From 018ef066c61c1cc8abaf6eca20fd684849616f1c Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Wed, 20 Oct 2021 15:12:26 -0700 Subject: [PATCH] updates to install directions and for v5.8.1, doc@90790be --- _sources/about.rst.txt | 1 + _sources/changes_to_master.rst.txt | 29 +- _sources/contents.rst.txt | 7 +- _sources/docker_image.rst.txt | 4 +- _sources/first_run_fortran.rst.txt | 5 +- _sources/first_run_pyclaw.rst.txt | 2 + _sources/galleries.rst.txt | 28 +- _sources/howto_release.rst.txt | 12 +- _sources/installing.rst.txt | 130 +++------ _sources/installing_fortcodes.rst.txt | 86 ++++++ _sources/installing_pip.rst.txt | 160 ++++++------ _sources/packages.rst.txt | 20 +- _sources/prereqs.rst.txt | 22 +- _sources/pyclaw/index.rst.txt | 44 +++- _sources/python.rst.txt | 88 +------ _sources/python_path.rst.txt | 36 +-- _sources/release_5_8_1.rst.txt | 111 ++++++++ _sources/releases.rst.txt | 2 + _sources/setenv.rst.txt | 16 +- _sources/setrun_geoclaw.rst.txt | 12 - 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dev/.doctrees/installing_fortcodes.doctree create mode 100644 dev/.doctrees/release_5_8_1.doctree create mode 100644 dev/_sources/installing_fortcodes.rst.txt create mode 100644 dev/_sources/release_5_8_1.rst.txt create mode 100644 dev/installing_fortcodes.html create mode 100644 dev/release_5_8_1.html create mode 100644 installing_fortcodes.html create mode 100644 release_5_8_1.html create mode 100644 v5.8.x/.doctrees/installing_fortcodes.doctree create mode 100644 v5.8.x/.doctrees/release_5_8_1.doctree create mode 100644 v5.8.x/_sources/installing_fortcodes.rst.txt create mode 100644 v5.8.x/_sources/release_5_8_1.rst.txt create mode 100644 v5.8.x/installing_fortcodes.html create mode 100644 v5.8.x/release_5_8_1.html diff --git a/_sources/about.rst.txt b/_sources/about.rst.txt index 247b4e0524..ecaf8a1487 100644 --- a/_sources/about.rst.txt +++ b/_sources/about.rst.txt @@ -133,6 +133,7 @@ Here's the bibtex:: Please fill in the version number that you used, and its year, with the appropriate DOI from `Zenodo `_, if available. See :ref:`releases`. + It is best to refer to the particular release used to obtain your results, but if you need to refer to multiple past releases, or to cite Clawpack more generally, you can also use the DOI diff --git a/_sources/changes_to_master.rst.txt b/_sources/changes_to_master.rst.txt index a5c9231fa3..6a0fd8514e 100644 --- a/_sources/changes_to_master.rst.txt +++ b/_sources/changes_to_master.rst.txt @@ -3,12 +3,12 @@ .. _changes_to_master: =============================== -Changes to master since v5.8.0 +Changes to master since v5.8.1 =============================== Follow the links to see changes that have been made to the master branch of -each repository since the last release (v5.8.0) on February 4, 2021. +each repository since the last release (v5.8.1) on October 19, 2021. These changes should appear in the next release. If you need them now, see :ref:`developers` for instructions on cloning and installing from the @@ -31,40 +31,41 @@ Changes to classic See `classic diffs -`_ +`_ Changes to clawutil ------------------- See `clawutil diffs -`_ +`_ Changes to visclaw ------------------ + See `visclaw diffs -`_ +`_ Changes to riemann ------------------ See `riemann diffs -`_ +`_ Changes to amrclaw ------------------ + See `amrclaw diffs -`_ +`_ Changes to geoclaw ------------------ - -See `geoclaw diffs -`_ + +See `geoclaw diffs `_ Changes to PyClaw @@ -75,7 +76,7 @@ For changes in PyClaw, see the `PyClaw changelog `_. See `pyclaw diffs -`_ +`_ =========================== Other Clawpack Repositories @@ -85,11 +86,13 @@ The repositories below are not included in the Clawpack tarfile or pip install, but changes to these repositories may also be of interest. - `apps diffs - `_ + `_ - `doc diffs `_ + shows changes in the `dev` branch not yet in the posted version of the + documentation. - `docker-files diffs - `_ + `_ diff --git a/_sources/contents.rst.txt b/_sources/contents.rst.txt index a2fc818d17..e9d0614902 100644 --- a/_sources/contents.rst.txt +++ b/_sources/contents.rst.txt @@ -10,7 +10,7 @@ the Clawpack open source software project. Full Table of Contents ==================================================== -This is the documentation for **Clawpack Version 5.8.0.** +This is the documentation for **Clawpack Version 5.8.1.** For documentation corresponding to older versions see the list of past releases in the menu to the left. The *future* version refers to new documentation for features that have been merged into the @@ -35,7 +35,7 @@ Overview and Getting Started packages installing installing_pip - installing_more_options + installing_fortcodes setenv first_run clawpack_components @@ -58,11 +58,14 @@ Examples and Applications :maxdepth: 1 apps + galleries fvmbook contribute_apps testing sphinxdoc +.. _contents_fortcodes: + Classic, AMRClaw, and GeoClaw ============================== diff --git a/_sources/docker_image.rst.txt b/_sources/docker_image.rst.txt index 99b442de51..8b060a6fed 100644 --- a/_sources/docker_image.rst.txt +++ b/_sources/docker_image.rst.txt @@ -9,8 +9,8 @@ you have `Docker `_ installed then you can now use a docker image from the `DockerHub Clawpack repositories `_. -Using Version 5.8.0 -------------------- +Using Version 5.8.0 or above +---------------------------- We are currently having problems creating a new Docker image for v5.8.0. However, you can follow the instructions below for v5.7.1 and then within a diff --git a/_sources/first_run_fortran.rst.txt b/_sources/first_run_fortran.rst.txt index 321321caa3..444efce460 100644 --- a/_sources/first_run_fortran.rst.txt +++ b/_sources/first_run_fortran.rst.txt @@ -7,7 +7,7 @@ This assumes that you have downloaded the Fortran components of Clawpack, see :ref:`install_fortran`. First ensure that you have :ref:`setenv` -and that you have the :ref:`install_prerequisites`. +and that you have the :ref:`prereqs`. As a first test of the Fortran code, try the following:: @@ -37,7 +37,8 @@ There are similar `tests` subdirectories of `$CLAW/amrclaw` and Running an example ------------------ -Many examples of Clawpack simulations can be seen in the :ref:`galleries`. +Many examples of Clawpack simulations can be seen in the +`gallery `__. Classic diff --git a/_sources/first_run_pyclaw.rst.txt b/_sources/first_run_pyclaw.rst.txt index 021aabf00c..dfe35a0ead 100644 --- a/_sources/first_run_pyclaw.rst.txt +++ b/_sources/first_run_pyclaw.rst.txt @@ -3,6 +3,8 @@ Testing a PyClaw installation and running an example ===================================================== +First ensure that you have :ref:`setenv` and that you have the :ref:`prereqs`. + If you downloaded Clawpack manually, you can test your :ref:`pyclaw` installation as follows (starting from your `clawpack` directory):: diff --git a/_sources/galleries.rst.txt b/_sources/galleries.rst.txt index f824c7c9e7..b6f89831f6 100644 --- a/_sources/galleries.rst.txt +++ b/_sources/galleries.rst.txt @@ -2,8 +2,30 @@ .. _galleries: -The Clawpack Gallery is available only for the latest release of Clawpack. +================== +Clawpack Gallery +================== + +The `Clawpack Gallery `__ +is available only for the latest release of Clawpack. + +The Gallery shows results obtained by running many of the examples that are +included with Clawpack, from the directories + +- `$CLAW/pyclaw/examples` +- `$CLAW/classic/examples` +- `$CLAW/amrclaw/examples` +- `$CLAW/geoclaw/examples` + +and also from + +- `$CLAW/apps` + +which must be obtained separately from the main installation of Clawpack, +see :ref:`apps`. +The directory `$CLAW/apps/notebooks` contains a number of Jupyter +notebooks that illustrate various aspects of Clawpack. +Many of these are also visible in rendered html form in the +`Gallery of Notebooks `__. -Please see -``_. diff --git a/_sources/howto_release.rst.txt b/_sources/howto_release.rst.txt index 069b683f30..05a7385843 100644 --- a/_sources/howto_release.rst.txt +++ b/_sources/howto_release.rst.txt @@ -176,6 +176,13 @@ on release since that would only archive a zip file of the main `clawpack` repository. Instead we want to archive the tar file containing all subrepositories too. +Open Science Framework (OSF) +---------------------------- + +Go to https://osf.io/kmw6h/files/ and upload the latest tarfile to the set +of versions that can be accessed with the single DOI +`10.17605/osf.io/kmw6h `__. + .. _howto_release_doc: Updating the documentation @@ -213,11 +220,12 @@ When making changes for a new release, the following pages in the directory Also update the bibtex and recommended citation in `about.rst`. - Modify several other files to point to the new version number, in particular - `installing.rst` , `installing_pip.rst`, `installing_more_options.rst`, + `installing_pip.rst`, `installing_fortcodes.rst`, `contents.rst`, `docker_image.rst`. - Modify the main landing page `_templates/index.html` to cite the - proper version number and DOI. + proper version number and DOI. + (No longer necessary -- This page has been changed to be more generic.) - Update `conf.py` to the new version number, and also `$CLAW/doc/gallery/conf.py` (For a major release.) diff --git a/_sources/installing.rst.txt b/_sources/installing.rst.txt index a77eaabcd3..a58a25a8f0 100644 --- a/_sources/installing.rst.txt +++ b/_sources/installing.rst.txt @@ -8,112 +8,44 @@ Installing Clawpack See also: -* :ref:`clawpack_packages` -* :ref:`releases` -* :ref:`trouble_installation` +- :ref:`releases` +- :ref:`docker_image` as an alternative to installing -**Prerequisites:** Before installing, check that you have the :ref:`prereqs`. - - -.. _installing_pipintro: - -pip install ------------ - -The recommended approach is to use `pip install`. -It is also possible to have multiple versions of Clawpack installed and -switch between them (i.e., modify your Python path) using `pip`. -(see :ref:`installing_pip`) -If you plan to do this, or if you also wish to directly use the Fortran -variants of Clawpack (classic, AMRClaw, and/or GeoClaw), then we recommend -using the following version of the `pip install` command -**(you might want to first read the notes below to see if you -want to change anything in this command)**:: - - pip install --src=$HOME/clawpack_src --user -e \ - git+https://github.com/clawpack/clawpack.git@v5.8.0#egg=clawpack-v5.8.0 - -This will download Clawpack (via a git clone) into the directory -`$HOME/clawpack_src/clawpack-v5.8.0`. The top -installation directory can be changed by modifying the ``--src`` target -(or omit this part to put it in your current working directory). -If you have already downloaded Clawpack via a different mechanism then -see :ref:`pip_switch_version` rather than using the above command. - - -See :ref:`clawpack_components` for a list of what's included in this top -level directory. - -**Note:** Using pip to install will also check some python -:ref:`prereqs` and may update these on your system, and will use f2py to -convert Fortran Riemann solvers to Python versions. See -:ref:`installing_options` if you want more control. - -The ``--user`` flag is necessary if you are installing on a shared computer -where you do not have root access. If you do have root access and want it -to be available to all users, you can omit this flag. +**Register:** Please `register `_ +if you have not already done so. This is very useful in helping +us track the extent of usage, and important to the :ref:`funding` agencies +who support this work. -The ``-e`` flag makes it an "editable" install, leaving the source code in -place and allowing you to modify it if desired. -(Otherwise, by default, pip would move the python code to some -`site-packages` directory and delete everything else.) - -In order to use the Fortran codes within Clawpack, -you should then set the environment -variable `CLAW` to point to the `clawpack-v5.8.0` directory within -the installation directory `$HOME/clawpack_src`, and `FC` to point -to the desired Fortran compiler, e.g. in the bash shell:: - - export CLAW=$HOME/clawpack_src/clawpack-v5.8.0 - export FC=gfortran - -See :ref:`setenv` for more information. - -For more discussion of `pip` installation, and troubleshooting hints, see -:ref:`installing_pip`. - - -.. _installing_options: - -Other Installation Options -===================================== - -In general, *installing* Clawpack requires downloading some version -and then setting -paths so that Python import statements (and possibly Fortran Makefiles) find -the desired version. Switching between versions already on your computer -simply requires resetting paths. For hints and troubleshooting, see: +**Prerequisites:** Before installing, check that you have the :ref:`prereqs`. + +**Please see** - - :ref:`setenv` - - :ref:`python_path` - - :ref:`installing_pip` +- :ref:`clawpack_packages` -Rather than using `pip`, there are several other options for using -Clawpack that may be useful depending on your needs. These are summarized -in :ref:`installing_more_options`, including: +before installing, particularly if you are not sure whether you will +be using the Fortran versions of the PDE solvers +(:ref:`contents_fortcodes`) or the :ref:`pyclaw` version of the PDE solvers. - - :ref:`installing_tarfile` - - :ref:`install_dev` - - :ref:`installing_conda` - - :ref:`installing_docker` - - :ref:`installing_aws` - - :ref:`install_pyclaw_parallel` +**Then choose the best installation option** for your needs from this list: -**Python path:** -If you download a tarfile or use `git clone` to download a version, you can -still use `pip install` to set the Python path appropriately. -See :ref:`installing_pip` for details. +- If you **only** plan to use PyClaw to solve the PDEs and Visclaw for plotting, + we suggest + + - :ref:`install_quick_pyclaw`. + +- If you **only** plan to use the Fortran variants of Clawpack + (:ref:`contents_fortcodes`) for solving the PDEs, together with + Visclaw for plotting and other Python tools (e.g. from geoclaw or clawutil), + then we suggest + + - :ref:`installing_fortcodes`. + +- If you are a power user who plans to use both PyClaw and the Fortran variants + for solving PDEs, we recommend + + - :ref:`install_quick_all`. -If you are *not* using `pip` to set paths, then you will need to set -the `PYTHONPATH` -environment variable to point to a particular version of Clawpack, -but this is `not recommended `_. -See :ref:`python_path` for more details and tips on sorting out your path. -**Components:** -See :ref:`clawpack_components` for a list of what is generally included -under the top level `clawpack` directory when using any of the approaches below. -(And what is not included, e.g. the :ref:`apps`.) Next steps: @@ -124,4 +56,6 @@ started: - :ref:`first_run_pyclaw` - :ref:`first_run_fortran` +- :ref:`trouble_installation` + diff --git a/_sources/installing_fortcodes.rst.txt b/_sources/installing_fortcodes.rst.txt new file mode 100644 index 0000000000..cc91b3497b --- /dev/null +++ b/_sources/installing_fortcodes.rst.txt @@ -0,0 +1,86 @@ +:orphan: + +.. _installing_fortcodes: + +********************************************** +Options for installing Clawpack Fortran codes +********************************************** + + +This page describes ways to download and "install" Clawpack in a way that +the Fortran versions of the PDE solvers (:ref:`contents_fortcodes`) +can be used, along with Python codes that support these solvers, including +the visualization tools in VisClaw. + +If you plan to use the PDE solvers directly from :ref:`pyclaw`, please +see :ref:`installing` for other options. If you are not sure, see +:ref:`clawpack_packages` + +.. _installing_tarfile: + +tar file +-------- + +You can download the most recent (or certain previous versions) of Clawpack +as a tar file. After untarring this, you can set environment variables +to point to this version. + +Download a tar file from one of these sources: + +- `Clawpack releases on Github + `_ + +- The Zenodo link for the current release, listed at + :ref:`releases` (which also lists DOIs for recent versions, useful for + :ref:`citing`) + +After downloading a tar file you can do, e.g. :: + + tar -xzf clawpack-v5.8.1.tar.gz + cd clawpack-v5.8.1 + export CLAW=/full/path/to/clawpack-v5.8.1 # in bash + +The last command sets an environment variable when using the bash shell. +The syntax may be different in other shells. Replace `/full/path/to` +with the appropriate full path. + +You must also add `$CLAW` to your `PYTHONPATH` environment variable, +see :ref:`python_path`. + +.. _install_dev: + +git clone +--------- + +You can clone the git repositories from ``_. +This is particularly useful if you +want the latest development version or a branch that is not in a release yet, +and/or if you plan to contribute to the code yourself via a pull request. +See :ref:`developers` for more details, but the basic commands are:: + + git clone git://github.com/clawpack/clawpack.git + cd clawpack + git checkout v5.8.1 # or an older version; `git tag -l` to list options + git submodule init # for repositories pyclaw, clawutil, visclaw, etc. + git submodule update # clones all the submodule repositories + export CLAW=/full/path/to/clawpack # in bash + +The last command sets an environment variable when using the bash shell. +The syntax may be different in other shells. Replace `/full/path/to` +with the appropriate full path. + +You must also add `$CLAW` to your `PYTHONPATH` environment variable, +see :ref:`python_path`. + +**Components:** +See :ref:`clawpack_components` for a list of what is generally included +under the top level `clawpack` directory when using any of these approaches. +(And what is not included, e.g. the :ref:`apps`.) + +Next steps: +=========== + +Once Clawpack is installed, you can get started: + +- :ref:`first_run_fortran` +- :ref:`trouble_installation` diff --git a/_sources/installing_pip.rst.txt b/_sources/installing_pip.rst.txt index 3ae014885d..8004d2553f 100644 --- a/_sources/installing_pip.rst.txt +++ b/_sources/installing_pip.rst.txt @@ -4,82 +4,106 @@ pip install instructions ************************************** -For other installation options, see :ref:`installing`. -See also: +**Note:** If you only plan to use the Fortran versions of the solvers +(rather than :ref:`pyclaw`), and you run into problems with pip, +then you might want to try :ref:`installing_fortcodes`. -* :ref:`clawpack_packages` -* :ref:`releases` -* :ref:`trouble_installation` -**Register:** Please `register `_ -if you have not already done so. This is very useful in helping -us track the extent of usage, and important to the :ref:`funding` agencies -who support this work. +.. _install_quick_pyclaw: + +Quick Installation of PyClaw with pip +===================================== + +Please see :ref:`clawpack_packages` before installing, particularly +if you are not sure whether you will +be using the Fortran versions of the PDE solvers +(:ref:`contents_fortcodes`) or the :ref:`pyclaw` version of the PDE solvers. +See :ref:`installing` for other installation options. **Prerequisites:** Before installing, check that you have the :ref:`prereqs`. -*Installing* Clawpack requires downloading some version and then setting -paths so that Python import statements (and possibly Fortran Makefiles) find -the desired version. `pip` can be used to reset Python paths as well as to -download a new version of Clawpack and set the path appropriately. See -:ref:`python_path` for more information. +If you only want to use PyClaw (and associated Python +tools, e.g. VisClaw for visualization), then the simplest way to install +Clawpack is via:: + + pip install --user clawpack + +or, more specifically, :: + + pip install --user clawpack==v5.8.1 + +or you can choose a previous version from the `PyPi history `__. + +However, note that this does not download the Fortran codes in a way that they +can be used for :ref:`contents_fortcodes`. + +If you think you might want to use the Fortran packages as well +(Classic, AMRClaw, GeoClaw) and/or want easier access to the Python source +code, it is recommended that you follow the pip instructions below. .. _install_quick_all: -Quick Installation of all packages -===================================== +Quick Installation of all packages with pip +============================================ The recommended way to install the latest release of Clawpack, for -using PyClaw and/or the Fortran packages, is to give the following pip -install command +using both PyClaw and the Fortran packages, is to use pip, e.g. with the +following command **(you might want to first read the notes below to see if you want to change anything in this command)**:: pip install --src=$HOME/clawpack_src --user -e \ - git+https://github.com/clawpack/clawpack.git@v5.8.0#egg=clawpack-v5.8.0 - -This will download Clawpack (via a git clone) into the directory -`$HOME/clawpack_src/clawpack-v5.8.0`. The top -installation directory can be changed by modifying the ``--src`` target -(or omit this part to put it in your current working directory). -If you have already downloaded Clawpack via a different mechanism then -see :ref:`pip_switch_version` rather than using the above command. - -See :ref:`clawpack_components` for a list of what's included in this top -level directory. - -**Note:** Using pip to install will also check some python -:ref:`prereqs` and may update these on your system, and will use f2py to -convert Fortran Riemann solvers to Python versions. See -:ref:`installing_options` if you want more control. - -The ``--user`` flag is necessary if you are installing on a shared computer -where you do not have root access. If you do have root access and want it -to be available to all users, you can omit this flag. See notes below for -more information. - -The ``-e`` flag makes it an "editable" install, leaving the source code in -place and allowing you to modify it if desired. -(Otherwise, by default, pip would move the python code to some -`site-packages` directory and delete everything else.) - -In order to use the Fortran codes within Clawpack (`classic`, -`amrclaw`, or `geoclaw`), you should then set the environment -variable `CLAW` to point to the `clawpack-v5.8.0` directory within -the installation directory `$HOME/clawpack_src`, and `FC` to point -to the desired Fortran compiler, e.g. in the bash shell:: - - export CLAW=$HOME/clawpack_src/clawpack-v5.8.0 - export FC=gfortran - + git+https://github.com/clawpack/clawpack.git@v5.8.1#egg=clawpack-v5.8.1 \ + --use-deprecated=legacy-resolver + + **Notes:** -You may want to set `CLAW` even if you are only using PyClaw, since `$CLAW` is -sometimes used in this documentation to indicate the top level of the -Clawpack source directory structure. +- With older versions of `pip`, the flag + `--use-deprecated=legacy-resolver` + may not be recognized and is not needed. + +- Using pip to install will also check some python + :ref:`prereqs` and may update these on your system, and will use f2py to + convert Fortran Riemann solvers to Python versions. See + :ref:`installing_options` if you want more control. + +- This will download Clawpack (via a git clone) into the directory + `$HOME/clawpack_src/clawpack-v5.8.1`. The top + installation directory can be changed by modifying the ``--src`` target + (or omit this part to put it in your current working directory). + If you have already downloaded Clawpack via a different mechanism then + see :ref:`pip_switch_version` rather than using the above command. + +- See :ref:`clawpack_components` for a list of what's included in this top + level directory. + +- The ``--user`` flag is necessary if you are installing on a shared computer + where you do not have root access. If you do have root access and want it + to be available to all users, you can omit this flag. See notes below for + more information. + +- The ``-e`` flag makes it an "editable" install, leaving the source code in + place and allowing you to modify it if desired. + (Otherwise, by default, pip would move the python code to some + `site-packages` directory and delete everything else.) + +- In order to use the Fortran codes within Clawpack (`classic`, + `amrclaw`, or `geoclaw`), you should then set the environment + variable `CLAW` to point to the `clawpack-v5.8.1` directory within + the installation directory `$HOME/clawpack_src`, and `FC` to point + to the desired Fortran compiler, e.g. in the bash shell:: + + export CLAW=$HOME/clawpack_src/clawpack-v5.8.1 + export FC=gfortran + + +- You may want to set `CLAW` even if you are only using PyClaw, since `$CLAW` is + sometimes used in this documentation to indicate the top level of the + Clawpack source directory structure. Installing with `pip` also compiles Riemann solvers written in Fortran for use in PyClaw. If you get a Fortran error message when installing, see @@ -88,26 +112,6 @@ use in PyClaw. If you get a Fortran error message when installing, see See :ref:`setenv` for more information, and :ref:`python_path` if you are having problems with importing Python modules. -.. _install_quick_pyclaw: - -Quick Installation of only PyClaw -===================================== - - -If you only want to use PyClaw (and associated Python -tools, e.g. VisClaw for visualization), they you could do:: - - pip install --user clawpack - -or, more specifically, :: - - pip install --user clawpack==v5.8.0 - -However, if you think you might want to use the Fortran packages as well -(Classic, AMRClaw, GeoClaw) and/or want easier access to the Python source -code, it is recommended that you follow the instructions above for -:ref:`install_quick_all` (or see other :ref:`installing_more_options`). - Next steps: ----------- @@ -117,6 +121,8 @@ started: - :ref:`first_run_pyclaw` - :ref:`first_run_fortran` +- :ref:`trouble_installation` + .. _pip_switch_version: diff --git a/_sources/packages.rst.txt b/_sources/packages.rst.txt index 8a758e40ab..8d2a104efe 100644 --- a/_sources/packages.rst.txt +++ b/_sources/packages.rst.txt @@ -7,10 +7,10 @@ Which Clawpack solver should I use? Clawpack includes a number of related hyperbolic PDE solvers: - - Classic - - :ref:`amrclaw` - - :ref:`geoclaw` - - :ref:`pyclaw` + - Classic (single grid solvers in Fortran) + - :ref:`amrclaw` (adaptive mesh refinement in Fortran) + - :ref:`geoclaw` (geophysical flows with AMR, in Fortran) + - :ref:`pyclaw` (Python version of solvers) All of them are built on common algorithmic ideas, make use of the same set of Riemann solvers, and can be used with VisClaw @@ -20,20 +20,26 @@ the main differences between them. Installation and user interface =============================== -The AMRClaw, GeoClaw, and Classic solvers are Fortran-based +The :ref:`contents_fortcodes` solvers are Fortran-based packages and rely on Makefiles and environment variables. Problems are specified partially through Python scripts at run time (`setrun.py`) and partially through custom Fortran code at compile time (to set initial conditions, for instance). -With PyClaw, problems are specified entirely at run time through +With :ref:`pyclaw`, problems are specified entirely at run time through Python script files, or interactively (e.g., in IPython or Jupyter notebooks). Typically, the user does not need to write any Fortran code (though custom routines can be written in Fortran when necessary for performance reasons). + PyClaw uses much of the same library of Fortran code, but that code is compiled during installation so that it can be imported dynamically within -Python programs. +Python programs. In particular, Fortran versions of all the :ref:`riemann` +available in Classic or AMRClaw are also exposed in PyClaw. These are +converted using `f2py `__, a step +that sometimes causes problems and is not required if you are only using +Fortran versions of the solvers. + Algorithmic differences diff --git a/_sources/prereqs.rst.txt b/_sources/prereqs.rst.txt index 047fd66e06..38a4609dca 100644 --- a/_sources/prereqs.rst.txt +++ b/_sources/prereqs.rst.txt @@ -22,10 +22,10 @@ Operating system Fortran ------- -PyClaw can now be installed without a Fortran compiler; see :ref:`installing_conda`. -To use the other packages, you will need -`gfortran `_ or another F90 compiler +To use the Fortran versions of the PDE solvers (:ref:`contents_fortcodes`), +you will need +`gfortran `_ or another F90 compiler. See :ref:`fortran_compilers` for more about which compilers work well with Clawpack. @@ -35,15 +35,14 @@ Clawpack. Python ------ -- Python Version 2.7 or above, or (**new in 5.4.0**) Python 3 +- Python Version 3.0 or above (much of the code works in Python2, but this + is no longer officially supported; see :ref:`python-three`). - `NumPy `_ (for PyClaw/VisClaw) - `matplotlib `_ (for PyClaw/VisClaw) -The `Anaconda Python Distribution `_ -is an easy way to get all of these. -See :ref:`python` for more information on -installing the required modules and to get started using Python if -you are not familiar with it. +There are many ways to install the Python scientific stack, e.g. via +`apt-get` or `brew`. On MacOS, you might check out +`ScipySuperpack for Homebrew `__. .. _prereqs_pip: @@ -51,9 +50,8 @@ pip --- If you are installing via `pip install` then you need `pip`. -You may already have it; in particular the Anaconda Python distribution -contains pip. If you need to install it, see -``_ +If you need to install it, see +``_ The version of `pip install` suggested for :ref:`install_quick_all` requires a recent version of `pip`, so you may need to upgrade if you run into diff --git a/_sources/pyclaw/index.rst.txt b/_sources/pyclaw/index.rst.txt index 43244cec0f..3da3e5f8fb 100644 --- a/_sources/pyclaw/index.rst.txt +++ b/_sources/pyclaw/index.rst.txt @@ -3,28 +3,44 @@ .. _pyclaw: -Pyclaw +PyClaw ====== +In this section of the documentation, PyClaw refers +a Python version of the hyperbolic PDE solvers that allows solving the +problem in Python (e.g. in a Jupyter notebook) without explicitly using +any Fortran code. Versions of the solvers are written in Python. +However, they use Riemann solvers that are converted from the Fortran +versions into Python-callable versions using +`f2py `__, +to facilitate using the same large set of solvers from either Fortran +or Python. Note that +in order for this to work the solvers must be precompiled, as is done +when using `pip install`, for example (see :ref:`installing_pip`). + +See :ref:`clawpack_packages` for more information about the different +capabilities of PyClaw relative to :ref:`contents_fortcodes`. + +**Note:** The `clawpack/pyclaw` directory also contains some +Python tools that are used many places in +Clawpack, e.g. when plotting with :ref:`visclaw` or when compiling and +running Fortran code using a `Makefile` and `setrun.py` file +(when using :ref:`contents_fortcodes`). +These modules are mostly used "under the hood". +Other Python tools of use in the Fortran versions +are described elsewhere; see e.g. :ref:`plotting` or :ref:`geoclaw`. +All of these modules are pure Python and should work fine as long +as the top level of Clawpack is on your :ref:`python_path`. + + .. _pyclaw_install: PyClaw installation ------------------- -Just do this:: - - pip install clawpack - -Installing with pip requires that you have a Fortran compiler installed. - -Alternatively, if you use `Anaconda `_ or -`Conda `_, you can:: - - conda install -c clawpack -c conda-forge clawpack +Using `pip install` is the recommended approach, see +:ref:`installing_pip`. -This option will also install optional dependencies including PETSc and HDF5, -which are useful for large-scale parallel runs. Installing with Conda does not -require that you have a Fortran compiler. Examples -------- diff --git a/_sources/python.rst.txt b/_sources/python.rst.txt index 77ef44350a..9d356e23bf 100644 --- a/_sources/python.rst.txt +++ b/_sources/python.rst.txt @@ -6,8 +6,6 @@ Python Hints *************** -.. contents:: - .. _python-three: Dropping support for Python 2.7 @@ -34,46 +32,9 @@ functions, but there are a few other changes. See e.g., https://docs.python.org/3/howto/pyporting.html and other online resources discussing the differences between Python 2 and 3. -.. _python-intro: - -What is Python? ---------------- - -Python is a powerful object-oriented interpreted scripting/programming -language. Some version of Python is almost certainly on your computer -already (on unix, linux, OSX type:: - - $ python --version - -to find out which version, or just:: - - $ python - -to start a python shell with a prompt that looks like:: - - >>> -You may prefer to use `IPython -`_, which is a nicer shell -than the pure python shell, with things like command completion and history. -See the `Quick IPython Tutorial -`_. - -.. _python-install: - -Installation of required modules --------------------------------- - -To effectively use the pyclaw and Clawpack plotting routines that are -written in Python, you will need version 2.7 or greater -(but **not** 3.0 or above, which is not backwards compatible). -some modules that are not included in the standard Python distribution. -Python modules are loaded with the *import* statement in Python and a wide -variety of specialized modules exist for various purposes since people use -Python for many different purposes. - -An alternative to installing the packages discussed below, you could also use the -:ref:`VM`, which has all the required Python modules pre-installed. +References and tutorials +------------------------ For use with Clawpack, you will need the `Numpy `_ module (*Numerical Python*) @@ -86,51 +47,22 @@ page for tips installing SciPy and NumPy on various platforms. For plotting you will also need the `matplotlib `_ module which provides Matlab-like plotting commands for 1d and 2d plots (e.g. contour and pcolor plots). -This is generally the hardest thing to get going properly. See the -`matplotlib Installation FAQ -`_. - -Often the easiest way to get all the modules you need is to install the - -`Anaconda Python Distribution `_ -or the -`Enthought Python Distribution -`_, which is free for academic -users. Versions are available for Windows, Mac OS X, and Redhat linux. - -With some versions of Linux (e.g. debian and Ubuntu), you can easily install -what's needed using ``apt-get``:: - - $ apt-get install python-numpy - $ apt-get install python-scipy - $ apt-get install python-matplotlib - -For OS X, you might also try the `Scipy Superpack -`_. -See also these `tips on installing matplotlib on OS X -`_. - - -References and tutorials ------------------------- Some useful links to get started learning Python: - * `Dive Into Python `_ - - * `Python tutorial `_ - * `NumPy User Guide `_ - * `NumPy for Matlab users `_ + * `NumPy User Guide `_ + * `NumPy for Matlab users `_ * `SciPy Reference Guide `_ - * `Matplotlib gallery `_ + * `Matplotlib gallery `_ * `LeVeque's class notes `_ - * `Langtangen's book `_ and - `Introductory slides `_ + Notebooks --------- -See :ref:`notebooks`. - +The `Clawpack Gallery of Jupyter +Notebooks `__ +contains a number of notebooks with other examples of using Python for +Clawpack. diff --git a/_sources/python_path.rst.txt b/_sources/python_path.rst.txt index b488236440..dc2d4a8997 100644 --- a/_sources/python_path.rst.txt +++ b/_sources/python_path.rst.txt @@ -10,10 +10,8 @@ When using PyClaw or other Python tools from Clawpack (e.g. the visualization tools in VisClaw or :ref:`topotools` from GeoClaw), you need to be able to import various modules. -For a general discussion of importing Python modules, see the tutorial in -the Python documentation: -`Python 2 `_, -`Python 3 `_. +For a general discussion of importing Python modules, see the tutorial in the +`Python3 documentation `_. Below are some hints in case you run into problems with import statements with modules not being found, or being imported from the wrong version of @@ -169,10 +167,24 @@ path to this via:: PYTHONPATH ---------- -.. warning :: Setting the environment variable `PYTHONPATH` is generally - considered bad practice in the Python community - and can lead to problems, see for example - `PYTHONPATH Considered Harmful `_. +If you install Clawpack with pip, then you do not need to include it in +environment variable `PYTHONPATH`. + +Setting the environment variable `PYTHONPATH` is often +considered bad practice in the Python community +and can lead to problems, see for example +`PYTHONPATH Considered Harmful `_. + + +In spite of the possible drawbacks, some Clawpack developers often +use `PYTHONPATH` to switch versions without difficulty, particularly +when using one of the :ref:`installing_fortcodes` rather than pip. + +If you do wish to use it, you should set `PYTHONPATH` to point to the top +level of the clawpack directory for the code you wish to use. +Then use the :ref:`whichclaw` utility to check that this is where Clawpack +is imported from, and there is not an `easy-install.pth` file generated by +pip that points to a different location. If you have an environment variable `PYTHONPATH` set, the paths specified here may be searched before or after what is specified in the users' @@ -191,11 +203,3 @@ possibly conflicting `easy-install.pth` files. See :ref:`setenv` for information on setting environment variables. -In spite of the possible drawbacks, some Clawpack developers often -use `PYTHONPATH` to switch versions without difficulty. If you do -wish to use it, you should set `PYTHONPATH` to point to the top -level of the clawpack directory for the code you wish to use. -Then use the :ref:`whichclaw` utility to check that this is where Clawpack -is imported from, and there is not a `easy-install.pth` that points to a -different location. - diff --git a/_sources/release_5_8_1.rst.txt b/_sources/release_5_8_1.rst.txt new file mode 100644 index 0000000000..4ba8cde17c --- /dev/null +++ b/_sources/release_5_8_1.rst.txt @@ -0,0 +1,111 @@ +:orphan: + +.. _release_5_8_1: + +=============================== +v5.8.1 release notes +=============================== + +Clawpack 5.8.1 was released on October 19, 2021. See :ref:`installing`. + +**The installation instructions have been reorganized (once again) +in an attempt to make the different options clearer.** + +Permanent DOI: http://doi.org/10.5281/zenodo.?? + + +Changes relative to Clawpack 5.8.0 (February 4, 2021) are shown below. + +To see more recent changes that are in the the master branch but not yet +released, see :ref:`changes_to_master`. + + +Changes that are not backward compatible +---------------------------------------- + + +General changes +--------------- + + +Changes to classic +------------------ + +No changes. + +See `classic diffs +`_ + +Changes to clawutil +------------------- + +No changes. + + +See `clawutil diffs +`_ + +Changes to visclaw +------------------ + +No major changes. + +See `visclaw diffs +`_ + +Changes to riemann +------------------ + +- Fix `rp1_shallow_hlle.f90` to work better near dry states. + +See `riemann diffs +`_ + +Changes to amrclaw +------------------ + +No changes. + +See `amrclaw diffs +`_ + +Changes to geoclaw +------------------ + +- Some improvements to storm tracks +- Reading (some) geotiff files now supported in `topotools` +- Added `kmltools.topo2kmz` to make Google Earth overlays showing topography +- Some other bug fixes. + +See `geoclaw diffs +`_ + + +Changes to PyClaw +------------------ + + +For changes in PyClaw, see the `PyClaw changelog +`_. + +See `pyclaw diffs +`_ + +=========================== +Other Clawpack Repositories +=========================== + +The repositories below are not included in the Clawpack tarfile or pip +install, but changes to these repositories may also be of interest. + +- `apps diffs + `_ + +- `doc diffs + `_ + shows changes in the `dev` branch not yet in the posted version of the + documentation. + +- `docker-files diffs + `_ + diff --git a/_sources/releases.rst.txt b/_sources/releases.rst.txt index 3faff132fd..22ff38421d 100644 --- a/_sources/releases.rst.txt +++ b/_sources/releases.rst.txt @@ -35,6 +35,8 @@ can also be referenced with the single DOI `10.17605/osf.io/kmw6h `__. See :ref:`citing` for more information on how best to cite Clawpack. +* :ref:`release_5_8_1` -- October 19, 2021 + `[DOI 10.5281/zenodo.??] `_ * :ref:`release_5_8_0` -- February 4, 2021 `[DOI 10.5281/zenodo.4503024] `_ * :ref:`release_5_7_1` -- September 11, 2020 diff --git a/_sources/setenv.rst.txt b/_sources/setenv.rst.txt index bf172d3bd1..52f11aff4e 100644 --- a/_sources/setenv.rst.txt +++ b/_sources/setenv.rst.txt @@ -5,6 +5,10 @@ Set environment variables ========================= +The `export` commands below work in the bash shell. The syntax may +be different in other shells. + + CLAW ---- @@ -42,6 +46,12 @@ should list the top level directory, and report for example:: PYTHONPATH ---------- -We do not recommend setting this environment variable. See -:ref:`python_path` for more information. Instead we recommend using `pip -install` to set the Python path appropriately, see :ref:`installing_pip`. +If you used `pip` to install Clawpack then you should not set this +environment variable. But if you installed without `pip`, e.g. following +:ref:`installing_fortcodes`, then you need to set `PYTHONPATH` to include +the directory `$CLAW`. If `PYTHONPATH` is already set, then you may want to +insert `$CLAW` into the list of directories searched by Python via:: + + export PYTHONPATH=$CLAW:$PYTHONPATH + +See :ref:`python_path` for more information. diff --git a/_sources/setrun_geoclaw.rst.txt b/_sources/setrun_geoclaw.rst.txt index e32dc9dfc0..bb90f697cf 100644 --- a/_sources/setrun_geoclaw.rst.txt +++ b/_sources/setrun_geoclaw.rst.txt @@ -74,18 +74,6 @@ is done should be specified for GeoClaw applications: speed of 2.0 would refine to level 3, and cells with a speed of 3.0 would refine to level 4. -.. attribute:: rundata.refinement_data.max_level_deep : int - - For simulations over the ocean, it is often useful to specify - a *maximum refinement level* allowed in deep parts of the ocean. This is - useful if a high level of refinement is specified on some rectangular - region but only the parts of this region near the shore actually need to - be refined. - -.. attribute:: rundata.refinement_data.deep_depth : float - - The deepness that triggers the refinement limitation imposed by - `max_level_deep` above. .. _setrun_geo: diff --git a/_sources/sharing.rst.txt b/_sources/sharing.rst.txt index ab7c875420..137a8e132b 100644 --- a/_sources/sharing.rst.txt +++ b/_sources/sharing.rst.txt @@ -36,9 +36,11 @@ To make it easy for others to view your code and the resulting plots, you can simply copy the example directory (containing the code and the _plots subdirectory) to your publicly visible web pages. -IPython notebooks +Jupyter notebooks ================= -You should also consider creating an IPython notebook to explain your +You should also consider creating an Jupyter notebook to explain your problem, illustrate your workflow, and present plots and animations all in -one. See :ref:`notebooks` for some examples. +one. See the +`Gallery of Notebooks `_ +for some examples. diff --git a/_sources/topo.rst.txt b/_sources/topo.rst.txt index a725cb607d..46909954eb 100644 --- a/_sources/topo.rst.txt +++ b/_sources/topo.rst.txt @@ -69,9 +69,11 @@ The recognized topotypes are: These files are larger than necessary since they store the x,y values at each point even though the points are required to be equally spaced. Many data sets come this way, but note that you can convert a file of - this type to one of the more compact types below using:: + this type to one of the more compact types below using e.g.:: - [insert python code] + from clawpack.geoclaw import topotools + topo = topotools.Topography(input_path, topo_type=1) + topo.write(output_path, topo_type=3) diff --git a/about.html b/about.html index b36bc3a81a..618d00093f 100644 --- a/about.html +++ b/about.html @@ -97,7 +97,7 @@

Navigation

Adaptive mesh refinement is included, see AMRClaw Description and Detailed Contents, and routines specialized to depth-averaged geophysical flows can be found in GeoClaw Description and Detailed Contents.

-

The Pyclaw software provides a more pythonic interface and +

The PyClaw software provides a more pythonic interface and parallelism that scales to tens of thousands of cores.

New users may wish to read Which Clawpack solver should I use? before starting.

The “wave propagation” algorithms implemented in Clawpack are discribed in @@ -187,8 +187,8 @@

LicenseZenodo, if available. -See Releases of Clawpack and release notes. -It is best to refer to the particular release used to obtain your results, +See Releases of Clawpack and release notes.

+

It is best to refer to the particular release used to obtain your results, but if you need to refer to multiple past releases, or to cite Clawpack more generally, you can also use the DOI 10.17605/osf.io/kmw6h.

diff --git a/apps.html b/apps.html index 266dd54c28..f6cce17561 100644 --- a/apps.html +++ b/apps.html @@ -20,7 +20,7 @@ - +
@@ -67,7 +67,7 @@

Navigation

modules |
  • - next |
  • Related Topics

    • diff --git a/changes_to_master.html b/changes_to_master.html index 000633f8a0..25902be66c 100644 --- a/changes_to_master.html +++ b/changes_to_master.html @@ -4,7 +4,7 @@ - Changes to master since v5.8.0 — Clawpack 5.8.x documentation + Changes to master since v5.8.1 — Clawpack 5.8.x documentation @@ -73,10 +73,10 @@

    Navigation

    -
    -

    Changes to master since v5.8.0

    +
    +

    Changes to master since v5.8.1

    Follow the links to see changes that have been made to the master branch of -each repository since the last release (v5.8.0) on February 4, 2021.

    +each repository since the last release (v5.8.1) on October 19, 2021.

    These changes should appear in the next release. If you need them now, see Developers’ Guide for instructions on cloning and installing from the master branch.

    @@ -91,32 +91,32 @@

    General changes

    Changes to classic

    -

    See classic diffs

    +

    See classic diffs

    Changes to clawutil

    -

    See clawutil diffs

    +

    See clawutil diffs

    Changes to visclaw

    -

    See visclaw diffs

    +

    See visclaw diffs

    Changes to riemann

    -

    See riemann diffs

    +

    See riemann diffs

    Changes to amrclaw

    -

    See amrclaw diffs

    +

    See amrclaw diffs

    Changes to geoclaw

    -

    See geoclaw diffs

    +

    See geoclaw diffs

    Changes to PyClaw

    For changes in PyClaw, see the PyClaw changelog.

    -

    See pyclaw diffs

    +

    See pyclaw diffs

    @@ -124,9 +124,11 @@

    Other Clawpack Repositories -

  • apps diffs

    • -

  • doc diffs

    • -

  • docker-files diffs

    • +

  • apps diffs

    • +

  • doc diffs +shows changes in the dev branch not yet in the posted version of the +documentation.

    • +

  • docker-files diffs

    • @@ -143,7 +145,7 @@

    Version 5.8.x

    Table of Contents

    Full Table of Contents

    -

    This is the documentation for Clawpack Version 5.8.0. +

    This is the documentation for Clawpack Version 5.8.1. For documentation corresponding to older versions see the list of past releases in the menu to the left. The future version refers to new documentation for features that have been merged into the @@ -132,7 +132,7 @@

    Overview and Getting StartedWhich Clawpack solver should I use?
  • Installing Clawpack
  • pip install instructions
    • -
  • Additional options for installing Clawpack
    • +
  • Options for installing Clawpack Fortran codes
  • Set environment variables
  • Running an example
  • Clawpack components
    • @@ -153,6 +153,7 @@

    Examples and Applications diff --git a/dev/fvmbook.html b/dev/fvmbook.html index 3ba4b64c2b..3e387fddcb 100644 --- a/dev/fvmbook.html +++ b/dev/fvmbook.html @@ -21,7 +21,7 @@ - +
    @@ -70,7 +70,7 @@

    Navigation

    next |
  • - previous |
  • Clawpack dev documentation »
    • @@ -129,7 +129,7 @@

    Table of Contents

    Related Topics

    diff --git a/dev/galleries.html b/dev/galleries.html index 2b4d45f27a..4644c1314e 100644 --- a/dev/galleries.html +++ b/dev/galleries.html @@ -4,7 +4,7 @@ - <no title> — Clawpack dev documentation + Clawpack Gallery — Clawpack dev documentation @@ -19,7 +19,9 @@ - + + +
    @@ -64,6 +66,12 @@

    Navigation

  • modules |
    • +
  • + next |
    • +
  • + previous |
  • Clawpack dev documentation »
    • @@ -73,9 +81,29 @@

    Navigation

    -

    The Clawpack Gallery is available only for the latest release of Clawpack.

    -

    Please see -http://www.clawpack.org/gallery/index.html.

    +
    @@ -90,6 +118,8 @@

    Version dev

    Related Topics

    diff --git a/dev/genindex.html b/dev/genindex.html index 5874e08383..6e2b83e5d5 100644 --- a/dev/genindex.html +++ b/dev/genindex.html @@ -1032,15 +1032,17 @@

    T

  • tfluct_solver (clawpack.pyclaw.sharpclaw.solver.SharpClawSolver attribute)
    • - - +
    @@ -124,7 +124,7 @@

    Version dev

    Related Topics

    @@ -360,7 +360,7 @@

    Table of Contents

    Related Topics

    @@ -182,7 +182,7 @@

    Final releaseChanges to master since v5.8.0 which generate diffs between the latest version and +Changes to master since v5.8.1 which generate diffs between the latest version and the current master branch of each repository.

    @@ -235,6 +235,12 @@

    Zenodo +

    Open Science Framework (OSF)

    +

    Go to https://osf.io/kmw6h/files/ and upload the latest tarfile to the set +of versions that can be accessed with the single DOI +10.17605/osf.io/kmw6h.

    +

    Updating the documentation

    See Guide for updating this documentation for general instructions on building the documentation @@ -263,10 +269,11 @@

    ZenodoTable of Contents

  • Final release
  • Pypi
  • Zenodo
    • +
  • Open Science Framework (OSF)
  • Updating the documentation
  • Updating the apps repository
  • Updating the Dockerfile
    • @@ -337,7 +345,7 @@

    Table of Contents

    Related Topics

    @@ -203,14 +149,10 @@

    Version dev

    Table of Contents

    Related Topics

    • Documentation overview
        diff --git a/dev/installing_fortcodes.html b/dev/installing_fortcodes.html new file mode 100644 index 0000000000..c03cff5e6a --- /dev/null +++ b/dev/installing_fortcodes.html @@ -0,0 +1,247 @@ + + + + + + + Options for installing Clawpack Fortran codes — Clawpack dev documentation + + + + + + + + + + + + + + + + + + +
        +
        + +
        +
        + + + +
        +
        +
        +
        + +
        +

        Options for installing Clawpack Fortran codes

        +

        This page describes ways to download and “install” Clawpack in a way that +the Fortran versions of the PDE solvers (Classic, AMRClaw, and GeoClaw) +can be used, along with Python codes that support these solvers, including +the visualization tools in VisClaw.

        +

        If you plan to use the PDE solvers directly from PyClaw, please +see Installing Clawpack for other options. If you are not sure, see +Which Clawpack solver should I use?

        +
        +

        tar file

        +

        You can download the most recent (or certain previous versions) of Clawpack +as a tar file. After untarring this, you can set environment variables +to point to this version.

        +

        Download a tar file from one of these sources:

        + +

        After downloading a tar file you can do, e.g.

        +
        tar -xzf clawpack-v5.8.1.tar.gz
+cd clawpack-v5.8.1
+export CLAW=/full/path/to/clawpack-v5.8.1  # in bash
+
        +
        +

        The last command sets an environment variable when using the bash shell. +The syntax may be different in other shells. Replace /full/path/to +with the appropriate full path.

        +

        You must also add $CLAW to your PYTHONPATH environment variable, +see Python path.

        +
        +
        +

        git clone

        +

        You can clone the git repositories from https://github.com/clawpack. +This is particularly useful if you +want the latest development version or a branch that is not in a release yet, +and/or if you plan to contribute to the code yourself via a pull request. +See Developers’ Guide for more details, but the basic commands are:

        +
        git clone git://github.com/clawpack/clawpack.git
+cd clawpack
+git checkout v5.8.1     # or an older version; `git tag -l` to list options
+git submodule init      # for repositories pyclaw, clawutil, visclaw, etc.
+git submodule update    # clones all the submodule repositories
+export CLAW=/full/path/to/clawpack    # in bash
+
        +
        +

        The last command sets an environment variable when using the bash shell. +The syntax may be different in other shells. Replace /full/path/to +with the appropriate full path.

        +

        You must also add $CLAW to your PYTHONPATH environment variable, +see Python path.

        +

        Components: +See Clawpack components for a list of what is generally included +under the top level clawpack directory when using any of these approaches. +(And what is not included, e.g. the Clawpack Applications repository.)

        +
        +

        Next steps:

        +

        Once Clawpack is installed, you can get started:

        + +
        +
        +
        + + +
        +
        +
        + +
        +
        +
        + © Copyright CC-BY 2020, The Clawpack Development Team. + Created using Sphinx. +
        + + + + \ No newline at end of file diff --git a/dev/installing_pip.html b/dev/installing_pip.html index 6b68368fa6..4fd7cf100f 100644 --- a/dev/installing_pip.html +++ b/dev/installing_pip.html @@ -20,7 +20,7 @@ - +
        @@ -67,7 +67,7 @@

        Navigation

        modules |
      • - next |
      • Navigation

    pip install instructions

    -

    For other installation options, see Installing Clawpack.

    -

    See also:

    - -

    Register: Please register -if you have not already done so. This is very useful in helping -us track the extent of usage, and important to the Funding agencies -who support this work.

    +

    Note: If you only plan to use the Fortran versions of the solvers +(rather than PyClaw), and you run into problems with pip, +then you might want to try Options for installing Clawpack Fortran codes.

    +
    +

    Quick Installation of PyClaw with pip

    +

    Please see Which Clawpack solver should I use? before installing, particularly +if you are not sure whether you will +be using the Fortran versions of the PDE solvers +(Classic, AMRClaw, and GeoClaw) or the PyClaw version of the PDE solvers. +See Installing Clawpack for other installation options.

    Prerequisites: Before installing, check that you have the Installation Prerequisites.

    -

    Installing Clawpack requires downloading some version and then setting -paths so that Python import statements (and possibly Fortran Makefiles) find -the desired version. pip can be used to reset Python paths as well as to -download a new version of Clawpack and set the path appropriately. See -Python path for more information.

    -
    -

    Quick Installation of all packages

    +

    If you only want to use PyClaw (and associated Python +tools, e.g. VisClaw for visualization), then the simplest way to install +Clawpack is via:

    +
    pip install --user clawpack
+
    +
    +

    or, more specifically,

    +
    pip install --user clawpack==v5.8.1
+
    +
    +

    or you can choose a previous version from the PyPi history.

    +

    However, note that this does not download the Fortran codes in a way that they +can be used for Classic, AMRClaw, and GeoClaw.

    +

    If you think you might want to use the Fortran packages as well +(Classic, AMRClaw, GeoClaw) and/or want easier access to the Python source +code, it is recommended that you follow the pip instructions below.

    +
    +
    +

    Quick Installation of all packages with pip

    The recommended way to install the latest release of Clawpack, for -using PyClaw and/or the Fortran packages, is to give the following pip -install command +using both PyClaw and the Fortran packages, is to use pip, e.g. with the +following command (you might want to first read the notes below to see if you want to change anything in this command):

    pip install --src=$HOME/clawpack_src --user -e \
-    git+https://github.com/clawpack/clawpack.git@v5.8.0#egg=clawpack-v5.8.0
+    git+https://github.com/clawpack/clawpack.git@v5.8.1#egg=clawpack-v5.8.1 \
+    --use-deprecated=legacy-resolver
    -

    This will download Clawpack (via a git clone) into the directory -$HOME/clawpack_src/clawpack-v5.8.0. The top +

    Notes:

    +
      +

    • With older versions of pip, the flag +–use-deprecated=legacy-resolver +may not be recognized and is not needed.

      • +

    • Using pip to install will also check some python +Installation Prerequisites and may update these on your system, and will use f2py to +convert Fortran Riemann solvers to Python versions. See +installing_options if you want more control.

      • +

    • This will download Clawpack (via a git clone) into the directory +$HOME/clawpack_src/clawpack-v5.8.1. The top installation directory can be changed by modifying the --src target (or omit this part to put it in your current working directory). If you have already downloaded Clawpack via a different mechanism then -see Using pip to install a different version rather than using the above command.

      -

      See Clawpack components for a list of what’s included in this top -level directory.

      -

      Note: Using pip to install will also check some python -Installation Prerequisites and may update these on your system, and will use f2py to -convert Fortran Riemann solvers to Python versions. See -Other Installation Options if you want more control.

      -

      The --user flag is necessary if you are installing on a shared computer +see Using pip to install a different version rather than using the above command.

      • +

    • See Clawpack components for a list of what’s included in this top +level directory.

      • +

    • The --user flag is necessary if you are installing on a shared computer where you do not have root access. If you do have root access and want it to be available to all users, you can omit this flag. See notes below for -more information.

      -

      The -e flag makes it an “editable” install, leaving the source code in +more information.

      • +

    • The -e flag makes it an “editable” install, leaving the source code in place and allowing you to modify it if desired. (Otherwise, by default, pip would move the python code to some -site-packages directory and delete everything else.)

      -

      In order to use the Fortran codes within Clawpack (classic, +site-packages directory and delete everything else.)

      • +

    • In order to use the Fortran codes within Clawpack (classic, amrclaw, or geoclaw), you should then set the environment -variable CLAW to point to the clawpack-v5.8.0 directory within +variable CLAW to point to the clawpack-v5.8.1 directory within the installation directory $HOME/clawpack_src, and FC to point to the desired Fortran compiler, e.g. in the bash shell:

      -
      export CLAW=$HOME/clawpack_src/clawpack-v5.8.0
+
      export CLAW=$HOME/clawpack_src/clawpack-v5.8.1
 export FC=gfortran
 
      
 
      
-
      Notes:
      
-
      You may want to set CLAW even if you are only using PyClaw, since $CLAW is
+
      • +

    • You may want to set CLAW even if you are only using PyClaw, since $CLAW is sometimes used in this documentation to indicate the top level of the -Clawpack source directory structure.

      +Clawpack source directory structure.

      • +

    Installing with pip also compiles Riemann solvers written in Fortran for use in PyClaw. If you get a Fortran error message when installing, see Setting the Fortran compiler to be used by f2py (pip).

    See Set environment variables for more information, and Python path if you are having problems with importing Python modules.

    -
    -
    -

    Quick Installation of only PyClaw

    -

    If you only want to use PyClaw (and associated Python -tools, e.g. VisClaw for visualization), they you could do:

    -
    pip install --user clawpack
-
    -
    -

    or, more specifically,

    -
    pip install --user clawpack==v5.8.0
-
    -
    -

    However, if you think you might want to use the Fortran packages as well -(Classic, AMRClaw, GeoClaw) and/or want easier access to the Python source -code, it is recommended that you follow the instructions above for -Quick Installation of all packages (or see other Additional options for installing Clawpack).

    Next steps:

    Once Clawpack is installed, you can go to one of the following pages to get @@ -172,6 +174,7 @@

    Next steps:

  • Testing a PyClaw installation and running an example

  • Testing your Fortran installation and running an example

    • +

  • Troubleshooting Installation

    • @@ -257,8 +260,8 @@

    Version dev

    Table of Contents

    • pip install instructions
        -
      • Quick Installation of all packages
        • -
      • Quick Installation of only PyClaw
          +
        • Quick Installation of PyClaw with pip
          • +
        • Quick Installation of all packages with pip
          • Next steps:
          • Using pip to install a different version
          • Experimenting with code in the examples directories
            • @@ -272,7 +275,7 @@

            Related Topics

            diff --git a/dev/kmltools_module.html b/dev/kmltools_module.html index 98e2b12d1a..e14a64fb6c 100644 --- a/dev/kmltools_module.html +++ b/dev/kmltools_module.html @@ -114,6 +114,7 @@

            Navigation

          • pcolorcells_for_kml - version of pcolormesh with appropriate dpi and size

          • png2kml - create kml file wrapping a png figure to be viewed on GE

          • kml_build_colorbar - create a colorbar to display on GE

            • +

          • topo2kmz - create kmz file showing onshore and offshore topography

          • kml_header - used internally

          • kml_footer - used internally

          • kml_region - used internally

            • @@ -223,7 +224,7 @@

            Navigation

            -clawpack.geoclaw.kmltools.kml_build_colorbar(cb_filename, cmap, cmin=None, cmax=None, norm=None, label=None, title=None, extend='neither')
            +clawpack.geoclaw.kmltools.kml_build_colorbar(cb_filename, cmap, cmin=None, cmax=None, norm=None, label=None, title=None, extend='neither', close_figs=True)

            Make a png file with a colorbar corresponding to cmap, norm. cmin, cmax are used only if nrm is not provided.

            @@ -335,7 +336,7 @@

            Navigation

            Internally the value dpi (dots per inch) for the png file is determined so that it is at least 16 and so that:

            -

            System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

            +

            System Message: ERROR/3 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

            Unexpected indentation.

            @@ -343,7 +344,7 @@

            Navigation

            dpi * y_inches = dcp * y_cells

            -

            System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 38)

            +

            System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 38)

            Block quote ends without a blank line; unexpected unindent.

            where x_cells, y_cells are the number of cells in each direction.

            @@ -353,14 +354,14 @@

            Navigation

            annotate the figure befor saving it as a png file, which should then be done with:

            -

            System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

            +

            System Message: ERROR/3 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

            Unexpected indentation.

            plt.savefig(png_filename, transparent=True, dpi=kml_dpi)

            -

            System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

            +

            System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

            Block quote ends without a blank line; unexpected unindent.

            The png_extent is needed in construcing a kml file to display the @@ -471,6 +472,39 @@

            Navigation

            Color is green by default.

            +
            +
            +clawpack.geoclaw.kmltools.topo2kmz(topo, zlim=(-20, 20), mask_outside_zlim=True, sea_level=0.0, name='topo', force_dry=None, close_figs=True)
            +

            Create kmz file showing onshore and offshore topography as separate layers. +Currently not very flexible but is useful in quickly creating kmz files +to open on Google Earth showing the onshore topography and offshore +bathymetry as two separate layers. Constant colors on rectangular grid +cells should be properly rendered to ease exploration of DEMs. +A colorbar png file is also created and included in the kmz file.

            +
            +
            Input
            +
              +

            • topo should be a topotools.Topography object,

              • +

            • zlim is the elevation z limits for choosing the color map

              • +

            • mask_outside_zlim if True, suppress plotting outsize zlim

              • +

            • sea_level is the break between water and land colors

              • +

            • name is used in the kml menu and file name

              • +

            • force_dry is currently not used

              • +

            • close_figs to close the pyplot figures after making png files

              • +
            +
            +
            Future
            +

            +
            +
            +

            System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.topo2kmz, line 18)

            +

            Field list ends without a blank line; unexpected unindent.

            +
            +

            If force_dry is an array of the same shape as topo.Z then another png +and kml file are created for land that is below sea_level but where +force_dry = True.

            +
            +
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    Clawpack includes a number of related hyperbolic PDE solvers:

    All of them are built on common algorithmic @@ -98,25 +98,29 @@

    Navigation

    the main differences between them.

    Installation and user interface

    -

    The AMRClaw, GeoClaw, and Classic solvers are Fortran-based +

    The Classic, AMRClaw, and GeoClaw solvers are Fortran-based packages and rely on Makefiles and environment variables. Problems are specified partially through Python scripts at run time (setrun.py) and partially through custom Fortran code at compile time (to set initial conditions, for instance).

    -

    With PyClaw, problems are specified entirely at run time through +

    With PyClaw, problems are specified entirely at run time through Python script files, or interactively (e.g., in IPython or Jupyter notebooks). Typically, the user does not need to write any Fortran code (though custom routines can be written in Fortran -when necessary for performance reasons). -PyClaw uses much of the same library of Fortran code, but that code is +when necessary for performance reasons).

    +

    PyClaw uses much of the same library of Fortran code, but that code is compiled during installation so that it can be imported dynamically within -Python programs.

    +Python programs. In particular, Fortran versions of all the Riemann solvers +available in Classic or AMRClaw are also exposed in PyClaw. These are +converted using f2py, a step +that sometimes causes problems and is not required if you are only using +Fortran versions of the solvers.

    Algorithmic differences

    All of the Clawpack solvers include the classic algorithms described in [LeVeque-FVMHP]; if you only require those, it’s easiest to use Classic or -Pyclaw. Most of the packages contain additional algorithms:

    +PyClaw. Most of the packages contain additional algorithms:

    • AMRClaw includes block-structured adaptive mesh refinement that allows one diff --git a/dev/plotexamples.html b/dev/plotexamples.html index 42d061c05f..44019219fe 100644 --- a/dev/plotexamples.html +++ b/dev/plotexamples.html @@ -84,7 +84,7 @@

      Navigation

      Plotting examples

      -

      See Using setplot.py to specify the desired plots and the examples in the galleries. +

      See Using setplot.py to specify the desired plots and the examples in the Clawpack Gallery. The code that produced each set of plots can be found in the Clawpack directory indicated.

      If you wish to use the Matlab tools, see the Matlab Gallery.

      diff --git a/dev/plotting_python.html b/dev/plotting_python.html index de23b689f4..0894132fbb 100644 --- a/dev/plotting_python.html +++ b/dev/plotting_python.html @@ -87,7 +87,7 @@

      Navigation

      Clawpack includes utilities for plotting using Python. Most of these are defined in the clawpack.visclaw module. In order to use these you will need to insure that you have the required -modules installed (see Installation of required modules).

      +modules installed (see python-install).

      See Python Hints for more information on Python and pointers to many tutorials.

      Producing html plots from the command line

      diff --git a/dev/prereqs.html b/dev/prereqs.html index 27b71feaf1..9e11818b2d 100644 --- a/dev/prereqs.html +++ b/dev/prereqs.html @@ -86,39 +86,37 @@

      Navigation

      Fortran

      -

      PyClaw can now be installed without a Fortran compiler; see Using conda (does not require a Fortran compiler).

      -

      To use the other packages, you will need -gfortran or another F90 compiler

      +

      To use the Fortran versions of the PDE solvers (Classic, AMRClaw, and GeoClaw), +you will need +gfortran or another F90 compiler.

      See Fortran Compilers for more about which compilers work well with Clawpack.

      Python

        -

      • Python Version 2.7 or above, or (new in 5.4.0) Python 3

        • +

      • Python Version 3.0 or above (much of the code works in Python2, but this +is no longer officially supported; see Dropping support for Python 2.7).

      • NumPy (for PyClaw/VisClaw)

      • matplotlib (for PyClaw/VisClaw)

      -

      The Anaconda Python Distribution -is an easy way to get all of these. -See Python Hints for more information on -installing the required modules and to get started using Python if -you are not familiar with it.

      +

      There are many ways to install the Python scientific stack, e.g. via +apt-get or brew. On MacOS, you might check out +ScipySuperpack for Homebrew.

      pip

      If you are installing via pip install then you need pip. -You may already have it; in particular the Anaconda Python distribution -contains pip. If you need to install it, see -https://pip.pypa.io/en/stable/installing/

      -

      The version of pip install suggested for Quick Installation of all packages requires +If you need to install it, see +https://pip.pypa.io/en/stable/installation/

      +

      The version of pip install suggested for Quick Installation of all packages with pip requires a recent version of pip, so you may need to upgrade if you run into problems.

      Git

      If you are installing via pip using the command in -Quick Installation of all packages, or via git clone, then you need Git. +Quick Installation of all packages with pip, or via git clone, then you need Git. You may already have it; in particular the Xcode tools on Mac OSX contains Git. If you need to install it, see the Git book.

      diff --git a/dev/pyclaw/about.html b/dev/pyclaw/about.html index d6094d9c75..a24af947e5 100644 --- a/dev/pyclaw/about.html +++ b/dev/pyclaw/about.html @@ -73,7 +73,7 @@

      Navigation

      previous |
    • Clawpack dev documentation »
      • -
    • Pyclaw »
      • +
    • PyClaw »
    @@ -167,7 +167,7 @@

    Table of Contents

    Related Topics

    @@ -129,7 +129,7 @@

    Version dev

    Related Topics

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    @@ -134,7 +134,7 @@

    From the command line

    Built-in examples

    -

    You can see results from many of the examples in the galleries.

    +

    You can see results from many of the examples in the Clawpack Gallery.

    Adding new examples

    @@ -171,7 +171,7 @@

    Table of Contents

    Related Topics

    @@ -769,7 +769,7 @@

    Table of Contents

    Related Topics

    • Documentation overview
        -
      • Pyclaw @@ -136,7 +136,7 @@

        Version dev

        Related Topics

        • Documentation overview
            -
          • Pyclaw
              +
            • PyClaw
              • diff --git a/dev/pyclaw/index.html b/dev/pyclaw/index.html index 0780623abc..5fcba6ed3a 100644 --- a/dev/pyclaw/index.html +++ b/dev/pyclaw/index.html @@ -4,7 +4,7 @@ - Pyclaw — Clawpack dev documentation + PyClaw — Clawpack dev documentation @@ -82,22 +82,34 @@

              Navigation

              -

              Pyclaw

              +

              PyClaw

              +

              In this section of the documentation, PyClaw refers +a Python version of the hyperbolic PDE solvers that allows solving the +problem in Python (e.g. in a Jupyter notebook) without explicitly using +any Fortran code. Versions of the solvers are written in Python. +However, they use Riemann solvers that are converted from the Fortran +versions into Python-callable versions using +f2py, +to facilitate using the same large set of solvers from either Fortran +or Python. Note that +in order for this to work the solvers must be precompiled, as is done +when using pip install, for example (see pip install instructions).

              +

              See Which Clawpack solver should I use? for more information about the different +capabilities of PyClaw relative to Classic, AMRClaw, and GeoClaw.

              +

              Note: The clawpack/pyclaw directory also contains some +Python tools that are used many places in +Clawpack, e.g. when plotting with visclaw or when compiling and +running Fortran code using a Makefile and setrun.py file +(when using Classic, AMRClaw, and GeoClaw). +These modules are mostly used “under the hood”. +Other Python tools of use in the Fortran versions +are described elsewhere; see e.g. Plotting with Visclaw or GeoClaw Description and Detailed Contents. +All of these modules are pure Python and should work fine as long +as the top level of Clawpack is on your Python path.

              PyClaw installation

              -

              Just do this:

              -
              pip install clawpack
-
              -
              -

              Installing with pip requires that you have a Fortran compiler installed.

              -

              Alternatively, if you use Anaconda or -Conda, you can:

              -
              conda install -c clawpack -c conda-forge clawpack
-
              -
              -

              This option will also install optional dependencies including PETSc and HDF5, -which are useful for large-scale parallel runs. Installing with Conda does not -require that you have a Fortran compiler.

              +

              Using pip install is the recommended approach, see +pip install instructions.

              Examples

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              • Documentation overview
                  -
                • Pyclaw
                    +
                  • PyClaw
                    • Going Further @@ -150,7 +150,7 @@

                      Table of Contents

                      Related Topics

                      • Documentation overview
                          -
                        • Pyclaw
                            +
                          • PyClaw
                            • PyClaw Basics @@ -279,7 +279,7 @@

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                              • Documentation overview
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                                • Pyclaw
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                                  • PyClaw
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                                                      • Documentation overview
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                                                        • Pyclaw
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                                                                          • PyClaw
                                                                            • PyClaw Basics @@ -321,7 +321,7 @@

                                                                              Table of Contents

                                                                              Related Topics

                                                                              • Documentation overview
                                                                                  -
                                                                                • Pyclaw
                                                                                    +
                                                                                  • PyClaw
                                                                                    • diff --git a/dev/python.html b/dev/python.html index babcdb7e16..15f4590d49 100644 --- a/dev/python.html +++ b/dev/python.html @@ -82,23 +82,9 @@

                                                                                    Navigation

                                                                                    -

                                                                                    Python Hints

                                                                                    - +

                                                                                    Python Hints

                                                                                    -

                                                                                    Dropping support for Python 2.7

                                                                                    +

                                                                                    Dropping support for Python 2.7

                                                                                    As of Clawpack v5.7.0 we are no longer supporting Python 2.7, and Python 3.x is expected, see v5.7.0 release notes. At this point we believe v5.7.0 still works with Python 2.7, but we are phasing out @@ -118,37 +104,8 @@

                                                                                    Navigation

                                                                                    https://docs.python.org/3/howto/pyporting.html and other online resources discussing the differences between Python 2 and 3.

                                                                                    -
                                                                                    -

                                                                                    What is Python?

                                                                                    -

                                                                                    Python is a powerful object-oriented interpreted scripting/programming -language. Some version of Python is almost certainly on your computer -already (on unix, linux, OSX type:

                                                                                    -
                                                                                    $ python --version
-
                                                                                    -
                                                                                    -

                                                                                    to find out which version, or just:

                                                                                    -
                                                                                    $ python
-
                                                                                    -
                                                                                    -

                                                                                    to start a python shell with a prompt that looks like:

                                                                                    -
                                                                                    >>>
-
                                                                                    -
                                                                                    -

                                                                                    You may prefer to use IPython, which is a nicer shell -than the pure python shell, with things like command completion and history. -See the Quick IPython Tutorial.

                                                                                    -
                                                                                    -
                                                                                    -

                                                                                    Installation of required modules

                                                                                    -

                                                                                    To effectively use the pyclaw and Clawpack plotting routines that are -written in Python, you will need version 2.7 or greater -(but not 3.0 or above, which is not backwards compatible). -some modules that are not included in the standard Python distribution. -Python modules are loaded with the import statement in Python and a wide -variety of specialized modules exist for various purposes since people use -Python for many different purposes.

                                                                                    -

                                                                                    An alternative to installing the packages discussed below, you could also use the -Clawpack Virtual Machine, which has all the required Python modules pre-installed.

                                                                                    +
                                                                                    +

                                                                                    References and tutorials

                                                                                    For use with Clawpack, you will need the Numpy module (Numerical Python) that allows working with arrays in much the same way as in Matlab. This is distributed as part of @@ -156,44 +113,24 @@

                                                                                    Navigation

                                                                                    See the Installing SciPy page for tips installing SciPy and NumPy on various platforms.

                                                                                    For plotting you will also need the matplotlib module which provides Matlab-like -plotting commands for 1d and 2d plots (e.g. contour and pcolor plots). -This is generally the hardest thing to get going properly. See the -matplotlib Installation FAQ.

                                                                                    -

                                                                                    Often the easiest way to get all the modules you need is to install the

                                                                                    -

                                                                                    Anaconda Python Distribution -or the -Enthought Python Distribution, which is free for academic -users. Versions are available for Windows, Mac OS X, and Redhat linux.

                                                                                    -

                                                                                    With some versions of Linux (e.g. debian and Ubuntu), you can easily install -what’s needed using apt-get:

                                                                                    -
                                                                                    $ apt-get install python-numpy
-$ apt-get install python-scipy
-$ apt-get install python-matplotlib
-
                                                                                    -
                                                                                    -

                                                                                    For OS X, you might also try the Scipy Superpack. -See also these tips on installing matplotlib on OS X.

                                                                                    -
                                                                                    -
                                                                                    -

                                                                                    Notebooks

                                                                                    -

                                                                                    See notebooks.

                                                                                    +

                                                                                    Notebooks

                                                                                    +

                                                                                    The Clawpack Gallery of Jupyter +Notebooks +contains a number of notebooks with other examples of using Python for +Clawpack.

                                                                                    @@ -212,8 +149,6 @@

                                                                                    Table of Contents

                                                                                    • Python Hints diff --git a/dev/python_path.html b/dev/python_path.html index 2e52fabc20..e0df731a4e 100644 --- a/dev/python_path.html +++ b/dev/python_path.html @@ -78,10 +78,8 @@

                                                                                      Navigation

                                                                                      When using PyClaw or other Python tools from Clawpack (e.g. the visualization tools in VisClaw or Python tools for working with topo and dtopo from GeoClaw), you need to be able to import various modules.

                                                                                      -

                                                                                      For a general discussion of importing Python modules, see the tutorial in -the Python documentation: -Python 2, -Python 3.

                                                                                      +

                                                                                      For a general discussion of importing Python modules, see the tutorial in the +Python3 documentation.

                                                                                      Below are some hints in case you run into problems with import statements with modules not being found, or being imported from the wrong version of Clawpack (if you have more than one on your computer).

                                                                                      @@ -219,13 +217,20 @@

                                                                                      easy-install.pth

                                                                                      PYTHONPATH

                                                                                      -
                                                                                      -

                                                                                      Warning

                                                                                      -

                                                                                      Setting the environment variable PYTHONPATH is generally +

                                                                                      If you install Clawpack with pip, then you do not need to include it in +environment variable PYTHONPATH.

                                                                                      +

                                                                                      Setting the environment variable PYTHONPATH is often considered bad practice in the Python community and can lead to problems, see for example PYTHONPATH Considered Harmful.

                                                                                      -
                                                                                      +

                                                                                      In spite of the possible drawbacks, some Clawpack developers often +use PYTHONPATH to switch versions without difficulty, particularly +when using one of the Options for installing Clawpack Fortran codes rather than pip.

                                                                                      +

                                                                                      If you do wish to use it, you should set PYTHONPATH to point to the top +level of the clawpack directory for the code you wish to use. +Then use the whichclaw.py utility to check that this is where Clawpack +is imported from, and there is not an easy-install.pth file generated by +pip that points to a different location.

                                                                                      If you have an environment variable PYTHONPATH set, the paths specified here may be searched before or after what is specified in the users’ site-packages/easy-install.pth, depending on how you set PYTHONPATH. @@ -240,13 +245,6 @@

                                                                                      PYTHONPATHwhichclaw.py utility to report this, along with any other possibly conflicting easy-install.pth files.

                                                                                      See Set environment variables for information on setting environment variables.

                                                                                      -

                                                                                      In spite of the possible drawbacks, some Clawpack developers often -use PYTHONPATH to switch versions without difficulty. If you do -wish to use it, you should set PYTHONPATH to point to the top -level of the clawpack directory for the code you wish to use. -Then use the whichclaw.py utility to check that this is where Clawpack -is imported from, and there is not a easy-install.pth that points to a -different location.

                                                                                    diff --git a/dev/regression.html b/dev/regression.html index 968f58ea09..8f2e7773b9 100644 --- a/dev/regression.html +++ b/dev/regression.html @@ -73,7 +73,7 @@

                                                                                    Navigation

                                                                                    previous |
                                                                                  • Clawpack dev documentation »
                                                                                    • -
                                                                                  • Pyclaw »
                                                                                    • +
                                                                                  • PyClaw »
                                                                                  • Developers’ Guide »
                                                                                  @@ -130,7 +130,7 @@

                                                                                  Fortran codesgalleries. An attempt at automating this +with those archived in the Clawpack Gallery. An attempt at automating this can be found in the $CLAW/amrclaw/examples directory, which uses the imagediff tool described below. This is still under development.

                                                                                  @@ -322,7 +322,7 @@

                                                                                  Table of Contents

                                                                                  Related Topics

                                                                                  • Documentation overview
                                                                                      -
                                                                                    • Pyclaw
                                                                                        +
                                                                                      • PyClaw
                                                                                        • Developers’ Guide
                                                                                          • diff --git a/dev/release_5_6_0.html b/dev/release_5_6_0.html index be5c8e4b1c..3f0b0f08a0 100644 --- a/dev/release_5_6_0.html +++ b/dev/release_5_6_0.html @@ -78,7 +78,7 @@

                                                                                          Navigation

                                                                                          Clawpack 5.6.0 was released on June 2, 2019. See Installing Clawpack.

                                                                                          Changes relative to Clawpack 5.5.0 (Aug 28, 2018) are shown below.

                                                                                          To see more recent changes that are in the the master branch but not yet -released, see Changes to master since v5.8.0.

                                                                                          +released, see Changes to master since v5.8.1.

                                                                                          Changes that are not backward compatible

                                                                                          diff --git a/dev/release_5_6_1.html b/dev/release_5_6_1.html index c5451a8ac4..8d5d04c2de 100644 --- a/dev/release_5_6_1.html +++ b/dev/release_5_6_1.html @@ -78,7 +78,7 @@

                                                                                          Navigation

                                                                                          Clawpack 5.6.1 was released on October 28, 2019. See Installing Clawpack.

                                                                                          Changes relative to Clawpack 5.6.0 (June 2, 2019) are shown below.

                                                                                          To see more recent changes that are in the the master branch but not yet -released, see Changes to master since v5.8.0.

                                                                                          +released, see Changes to master since v5.8.1.

                                                                                          Changes that are not backward compatible

                                                                                          $CLAW/amrclaw/src/2d/amr_module.f90 has changed, so do a make new in diff --git a/dev/release_5_7_0.html b/dev/release_5_7_0.html index fbaefe70a8..848201f6af 100644 --- a/dev/release_5_7_0.html +++ b/dev/release_5_7_0.html @@ -80,7 +80,7 @@

                                                                                          Navigation

                                                                                          [DOI 10.5281/zenodo.3764278].

                                                                                          Changes relative to Clawpack 5.6.1 (October 28, 2019) are shown below.

                                                                                          To see more recent changes that are in the the master branch but not yet -released, see Changes to master since v5.8.0.

                                                                                          +released, see Changes to master since v5.8.1.

                                                                                          Python support

                                                                                          As of v5.7.0 we are no longer supporting Python 2.7, and Python 3.x is diff --git a/dev/release_5_7_1.html b/dev/release_5_7_1.html index 4e6c150849..000bc19c32 100644 --- a/dev/release_5_7_1.html +++ b/dev/release_5_7_1.html @@ -80,7 +80,7 @@

                                                                                          Navigation

                                                                                          [DOI 10.5281/zenodo.4025432].

                                                                                          Changes relative to Clawpack 5.7.0 (April 23, 2020) are shown below.

                                                                                          To see more recent changes that are in the the master branch but not yet -released, see Changes to master since v5.8.0.

                                                                                          +released, see Changes to master since v5.8.1.

                                                                                          Changes that are not backward compatible

                                                                                            diff --git a/dev/release_5_8_0.html b/dev/release_5_8_0.html index 988c8e3cff..50fa4602ca 100644 --- a/dev/release_5_8_0.html +++ b/dev/release_5_8_0.html @@ -79,7 +79,7 @@

                                                                                            Navigation

                                                                                            Permanent DOI: http://doi.org/10.5281/zenodo.4503024

                                                                                            Changes relative to Clawpack 5.7.1 (Sept. 11, 2020) are shown below.

                                                                                            To see more recent changes that are in the the master branch but not yet -released, see Changes to master since v5.8.0.

                                                                                            +released, see Changes to master since v5.8.1.

                                                                                            Changes that are not backward compatible

                                                                                              diff --git a/dev/release_5_8_1.html b/dev/release_5_8_1.html new file mode 100644 index 0000000000..3576f60c75 --- /dev/null +++ b/dev/release_5_8_1.html @@ -0,0 +1,245 @@ + + + + + + + v5.8.1 release notes — Clawpack dev documentation + + + + + + + + + + + + + + + + +
                                                                                              +
                                                                                              + +
                                                                                              +
                                                                                              + + + +
                                                                                              +
                                                                                              +
                                                                                              +
                                                                                              + +
                                                                                              +

                                                                                              v5.8.1 release notes

                                                                                              +

                                                                                              Clawpack 5.8.1 was released on October 19, 2021. See Installing Clawpack.

                                                                                              +

                                                                                              The installation instructions have been reorganized (once again) +in an attempt to make the different options clearer.

                                                                                              +

                                                                                              Permanent DOI: http://doi.org/10.5281/zenodo.??

                                                                                              +

                                                                                              Changes relative to Clawpack 5.8.0 (February 4, 2021) are shown below.

                                                                                              +

                                                                                              To see more recent changes that are in the the master branch but not yet +released, see Changes to master since v5.8.1.

                                                                                              +
                                                                                              +

                                                                                              Changes that are not backward compatible

                                                                                              +
                                                                                              +
                                                                                              +

                                                                                              General changes

                                                                                              +
                                                                                              +
                                                                                              +

                                                                                              Changes to classic

                                                                                              +

                                                                                              No changes.

                                                                                              +

                                                                                              See classic diffs

                                                                                              +
                                                                                              +
                                                                                              +

                                                                                              Changes to clawutil

                                                                                              +

                                                                                              No changes.

                                                                                              +

                                                                                              See clawutil diffs

                                                                                              +
                                                                                              +
                                                                                              +

                                                                                              Changes to visclaw

                                                                                              +

                                                                                              No major changes.

                                                                                              +

                                                                                              See visclaw diffs

                                                                                              +
                                                                                              +
                                                                                              +

                                                                                              Changes to riemann

                                                                                              +
                                                                                                +

                                                                                              • Fix rp1_shallow_hlle.f90 to work better near dry states.

                                                                                                • +
                                                                                              +

                                                                                              See riemann diffs

                                                                                              +
                                                                                              +
                                                                                              +

                                                                                              Changes to amrclaw

                                                                                              +

                                                                                              No changes.

                                                                                              +

                                                                                              See amrclaw diffs

                                                                                              +
                                                                                              +
                                                                                              +

                                                                                              Changes to geoclaw

                                                                                              +
                                                                                                +

                                                                                              • Some improvements to storm tracks

                                                                                                • +

                                                                                              • Reading (some) geotiff files now supported in topotools

                                                                                                • +

                                                                                              • Added kmltools.topo2kmz to make Google Earth overlays showing topography

                                                                                                • +

                                                                                              • Some other bug fixes.

                                                                                                • +
                                                                                              +

                                                                                              See geoclaw diffs

                                                                                              +
                                                                                              +
                                                                                              +

                                                                                              Changes to PyClaw

                                                                                              +

                                                                                              For changes in PyClaw, see the PyClaw changelog.

                                                                                              +

                                                                                              See pyclaw diffs

                                                                                              +
                                                                                              +
                                                                                              +
                                                                                              +

                                                                                              Other Clawpack Repositories

                                                                                              +

                                                                                              The repositories below are not included in the Clawpack tarfile or pip +install, but changes to these repositories may also be of interest.

                                                                                              + +
                                                                                              + + +
                                                                                              +
                                                                                              +
                                                                                              + +
                                                                                              +
                                                                                              +
                                                                                              + © Copyright CC-BY 2020, The Clawpack Development Team. + Created using Sphinx. +
                                                                                              + + + + \ No newline at end of file diff --git a/dev/releases.html b/dev/releases.html index 7a555d2dc2..d5d140b2ea 100644 --- a/dev/releases.html +++ b/dev/releases.html @@ -92,7 +92,7 @@

                                                                                              Other notes:Citing this work for the suggested way to cite the version of Clawpack that you are using in publications.

                                                                                            • For changes in PyClaw, see the PyClaw changelog.

                                                                                              • -

                                                                                            • See Changes to master since v5.8.0 for changes to the master branch on Github +

                                                                                            • See Changes to master since v5.8.1 for changes to the master branch on Github that are not in the most recent release.

                                                                                            • The “dev” branch of the documentation (selected under Versions on the menu @@ -109,6 +109,8 @@

                                                                                              Releases:10.17605/osf.io/kmw6h. See Citing this work for more information on how best to cite Clawpack.

                                                                                                +

                                                                                              • v5.8.1 release notes – October 19, 2021 +[DOI 10.5281/zenodo.??]

                                                                                              • v5.8.0 release notes – February 4, 2021 [DOI 10.5281/zenodo.4503024]

                                                                                              • v5.7.1 release notes – September 11, 2020 diff --git a/dev/searchindex.js b/dev/searchindex.js index 94be04cfc2..794aa99b41 100644 --- a/dev/searchindex.js +++ b/dev/searchindex.js @@ -1 +1 @@ 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155],alloc:[20,99,117,126,138],allocat:117,allot:59,allow:[4,6,13,22,27,28,29,32,38,39,44,45,47,50,51,53,54,56,58,64,66,67,70,71,73,76,77,86,92,93,99,101,104,105,106,110,111,113,114,117,118,119,120,121,123,124,126,129,131,137,139,140,141,142,146,150,152,154],almost:105,alon:[16,51],along:[6,14,16,24,27,30,32,39,44,51,54,68,70,106,110,117,128,131,133,140,146,154],alpha:[51,55,99],alphabet:81,alreadi:[0,1,6,12,13,18,28,29,41,55,56,57,58,59,60,66,79,80,94,98,100,103,105,114,122,152],also:[3,4,5,6,7,8,9,11,12,16,17,18,20,22,23,24,25,28,29,30,32,33,35,36,37,38,39,41,42,44,47,48,51,52,53,54,55,56,57,58,59,62,63,66,67,68,70,71,72,73,76,77,79,83,85,86,89,91,93,94,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,135,137,138,139,140,141,142,144,145,146,147,148,149,150,152,153,154,155,157,158],alter:51,altern:[30,35,36,44,47,51,57,60,62,67,76,91,94,105,106,110,117,118,119],although:[30,51,63,67,95,96,98,110,122,152],alwai:[16,22,26,27,28,32,41,53,54,58,67,83,92,109,110,113,114,126,133,139,140,141,150,155],amal:[4,17,81,91],amazon:25,amazonaw:13,amdq:[97,129],ami:25,among:124,amount:[44,48,54],amplitud:[5,119],amr:[4,7,8,16,20,23,25,27,28,32,34,38,44,45,52,59,67,72,73,76,81,89,118,120,121,122,124,126,133,136,137,139,141,149,155],amr_1d:122,amr_2d:[121,122],amr_:[3,7],amr_celledges_show:3,amr_contour_color:3,amr_contour_show:3,amr_data_show:118,amr_level:72,amr_level_max:139,amr_levels_max:[32,110,138,139],amr_modul:[71,110,117,123,124],amrclaw:[4,5,6,12,15,16,19,20,22,23,24,28,36,38,39,41,44,45,46,52,55,56,57,58,60,66,67,68,71,72,73,100,106,107,110,111,128,129,131,134,135,137,140,144,145,148,149,153],amrdata:[5,22,32,110,124,126,138,139,140],amrflag:110,amrlib:117,amrnez:110,an11:54,anaconda:[51,80,91,100,105],anal:17,analog:[137,138],analysi:17,andi:4,angl:[16,30,47,70],ani:[3,4,5,6,8,13,16,18,19,20,22,27,28,29,32,35,36,37,45,48,50,51,54,55,56,58,61,62,64,66,67,69,71,72,73,77,81,87,88,89,91,92,93,94,96,98,100,104,106,109,110,111,117,121,123,128,131,132,133,136,137,138,140,146,155,158],anim:[12,16,42,51,117,124,125,142],animation_tool:[124,125],anisotrop:[6,22],anl:94,annot:[27,59],annual:24,anoth:[3,22,39,44,51,55,57,58,72,76,80,88,99,102,111,121,146,155],answer:24,anyth:[3,6,28,29,56,58,63,111,121],anywher:110,aoml:146,apach:13,apdq:[97,129],api:[47,121],app:[12,13,18,23,26,28,29,32,37,42,70,108,109,116,120,121,122,123,124,125,126,130],appar:[30,32,71],appeal:51,appear:[0,1,3,5,8,13,18,23,32,44,45,51,54,57,59,62,65,77,93,98,101,119,126,140,142,150],append:[5,20,32,38,39,44,51,60,77,86,98,110,118,119,128,129,139],appl:17,appli:[3,4,5,6,13,16,25,30,48,51,53,64,66,70,77,79,87,89,92,99,110,128,137,140,155],applic:[4,6,15,16,19,20,22,23,24,28,29,32,35,36,37,41,42,45,46,55,56,58,63,66,68,71,79,88,89,90,91,93,99,104,107,109,110,111,113,116,117,119,120,121,123,124,129,131,133,134,137,140,144,145,150,152,153,155,156],appreci:81,approach:[5,7,13,28,29,38,44,54,56,69,76,84,94,96,104,110,117,119,120,122,129,130,136,140,155,158],appropri:[4,5,6,13,16,24,28,45,48,49,51,55,56,58,59,60,64,67,68,69,71,83,86,87,88,92,94,95,96,97,98,111,123,129,132,135,137,146,155,158],approv:48,approxim:[6,16,25,33,48,51,70,129],april:[24,124,125,127],apt:[13,105],arbitrari:[32,59,99,113,131,140],arbitrarili:66,arc:132,arcgi:152,architectur:94,archiv:[12,21,36,51,55,111,142,148,152,154],arcminut:[70,150],arcsecond:[45,150],area:[15,22,45,99,108,119,133,134],arg:[89,98],argument:[0,1,2,3,27,30,45,47,50,51,53,77,83,84,88,89,92,96,98,99,101,104,111,121,129,131,136,137,138,146,152,155],argv:[139,141],aris:[61,81],arithmet:64,aron:[4,17,81,91],arora:87,arora_ro:87,around:[6,30,32,39,59,92,108,111,124,138,139,146,152,155],arrai:[0,3,6,15,20,22,27,30,32,33,38,44,45,47,49,53,59,77,83,84,86,87,89,91,92,93,96,97,98,99,101,103,104,105,113,114,115,119,121,124,126,129,130,131,134,137,138,139,140,141,146,150,152,155],arrang:152,arriv:[22,32,34,39,45,119,132,133],arrival_tol:32,articl:[4,17,91,142],artifici:[16,133],arxiv:52,asc:152,ascii:[44,53,67,83,86,93,98,119,128,137,139,141,150,156],ascii_output_format:68,ask:24,ask_us:152,aspect:[12,24,29,48,49,67],assembl:57,assert:[139,141],assess:[4,48,132],assign:[30,32,83,86,92,98],assist:[22,124],associ:[0,1,2,6,22,51,58,71,89,92,93,111],assum:[3,5,20,22,30,32,36,39,47,48,51,53,54,55,59,67,70,76,92,93,95,96,97,103,104,110,117,131,132,137,140,146,147,150,152,154,158],assumpt:[51,54],asteroid:4,astronom:132,atcf:[108,121,146,147],aterrel:4,atmospher:4,attach:[55,92,101],attempt:[5,8,11,20,33,35,36,62,92,104,111,113,146,152,153],attirbut:22,attr:[89,98],attribur:5,attribut:[5,7,22,30,38,44,66,70,76,78,79,83,86,89,92,94,96,98,99,110,113,118,122,128,136,137,138,140,146,152],attributeerror:77,aug:[17,122],aug_glob:97,augment:[66,130],august:[24,121,127],austin:4,author:[17,25,45,48,87,91,92,97,109],auto:[0,44,84],autom:[14,54,84,111],automat:[0,2,3,8,11,16,30,35,36,41,51,55,62,76,77,79,83,88,92,94,100,101,102,104,111,113,124,126,137,138,140,150],au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rown:[81,152],brows:[11,24,42,51,67,142,155],browser:[13,28,29,35,36,51,54,142],bsd:[4,61,81,121],buffer:[30,39,44,110,118,119,138,139,152],buffer_length:152,buffer_s:[30,70],bug:[4,8,12,22,24,41,51,64,71,77,81,116,117,118,119,121,126],build:[4,17,28,29,54,55,67,84,94,104,120,131],buildsystem:94,built:[28,29,64,73,82,91,94,96,98,110,111,144,145],bulk:[19,83,97,103,129,139,155],bull:[17,30],buoi:45,burger:[91,129,155],burgers_1d:97,burgers_1d_pi:97,busi:[61,81],butcher:99,button:[12,13,28,51,59,120],bzip2:124,c210:[17,91],c231:[17,91],c_center:89,c_centers_with_ghost:89,c_l:97,c_node:89,c_nodes_with_ghost:89,c_r:97,cach:[22,47,55,79,81,124,138],cache_dir:47,cada:87,cada_torrilhon_limit:87,cada_torrilhon_limiter_nonlinear:87,cake:74,cal:[129,155,158],calcul:[3,5,6,27,30,33,45,47,67,70,77,89,97,99,114,119,152],calculate_geometri:30,calculate_geometry_triangl:30,calhellev08:17,calhoun:[4,17,51],calhounhelzellevequ:16,call:[1,6,9,20,22,27,30,38,41,44,50,51,63,66,67,70,72,77,79,83,84,86,87,92,93,96,98,99,101,103,104,110,111,113,117,118,120,121,129,131,133,135,137,139,140,141,146,152,155],call_before_step_each_stag:99,call_setplot:77,callabl:104,calucl:97,cambridg:17,came:14,camera:51,can:[0,2,3,4,5,6,7,8,9,11,12,13,14,15,16,19,20,22,24,26,27,28,29,30,32,35,36,37,38,39,40,41,42,44,45,46,47,48,51,52,53,54,55,56,57,58,59,60,62,63,64,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,83,84,85,87,88,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,110,111,113,114,117,118,119,120,121,124,125,126,127,128,129,131,132,133,134,135,136,137,138,139,140,141,142,144,145,146,148,150,152,153,154,155,156,158],cannot:[52,58,92,126,133,146],canopi:100,capa:98,capa_index:[137,139,141],capab:152,capabili:121,capabilit:119,capabilti:121,capabl:[7,12,22,32,34,48,52,66,73,84,113,118,119,121,122,123,124,125,152,154],capac:[15,97,134,137,138,139,141],captur:[32,48,131,150],car_nam:146,care:[32,39,45,94],carefulli:[20,22,64],cartesian:[32,46,59,84,140],cartopi:146,cascad:4,cast:152,cat_nam:146,catalog:154,categor:146,categori:146,category_color:146,caus:[22,48,51,54,61,62,79,81,102,111,118,119,120,122,126,136,138,150,152],caut:87,caution:48,cautionari:[25,45,63,140],cautiou:48,caxi:67,cb_file:59,cb_filenam:59,cb_kwarg:152,cb_name:59,cb_xfrac:59,cb_yfrac:59,cbar:[97,152],cdot:[64,96,131],ceas:105,cell:[3,4,5,7,8,15,16,20,22,25,27,32,33,44,45,51,53,59,66,67,71,72,73,83,89,94,97,99,101,103,110,113,114,118,119,120,121,122,123,124,126,129,132,133,134,137,138,139,140,141,147,149,150,155,158],celledg:3,celledges_show:[3,22],cellgridintegr:113,cellgridintegrate2:113,cellsiz:[39,53,117,150],center:[4,5,27,30,32,33,39,44,51,53,59,70,83,89,96,97,103,110,121,131,133,138,139,140,146,147,150,155],centerlin:30,centers_with_ghost:89,central:[137,146,147],central_pressur:146,centroid:[30,70],certain:[14,32,45,57,66,93,110,118,131,137],certainli:[94,105],certik:[4,81],cf2py:84,cfl:[6,89,93,99,103,113,118,137,139,140,141],cfl_desir:[99,137,139,141],cfl_max:[99,137,139,141],cfl_superbe:87,cfl_superbee_theta:87,challeng:120,chanc:81,chang:[1,6,8,13,15,16,19,20,25,28,29,30,32,40,41,50,51,52,53,54,55,56,58,59,62,63,64,66,67,68,71,72,73,76,79,83,84,90,92,93,101,104,105,108,109,110,111,127,129,133,134,137,138,139,140,141,144,145,150,153,155],changelog:[18,22,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127],changes_to_mast:55,channel:24,chapter:[16,129,137,155],char_decomp:99,charact:47,characterist:99,charg:13,chava:140,cheaper:13,check:[6,14,15,16,20,32,35,36,40,41,50,51,52,54,55,56,58,62,67,77,83,84,86,91,94,98,99,101,103,104,106,107,110,114,123,131,133,134,138,139,144,145,146,152,153,154,155],check_3rd_ord_cond:99,check_diff:[104,111],check_lmm_cond:99,check_valid:86,check_valu:[104,111],checkout:[28,52,54,55],checkpoint:[25,44,118,119,121,123,126,137,139,141],checkpt_interv:[137,139],checkpt_styl:[118,128,137,139],checkpt_tim:[137,139],checksum:92,chen:[30,154],chile2010:[51,109,110,113,116,122,150],chile2010_adjoint:5,chile2010_fgmax:32,chile2010a:[29,109],chile2010b:109,chile:[45,59,70],chile_2010:51,chile_dtopo:70,chk00006:[139,141],chk00100:118,chk:118,chkaaaaa:118,chkbbbbb:118,chknnnnn:[128,137,139,141],choic:[16,45,76,99,137,139,140,141,155],choos:[0,7,70,96,137,140],chose:64,chosen:[3,29,32,38,39,51,53,66,103,110,126,132,138],chri:4,chunk:92,chunksiz:92,circl:[3,47,77],circular:17,cise:17,citat:[4,55],cite:[25,55,57,127],cjvogl:4,clamshel:114,clarifi:22,clariti:38,clash:67,classic4:141,classic:[4,6,12,15,16,19,20,22,23,24,28,41,42,46,55,56,57,58,63,69,71,72,73,81,83,86,88,89,90,91,92,96,106,107,111,128,129,134,135,138,140,145,153,155],classic_1d:63,claw1:[63,104],claw1ez:63,claw:[5,6,8,11,12,13,14,15,16,19,20,22,24,28,30,32,33,35,36,37,38,40,41,44,45,47,49,50,52,54,55,56,57,58,59,62,63,67,69,70,71,78,83,86,88,91,92,93,94,100,102,106,107,108,109,110,111,113,114,116,117,120,121,123,129,133,134,139,140,141,143,144,145,148,149,150,152,153,155,156],claw_1dnoncon:158,claw_git_diff:[28,50,55],claw_git_statu:[28,50,55,125],claw_lib:68,claw_outdir:[62,77],claw_packag:99,claw_pkg:[137,138,139,140,141],claw_topo_download:152,claw_vers:58,clawdata2pyclaw:84,clawdata:[5,38,113,117,128,137,138,139,140,141],clawdev2013:54,clawdev:54,clawgraph:67,clawicon:54,clawlogo:54,clawpack:[1,4,5,6,7,11,16,26,28,30,32,33,34,35,36,37,38,39,41,42,43,44,45,46,47,48,50,51,58,59,60,61,63,66,67,69,70,71,75,76,77,78,79,80,81,82,83,85,86,88,89,90,91,92,93,94,95,96,97,98,101,102,103,104,105,106,109,111,112,113,114,115,116,117,118,119,128,129,131,135,137,138,139,140,142,143,146,148,150,152,153,155,156,158],clawpack_gpu:52,clawpack_src:[56,58,106],clawplotax:[1,2,3,27,77,121,126,136],clawplotdata:[2,3,27,44,51,77,79,86,136],clawplotfigur:[0,1,51,77,136],clawplotitem:[0,1,7,22,27,76,78,118,121,136],clawrundata:[5,44,59,122,128,137,138,139,141],clawsolut:1,clawsolv:[99,129],clawsolver1d:[83,86,89,99,103,129],clawsolver2d:[89,99],clawutil:[5,11,14,19,20,23,28,40,41,50,55,57,62,106,111,135,137,138,139,141,152,153],clean:[22,54,55,104,117,121],cleaner:[28,119],cleanup:120,clear:[1,2,6,67,79],clearer:[123,126],clearfigur:1,clearfram:[1,79],cleargaug:44,clearli:[44,48,51,131],clf:2,clf_each_fram:2,click:[4,12,13,18,28,51,54,111,120,127],clifford:24,clint:17,clobber:[92,118],clockwis:[32,47,70,152],clone:[12,18,23,24,42,52,54,55,56,58,80,94,100,109,153],close:[13,39,51,54,66,67,92,110,124,138,146],closer:[70,139],closest:146,cloud:13,cluster:[6,17,57,110,138,139],clustering_cutoff:[110,138,139],cma:146,cmap:[39,51,59,66,77,131,152],cmap_dri:[39,66],cmap_land:66,cmap_sea:66,cmap_sea_dri:66,cmap_slip:30,cmap_topo:66,cmax:[51,59],cmax_dz:30,cmax_slip:30,cmdline:106,cmin:[51,59],cmin_slip:30,cmmi:4,cname:54,coars:[3,32,51,110,119,126,137,150,155],coarsen:[53,110,121,122,138,150,152],coarsen_method:53,coarser:[3,16,53,119,133,137,138,155],coarsest:[6,51,72,113,128,137],coast:[39,66,110,133,152],coastal:[48,124,132,133,140,150],coastlin:[32,51,66,124,131,140,154],code:[4,5,6,7,8,12,14,16,19,20,21,22,23,24,27,29,32,35,36,38,40,41,42,44,45,48,50,52,53,54,56,57,61,62,63,64,68,69,70,71,72,73,75,77,79,81,83,84,89,91,92,93,94,96,99,100,103,105,106,109,112,113,114,117,118,119,120,121,122,123,124,126,128,129,130,131,137,138,139,140,141,142,146,148,149,150],code_of_conduct:121,coeffici:[5,64,96,97,99,101,102,103,129,140],colella:[6,17],collabor:[51,142],collect:[12,25,26,28,30,32,70,76,83,99,142],collela:120,color:[3,30,39,51,59,66,67,76,131,136,146,152],colorado:24,colorbar:[3,39,59,66,121,124,131,152],colorbar_kwarg:121,colorbar_labels:30,colorbar_shrink:30,colorbar_ticks:30,colormap:[3,30,39,46,51,66,67,76,78,118,124,152],column:[10,30,32,44,48,60,93,97,117,131,152],column_list:30,column_map:30,com:[12,13,23,24,26,28,29,52,54,55,56,57,58,92,94,96,100,116,118,119,120,127,130],combin:[20,54,59,118,154],combinatori:111,come:[3,28,77,79,88,94,99,117,150,155],comfort:[58,96],comm_world:104,command:[0,1,2,3,11,13,14,28,40,50,51,52,55,56,57,58,62,69,76,77,80,83,84,86,91,94,95,99,103,104,105,106,111,129,135,136,137,138,150,152],commenc:128,comment:[5,11,24,49,55,120,128],commit:[25,30,50,54,55,111],common:[3,23,28,35,36,40,41,62,63,73,76,83,97,99,101,102,119,121,124,153,155],common_sourc:63,commonli:[3,67,77,79],commun:[25,51,81,101,104,106,110,121],comot:4,compact:[66,150],compactli:131,compar:[5,22,36,44,48,51,55,77,93,110,111,132,138,140,148,154,158],compare_gaug:117,comparison:52,compat:[28,30,47,51,59,70,76,94,102,105,114,115,119,120,152],compil:[13,25,35,36,40,46,56,58,63,71,73,79,80,84,91,92,96,100,104,113,129,130,135],compile_librari:104,complet:[20,22,28,47,62,79,83,84,94,104,105,111],complevel:92,complex:[12,38,89],compliant:41,complic:[16,77,84,131,136],compon:[3,16,20,22,25,36,44,56,58,67,72,76,96,98,100,101,110,117,126,130,137,138,139,150,155],compos:[30,83],comprehens:111,compress:[30,92,152],compris:[22,91,152],comput:[3,4,5,6,13,16,17,27,29,30,32,33,39,44,47,51,53,56,58,59,60,62,68,70,76,77,79,84,86,89,91,92,93,94,99,103,105,106,108,110,113,114,118,119,123,126,129,133,137,139,140,141,147,150,155,158],computation:[84,99],compute_f:[86,93],compute_gauge_valu:93,compute_p:[83,86],concentr:108,concept:[25,129],concern:[22,45,138],conclus:[4,51],conda:[51,56,80,91],condit:[5,7,20,25,61,63,73,81,82,83,84,86,93,99,107,113,114,117,121,132,137,139,140,141],conduct:121,conf:[54,55],confer:24,config:94,config_fc:153,configur:[77,83,94,152],confirm:48,conflict:[6,28,58,62,67,102,106],conform:[22,28,33,98,121,150],confus:[3,53,58,106,126,129],conjunct:[24,39,66,92,110],conlict:62,connect:[32,54,59,66,124,131],consequenti:[61,81],conserv:[4,5,6,17,93,99,101,122,130,155,158],consid:[6,39,48,57,58,66,84,106,135,142,152],consider:[48,83],consist:[6,25,32,47,51,55,59,94,105,119,129,131,140,150,155],consol:[13,93,140],consolid:117,constant:[30,32,48,59,64,94,97,129,130,131,133,140,152,155],constant_storm_modul:117,constrain:110,constraint:[39,44,131,138,158],construc:59,construct:[22,30,32,53,83,89,104,146,147,150],construct_function_handl:104,constructor:101,consult:102,contact:[12,88,91,100],contain:[1,3,5,12,13,20,23,25,26,30,32,33,35,36,37,40,42,44,45,47,49,50,51,52,53,54,55,57,59,60,62,63,66,67,68,72,73,77,79,80,83,84,86,87,89,92,94,96,97,98,99,101,103,104,106,110,111,113,114,121,122,127,129,131,136,137,140,142,146,150,152,153,155],containing_rect:30,contains:29,containt:128,contamin:137,contan:51,content:[4,6,23,51,55,73,84,140,150,155,156],context:[27,51,155],contigu:[72,92,101,131],continent:[7,66],contingu:22,continu:[13,22,28,30,49,54,81,105,129,137,158],contour:[3,30,44,51,53,67,105,136,152],contour_color:3,contour_kwarg:[3,152],contour_level:[3,152],contour_max:3,contour_min:3,contour_nlevel:3,contour_show:3,contourf:[51,76],contract:[4,61,81],contrast:[53,131],contribut:[4,24,25,57,81,84,91,96,99,108,111],contributor:[4,24,61,91],control:[6,7,23,25,32,41,44,54,56,58,60,67,79,82,87,89,91,92,93,94,96,110,119,124,130,140],conveni:[1,27,32,35,36,39,44,51,79,86,88,91,93,95,103,155,158],convens:150,convent:[3,22,30,46,53,70,97,150],converg:[66,76],convers:[19,25,84,92,110,131,150,154],convert43to46:19,convert46to50:20,convert:[3,22,25,30,33,42,47,51,56,58,59,62,70,84,96,104,105,121,124,137,138,146,150,154],convert_fort_double_to_float:104,convert_readm:11,convert_to_standard_unit:30,convex:[7,32],coodin:30,coord:[47,51],coordin:[4,23,30,32,47,72,76,83,89,93,94,103,110,131,140,152],coordinate_specif:[30,70],coordinate_system:[15,60,134,140],coorind:152,copi:[6,14,15,16,35,36,44,51,54,55,58,67,83,86,96,101,107,108,109,110,114,118,121,125,133,134,138,142,144,145,150,155],copyq1:63,copyright:[61,81],core:[4,12,73,111,121],corioli:[48,140,144,145],coriolis_forc:[48,140],corner:[3,30,32,53,70,72,89,131,137,139,141,150,152],correct:[20,28,41,54,55,63,64,67,77,83,89,94,98,104,113,114,118,133,137,139,140,141],correctli:[28,32,84,90,117,140],correspond:[3,6,12,23,25,27,30,44,47,48,53,54,55,59,67,70,77,83,87,89,92,93,96,98,101,110,111,129,131,132,137,138,139,140,141,146,150,154,155],correspondingli:32,cos:[39,47,49,66,83,96],cosin:83,cost:[13,99],costli:130,could:[5,12,13,27,32,35,36,39,44,53,58,60,66,70,71,77,79,83,89,93,101,102,105,106,117,126,131,133,138,139,140,141,152,155],council:4,count:83,count_from_zero:83,counter:[104,152],counterclockwis:70,coupl:[119,158],courant:[4,6,110,120,137,138,139,141],cours:[13,26,32,44,46,60,70,94,95,103,105,108,140,150],cover:[6,7,27,28,30,32,38,39,51,59,66,70,110,114,119,133,139,150],coverag:[91,111],covert:11,covid:24,cparam:[83,101],cpp:52,cpu:[13,52,118,121,123,149],crash:[118,137,138],creat:[0,1,2,3,5,6,7,19,24,25,28,30,32,33,35,36,38,40,42,44,45,46,50,52,54,57,58,59,62,70,72,76,77,79,84,85,88,89,91,92,95,98,101,102,103,104,110,111,113,117,118,119,121,122,123,126,131,136,137,138,139,142,143,146,152,154,155,156],create_dtopo_xi:[30,70],create_dtopographi:[30,70],create_topo_func:152,creation:[39,77,91,113],criteria:[6,7,22,25,32,66,101],criterion:[32,110,139],critic:[51,93,129],crop:[53,152],cross:28,crucial:[51,150],csdm:24,cse:24,csh:94,csv:[30,70,121],csvfault:[30,70],ctrl:[29,77],cube:67,cultu:66,cumul:121,current:[3,5,13,14,20,22,24,27,28,29,30,32,38,39,41,44,45,48,53,54,55,56,57,58,59,60,67,68,72,77,79,89,92,93,94,99,101,104,106,110,111,118,120,121,128,132,136,137,138,139,140,141,146,147,150,152,154],current_data:[0,3,25,44,76,77],curv:[3,44,76,131],custom:[0,13,16,20,22,25,63,67,73,76,84,90,96,133],custom_bc:96,customari:93,cut:138,cutoff:[6,139],cvf:55,cvs:51,cxx:94,cyber:17,cygwin:86,cython:94,dai:[6,13,51,140],dalcin:81,dam:[51,133],dam_break:130,damag:[6,61,81],damian:57,damiansra:96,dark:131,darker:51,darryl:17,dart:45,dash:[3,94],daspect:67,dat:[30,146],data:[0,1,3,5,25,27,30,32,35,36,38,39,40,42,44,45,46,47,53,54,59,60,61,62,66,67,76,77,78,79,81,83,86,89,92,93,95,97,98,99,101,104,107,108,109,110,113,115,116,118,119,121,122,123,124,126,129,131,132,138,139,141,146,149,151,156],data_break:[39,66,152],data_fil:33,data_limit:[39,66],data_storm:146,data_typ:104,databas:[13,30,70,104,108,121,150],datadir:118,dataset:[150,152,154],date:[5,28,40,47,51,54,55,62,77,146,153],date_tim:47,datetiem:146,datetim:[47,146],datum:[47,48,97,132,140,154],dave:30,davi:[4,17],david:[4,17,81,91,99],davis2018:[5,17],davisleveque2016:[5,17],davisleveque2018:[5,17],dawson:17,daylight:59,dcp:59,deal:[30,48,76,93,94,101,146,152],dealt:[32,39],debian:105,debug:[7,41,62,72,76,93,101,106,111,137,139],debugg:77,decid:[83,99],decim:[47,59],decimc:146,decis:51,declar:[20,22,101,126,155],decompos:[72,129,158],decomposit:137,decor:104,decoupl:54,decreas:[44,133,150],deduc:150,deep:[5,66,140],deep_depth:140,deeper:[131,140,150],deepli:103,def:[0,1,3,44,51,66,77,83,89,93,96,99,139,141,146],default_tfluct:99,defenc:4,defens:4,defin:[0,1,3,5,6,7,22,27,30,32,38,39,41,51,59,60,62,66,67,70,77,79,83,86,89,95,96,98,99,101,103,104,110,113,121,126,129,139,141,146,150,152,153,155,158],definit:[30,67,83,110,116],deform:[17,30,33,45,70,154],deg2dm:59,degener:131,degre:[30,47,51,59,70],delet:[20,28,56,58],delimit:30,delin:140,delta:[87,89,96,99,129,152,155,158],delta_h:97,delta_hu:97,delta_i:152,delta_limit:152,delta_x:152,dem:[32,45,53,121,150,152,154],demo:94,demonstr:[12,25,88,94],denot:[6,22,44,53,129,152],dens:147,densiti:[86,93,97,101,103,138,139,155],depart:[4,146],depdend:87,depend:[3,13,16,28,29,30,32,35,36,40,41,46,48,51,56,57,62,64,67,70,77,82,91,92,97,98,99,104,106,110,121,133,138,140,152,153,155,158],deprec:[7,30,34,54,117,121,140,150,152],depress:32,depth:[4,5,16,17,22,30,32,33,39,44,45,48,64,70,76,78,130,132,133,140,150],deriv:[61,70,81,86,90,91,101,111],describ:[3,4,5,6,7,13,14,16,19,26,28,30,31,32,35,36,38,39,44,46,47,48,51,52,54,55,59,60,62,63,66,67,70,72,73,76,77,78,89,92,98,104,108,110,111,119,122,123,129,131,132,136,137,138,140,146,147,150,152,154,155,158],descript:[3,4,6,9,22,23,25,30,59,67,70,73,76,92,104,108,110,129,130,140,146,150,158],design:[4,27,28,51,81,83,103,131,154],desir:[0,1,2,3,6,7,16,22,25,26,30,32,33,39,42,44,55,56,58,59,60,66,70,75,76,77,79,83,84,86,93,98,99,107,119,121,124,133,135,137,138,139,141,146,150,152,153],desktop:94,destin:51,detail:[4,5,10,16,22,23,25,26,28,29,30,32,35,36,38,41,46,48,51,54,56,57,58,61,62,66,67,70,73,77,81,86,87,88,89,92,93,94,95,96,97,99,109,110,111,114,119,121,126,129,131,136,137,140,142,146,150,153,154,155,158],detect:[51,62,92,100,104,153],deterimin:[140,152],determin:[3,5,6,30,32,39,44,45,48,50,51,54,59,70,77,87,89,92,97,101,106,110,114,118,119,128,131,132,136,137,138,140,152,155],determine_topo_typ:152,dev:[18,24,28,54,55,94,121,122,127],develop:[4,6,7,12,13,18,22,23,48,52,54,57,58,61,66,67,76,80,81,84,91,96,99,100,106,108,111,121,122,124,126,129,132,133,139],dict:[30,86,92,97,98,101,146,152],dictionari:[0,1,2,3,30,44,60,77,83,86,92,97,98,101,103,106,146,150,152],dicuss:30,did:[121,126,131,150],didn:116,died:113,diff:[18,50,55,113,114,115,116,117,118,119,120,121,122,123,124,125,126],differ:[1,3,6,7,12,15,16,22,28,30,31,35,36,39,44,46,48,50,53,56,59,62,64,66,67,70,71,76,79,83,84,86,88,89,92,97,99,104,105,106,107,110,111,117,118,119,120,121,124,126,129,132,133,134,137,138,139,140,144,145,150,152,153,154,155,158],differenti:[17,30],difficult:44,difficulti:[100,102,106],diffus:96,digit:[32,39,53,59,60,77,119,120,121,152],dike:[39,66,124],dim:[96,97,99],dimens:[5,6,7,16,20,22,25,44,47,53,59,67,83,84,86,92,94,96,97,98,101,103,110,121,124,129,137,138,139,141,152,155],dimension:[3,7,8,17,22,25,30,32,35,36,44,48,52,67,89,96,117,118,120,123,139,140,141,152,155],dimensional_split:[89,117,137,139,141],dip:[30,70],dir:[55,94,156],direct:[6,8,16,22,30,32,35,36,44,47,51,55,59,61,62,67,70,71,77,81,86,96,103,110,120,129,137,138,140,152],directli:[8,19,23,32,48,56,67,70,77,79,83,84,87,91,101,104,106,121,152,156],directori:[1,3,5,6,11,12,13,14,15,16,19,20,22,23,25,28,29,31,32,35,36,37,40,42,44,45,47,50,51,54,55,56,57,59,63,67,68,71,75,76,79,86,88,89,91,92,93,96,103,106,107,108,110,111,113,118,119,120,121,123,128,129,133,134,135,136,137,138,142,144,145,148,149,150,153,155,156],directorti:108,disabl:[49,100,140],disable_petsc:104,discard:[32,99],disclaim:[61,81],discontinu:[4,99,158],discov:64,discoveri:111,discret:99,discrib:4,discuss:[5,24,28,30,48,53,56,66,70,92,103,105,106,110,119,121,129,140,158],disk:[13,44,83,92,93,111,119],dispers:48,displac:[30,45,48,70,133,140,154],displai:[1,13,35,36,40,44,51,59,77,93,111,140],display_format:[44,60],display_landfall_tim:140,dist:55,dist_latlong2met:47,dist_meters2latlong:47,distanc:[30,47,51,70,140,150,152],distant:[108,110],distinct:[44,119],distinguish:39,distribut:[4,12,13,29,30,54,61,70,73,80,81,99,105,124],disturb:51,distutil:84,dive:105,divid:[110,137],divis:[4,51],dlgeorg:4,dms2decim:47,dnetcdf:[41,150],doc:[18,23,24,28,30,51,55,87,104,105,106,120,121,122,123,124,125,126,143],docker:[18,25,55,56,120,121,122,123,124,125,126,157],docker_disk:29,docker_imag:55,dockerfile_v5:29,dockerhub:[29,55],dockeril:29,docstr:[84,88,111],doctest:89,documen:54,document:[0,1,2,3,6,7,18,21,22,23,24,25,28,29,32,45,48,53,58,61,70,76,77,78,79,81,87,89,92,93,94,95,99,101,104,106,114,127,136,139,156,157],dodsc:[39,66],doe:[4,5,11,16,20,27,28,39,40,48,51,53,54,56,67,73,77,80,89,91,98,101,104,110,111,114,119,123,126,128,129,130,133,146,152,153,155],doesn:[28,32,58,63,101],doflag:110,doi:[4,17,52,55,57,124,125,126,127],doing:[6,11,19,25,28,33,39,44,48,50,52,54,58,63,77,79,89,91,110,111,118,119,120,121],domain:[5,6,16,17,33,38,39,48,51,54,59,70,72,82,83,84,86,94,96,98,101,108,110,138,139,141,150],don:[13,27,28,54,55,77,93,94,100,111,139,153],done:[1,6,7,8,11,13,16,19,20,28,35,36,39,44,46,51,53,54,58,59,62,66,67,70,76,77,79,83,87,88,104,110,114,118,119,123,128,129,131,136,138,140,149,152,153,154],donna:[4,17],donnabois:4,donor:[137,139,141],dontflag:110,dot:[40,44,51,57,58,59,62,153],doubl:[67,84,89,104,129,138],down:[13,30,93,118,146,150,152],download:[12,13,28,29,30,36,37,39,45,51,55,56,57,58,68,88,94,100,121,122,127,148,152,153,154],downward:70,doxygen:[6,7,25,120],dpc:59,dpi:[51,59],dpng:67,dprint:[138,139],dq_src:[96,99],dqdt:99,draft:55,drag:140,drag_law:140,draw:3,drawback:106,drawcontourlin:67,drawn:[30,51,136],driver:[20,63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106,108,110,119,134,142,144,145,153],within:[6,16,28,29,54,56,58,66,73,77,95,104,106,110,129,131,136,142,152],without:[16,22,40,44,48,57,59,61,62,63,66,67,77,79,80,81,87,92,93,104,106,111,131,139,141,146,153,155],wkt:51,wmo:146,wmo_:146,wmo_ag:146,won:[12,13,66,84,152],woodward:120,word:[93,121,146],work:[3,5,8,13,16,19,20,22,24,25,26,28,29,32,35,36,40,45,48,51,52,53,54,55,56,57,58,59,66,67,69,70,71,77,80,81,82,83,85,86,87,91,92,93,94,97,99,100,105,106,108,109,110,111,115,116,117,118,119,120,121,124,126,127,129,136,137,138,140,142,147,150,153,157],workflow:[108,142,146],workshop:[108,124],workspac:[24,67,101],world:[48,64,91,94,146],worst:132,worth:101,worthwhil:96,would:[2,3,12,13,16,24,27,28,32,38,41,51,53,55,56,58,60,62,63,66,70,72,77,81,83,86,89,93,104,111,119,131,132,133,136,137,140,146,150,155],wouldn:63,wpalg:17,wrap:[59,81,84,89,99,104,146],wrapper:152,write:[7,28,30,38,39,44,45,50,53,54,64,70,72,73,76,83,86,89,90,92,93,94,98,119,121,139,141,146,150,152],write_:92,write_arrai:92,write_atcf:146,write_aux:[92,98],write_aux_alwai:[83,86,93],write_aux_init:[83,86],write_aux_int:93,write_geoclaw:146,write_hurdat:146,write_imd:146,write_jma:146,write_p:[92,98],write_tcvit:146,written:[6,11,25,30,32,40,44,58,59,60,61,70,72,73,77,81,90,92,96,105,119,129,137,138,139,140,141,146,152,155],wrong:[58,63,67,93,106],www:[4,13,17,30,39,43,45,54,60,61,66,68,81,84,89,92,94,120,122,146,152],x1_desir:33,x1_domain:33,x1_new:33,x2_desir:33,x2_new:33,x_1:[5,131],x_2:[5,131],x_c:131,x_cell:59,x_center:131,x_edg:[59,131],x_i:[129,155,158],x_inch:59,x_mask:152,xarr:89,xarrai:152,xarray_d:152,xclaw:[35,36,86],xclawcmd:86,xclawerr:86,xclawout:86,xcode:80,xdir:86,xiaom:30,xinsheng:[4,52],xinshengqin:[4,52],xleft:[138,139],xlf:100,xlimit:[0,44,51,124],xllcenter:[53,121,150],xllcorner:[53,150],xllower:121,xlow:72,xlower:[0,3,16,22,27,39,84,121,139,141,150,152,155],xlowerg:84,xmax:0,xmin:0,xpoint:140,xrang:96,xtick:[39,49],xupper:[0,22,139,141,152],xxdiff:111,xxx:150,xxxx:67,xy_fil:32,xy_fnam:33,xylim:30,xzf:57,y_c:131,y_cell:59,y_center:131,y_edg:[59,131],y_inch:59,year:[4,17,22,51,59,91,112,122,146],yellow:[59,77,146],yellow_red_blu:77,yes:67,yet:[1,13,20,25,48,52,54,57,59,76,99,119,120,121,122,123,124,125,126,127,129,137,139,157],yianni:[4,17,81],yield:3,yleft:[138,139],ylimit:[0,44,51,124,136],yllcenter:[53,121,150],yllcorner:[53,150],yllower:121,ylow:72,ylower:[3,22,27,39,84,121,139,150,152],ylowerg:84,ymax:0,ymin:0,yml:111,yong:17,you:[0,3,4,5,12,13,14,15,16,18,19,20,22,23,24,25,26,27,28,29,32,35,36,37,38,40,41,42,44,47,50,51,52,53,54,55,56,57,58,59,62,63,66,67,68,69,70,71,72,73,75,76,77,79,80,81,83,84,85,86,88,91,92,93,94,95,96,97,99,100,101,102,103,105,106,107,108,109,111,113,118,119,120,121,124,126,127,128,129,130,131,132,133,134,135,136,138,139,140,141,142,143,144,145,146,148,150,153,154,155,157],your:[4,6,15,16,19,20,24,25,26,35,37,41,44,53,54,55,56,57,58,68,71,76,77,79,81,82,83,84,85,88,90,91,93,102,103,105,106,107,108,110,111,113,121,129,134,135,144,145,150,153,155],yourself:[41,44,57],youtub:[24,108,124],ypoint:140,yupper:[22,139,152],z_allow_wet:39,z_dry:39,z_format:[39,66,152],zdry:[39,66],zenodo:[4,57,124,125,126,127],zero:[3,16,30,32,39,41,59,67,83,96,97,101,103,126,131,132],zip:[12,51,55],zipinfo:51,zlib:92,zlower:22,zmask:66,zmax:[39,66],zmin:[39,66],znearshor:66,zone:[48,51,59,138,139],zoom:[24,51],zsh:94,zshallow:66,ztopo:66,zupper:22,zvar:152},titles:["ClawPlotAxes","ClawPlotData","ClawPlotFigure","ClawPlotItem","About this software","Guiding AMR with adjoint flagging","Adaptive mesh refinement (AMR) algorithms","AMRClaw Description and Detailed Contents","AMRClaw for 1d problems","Doxygen documentation of AMRClaw","AMRClaw Flowcharts","Application documentation","Clawpack Applications repository","Amazon Web Services EC2 Clawpack AMI","b4run function","b4step default routines","Boundary conditions","Bibliography","Changes to master since v5.8.0","Converting from Clawpack 4.3 to 4.6","Converting from Clawpack 4.6 to 5.0","Clawpack 4.x links","Changes in Clawpack 5.0","Clawpack components","Clawpack Community","Full Table of Contents","Contributing examples and applications","current_data","Developers\u2019 Guide","Docker for Clawpack","dtopotools module for moving topography","Fortran 77 vs. Fortran 90 files","Fixed grid monitoring","fgmax_tools module for working with topography data","Fixed grid output","Running an example","Testing your Fortran installation and running an example","Testing a PyClaw installation and running an example","Specifying flagregions for adaptive refinement","Force Cells to be Dry Initially","Fortran version","Fortran Compilers","Examples from the book FVMHP","<no title>","Gauges","GeoClaw Description and Detailed Contents","Getting started with GeoClaw","geoclaw.util module of utility functions","Cautionary Hints on using GeoClaw","GeoClaw plotting tools","Keeping track of repository versions with Git","Visualizing GeoClaw results in Google Earth","Using the GPU version of Clawpack","Grid registration","Guide for updating this documentation","Guide for doing a Clawpack release","Installing Clawpack","Additional options for installing Clawpack","pip install instructions","kmltools module of utility functions","Lagrangian gauges for particle tracking","License","Clawpack Makefiles","Library routines in Makefiles","Manning friction term","The mapc2p function","Marching Front algorithm","Plotting using Matlab","Using NetCDF output","Creating a new application directory","Earthquake sources: Fault slip and the Okada model","Using OpenMP","Output data formats","Which Clawpack solver should I use?","Clawpack Community Photos","Plotting examples","Plotting with Visclaw","Plotting hints and FAQ","Plotting routines for GeoClaw","Plotting options in Python","Installation Prerequisites","About PyClaw","PyClaw Basics","Understanding Pyclaw Classes","Porting a problem from Clawpack 4.6.x to PyClaw","Running PyClaw in the cloud","Pyclaw Controller Class","Pyclaw Limiters","Working with PyClaw\u2019s built-in examples","PyClaw Geometry","Going Further","Pyclaw","Pyclaw Input/Output Package","PyClaw output","Running in parallel","Plotting PyClaw results","Setting up your own problem","Riemann Solver Package","PyClaw Solutions","Using PyClaw\u2019s solvers: Classic and SharpClaw","Installing PyClaw","PyClaw State","Troubleshooting","PyClaw tutorial: Solve the acoustics equations","Pyclaw Utility Module","Python Hints","Python path","qinit 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,allocat:117,allot:59,allow:[4,6,13,22,27,28,29,32,38,39,44,45,47,50,51,53,54,58,64,66,67,70,71,73,76,77,86,91,92,93,99,101,104,105,106,110,111,113,114,117,118,119,120,121,123,124,126,130,132,138,140,141,142,143,147,151,153,155],alon:[16,51],along:[6,14,16,24,27,30,32,39,44,51,54,57,68,70,106,110,117,129,132,134,141,147,155],alpha:[51,55,99],alphabet:81,alreadi:[0,1,6,12,13,18,28,29,41,55,56,58,59,60,66,79,80,94,98,100,103,105,114,122,136,153],also:[3,4,5,6,7,8,9,11,12,16,17,18,20,22,23,24,25,28,29,30,32,33,35,36,37,38,39,41,42,43,44,47,48,51,52,53,54,55,56,57,58,59,62,63,66,67,68,70,71,72,73,76,77,79,83,85,86,89,91,93,94,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,138,139,140,141,142,143,145,146,147,148,149,150,151,153,154,155,156,158,159],alter:51,altern:[30,35,36,44,47,51,56,60,62,67,76,91,94,106,110,117,118,119],although:[30,51,63,67,95,96,98,110,122,153],alwai:[16,22,26,27,28,32,41,53,54,58,67,83,92,109,110,113,114,126,134,140,141,142,151,156],amal:[4,17,81,91],amazon:25,amazonaw:13,amdq:[97,130],ami:25,among:124,amount:[44,48,54],amplitud:[5,119],amr:[4,7,8,16,20,23,25,27,28,32,34,38,44,45,52,59,67,72,73,76,81,89,118,120,121,122,124,126,134,137,138,140,142,150,156],amr_1d:122,amr_2d:[121,122],amr_:[3,7],amr_celledges_show:3,amr_contour_color:3,amr_contour_show:3,amr_data_show:118,amr_level:72,amr_level_max:140,amr_levels_max:[32,110,139,140],amr_modul:[71,110,117,123,124],amrclaw:[4,5,6,12,15,16,19,20,22,23,24,28,36,38,39,41,43,44,45,46,52,55,56,57,58,60,66,67,68,71,72,73,80,91,100,106,107,110,111,129,130,132,135,136,138,141,145,146,149,150,154],amrdata:[5,22,32,110,124,126,139,140,141],amrflag:110,amrlib:117,amrnez:110,an11:54,anaconda:[51,100],anal:17,analog:[138,139],analysi:17,andi:4,angl:[16,30,47,70],ani:[3,4,5,6,8,13,16,18,19,20,22,27,28,29,32,35,36,37,45,48,50,51,54,55,57,58,61,62,64,66,67,69,71,72,73,77,81,87,88,89,91,92,93,94,96,98,100,104,106,109,110,111,117,121,123,129,132,133,134,137,138,139,141,147,156,159],anim:[12,16,42,51,117,124,125,143],animation_tool:[124,125],anisotrop:[6,22],anl:94,annot:[27,59],annual:24,anoth:[3,22,39,44,51,55,58,59,72,76,80,88,99,102,111,121,147,156],answer:24,anyth:[3,6,28,29,58,63,111,121],anywher:110,aoml:147,apach:13,apdq:[97,130],api:[47,121],app:[12,13,18,23,26,28,29,32,37,42,43,70,108,109,116,120,121,122,123,124,125,126,127,131],appar:[30,32,71],appeal:51,appear:[0,1,3,5,8,13,18,23,32,44,45,51,54,59,62,65,77,93,98,101,119,126,141,143,151],append:[5,20,32,38,39,44,51,60,77,86,98,110,118,119,129,130,140],appl:17,appli:[3,4,5,6,13,16,25,30,48,51,53,64,66,70,77,79,87,89,92,99,110,129,138,141,156],applic:[4,6,15,16,19,20,22,23,24,28,29,32,35,36,37,41,42,43,45,46,55,57,58,63,66,68,71,79,88,89,90,91,93,99,104,107,109,110,111,113,116,117,119,120,121,123,124,130,132,134,135,138,141,145,146,151,153,154,156,157],appreci:81,approach:[5,7,13,28,29,38,44,54,57,69,76,84,91,94,96,104,110,117,119,120,122,130,131,137,141,156,159],appropri:[4,5,6,13,16,24,28,45,48,49,51,55,57,59,60,64,67,68,69,71,83,86,87,88,92,94,95,96,97,98,111,123,130,133,138,147,156,159],approv:48,approxim:[6,16,25,33,48,51,70,130],april:[24,124,125,128],apt:[13,80],arbitrari:[32,59,99,113,132,141],arbitrarili:66,arc:133,arcgi:153,architectur:94,archiv:[12,21,36,51,55,111,143,149,153,155],arcminut:[70,151],arcsecond:[45,151],area:[15,22,45,99,108,119,134,135],arg:[89,98],argument:[0,1,2,3,27,30,45,47,50,51,53,77,83,84,88,89,92,96,98,99,101,104,111,121,130,132,137,138,139,147,153,156],argv:[140,142],aris:[61,81],arithmet:64,aron:[4,17,81,91],arora:87,arora_ro:87,around:[6,30,32,39,59,92,108,111,124,139,140,147,153,156],arrai:[0,3,6,15,20,22,27,30,32,33,38,44,45,47,49,53,59,77,83,84,86,87,89,91,92,93,96,97,98,99,101,103,104,105,113,114,115,119,121,124,126,130,131,132,135,138,139,140,141,142,147,151,153,156],arrang:153,arriv:[22,32,34,39,45,119,133,134],arrival_tol:32,articl:[4,17,91,143],artifici:[16,134],arxiv:52,asc:153,ascii:[44,53,67,83,86,93,98,119,129,138,140,142,151,157],ascii_output_format:68,ask:24,ask_us:153,aspect:[12,24,29,43,48,49,67,153],assert:[140,142],assess:[4,48,133],assign:[30,32,83,86,92,98],assist:[22,124],associ:[0,1,2,6,22,51,58,71,89,92,93,111],assum:[3,5,20,22,30,32,36,39,47,48,51,53,54,55,59,67,70,76,92,93,95,96,97,103,104,110,117,132,133,138,141,147,148,151,153,155,159],assumpt:[51,54],asteroid:4,astronom:133,atcf:[108,121,147,148],aterrel:4,atmospher:4,attach:[55,92,101],attempt:[5,8,11,20,33,35,36,62,92,104,111,113,127,147,153,154],attirbut:22,attr:[89,98],attribur:5,attribut:[5,7,22,30,38,44,66,70,76,78,79,83,86,89,92,94,96,98,99,110,113,118,122,129,137,138,139,141,147,153],attributeerror:77,aug:[17,122],aug_glob:97,augment:[66,131],august:[24,121,128],austin:4,author:[17,25,45,48,87,91,92,97,109],auto:[0,44,84],autom:[14,54,84,111],automat:[0,2,3,8,11,16,30,35,36,41,51,55,62,76,77,79,83,88,92,94,100,101,102,104,111,113,124,126,138,139,141,151],autonom:5,aux1:32,aux1d:156,aux:[5,6,1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,23,25,26,30,32,33,35,36,37,40,42,43,44,45,47,49,50,51,52,53,54,55,59,60,62,63,66,67,68,72,73,77,79,80,83,84,86,87,89,91,92,94,96,97,98,99,101,103,104,105,106,110,111,113,114,121,122,128,130,132,137,138,141,143,147,151,153,154,156],containing_rect:30,contains:29,containt:129,contamin:138,contan:51,content:[4,6,23,51,55,73,84,91,141,151,156,157],context:[27,51,156],contigu:[72,92,101,132],continent:[7,66],contingu:22,continu:[13,22,28,30,49,54,81,105,130,138,159],contour:[3,30,44,51,53,67,105,137,153],contour_color:3,contour_kwarg:[3,153],contour_level:[3,153],contour_max:3,contour_min:3,contour_nlevel:3,contour_show:3,contourf:[51,76],contract:[4,61,81],contrast:[53,132],contribut:[4,24,25,57,81,84,91,96,99,108,111],contributor:[4,24,61,91],control:[6,7,23,25,32,41,44,54,58,60,67,79,82,87,89,91,92,93,94,96,110,119,124,131,141],conveni:[1,27,32,35,36,39,44,51,79,86,88,91,93,95,103,156,159],convens:151,convent:[3,22,30,46,53,70,97,151],converg:[66,76],convers:[19,25,84,92,110,132,151,155],convert43to46:19,convert46to50:20,convert:[3,22,25,30,33,42,47,51,58,59,62,70,73,84,91,96,104,105,121,124,138,139,147,151,155],convert_fort_double_to_float:104,convert_readm:11,convert_to_standard_unit:30,convex:[7,32],coodin:30,coord:[47,51],coordin:[4,23,30,32,47,72,76,83,89,93,94,103,110,132,141,153],coordinate_specif:[30,70],coordinate_system:[15,60,135,141],coorind:153,copi:[6,14,15,16,35,36,44,51,54,55,58,67,83,86,96,101,107,108,109,110,114,118,121,125,134,135,139,143,145,146,151,156],copyq1:63,copyright:[61,81],core:[4,12,73,111,121],corioli:[48,141,145,146],coriolis_forc:[48,141],corner:[3,30,32,53,70,72,89,132,138,140,142,151,153],correct:[20,28,41,54,55,63,64,67,77,83,89,94,98,104,113,114,118,134,138,140,141,142],correctli:[28,32,84,90,117,141],correspond:[3,6,12,23,25,27,30,44,47,48,53,54,55,59,67,70,77,83,87,89,92,93,96,98,101,110,111,130,132,133,138,139,140,141,142,147,151,155,156],correspondingli:32,cos:[39,47,49,66,83,96],cosin:83,cost:[13,99],costli:131,could:[5,12,13,27,32,35,36,39,44,53,60,66,70,71,77,79,83,89,93,101,102,106,117,126,132,134,139,140,141,142,153,156],council:4,count:83,count_from_zero:83,counter:[104,153],counterclockwis:70,coupl:[119,159],courant:[4,6,110,120,138,139,140,142],cours:[13,26,32,44,46,60,70,94,95,103,105,108,141,151],cover:[6,7,27,28,30,32,38,39,51,59,66,70,110,114,119,134,140,151],coverag:[91,111],covert:11,covid:24,cparam:[83,101],cpp:52,cpu:[13,52,118,121,123,150],crash:[118,138,139],creat:[0,1,2,3,5,6,7,19,24,25,28,30,32,33,35,36,38,40,42,44,45,46,50,52,54,58,59,62,70,72,76,77,79,84,85,88,89,91,92,95,98,101,102,103,104,110,111,113,117,118,119,121,122,123,126,132,137,138,139,140,143,144,147,153,155,156,157],create_dtopo_xi:[30,70],create_dtopographi:[30,70],create_topo_func:153,creation:[39,77,91,113],criteria:[6,7,22,25,32,66,101],criterion:[32,110,140],critic:[51,93,130],crop:[53,153],cross:28,crucial:[51,151],csdm:24,cse:24,csh:94,csv:[30,70,121],csvfault:[30,70],ctrl:[29,77],cube:67,cultu:66,cumul:121,current:[3,5,13,14,20,22,24,27,28,29,30,32,38,39,41,44,45,48,53,54,55,57,58,59,60,67,68,72,77,79,89,92,93,94,99,101,104,106,110,111,118,120,121,129,133,137,138,139,140,141,142,147,148,151,153,155],current_data:[0,3,25,44,76,77],curv:[3,44,76,132],custom:[0,13,16,20,22,25,63,67,73,76,84,90,96,134],custom_bc:96,customari:93,cut:139,cutoff:[6,140],cvf:55,cvs:51,cxx:94,cyber:17,cygwin:86,cython:94,dai:[6,13,51,141],dalcin:81,dam:[51,134],dam_break:131,damag:[6,61,81],damiansra:96,dark:132,darker:51,darryl:17,dart:45,dash:[3,94],daspect:67,dat:[30,147],data:[0,1,3,5,25,27,30,32,35,36,38,39,40,42,44,45,46,47,53,54,59,60,61,62,66,67,76,77,78,79,81,83,86,89,92,93,95,97,98,99,101,104,107,108,109,110,113,115,116,118,119,121,122,123,124,126,130,132,133,139,140,142,147,150,152,157],data_break:[39,66,153],data_fil:33,data_limit:[39,66],data_storm:147,data_typ:104,databas:[13,30,70,104,108,121,151],datadir:118,dataset:[151,153,155],date:[5,28,40,47,51,54,55,62,77,147,154],date_tim:47,datetiem:147,datetim:[47,147],datum:[47,48,97,133,141,155],dave:30,davi:[4,17],david:[4,17,81,91,99],davis2018:[5,17],davisleveque2016:[5,17],davisleveque2018:[5,17],dawson:17,daylight:59,dcp:59,deal:[30,48,76,93,94,101,147,153],dealt:[32,39],debug:[7,41,62,72,76,93,101,106,111,138,140],debugg:77,decid:[83,99],decim:[47,59],decimc:147,decis:51,declar:[20,22,101,126,156],decompos:[72,130,159],decomposit:138,decor:104,decoupl:54,decreas:[44,134,151],deduc:151,deep:[5,66],deeper:[132,141,151],deepli:103,def:[0,1,3,44,51,66,77,83,89,93,96,99,140,142,147],default_tfluct:99,defenc:4,defens:4,defin:[0,1,3,5,6,7,22,27,30,32,38,39,41,51,59,60,62,66,67,70,77,79,83,86,89,95,96,98,99,101,103,104,110,113,121,126,130,140,142,147,151,153,154,156,159],definit:[30,67,83,110,116],deform:[17,30,33,45,70,155],deg2dm:59,degener:132,degre:[30,47,51,59,70],delet:[20,28,58],delimit:30,delin:141,delta:[87,89,96,99,130,153,156,159],delta_h:97,delta_hu:97,delta_i:153,delta_limit:153,delta_x:153,dem:[32,45,53,59,121,151,153,155],demo:94,demonstr:[12,25,88,94],denot:[6,22,44,53,130,153],dens:148,densiti:[86,93,97,101,103,139,140,156],depart:[4,147],depdend:87,depend:[3,13,16,28,29,30,32,35,36,40,41,46,48,51,62,64,67,70,77,82,92,97,98,99,104,106,110,121,134,139,141,153,154,156,159],deprec:[7,30,34,54,58,117,121,141,151,153],depress:32,depth:[4,5,16,17,22,30,32,33,39,44,45,48,64,70,76,78,131,133,134,141,151],deriv:[61,70,81,86,90,91,101,111],describ:[3,4,5,6,7,13,14,16,19,26,28,30,31,32,35,36,38,39,44,46,47,48,51,52,54,55,57,59,60,62,63,66,67,70,72,73,76,77,78,89,91,92,98,104,108,110,111,119,122,123,130,132,133,137,138,139,141,147,148,151,153,155,156,159],descript:[3,4,6,9,22,23,25,30,59,67,70,73,76,91,92,104,108,110,130,131,141,147,151,159],design:[4,27,28,51,81,83,103,132,155],desir:[0,1,2,3,6,7,16,22,25,26,30,32,33,39,42,44,55,58,59,60,66,70,75,76,77,79,83,84,86,93,98,99,107,119,121,124,134,136,138,139,140,142,147,151,153,154],desktop:94,destin:51,detail:[4,5,10,16,22,23,25,26,28,29,30,32,35,36,38,41,46,48,51,54,57,58,61,62,66,67,70,73,77,81,86,87,88,89,91,92,93,94,95,96,97,99,109,110,111,114,119,121,126,130,132,137,138,141,143,147,151,154,155,156,159],detect:[51,62,92,100,104,154],deterimin:[141,153],determin:[3,5,6,30,32,39,44,45,48,50,51,54,59,70,77,87,89,92,97,101,106,110,114,118,119,129,132,133,137,138,139,141,153,156],determine_topo_typ:153,dev:[18,24,28,54,55,94,121,122,127,128],develop:[4,6,7,12,13,18,22,23,48,52,54,57,58,61,66,67,76,80,81,84,91,96,99,100,106,108,111,121,122,124,126,130,133,134,140],dict:[30,86,92,97,98,101,147,153],dictionari:[0,1,2,3,30,44,60,77,83,86,92,97,98,101,103,106,147,151,153],dicuss:30,did:[121,126,132,151],didn:116,died:113,diff:[18,50,55,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127],differ:[1,3,6,7,12,15,16,22,28,30,31,35,36,39,44,46,48,50,53,57,59,62,64,66,67,70,71,76,79,83,84,86,88,89,91,92,97,99,104,105,106,107,110,111,117,118,119,120,121,124,126,127,130,133,134,135,136,138,139,140,141,145,146,151,153,154,155,156,159],differenti:[17,30],difficult:44,difficulti:[100,102,106],diffus:96,digit:[32,39,53,59,60,77,119,120,121,153],dike:[39,66,124],dim:[96,97,99],dimens:[5,6,7,16,20,22,25,44,47,53,59,67,83,84,86,92,94,96,97,98,101,103,110,121,124,130,138,139,140,142,153,156],dimension:[3,7,8,17,22,25,30,32,35,36,44,48,52,67,89,96,117,118,120,123,140,141,142,153,156],dimensional_split:[89,117,138,140,142],dip:[30,70],dir:[55,94,157],direct:[6,8,16,22,30,32,35,36,44,47,51,55,59,61,62,67,70,71,77,81,86,96,103,110,120,130,138,139,141,153],directli:[8,19,23,32,48,57,67,70,77,79,83,84,87,91,101,104,106,121,153,157],directori:[1,3,5,6,11,12,13,14,15,16,19,20,22,23,25,28,29,31,32,35,36,37,40,42,43,44,45,47,50,51,54,55,57,59,63,67,68,71,75,76,79,86,88,89,91,92,93,96,103,106,107,108,110,111,113,118,119,120,121,123,129,130,134,135,136,137,138,139,143,145,146,149,150,151,154,156,157],directorti:108,disabl:[49,100,141],disable_petsc:104,discard:[32,99],disclaim:[61,81],discontinu:[4,99,159],discov:64,discoveri:111,discret:99,discrib:4,discuss:[5,24,28,30,48,53,66,70,92,103,105,106,110,119,121,130,141,159],disk:[13,44,83,92,93,111,119],dispers:48,displac:[30,45,48,70,134,141,155],displai:[1,13,35,36,40,44,51,59,77,93,111,141],display_format:[44,60],display_landfall_tim:141,dist:55,dist_latlong2met:47,dist_meters2latlong:47,distanc:[30,47,51,70,141,151,153],distant:[108,110],distinct:[44,119],distinguish:39,distribut:[4,12,13,29,30,54,61,70,73,81,99,105,124],disturb:51,distutil:84,divid:[110,138],divis:[4,51],dlgeorg:4,dms2decim:47,dnetcdf:[41,151],doc:[18,23,24,28,30,51,55,87,104,105,106,120,121,122,123,124,125,126,127,144],docker:[18,25,55,56,120,121,122,123,124,125,126,127,158],docker_disk:29,docker_imag:55,dockerfile_v5:29,dockerhub:[29,55],dockeril:29,docstr:[84,88,111],doctest:89,documen:54,document:[0,1,2,3,6,7,18,21,22,23,24,25,28,29,32,45,48,53,58,61,70,76,77,78,79,81,87,89,92,93,94,95,99,101,104,106,114,127,128,137,140,157,158],dodsc:[39,66],doe:[4,5,11,16,20,27,28,39,40,48,51,53,54,58,67,73,77,80,89,98,101,104,110,111,114,119,123,126,129,130,131,134,147,153,154,156],doesn:[28,32,58,63,101],doflag:110,doi:[4,17,52,55,57,124,125,126,127,128],doing:[6,11,19,25,28,33,39,44,48,50,52,54,58,63,77,79,89,91,110,111,118,119,120,121],domain:[5,6,16,17,33,38,39,48,51,54,59,70,72,82,83,84,86,94,96,98,101,108,110,139,140,142,151],don:[13,27,28,54,55,77,93,94,100,111,140,154],done:[1,6,7,8,11,13,16,19,20,28,35,36,39,44,46,51,53,54,56,59,62,66,67,70,76,77,79,83,87,88,91,104,110,114,118,119,123,129,130,132,137,139,141,150,153,154,155],donna:[4,17],donnabois:4,donor:[138,140,142],dontflag:110,dot:[40,44,51,58,59,62,154],doubl:[67,84,89,104,130,139],down:[13,30,93,118,147,151,153],download:[12,13,28,29,30,36,37,39,45,51,55,57,58,68,88,94,100,121,122,128,149,153,154,155],downward:70,doxygen:[6,7,25,120],dpc:59,dpi:[51,59],dpng:67,dprint:[139,140],dq_src:[96,99],dqdt:99,draft:55,drag:141,drag_law:141,draw:3,drawback:106,drawcontourlin:67,drawn:[30,51,137],driver:[20,63],drop:[13,54,80,124,126,134,138],dry:[16,17,25,32,45,97,124,127,131,134],dry_point:39,dry_points_sum:39,dry_toler:97,ds824:147,dst:59,dt_check:32,dt_initi:[113,138,140,141,142],dt_max:[138,140,142],dt_max_dtopo:[113,141],dt_variabl:[138,140,142],dtdtopo:116,dtdx1d:115,dtdx:87,dtdy1d:115,dtfe:99,dtopo2kml:59,dtopo:[25,30,33,45,48,53,59,70,106,113,115,116,124,126,134,141,151,153,155],dtopo_data:[113,141],dtopo_file_nam:59,dtopo_modul:113,dtopo_path:33,dtopo_typ:[30,33,59,70],dtopofil:[59,70,141],dtopographi:[30,70],dtopotool:[45,70,115,116,118,121,122,151,152],dtopotools_exampl:[30,70,109],dtopotyp:[141,151],due:[17,24,30,39,47,70,111,120,121,126,134,154],dummi:[84,99,156],dump:[72,138],dumpgaug:117,duplic:[77,116,129],durat:[30,126,133],dure:[5,22,32,39,44,59,70,73,113,133,134,140,141,142,151],dxc:84,dyc:84,dylib:51,dynam:[6,20,30,48,70,73,139],dynamic_slip:[30,122],dz_at_t:30,dz_interv:30,dz_max:30,e10:32,e15:44,e26:44,e68:[4,17],e_format_bst:147,e_l:97,e_r:97,each:[1,2,3,5,6,7,12,16,18,22,30,32,34,44,47,51,53,54,55,59,60,63,66,67,70,71,72,75,76,77,79,83,84,87,89,92,93,94,96,97,98,99,101,103,110,111,113,114,118,119,121,122,124,129,130,131,132,134,137,138,139,140,141,142,147,150,151,153,155,159],each_fram:44,each_gaug:44,ear:4,earli:[6,20,134],earlier:[5,20,22,30,32,38,53,70,83,96,113,120,151,153],earth:[25,39,45,52,59,66,70,117,119,127,132,141],earth_radiu:141,earthquak:[25,30,45,48,109,134,141,148,151],eas:59,easi:[4,6,11,29,38,58,67,84,93,94,95,132,143,156],easier:[58,76,119,121,132,156],easiest:[19,28,41,73,77,79,110,156],easili:[3,13,28,32,51,54,67,77,84,89,100,104,111,124,143,147],east:[13,151],easy_instal:94,ec2:25,echo:106,ecosystem:[4,17],edebug:[139,140],edg:[3,6,15,16,27,30,32,33,38,59,70,89,97,130,132,135,139,140,142,156],edgecolor:132,edit:[51,54,55,58,79],editabl:28,editor:72,edu:[30,51,68,92,123],effect:[44,51,64,67,89,93,110,111,133,141,153],effici:[48,52,81,91,92,93,101,110,132,139],effort:92,efix:[97,131],egg:[29,58],eigenvalu:5,eigenvector:[5,130,159],either:[12,16,20,30,32,39,45,46,51,60,62,66,67,70,77,79,83,89,91,92,93,99,104,106,110,111,117,118,119,121,130,132,134,139,141,147,151,153,156,159],elast:[13,70],element:[0,3,22,59,97,99,101,138,139,140,141],elementwis:93,elev:[22,25,32,39,45,46,48,51,53,59,76,107,110,124,132,133,141,151,153,155],elif:[140,142],elimin:[8,22,66,84,106,121,141],ell:130,els:[27,28,58,66,101,121,132,134,142],elsewher:[5,24,39,91,132],emerg:4,emmanuel:141,emmett:[17,81,91],empir:[48,64],empti:[12,44,98,101,104,106,138,147,153],empyclaw:96,enabl:[89,93,100,104,119],encapsul:48,encount:[40,51,77,100,102],encourag:67,end:[13,29,30,32,44,47,51,55,59,86,93,97,103,105,108,110,118,119,121,129,131,132,140,142,147,150],end_dat:47,enddo:156,endian:92,endors:[61,81],energi:[93,97],enforc:132,eng:147,engin:[17,51],enhanc:[64,81,121],enlarg:119,enough:[5,54,66,139,148,150,151],ensembl:147,ensur:[35,36,37,67,108],enter:[67,92,94,100],enthought:[100,102],entir:[5,6,38,48,51,59,66,70,71,73,83,93,98,108,110,114,132,153],entireti:86,entri:[51,60,83,93,104,147],entropi:[97,131],enumer:[89,99],environ:[14,25,28,35,36,37,40,50,51,54,57,58,67,69,71,73,95,102,104,106,119,153,154],envis:16,epd:102,eprint:[139,140],epsg:51,epsilon:87,eqn:159,eqnarrai:103,equal:[16,30,32,51,70,94,96,110,129,132,138,140,142,151,153],equat:[4,5,16,17,25,35,36,45,48,60,64,77,82,83,84,86,91,92,93,96,99,100,101,114,117,119,121,122,130,138,140,141,142,151,156,159],equiv:159,equival:[6,44,52,53,59,60,123,151],err:140,errest:110,erron:[30,70],error:[5,16,20,35,36,40,51,58,67,71,77,86,91,92,93,104,110,111,122,126,139,140,147,154],escap:[110,140],escienc:13,especi:[28,51,84,96],esri:[53,151],essenti:[5,53,67,99,141,151],est:140,establis:121,establish:4,estim:[5,64,110,139,141],estimat:[5,140],eta:[25,30,32,39,44,45,110,117,124,133],eta_init:134,eta_tild:32,etc:[0,2,16,19,20,24,27,28,32,33,48,51,54,57,59,63,72,76,84,130,137,138,141,147,156],etopo1:[121,132,133,151,153,155],etopo_sample_2min:153,etopotool:[121,151],euler:[60,91,99,115,117,120,122,130,156],euler_1d_pi:97,euler_2d:[35,37,91,96],euler_exact_1d:97,euler_hll_1d:97,euler_hllc_1d:97,euler_roe_1d:97,evalu:[17,27,30,64,83,89,99,153,156],even:[39,48,51,58,61,70,81,104,110,124,139,140,151,154,156],evenli:[51,93],event:[33,45,48,59,61,70,81,133,134,138],event_tim:59,eventu:[13,45,124],ever:[137,141],everi:[6,12,28,32,44,60,62,63,83,86,88,92,93,101,110,111,119,120,130,134,136,138,140,142,147,151,153,156],everyth:[32,55,58,71,94,103,104,111,121],everywher:[38,39,47,64,101,134],evolv:[22,83,86,99],evolve_to_tim:[83,99],exact:97,exactli:[28,50,52,101,132,138],exam:77,examin:[16,35,36,44,66,106],exampl:[0,1,2,3,4,5,6,7,8,9,13,14,16,20,22,24,27,28,29,30,38,40,41,43,45,47,53,54,55,56,57,59,60,62,63,64,68,70,71,72,76,77,79,81,82,83,84,86,89,90,92,93,96,97,98,99,100,103,104,105,106,108,109,110,111,113,115,116,117,118,119,120,121,122,123,124,125,129,130,131,133,134,136,137,138,139,140,141,142,143,147,149,150,151,153,154,155,156],exce:[32,51,110,139],exceed:[110,121],except:[22,27,30,39,92,97,104,124,138,141,147,151],ex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this software","Guiding AMR with adjoint flagging","Adaptive mesh refinement (AMR) algorithms","AMRClaw Description and Detailed Contents","AMRClaw for 1d problems","Doxygen documentation of AMRClaw","AMRClaw Flowcharts","Application documentation","Clawpack Applications repository","Amazon Web Services EC2 Clawpack AMI","b4run function","b4step default routines","Boundary conditions","Bibliography","Changes to master since v5.8.1","Converting from Clawpack 4.3 to 4.6","Converting from Clawpack 4.6 to 5.0","Clawpack 4.x links","Changes in Clawpack 5.0","Clawpack components","Clawpack Community","Full Table of Contents","Contributing examples and applications","current_data","Developers\u2019 Guide","Docker for Clawpack","dtopotools module for moving topography","Fortran 77 vs. Fortran 90 files","Fixed grid monitoring","fgmax_tools module for working with topography data","Fixed grid output","Running an example","Testing your Fortran installation and running an example","Testing a PyClaw installation and running an example","Specifying flagregions for adaptive refinement","Force Cells to be Dry Initially","Fortran version","Fortran Compilers","Examples from the book FVMHP","Clawpack Gallery","Gauges","GeoClaw Description and Detailed Contents","Getting started with GeoClaw","geoclaw.util module of utility functions","Cautionary Hints on using GeoClaw","GeoClaw plotting tools","Keeping track of repository versions with Git","Visualizing GeoClaw results in Google Earth","Using the GPU version of Clawpack","Grid registration","Guide for updating this documentation","Guide for doing a Clawpack release","Installing Clawpack","Options for installing Clawpack Fortran codes","pip install instructions","kmltools module of utility functions","Lagrangian gauges for particle tracking","License","Clawpack Makefiles","Library routines in Makefiles","Manning friction term","The mapc2p function","Marching Front algorithm","Plotting using Matlab","Using NetCDF output","Creating a new application directory","Earthquake sources: Fault slip and the Okada model","Using OpenMP","Output data formats","Which Clawpack solver should I use?","Clawpack Community Photos","Plotting examples","Plotting with Visclaw","Plotting hints and FAQ","Plotting routines for GeoClaw","Plotting options in Python","Installation Prerequisites","About PyClaw","PyClaw Basics","Understanding Pyclaw Classes","Porting a problem from Clawpack 4.6.x to PyClaw","Running PyClaw in the cloud","Pyclaw Controller Class","Pyclaw Limiters","Working with PyClaw\u2019s built-in examples","PyClaw Geometry","Going Further","PyClaw","Pyclaw Input/Output Package","PyClaw output","Running in parallel","Plotting PyClaw results","Setting up your own problem","Riemann Solver Package","PyClaw Solutions","Using PyClaw\u2019s solvers: Classic and SharpClaw","Installing PyClaw","PyClaw State","Troubleshooting","PyClaw tutorial: Solve the acoustics equations","Pyclaw Utility Module","Python Hints","Python path","qinit default routines","Quick start guide for storm surge modeling","Quick start guide for tsunami modeling","AMR refinement criteria","Regression testing","v5.0.0 release notes","v5.1.0 release notes","v5.2.0 release notes","v5.2.1 release notes","v5.2.2 release notes","v5.3.0 release notes","v5.3.1 release notes","v5.4.0 release notes","v5.4.1 release notes","v5.5.0 release notes","v5.6.0 release notes","v5.6.1 release notes","v5.7.0 release notes","v5.7.1 release notes","v5.8.0 release notes","v5.8.1 release notes","Releases of Clawpack and release notes","Checkpointing and restarting","Riemann solvers","Shallow water Riemann solvers in Clawpack","Ruled Rectangles","Setting sealevel","Set Eta Init \u2013 spatially varying initial surface elevation","setaux default routines","Set environment variables","Using setplot.py to specify the desired plots","Specifying classic run-time parameters in setrun.py","Specifying AMRClaw run-time parameters in setrun.py","Sample setrun.py module for AMRClaw","Specifying GeoClaw parameters in setrun.py","Sample setrun.py module for classic Clawpack","Saving and sharing results","Compiling the Sphinx documentation locally","src1d default routines","src default routines","Storm Specification Class and Tools","Sources for Storm Surge Data","Testing your installation","Timing Statistics","Topography data","Python tools for working with topo and dtopo","topotools module for working with topography data","Troubleshooting","Some sources of tsunami data","User files required for the Fortran code","Plotting with VisIt","Clawpack Virtual Machine","Wave-propagation algorithms"],titleterms:{"1d_fill_between":3,"1d_from_2d_data":3,"1d_plot":3,"2d_contour":3,"2d_pcolor":3,"case":134,"catch":28,"class":[83,86,147],"default":[15,107,134,135,145,146],"final":55,"function":[14,47,59,65,66,79,93,99,159],"import":106,"new":[46,54,69,88,111],"switch":67,"true":77,Adding:[28,51,88,96,130],For:6,Going:90,One:[130,131,159],The:[51,65,66,67,103],Use:102,Using:[5,13,25,29,38,52,58,63,68,71,93,96,99,130,137,156],about:[4,81],abov:29,access:79,acoust:[97,103],adapt:[6,16,25,38],add:77,addit:[51,139,141],adjoint:5,adjust:134,advect:97,after:129,afterfram:67,algorithm:[6,17,66,73,159],alias:51,all:[3,58,66],along:66,amazon:13,ami:13,amr:[3,5,6,22,66,71,110,132,139,141],amrclaw:[7,8,9,10,18,25,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,139,140,156],anoth:77,app:55,applic:[11,12,17,25,26,62,69,94],approach:8,arcsecond:[39,66],area:66,argument:66,arrai:[39,66,72,102],arriv:141,artifact:51,ascii:[72,92],attribut:[0,1,2,3,27,32,51,77,132],author:4,auto:[30,33,47,59,153],aux:[72,83],auxiliari:96,avail:[24,42],axes:49,b4run:14,b4step:[15,156],background:77,backward:[18,121,122,123,124,125,126,127],base:62,basic:[51,82,95],bathymetri:155,befor:156,behavior:134,below:66,better:29,between:[29,77],bibliographi:17,binari:72,binder:29,book:42,boundari:[6,16,96,156,159],bounding_box:132,branch:[28,54],buffer:66,bug:28,built:[54,88],buoi:155,burger:97,candid:55,capac:159,cautionari:48,cell:[6,39,132],cfl:87,chang:[18,22,77,99,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127],chardiff:111,check:[28,111],checkpoint:129,chile:51,choic:32,choos:[6,66],cite:[4,91],clamshel:16,classic:[18,25,35,36,99,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,138,142,149],claw:[74,136],clawcode2html:11,clawpack:[12,13,17,18,19,20,21,22,23,24,25,29,43,52,54,55,56,57,62,73,74,84,87,99,100,120,121,122,123,124,125,126,127,128,131,142,158],clawplotax:0,clawplotdata:1,clawplotfigur:2,clawplotitem:[3,77],clawutil:[18,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127],clinic:24,clone:[28,57],cloud:85,code:[11,25,28,39,46,57,58,74,111,154,156],color:77,colorbar:51,colormap:77,command:[29,37,67,79,88,154],commit:28,commun:[24,28,74],comparison:111,compat:[18,121,122,123,124,125,126,127],compil:[41,62,68,102,144,154],compon:[23,77],comput:[73,129],condit:[6,16,96,103,156,159],configur:54,contain:29,content:[7,25,28,39,45,66,77,83,93,99,111,132],continent:132,continu:111,contourf:77,contribut:[26,28,131],contributor:81,control:[83,86,103],convers:20,convert:[11,19,20],convex:132,coordin:[49,51],copi:69,correctli:94,cover:132,coverag:28,creat:[13,29,39,51,55,66,67,69,83],creation:83,criteria:110,current_data:[27,79],curv:77,custom:[99,130],dart:155,data:[33,51,72,137,141,148,151,153,154,155,156],debug:[77,139],defin:[16,132],deform:134,dem:[39,66],demonstr:131,depend:[87,100],deprec:8,depth:49,deriv:[83,93],describ:17,descript:[7,45],desir:137,detail:[6,7,45],determin:66,dev:74,develop:[24,25,28,74],diff:111,differ:[32,51,58,63,73,77],dimens:[89,131,159],dimension:130,directli:13,directori:[58,62,69,77],displac:151,doc:54,docker:29,dockerfil:[29,55],docstr:[30,33,47,59,153],doctest:111,document:[9,11,30,33,47,54,55,59,91,120,121,144,153],doing:55,domain:[89,103],done:156,download:151,doxygen:9,drop:105,dry:[39,66],dtopo:152,dtopotool:30,duplic:62,each:[28,156],earth:51,earthquak:[70,155],easi:106,ec2:13,elev:[49,66,134],environ:[41,136],equat:[97,103,131],error:[28,102],eta:134,euler:97,event:[24,51],exampl:[12,25,26,32,35,36,37,39,42,44,46,51,58,66,67,69,75,88,91,94,132],exe:154,exist:69,experi:58,extra:54,extrapol:110,f2py:154,faq:77,faster:51,fault:70,featur:91,fflag:41,fgmax:[32,66],fgmax_tool:33,figur:[51,77],file:[13,29,31,32,39,51,53,54,55,57,63,67,77,79,111,129,132,141,151,156],fileio:92,find:[13,66,77],finer:6,fix:[28,32,34,71,141],flag2refin:110,flag:[5,6,62,66,110,132,139],flagregion:38,flow:[25,83],flowchart:10,fly:76,forc:39,force_dry_init:39,fork:28,format:[32,72,151],formul:159,fort:[72,77],fortran:[22,25,31,36,39,40,41,57,80,102,111,154,156],found:67,frame:93,framework:55,friction:64,from:[13,19,20,22,25,28,30,33,37,39,42,47,54,59,66,79,84,88,95,132,153],front:66,full:25,fund:[4,81],further:90,fvmhp:42,galleri:[43,54,67],gaug:[44,51,60,93,155],gdal:51,gener:[18,22,30,33,47,54,59,121,122,123,124,125,126,127,141,153],geo:141,geoclaw:[5,15,16,18,22,25,29,39,45,46,47,48,49,51,71,74,78,107,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,132,135,141,145,146],geometri:89,geophys:25,get:[25,29,46,67],gfortran:[41,100],ghost:6,git:[28,50,54,57,80],github:[28,55],given:66,global:119,godunov:159,googl:51,gpu:52,grid:[6,16,32,34,53,71,89,141],guid:[5,28,54,55,108,109],guidelin:28,hack:74,hazard:48,hdf5:92,help:67,high:159,hint:[48,77,105],hll:131,host:29,how:[77,79,93],hpc3:74,html:[11,79],imag:[29,51],imagediff:111,implement:110,includ:[12,54],independ:87,indic:[66,91],init:134,initi:[6,39,66,96,103,134,156],input:[22,32,92,138,139],instal:[28,36,37,56,57,58,68,73,80,91,94,100,102,106,149,154],instanc:13,instanti:132,instruct:[28,58],integr:111,intel:41,interact:[79,88],interfac:73,intern:39,interpol:32,interpret:37,iplotclaw:79,ipython:[37,88],issu:28,item:77,jupyt:[12,29,37,143],kaust:74,keep:50,kinemat:70,kml:51,kmltool:59,kmz:51,lagrangian:60,latest:28,latex:79,latitud:[49,51],launch:13,layer:131,level:[28,134],lflag:41,librari:[51,63],licens:[4,61,81],limit:87,line:[37,79,88,111,154],link:21,load:51,local:144,locat:44,log:[13,93],longitud:[49,51],machin:[29,158],make:[77,94,143,154],make_kml:132,makefil:[40,62,63,96,129],man:64,map:51,mapc2p:65,march:66,mask:66,mask_outsid:132,master:[18,28],math:85,matlab:67,matplotlib:100,maxfram:67,maximum:141,mesh:[6,25],method:[0,1,2,3,132,159],mhw:66,migrat:25,miss:131,model:[48,70,108,109,155],modif:39,modifi:[28,63,129],modul:[30,33,47,59,91,104,140,142,153],monitor:[32,141],more:[6,36,40],most:28,move:[29,30],multipl:51,name:[62,63],need:51,netcdf:[53,68,72,92,151],never:28,next:[56,57,58,100],nose:100,note:[112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128],notebook:[12,29,37,105,143],number:55,numpi:100,object:[89,137],obtain:100,okada:70,old:8,older:25,onli:66,open:55,openmp:71,oper:80,option:[51,57,79,94,96],order:102,osf:55,other:[17,18,23,24,29,32,54,77,120,121,122,123,124,125,126,127,128,132,134],out:[28,66],outdir:77,output:[32,34,62,66,67,68,71,72,83,92,93,111,129,138,139,141,154],overlai:51,overview:[25,137],own:[13,29,96],packag:[22,58,92,97],page:54,paper:17,parallel:[73,89,94,95,101],paramet:[22,44,77,79,103,138,139,141],particl:60,pass:94,patch:89,path:[67,106],pcolor:77,petclaw:[89,101],petsc:94,photo:74,pip:[58,80,154],pixel:111,plot:[3,13,22,25,32,44,46,49,51,60,62,67,68,75,76,77,78,79,88,94,95,111,137,143,154,157],plot_typ:3,plotax:51,plotclaw:67,plotdata:51,plotfigur:51,plotitem:51,point:[32,66],pointwis:130,polygon:132,port:84,post:76,potenti:131,ppflag:41,pre:41,prepar:55,prerequisit:80,previou:[24,54],previous_pts_chosen:66,print:139,printfram:79,problem:[8,84,96,103,156],procedur:32,process:[32,76],processor:41,produc:79,propag:159,provid:77,pth:106,publish:51,pull:28,pyclaw:[18,22,25,35,37,58,81,82,83,84,85,86,87,88,89,91,92,93,95,98,99,100,101,103,104,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,149],pyflak:28,pylint:28,pypi:55,python:[20,79,80,100,105,106,124,152],pythonpath:[106,136],q0002:72,qinit:[107,141,151],quantiti:[83,93],quick:[58,108,109],raw:72,read:[39,132],readm:11,recent:[24,28],rectangl:[38,132],rectangular:70,refer:[17,25,52,91,105],refin:[6,16,25,38,110,141],region:[66,110,132,141],registr:53,regress:111,relat:132,releas:[54,55,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128],remot:28,remov:51,replac:63,report:28,repositori:[12,18,23,28,50,54,55,120,121,122,123,124,125,126,127,130],request:28,requir:[51,156],resolut:[51,159],resourc:25,restart:[29,83,129],result:[13,46,51,68,95,143],richardson:110,riemann:[18,25,91,96,97,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,130,131,156],roe:131,routin:[15,22,63,78,107,135,145,146],rst:11,rule:[38,132],run:[29,35,36,37,46,83,85,88,94,95,111,138,139,154],ruptur:70,sage:85,same:63,sampl:[39,66,140,142],save:[93,143],scienc:55,script:96,sea:134,sealevel:133,search:67,seismic:134,select:132,serial:[89,101,111],servic:13,session:24,set:[46,67,77,79,96,133,134,136,154],setaux:[135,156],setplot:[67,77,79,137],setrun:[22,44,138,139,140,141,142],shallow:[97,131],share:143,sharpclaw:99,shelf:132,shoot:[28,67],shore:66,should:73,signatur:99,simpl:[32,132],simul:83,simultan:111,sinc:18,size:77,slip:70,slu:132,softwar:[4,17],solut:[77,83,98],solv:103,solver:[73,83,91,96,97,99,103,130,131,156],some:[29,77,155],someth:77,sourc:[62,70,96,148,155,156,159],space:159,spatial:[134,156],special:[3,139],specif:[32,103,111,141,147,156],specifi:[38,60,77,79,110,137,138,139,141,156],sphere:16,sphinx:[54,144],sprint:[24,74],src1d:[145,156],src:[146,156],start:[25,29,46,108,109],state:101,statist:150,step:[56,57,58,100,156],stop:[13,29],storm:[108,141,147,148],stream:24,style:[32,54],subfault:70,submodul:12,support:[105,124],surfac:[49,134],surg:[108,148],sys:106,system:80,t0002:72,tabl:[25,91],tag:54,tar:[55,57],term:[64,96,156,159],test:[28,36,37,94,100,111,149],than:77,thi:[4,54],tide:155,tile:51,time:[138,139,141,150,156],tip:[28,40,49,51,94],titl:77,tool:[20,25,44,49,60,111,147,152],top:28,topo:152,topofil:66,topographi:[30,33,39,46,51,66,141,151,153,155],topotool:153,track:[50,60],transfer:13,travi:111,triangular:70,troubl:[28,67,154],troubleshoot:[58,102,154],tsunami:[48,51,109,155],tutori:[24,103,105],tvd:87,two:131,understand:83,univers:74,upcom:24,updat:[28,54,55],usag:39,use:[73,134],used:154,useful:[29,131],user:[16,24,29,73,156],using:[48,67,156],utah:74,util:[47,59,104],valu:[32,83],vari:[134,156],variabl:[41,62,96,136],version:[25,29,40,50,52,54,55,58,106],view:13,virtual:158,visclaw:[18,25,60,76,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127],visit:157,visual:[25,51],washington:74,water:[49,97,131],wave:[130,159],web:13,webpag:[13,54,143],what:[77,79,93,131],when:93,where:93,which:[73,106],whichclaw:106,work:[4,33,88,152,153,156],workflow:28,workshop:[24,74],write:[66,96,111,132],written:93,your:[13,28,29,36,51,94,96,100,143,149],zenodo:55,zone:66}}) \ No newline at end of file diff --git a/dev/setenv.html b/dev/setenv.html index b8616d4152..9633609dbc 100644 --- a/dev/setenv.html +++ b/dev/setenv.html @@ -21,7 +21,7 @@ - +

                                                                                                @@ -70,7 +70,7 @@

                                                                                                Navigation

                                                                                                next |
                                                                                              • - previous |
                                                                                              • Clawpack dev documentation »
                                                                                              @@ -83,6 +83,8 @@

                                                                                              Navigation

                                                                                              Set environment variables

                                                                                              +

                                                                                              The export commands below work in the bash shell. The syntax may +be different in other shells.

                                                                                              CLAW

                                                                                              To use the Fortran versions of Clawpack you will need to set the @@ -117,9 +119,15 @@

                                                                                              FC

                                                                                              PYTHONPATH

                                                                                              -

                                                                                              We do not recommend setting this environment variable. See -Python path for more information. Instead we recommend using pip -install to set the Python path appropriately, see pip install instructions.

                                                                                              +

                                                                                              If you used pip to install Clawpack then you should not set this +environment variable. But if you installed without pip, e.g. following +Options for installing Clawpack Fortran codes, then you need to set PYTHONPATH to include +the directory $CLAW. If PYTHONPATH is already set, then you may want to +insert $CLAW into the list of directories searched by Python via:

                                                                                              +
                                                                                              export PYTHONPATH=$CLAW:$PYTHONPATH
+
                                                                                              +
                                                                                              +

                                                                                              See Python path for more information.

                                                                                              @@ -146,7 +154,7 @@

                                                                                              Table of Contents

                                                                                              Related Topics

                                                                                              diff --git a/dev/setrun_geoclaw.html b/dev/setrun_geoclaw.html index bbbe595073..b55b4210ff 100644 --- a/dev/setrun_geoclaw.html +++ b/dev/setrun_geoclaw.html @@ -142,23 +142,6 @@

                                                                                              Additional AMR parameters -
                                                                                              -rundata.refinement_data.max_level_deep : int
                                                                                              -

                                                                                              For simulations over the ocean, it is often useful to specify -a maximum refinement level allowed in deep parts of the ocean. This is -useful if a high level of refinement is specified on some rectangular -region but only the parts of this region near the shore actually need to -be refined.

                                                                                              -
                                                                                              - -
                                                                                              -
                                                                                              -rundata.refinement_data.deep_depth : float
                                                                                              -

                                                                                              The deepness that triggers the refinement limitation imposed by -max_level_deep above.

                                                                                              -
                                                                                              -

                                                                                              • General geo parameters

                                                                                              diff --git a/dev/sharing.html b/dev/sharing.html index 946aaeb8e7..3f257f6f1f 100644 --- a/dev/sharing.html +++ b/dev/sharing.html @@ -87,7 +87,7 @@

                                                                                              Navigation

                                                                                              results that you have obtained with this software. These make it relatively easy to generate a set of webpages such as those seen when browsing the examples collected in -galleries.

                                                                                              +Clawpack Gallery.

                                                                                              These webpages can easily be posted on your own website to be viewed by others if you wish, for example to share on-going work with collaborators or to supplement a journal article.

                                                                                              @@ -106,11 +106,13 @@

                                                                                              Sharing your results

                                                                                              -
                                                                                              -

                                                                                              IPython notebooks

                                                                                              -

                                                                                              You should also consider creating an IPython notebook to explain your +

                                                                                              +

                                                                                              Jupyter notebooks

                                                                                              +

                                                                                              You should also consider creating an Jupyter notebook to explain your problem, illustrate your workflow, and present plots and animations all in -one. See notebooks for some examples.

                                                                                              +one. See the +Gallery of Notebooks +for some examples.

                                                                                              @@ -130,7 +132,7 @@

                                                                                              Table of Contents

                                                                                            • Saving and sharing results
                                                                                            diff --git a/dev/storm_module.html b/dev/storm_module.html index e94d2c3fa4..7169651601 100644 --- a/dev/storm_module.html +++ b/dev/storm_module.html @@ -586,7 +586,7 @@

                                                                                            Navigation

                                                                                            -

                                                                                            System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/surge/storm.py:docstring of clawpack.geoclaw.surge.storm.fill_rad_w_other_source, line 15)

                                                                                            +

                                                                                            System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/surge/storm.py:docstring of clawpack.geoclaw.surge.storm.fill_rad_w_other_source, line 15)

                                                                                            Field list ends without a blank line; unexpected unindent.

                                                                                              @@ -617,7 +617,7 @@

                                                                                              Navigation

                                                                                              -

                                                                                              System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/surge/storm.py:docstring of clawpack.geoclaw.surge.storm.fill_rad_w_other_source, line 26)

                                                                                              +

                                                                                              System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/surge/storm.py:docstring of clawpack.geoclaw.surge.storm.fill_rad_w_other_source, line 26)

                                                                                              Field list ends without a blank line; unexpected unindent.

                                                                                                diff --git a/dev/testing.html b/dev/testing.html index 851183f696..048225812a 100644 --- a/dev/testing.html +++ b/dev/testing.html @@ -85,7 +85,7 @@

                                                                                                Navigation

                                                                                                Testing your installation

                                                                                                PyClaw

                                                                                                -

                                                                                                If you downloaded Clawpack manually, you can test your Pyclaw +

                                                                                                If you downloaded Clawpack manually, you can test your PyClaw installation as follows (starting from your clawpack directory):

                                                                                                cd pyclaw
 nosetests
@@ -118,7 +118,7 @@ 
                                                                                                Classicgalleries.  See also Regression testing.
                                                                                                
+archived in the Clawpack Gallery.  See also Regression testing.
                                                                                                diff --git a/dev/topo.html b/dev/topo.html index c838059186..181de4ee1c 100644 --- a/dev/topo.html +++ b/dev/topo.html @@ -147,8 +147,10 @@

                                                                                                Navigation

                                                                                                These files are larger than necessary since they store the x,y values at each point even though the points are required to be equally spaced. Many data sets come this way, but note that you can convert a file of -this type to one of the more compact types below using:

                                                                                                -
                                                                                                [insert python code]
+this type to one of the more compact types below using e.g.:
                                                                                                
+
                                                                                                from clawpack.geoclaw import topotools
+topo = topotools.Topography(input_path, topo_type=1)
+topo.write(output_path, topo_type=3)
                                                                                          diff --git a/dev/topotools_module.html b/dev/topotools_module.html index 5a656c9a55..eb94ff698a 100644 --- a/dev/topotools_module.html +++ b/dev/topotools_module.html @@ -314,7 +314,7 @@

                                                                                          Navigation

                                                                                          -plot(axes=None, contour_levels=None, contour_kwargs={}, limits=None, cmap=None, add_colorbar=True, plot_box=False, fig_kwargs={}, data_break=0.0, cb_kwargs={})
                                                                                          +plot(axes=None, contour_levels=None, contour_kwargs={}, limits=None, cmap=None, add_colorbar=True, plot_box=False, long_lat=True, fig_kwargs={}, data_break=0.0, cb_kwargs={})

                                                                                          Plot the topography.

                                                                                          Input
                                                                                          @@ -334,6 +334,9 @@

                                                                                          Navigation

                                                                                        • fig_kwargs (dict) - keyword arguments to be passed to figure.

                                                                                        • plot_box (bool or color specifier) - If evaluates to True, plot a box around limits of this topo.

                                                                                          • +

                                                                                        • long_lat (bool) - If this is a longitude-latitude plot then set the +aspect of the plot to compensate for stretching. If not then the +aspect is set to “equal”.

                                                                                        • data_break (float) - when default cmap is used, the value to use to break between water and land colormaps. Defaults to 0., but for some topo files may need to use e.g. 0.01 diff --git a/dev/user_routines.html b/dev/user_routines.html index c5bb12b392..603bef11dd 100644 --- a/dev/user_routines.html +++ b/dev/user_routines.html @@ -101,7 +101,7 @@

                                                                                          Navigation

                                                                                        • $CLAW/amrclaw/examples

                                                                                        • $CLAW/geoclaw/examples

                                                                                        -

                                                                                        You can also browse from the galleries to the README file for an +

                                                                                        You can also browse from the Clawpack Gallery to the README file for an example and then to the source code for the application-specific codes.

                                                                                        Specifying the initial conditions

                                                                                        diff --git a/developers.html b/developers.html index 61213066d4..9881ec9196 100644 --- a/developers.html +++ b/developers.html @@ -73,7 +73,7 @@

                                                                                        Navigation

                                                                                        previous |
                                                                                      • Clawpack 5.8.x documentation »
                                                                                        • -
                                                                                      • Pyclaw »
                                                                                        • +
                                                                                      • PyClaw »
                                                                                      @@ -513,7 +513,7 @@

                                                                                      Table of Contents

                                                                                      Related Topics

                                                                                      • Documentation overview
                                                                                          -
                                                                                        • Pyclaw @@ -73,9 +81,29 @@

                                                                                          Navigation

                                                                                          -

                                                                                          The Clawpack Gallery is available only for the latest release of Clawpack.

                                                                                          -

                                                                                          Please see -http://www.clawpack.org/gallery/index.html.

                                                                                          +
                                                                                          @@ -90,6 +118,8 @@

                                                                                          Version 5.8.x

                                                                                          Related Topics

                                                                                          diff --git a/gallery/_sources/notebooks.rst.txt b/gallery/_sources/notebooks.rst.txt index 1c85dde44b..75f0cc78f4 100644 --- a/gallery/_sources/notebooks.rst.txt +++ b/gallery/_sources/notebooks.rst.txt @@ -157,9 +157,7 @@ The notebook * `animation tools demo <_static/apps/notebooks/visclaw/animation_tools_demo.html>`__ -shows some other related animation tools, including ways to create interactive -animations using Jupyter widgets or as embedded or stand-alone javascript -or mp4 files. +shows some other related animation tools. .. _notebooks_vis: @@ -179,6 +177,11 @@ show how to use various plotting and visualization tools available in Clawpack: extract a uniform grid or a 1D transect that uses the finest available grid info at each point. +* `animation tools demo <_static/apps/notebooks/visclaw/animation_tools_demo.html>`__ + illustrates animation tools, including ways to create interactive + animations using Jupyter widgets or as embedded or stand-alone javascript + or mp4 files. (These tools may be useful for plots created outside of + Clawpack as well.) .. _notebooks_riemann: diff --git a/gallery/notebooks.html b/gallery/notebooks.html index c01057cf9e..ff2088ee40 100644 --- a/gallery/notebooks.html +++ b/gallery/notebooks.html @@ -197,9 +197,7 @@

                                                                                          Tohoku 2011

                                                                                        • animation tools demo

                                                                                        -

                                                                                        shows some other related animation tools, including ways to create interactive -animations using Jupyter widgets or as embedded or stand-alone javascript -or mp4 files.

                                                                                        +

                                                                                        shows some other related animation tools.

                                                                                        Plotting and visualization

                                                                                        @@ -213,6 +211,11 @@

                                                                                        Tohoku 2011animation tools demo +illustrates animation tools, including ways to create interactive +animations using Jupyter widgets or as embedded or stand-alone javascript +or mp4 files. (These tools may be useful for plots created outside of +Clawpack as well.)

                                                                                      diff --git a/gallery/searchindex.js b/gallery/searchindex.js index bc5c0d71a4..55b4f7b0a4 100644 --- a/gallery/searchindex.js +++ b/gallery/searchindex.js @@ -1 +1 @@ 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1D \u2013 Heterogeneous example","Acoustics 1D \u2014 Homogeneous example","Two-dimensional acoustics with radially symmetric initial data","Advection 1D Example 1","Two-dimensional advection around an annulus","Two-dimensional advection with inflow boundaries","Two-dimensional advection of a square pulse","Two-dimensional advection with a swirling flowfield","Two-dimensional Burgers\u2019 equation","Euler equations in 1d \u2013 Woodward-Colella blast wave problem","Two-dimensional Euler equations","TVB Method of Shu on Advection","Chapter 11","Chapter 11","Chapter 11","Chapter 11","Entropy Fix Examples with Burger\u2019s Eqn","Two colliding 2-shocks","Variable-Coefficient Traffic Flow Model","Advection Diffusion Equation","Traffic Flow equation with an on ramp source","2D Burgers\u2019 equation at angle theta to the x-axis","1D Acoustics with simple waves","Compare Limiters for Advection","Advection with wave packet data","Inflow BCs for acoustics","Advection with inflow boundary conditions.","Acoustics with a standing wave","Tohoku tsunami and comparison with gauge data in Hawaii","Radial bowl test case for fgmax routines","Chile 2010 test case for fgmax routines","Tsunami interacting with 1d continental shelf","Acoustics 1D Example 1","Acoustics 1D Example 1","Two-dimensional acoustics with radially symmetric initial data","Advection 1D Example 1","Two-dimensional advection around an annulus","Euler equations in 1d \u2013 Woodward-Colella blast wave problem","Gallery of 1d Classic applications","Gallery of 2d Clawpack applications","Gallery of Classic and AMRClaw applications","Gallery of fvmbook applications","Gallery of GeoClaw applications","Tsunami in a parabolic bowl shaped ocean","Basic 2D Multi-Layer Shallow Water Examples","Basic Example of Storm Surge from Hurricane Ike","Basic Example of Storm Surge from Hurricane Isaac","Tsunami in a parabolic bowl shaped ocean","Sloshing water in a parabolic bowl","Tsunami arising offshore Maule, Chile, Feb. 27, 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1D \u2013 Heterogeneous example","Acoustics 1D \u2014 Homogeneous example","Two-dimensional acoustics with radially symmetric initial data","Advection 1D Example 1","Two-dimensional advection around an annulus","Two-dimensional advection with inflow boundaries","Two-dimensional advection of a square pulse","Two-dimensional advection with a swirling flowfield","Two-dimensional Burgers\u2019 equation","Euler equations in 1d \u2013 Woodward-Colella blast wave problem","Two-dimensional Euler equations","TVB Method of Shu on Advection","Chapter 11","Chapter 11","Chapter 11","Chapter 11","Entropy Fix Examples with Burger\u2019s Eqn","Two colliding 2-shocks","Variable-Coefficient Traffic Flow Model","Advection Diffusion Equation","Traffic Flow equation with an on ramp source","2D Burgers\u2019 equation at angle theta to the x-axis","1D Acoustics with simple waves","Compare Limiters for Advection","Advection with wave packet data","Inflow BCs for acoustics","Advection with inflow boundary conditions.","Acoustics with a standing wave","Tohoku tsunami and comparison with gauge data in Hawaii","Radial bowl test case for fgmax routines","Chile 2010 test case for fgmax routines","Tsunami interacting with 1d continental shelf","Acoustics 1D Example 1","Acoustics 1D Example 1","Two-dimensional acoustics with radially symmetric initial data","Advection 1D Example 1","Two-dimensional advection around an annulus","Euler equations in 1d \u2013 Woodward-Colella blast wave problem","Gallery of 1d Classic applications","Gallery of 2d Clawpack applications","Gallery of Classic and AMRClaw applications","Gallery of fvmbook applications","Gallery of GeoClaw applications","Tsunami in a parabolic bowl shaped ocean","Basic 2D Multi-Layer Shallow Water Examples","Basic Example of Storm Surge from Hurricane Ike","Basic Example of Storm Surge from Hurricane Isaac","Tsunami in a parabolic bowl shaped ocean","Sloshing water in a parabolic bowl","Tsunami arising offshore Maule, Chile, Feb. 27, 2010","Tsunami arising offshore Maule, Chile, Feb. 27, 2010","Adjoint solution for Chile 2010 with adjoint flagging","Tsunami modeling example with subsidence and dry regions below sea level","Flow past an island with particle tracking","Radial ocean with an island and fgmax grids","Test Gallery","Galleries of all Clawpack applications","Clawpack Gallery of Jupyter Notebooks","2-dimensional shallow water on the sphere","1-dimensional acoustics","2-dimensional acoustics","2-dimensional variable-coefficient acoustics","2-dimensional variable-coefficient acoustics","1-dimensional advection","2-dimensional advection","2-dimensional variable-coefficient advection","2-dimensional advection-reaction","1-dimensional Burgers\u2019 equation","1-dimensional shallow water equation","Gallery of all PyClaw applications","2-dimensional KPP equation","2-dimensional p-system","2-dimensional Euler equations","2-dimensional shallow water equations","2-dimensional Euler equations","1-dimensional Euler equations","1-dimensional Euler equations","1-dimensional shallow water equation","1-dimensional nonlinear elasticity","1-dimensional variable-velocity advection","1-dimensional Euler equations"],titleterms:{"break":73,"case":[29,30],BCs:25,Ike:45,One:[59,63,79],acoust:[0,1,2,22,25,27,32,33,34,38,39,40,59,60,61,62,69],adjoint:[42,50,51,55],advect:[3,4,5,6,7,11,19,23,24,26,35,36,38,39,40,55,63,64,65,66,69,79],all:[56,69],amr:42,amrclaw:[40,57],angl:21,annular:65,annulu:[4,36],applic:[38,39,40,41,42,56,69],approach:41,aris:[49,50],around:[4,36],axi:21,balanc:41,basic:[44,45,46],below:52,blast:[9,37,80],boundari:[5,26,41],bowl:[29,42,43,47,48],burger:[8,16,21,39,40,67,69],cell:41,chapter:[12,13,14,15,41],chile:[30,42,49,50,51,57],classic:[38,40,57],clawpack:[39,56,57],code:50,coeffici:[18,39,40,61,62,65,69],colella:[9,37,80],collid:17,compar:23,comparison:28,compress:74,condit:[26,41],conserv:41,content:[38,39,40,41,42,55,69],continent:31,convex:70,cylindr:74,dam:73,data:[2,24,28,34],diffus:19,dimension:[2,4,5,6,7,8,10,34,36,38,39,40,55,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80],domain:65,dry:52,elast:[69,78],entropi:16,eqn:16,equat:[8,9,10,19,20,21,37,39,40,41,67,68,69,70,72,73,74,75,76,77,80],eta_init:[42,55],euler:[9,10,37,38,39,40,69,72,74,75,76,80],exampl:[0,1,3,16,32,33,35,42,44,45,46,52,57,72],feb:[49,50],fgmax:[29,30,42,54],finit:41,fix:16,flag:[42,50,51],flow:[18,20,53,58,68,74,77],flowfield:7,flux:70,folder:50,force_dri:[42,55],format:78,fortran:57,from:[45,46],fvmbook:41,galleri:[38,39,40,41,42,55,56,57,69],gaug:[28,42],geoclaw:[42,55,57],ghost:41,grid:[54,61],hawaii:28,heterogen:0,high:41,histori:[29,30],homogen:1,hurrican:[45,46],hyperbol:41,illustr:57,inflow:[5,25,26],initi:[2,34],interact:31,isaac:46,island:[53,54],jupyt:57,kpp:[69,70],lagrangian:42,law:41,layer:[42,44],level:52,limit:23,linear:41,mani:[],map:61,maul:[49,50],media:78,method:[11,41,57],model:[18,52,57,70],multi:[42,44],multidimension:41,need:[],non:70,nonclass:41,nonlinear:[41,69,78],notebook:57,numer:57,ocean:[43,47,54,57],offshor:[49,50],old:[],organ:50,osher:75,other:41,output:[58,59,60,61,62,63,64,65,66,67,68,70,71,72,73,74,75,76,77,78,79,80],packet:24,parabol:[42,43,47,48],particl:53,past:53,period:78,plot:57,problem:[9,37,41,42,55,75,76,80],puls:6,pyclaw:[57,69],quadrant:72,radial:[2,29,34,42,54,57,73],ramp:20,reaction:[66,69],refer:48,region:52,resolut:41,result:57,riemann:57,routin:[29,30],run:[50,52,57],scalar:[41,70],sea:52,shallow:[42,44,58,68,69,73,77],shape:[43,47],shelf:31,shock:[17,76],shu:[11,75],simpl:22,slosh:[42,48],solitari:78,solut:51,solver:57,some:41,sourc:[20,41,58,59,60,61,62,63,64,65,66,67,68,70,71,72,73,74,75,76,77,78,79,80],sphere:[58,69],squar:6,stand:27,storm:[42,45,46],subsid:52,surg:[42,45,46],swirl:7,symmetr:[2,34,42],symmetri:74,system:[41,69,71],term:41,test:[29,30,55],theta:21,thi:52,tohoku:[28,57],tool:57,track:53,traffic:[18,20],tsuanami:42,tsunami:[28,31,42,43,47,49,50,52,57],tube:76,tvb:11,two:[2,4,5,6,7,8,10,17,34,36,60,61,62,64,71],updat:[],using:57,variabl:[18,39,40,61,62,65,69,79],variat:50,veloc:[69,79],version:[28,29,30,31,44,48,49,50,52,54],visclaw:[],visual:57,volum:41,water:[42,44,48,58,68,69,73,77],wave:[9,22,24,27,37,78,80],woodward:[9,37,80]}}) \ No newline at end of file diff --git a/genindex.html b/genindex.html index e9749f41c1..b124b1eb18 100644 --- a/genindex.html +++ b/genindex.html @@ -1032,15 +1032,17 @@

                                                                                      T

                                                                                    • tfluct_solver (clawpack.pyclaw.sharpclaw.solver.SharpClawSolver attribute)
                                                                                      • -
                                                                                    - + @@ -124,7 +124,7 @@

                                                                                    Version 5.8.x

                                                                                    Related Topics

                                                                                    • Documentation overview
                                                                                        -
                                                                                      • Pyclaw
                                                                                          +
                                                                                        • PyClaw
                                                                                          • Developers’ Guide @@ -360,7 +360,7 @@

                                                                                            Table of Contents

                                                                                            Related Topics

                                                                                            • Documentation overview
                                                                                                -
                                                                                              • Pyclaw
                                                                                                  +
                                                                                                • PyClaw
                                                                                                  • Developers’ Guide @@ -182,7 +182,7 @@

                                                                                                    Final releaseChanges to master since v5.8.0 which generate diffs between the latest version and +Changes to master since v5.8.1 which generate diffs between the latest version and the current master branch of each repository.

                                                                                                    @@ -235,6 +235,12 @@

                                                                                                    Zenodo +

                                                                                                    Open Science Framework (OSF)

                                                                                                    +

                                                                                                    Go to https://osf.io/kmw6h/files/ and upload the latest tarfile to the set +of versions that can be accessed with the single DOI +10.17605/osf.io/kmw6h.

                                                                                                    +

                                                                                                    Updating the documentation

                                                                                                    See Guide for updating this documentation for general instructions on building the documentation @@ -263,10 +269,11 @@

                                                                                                    ZenodoTable of Contents

                                                                                                  • Final release
                                                                                                  • Pypi
                                                                                                  • Zenodo
                                                                                                    • +
                                                                                                  • Open Science Framework (OSF)
                                                                                                  • Updating the documentation
                                                                                                  • Updating the apps repository
                                                                                                  • Updating the Dockerfile
                                                                                                    • @@ -337,7 +345,7 @@

                                                                                                    Table of Contents

                                                                                                    Related Topics

                                                                                                    @@ -203,14 +149,10 @@

                                                                                                    Version 5.8.x

                                                                                                    Table of Contents

                                                                                                    Related Topics

                                                                                                    • Documentation overview
                                                                                                        diff --git a/installing_fortcodes.html b/installing_fortcodes.html new file mode 100644 index 0000000000..58a9861bc9 --- /dev/null +++ b/installing_fortcodes.html @@ -0,0 +1,247 @@ + + + + + + + Options for installing Clawpack Fortran codes — Clawpack 5.8.x documentation + + + + + + + + + + + + + + + + + + +
                                                                                                        +
                                                                                                        + +
                                                                                                        +
                                                                                                        + + + +
                                                                                                        +
                                                                                                        +
                                                                                                        +
                                                                                                        + +
                                                                                                        +

                                                                                                        Options for installing Clawpack Fortran codes

                                                                                                        +

                                                                                                        This page describes ways to download and “install” Clawpack in a way that +the Fortran versions of the PDE solvers (Classic, AMRClaw, and GeoClaw) +can be used, along with Python codes that support these solvers, including +the visualization tools in VisClaw.

                                                                                                        +

                                                                                                        If you plan to use the PDE solvers directly from PyClaw, please +see Installing Clawpack for other options. If you are not sure, see +Which Clawpack solver should I use?

                                                                                                        +
                                                                                                        +

                                                                                                        tar file

                                                                                                        +

                                                                                                        You can download the most recent (or certain previous versions) of Clawpack +as a tar file. After untarring this, you can set environment variables +to point to this version.

                                                                                                        +

                                                                                                        Download a tar file from one of these sources:

                                                                                                        + +

                                                                                                        After downloading a tar file you can do, e.g.

                                                                                                        +
                                                                                                        tar -xzf clawpack-v5.8.1.tar.gz
+cd clawpack-v5.8.1
+export CLAW=/full/path/to/clawpack-v5.8.1  # in bash
+
                                                                                                        +
                                                                                                        +

                                                                                                        The last command sets an environment variable when using the bash shell. +The syntax may be different in other shells. Replace /full/path/to +with the appropriate full path.

                                                                                                        +

                                                                                                        You must also add $CLAW to your PYTHONPATH environment variable, +see Python path.

                                                                                                        +
                                                                                                        +
                                                                                                        +

                                                                                                        git clone

                                                                                                        +

                                                                                                        You can clone the git repositories from https://github.com/clawpack. +This is particularly useful if you +want the latest development version or a branch that is not in a release yet, +and/or if you plan to contribute to the code yourself via a pull request. +See Developers’ Guide for more details, but the basic commands are:

                                                                                                        +
                                                                                                        git clone git://github.com/clawpack/clawpack.git
+cd clawpack
+git checkout v5.8.1     # or an older version; `git tag -l` to list options
+git submodule init      # for repositories pyclaw, clawutil, visclaw, etc.
+git submodule update    # clones all the submodule repositories
+export CLAW=/full/path/to/clawpack    # in bash
+
                                                                                                        +
                                                                                                        +

                                                                                                        The last command sets an environment variable when using the bash shell. +The syntax may be different in other shells. Replace /full/path/to +with the appropriate full path.

                                                                                                        +

                                                                                                        You must also add $CLAW to your PYTHONPATH environment variable, +see Python path.

                                                                                                        +

                                                                                                        Components: +See Clawpack components for a list of what is generally included +under the top level clawpack directory when using any of these approaches. +(And what is not included, e.g. the Clawpack Applications repository.)

                                                                                                        +
                                                                                                        +

                                                                                                        Next steps:

                                                                                                        +

                                                                                                        Once Clawpack is installed, you can get started:

                                                                                                        + +
                                                                                                        +
                                                                                                        +
                                                                                                        + + +
                                                                                                        +
                                                                                                        +
                                                                                                        + +
                                                                                                        +
                                                                                                        +
                                                                                                        + © Copyright CC-BY 2020, The Clawpack Development Team. + Created using Sphinx. +
                                                                                                        + + + + \ No newline at end of file diff --git a/installing_pip.html b/installing_pip.html index 3a44fee24b..ebf1f6ba3d 100644 --- a/installing_pip.html +++ b/installing_pip.html @@ -20,7 +20,7 @@ - +
                                                                                                        @@ -67,7 +67,7 @@

                                                                                                        Navigation

                                                                                                        modules |
                                                                                                      • - next |
                                                                                                      • Navigation

                                                                                                        pip install instructions

                                                                                                        -

                                                                                                        For other installation options, see Installing Clawpack.

                                                                                                        -

                                                                                                        See also:

                                                                                                        - -

                                                                                                        Register: Please register -if you have not already done so. This is very useful in helping -us track the extent of usage, and important to the Funding agencies -who support this work.

                                                                                                        +

                                                                                                        Note: If you only plan to use the Fortran versions of the solvers +(rather than PyClaw), and you run into problems with pip, +then you might want to try Options for installing Clawpack Fortran codes.

                                                                                                        +
                                                                                                        +

                                                                                                        Quick Installation of PyClaw with pip

                                                                                                        +

                                                                                                        Please see Which Clawpack solver should I use? before installing, particularly +if you are not sure whether you will +be using the Fortran versions of the PDE solvers +(Classic, AMRClaw, and GeoClaw) or the PyClaw version of the PDE solvers. +See Installing Clawpack for other installation options.

                                                                                                        Prerequisites: Before installing, check that you have the Installation Prerequisites.

                                                                                                        -

                                                                                                        Installing Clawpack requires downloading some version and then setting -paths so that Python import statements (and possibly Fortran Makefiles) find -the desired version. pip can be used to reset Python paths as well as to -download a new version of Clawpack and set the path appropriately. See -Python path for more information.

                                                                                                        -
                                                                                                        -

                                                                                                        Quick Installation of all packages

                                                                                                        +

                                                                                                        If you only want to use PyClaw (and associated Python +tools, e.g. VisClaw for visualization), then the simplest way to install +Clawpack is via:

                                                                                                        +
                                                                                                        pip install --user clawpack
+
                                                                                                        +
                                                                                                        +

                                                                                                        or, more specifically,

                                                                                                        +
                                                                                                        pip install --user clawpack==v5.8.1
+
                                                                                                        +
                                                                                                        +

                                                                                                        or you can choose a previous version from the PyPi history.

                                                                                                        +

                                                                                                        However, note that this does not download the Fortran codes in a way that they +can be used for Classic, AMRClaw, and GeoClaw.

                                                                                                        +

                                                                                                        If you think you might want to use the Fortran packages as well +(Classic, AMRClaw, GeoClaw) and/or want easier access to the Python source +code, it is recommended that you follow the pip instructions below.

                                                                                                        +
                                                                                                        +
                                                                                                        +

                                                                                                        Quick Installation of all packages with pip

                                                                                                        The recommended way to install the latest release of Clawpack, for -using PyClaw and/or the Fortran packages, is to give the following pip -install command +using both PyClaw and the Fortran packages, is to use pip, e.g. with the +following command (you might want to first read the notes below to see if you want to change anything in this command):

                                                                                                        pip install --src=$HOME/clawpack_src --user -e \
-    git+https://github.com/clawpack/clawpack.git@v5.8.0#egg=clawpack-v5.8.0
+    git+https://github.com/clawpack/clawpack.git@v5.8.1#egg=clawpack-v5.8.1 \
+    --use-deprecated=legacy-resolver
                                                                                                        -

                                                                                                        This will download Clawpack (via a git clone) into the directory -$HOME/clawpack_src/clawpack-v5.8.0. The top +

                                                                                                        Notes:

                                                                                                        +
                                                                                                          +

                                                                                                        • With older versions of pip, the flag +–use-deprecated=legacy-resolver +may not be recognized and is not needed.

                                                                                                          • +

                                                                                                        • Using pip to install will also check some python +Installation Prerequisites and may update these on your system, and will use f2py to +convert Fortran Riemann solvers to Python versions. See +installing_options if you want more control.

                                                                                                          • +

                                                                                                        • This will download Clawpack (via a git clone) into the directory +$HOME/clawpack_src/clawpack-v5.8.1. The top installation directory can be changed by modifying the --src target (or omit this part to put it in your current working directory). If you have already downloaded Clawpack via a different mechanism then -see Using pip to install a different version rather than using the above command.

                                                                                                          -

                                                                                                          See Clawpack components for a list of what’s included in this top -level directory.

                                                                                                          -

                                                                                                          Note: Using pip to install will also check some python -Installation Prerequisites and may update these on your system, and will use f2py to -convert Fortran Riemann solvers to Python versions. See -Other Installation Options if you want more control.

                                                                                                          -

                                                                                                          The --user flag is necessary if you are installing on a shared computer +see Using pip to install a different version rather than using the above command.

                                                                                                          • +

                                                                                                        • See Clawpack components for a list of what’s included in this top +level directory.

                                                                                                          • +

                                                                                                        • The --user flag is necessary if you are installing on a shared computer where you do not have root access. If you do have root access and want it to be available to all users, you can omit this flag. See notes below for -more information.

                                                                                                          -

                                                                                                          The -e flag makes it an “editable” install, leaving the source code in +more information.

                                                                                                          • +

                                                                                                        • The -e flag makes it an “editable” install, leaving the source code in place and allowing you to modify it if desired. (Otherwise, by default, pip would move the python code to some -site-packages directory and delete everything else.)

                                                                                                          -

                                                                                                          In order to use the Fortran codes within Clawpack (classic, +site-packages directory and delete everything else.)

                                                                                                          • +

                                                                                                        • In order to use the Fortran codes within Clawpack (classic, amrclaw, or geoclaw), you should then set the environment -variable CLAW to point to the clawpack-v5.8.0 directory within +variable CLAW to point to the clawpack-v5.8.1 directory within the installation directory $HOME/clawpack_src, and FC to point to the desired Fortran compiler, e.g. in the bash shell:

                                                                                                          -
                                                                                                          export CLAW=$HOME/clawpack_src/clawpack-v5.8.0
+
                                                                                                          export CLAW=$HOME/clawpack_src/clawpack-v5.8.1
 export FC=gfortran
 
                                                                                                          
 
                                                                                                          
-
                                                                                                          Notes:
                                                                                                          
-
                                                                                                          You may want to set CLAW even if you are only using PyClaw, since $CLAW is
+
                                                                                                          • +

                                                                                                        • You may want to set CLAW even if you are only using PyClaw, since $CLAW is sometimes used in this documentation to indicate the top level of the -Clawpack source directory structure.

                                                                                                          +Clawpack source directory structure.

                                                                                                          • +

                                                                                                        Installing with pip also compiles Riemann solvers written in Fortran for use in PyClaw. If you get a Fortran error message when installing, see Setting the Fortran compiler to be used by f2py (pip).

                                                                                                        See Set environment variables for more information, and Python path if you are having problems with importing Python modules.

                                                                                                        -
                                                                                                        -
                                                                                                        -

                                                                                                        Quick Installation of only PyClaw

                                                                                                        -

                                                                                                        If you only want to use PyClaw (and associated Python -tools, e.g. VisClaw for visualization), they you could do:

                                                                                                        -
                                                                                                        pip install --user clawpack
-
                                                                                                        -
                                                                                                        -

                                                                                                        or, more specifically,

                                                                                                        -
                                                                                                        pip install --user clawpack==v5.8.0
-
                                                                                                        -
                                                                                                        -

                                                                                                        However, if you think you might want to use the Fortran packages as well -(Classic, AMRClaw, GeoClaw) and/or want easier access to the Python source -code, it is recommended that you follow the instructions above for -Quick Installation of all packages (or see other Additional options for installing Clawpack).

                                                                                                        Next steps:

                                                                                                        Once Clawpack is installed, you can go to one of the following pages to get @@ -172,6 +174,7 @@

                                                                                                        Next steps:

                                                                                                      • Testing a PyClaw installation and running an example

                                                                                                      • Testing your Fortran installation and running an example

                                                                                                        • +

                                                                                                      • Troubleshooting Installation

                                                                                                      @@ -257,8 +260,8 @@

                                                                                                      Version 5.8.x

                                                                                                      Table of Contents

                                                                                                      • pip install instructions
                                                                                                          -
                                                                                                        • Quick Installation of all packages
                                                                                                          • -
                                                                                                        • Quick Installation of only PyClaw
                                                                                                            +
                                                                                                          • Quick Installation of PyClaw with pip
                                                                                                            • +
                                                                                                          • Quick Installation of all packages with pip
                                                                                                            • Next steps:
                                                                                                            • Using pip to install a different version
                                                                                                            • Experimenting with code in the examples directories
                                                                                                              • @@ -272,7 +275,7 @@

                                                                                                              Related Topics

                                                                                                              diff --git a/kmltools_module.html b/kmltools_module.html index c565dd66b3..9c2e46489a 100644 --- a/kmltools_module.html +++ b/kmltools_module.html @@ -114,6 +114,7 @@

                                                                                                              Navigation

                                                                                                            • pcolorcells_for_kml - version of pcolormesh with appropriate dpi and size

                                                                                                            • png2kml - create kml file wrapping a png figure to be viewed on GE

                                                                                                            • kml_build_colorbar - create a colorbar to display on GE

                                                                                                              • +

                                                                                                            • topo2kmz - create kmz file showing onshore and offshore topography

                                                                                                            • kml_header - used internally

                                                                                                            • kml_footer - used internally

                                                                                                            • kml_region - used internally

                                                                                                              • @@ -223,7 +224,7 @@

                                                                                                              Navigation

                                                                                                              -clawpack.geoclaw.kmltools.kml_build_colorbar(cb_filename, cmap, cmin=None, cmax=None, norm=None, label=None, title=None, extend='neither')
                                                                                                              +clawpack.geoclaw.kmltools.kml_build_colorbar(cb_filename, cmap, cmin=None, cmax=None, norm=None, label=None, title=None, extend='neither', close_figs=True)

                                                                                                              Make a png file with a colorbar corresponding to cmap, norm. cmin, cmax are used only if nrm is not provided.

                                                                                                              @@ -335,7 +336,7 @@

                                                                                                              Navigation

                                                                                                              Internally the value dpi (dots per inch) for the png file is determined so that it is at least 16 and so that:

                                                                                                              -

                                                                                                              System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

                                                                                                              +

                                                                                                              System Message: ERROR/3 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

                                                                                                              Unexpected indentation.

                                                                                                              @@ -343,7 +344,7 @@

                                                                                                              Navigation

                                                                                                              dpi * y_inches = dcp * y_cells

                                                                                                              -

                                                                                                              System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 38)

                                                                                                              +

                                                                                                              System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 38)

                                                                                                              Block quote ends without a blank line; unexpected unindent.

                                                                                                              where x_cells, y_cells are the number of cells in each direction.

                                                                                                              @@ -353,14 +354,14 @@

                                                                                                              Navigation

                                                                                                              annotate the figure befor saving it as a png file, which should then be done with:

                                                                                                              -

                                                                                                              System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

                                                                                                              +

                                                                                                              System Message: ERROR/3 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

                                                                                                              Unexpected indentation.

                                                                                                              plt.savefig(png_filename, transparent=True, dpi=kml_dpi)

                                                                                                              -

                                                                                                              System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

                                                                                                              +

                                                                                                              System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

                                                                                                              Block quote ends without a blank line; unexpected unindent.

                                                                                                              The png_extent is needed in construcing a kml file to display the @@ -471,6 +472,39 @@

                                                                                                              Navigation

                                                                                                              Color is green by default.

                                                                                                              +
                                                                                                              +
                                                                                                              +clawpack.geoclaw.kmltools.topo2kmz(topo, zlim=(-20, 20), mask_outside_zlim=True, sea_level=0.0, name='topo', force_dry=None, close_figs=True)
                                                                                                              +

                                                                                                              Create kmz file showing onshore and offshore topography as separate layers. +Currently not very flexible but is useful in quickly creating kmz files +to open on Google Earth showing the onshore topography and offshore +bathymetry as two separate layers. Constant colors on rectangular grid +cells should be properly rendered to ease exploration of DEMs. +A colorbar png file is also created and included in the kmz file.

                                                                                                              +
                                                                                                              +
                                                                                                              Input
                                                                                                              +
                                                                                                                +

                                                                                                              • topo should be a topotools.Topography object,

                                                                                                                • +

                                                                                                              • zlim is the elevation z limits for choosing the color map

                                                                                                                • +

                                                                                                              • mask_outside_zlim if True, suppress plotting outsize zlim

                                                                                                                • +

                                                                                                              • sea_level is the break between water and land colors

                                                                                                                • +

                                                                                                              • name is used in the kml menu and file name

                                                                                                                • +

                                                                                                              • force_dry is currently not used

                                                                                                                • +

                                                                                                              • close_figs to close the pyplot figures after making png files

                                                                                                                • +
                                                                                                              +
                                                                                                              +
                                                                                                              Future
                                                                                                              +

                                                                                                              +
                                                                                                              +
                                                                                                              +

                                                                                                              System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.topo2kmz, line 18)

                                                                                                              +

                                                                                                              Field list ends without a blank line; unexpected unindent.

                                                                                                              +
                                                                                                              +

                                                                                                              If force_dry is an array of the same shape as topo.Z then another png +and kml file are created for land that is below sea_level but where +force_dry = True.

                                                                                                              +
                                                                                                              +
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                                                                                                      Clawpack includes a number of related hyperbolic PDE solvers:

                                                                                                      All of them are built on common algorithmic @@ -98,25 +98,29 @@

                                                                                                      Navigation

                                                                                                      the main differences between them.

                                                                                                      Installation and user interface

                                                                                                      -

                                                                                                      The AMRClaw, GeoClaw, and Classic solvers are Fortran-based +

                                                                                                      The Classic, AMRClaw, and GeoClaw solvers are Fortran-based packages and rely on Makefiles and environment variables. Problems are specified partially through Python scripts at run time (setrun.py) and partially through custom Fortran code at compile time (to set initial conditions, for instance).

                                                                                                      -

                                                                                                      With PyClaw, problems are specified entirely at run time through +

                                                                                                      With PyClaw, problems are specified entirely at run time through Python script files, or interactively (e.g., in IPython or Jupyter notebooks). Typically, the user does not need to write any Fortran code (though custom routines can be written in Fortran -when necessary for performance reasons). -PyClaw uses much of the same library of Fortran code, but that code is +when necessary for performance reasons).

                                                                                                      +

                                                                                                      PyClaw uses much of the same library of Fortran code, but that code is compiled during installation so that it can be imported dynamically within -Python programs.

                                                                                                      +Python programs. In particular, Fortran versions of all the Riemann solvers +available in Classic or AMRClaw are also exposed in PyClaw. These are +converted using f2py, a step +that sometimes causes problems and is not required if you are only using +Fortran versions of the solvers.

                                                                                                      Algorithmic differences

                                                                                                      All of the Clawpack solvers include the classic algorithms described in [LeVeque-FVMHP]; if you only require those, it’s easiest to use Classic or -Pyclaw. Most of the packages contain additional algorithms:

                                                                                                      +PyClaw. Most of the packages contain additional algorithms:

                                                                                                      • AMRClaw includes block-structured adaptive mesh refinement that allows one diff --git a/plotexamples.html b/plotexamples.html index 7726c1573f..2edee74363 100644 --- a/plotexamples.html +++ b/plotexamples.html @@ -84,7 +84,7 @@

                                                                                                        Navigation

                                                                                                        Plotting examples

                                                                                                        -

                                                                                                        See Using setplot.py to specify the desired plots and the examples in the galleries. +

                                                                                                        See Using setplot.py to specify the desired plots and the examples in the Clawpack Gallery. The code that produced each set of plots can be found in the Clawpack directory indicated.

                                                                                                        If you wish to use the Matlab tools, see the Matlab Gallery.

                                                                                                        diff --git a/plotting_python.html b/plotting_python.html index 4e29a43189..d8e6915ed4 100644 --- a/plotting_python.html +++ b/plotting_python.html @@ -87,7 +87,7 @@

                                                                                                        Navigation

                                                                                                        Clawpack includes utilities for plotting using Python. Most of these are defined in the clawpack.visclaw module. In order to use these you will need to insure that you have the required -modules installed (see Installation of required modules).

                                                                                                        +modules installed (see python-install).

                                                                                                        See Python Hints for more information on Python and pointers to many tutorials.

                                                                                                        Producing html plots from the command line

                                                                                                        diff --git a/prereqs.html b/prereqs.html index 72107b7440..51b7059353 100644 --- a/prereqs.html +++ b/prereqs.html @@ -86,39 +86,37 @@

                                                                                                        Navigation

                                                                                                        Fortran

                                                                                                        -

                                                                                                        PyClaw can now be installed without a Fortran compiler; see Using conda (does not require a Fortran compiler).

                                                                                                        -

                                                                                                        To use the other packages, you will need -gfortran or another F90 compiler

                                                                                                        +

                                                                                                        To use the Fortran versions of the PDE solvers (Classic, AMRClaw, and GeoClaw), +you will need +gfortran or another F90 compiler.

                                                                                                        See Fortran Compilers for more about which compilers work well with Clawpack.

                                                                                                        Python

                                                                                                          -

                                                                                                        • Python Version 2.7 or above, or (new in 5.4.0) Python 3

                                                                                                          • +

                                                                                                        • Python Version 3.0 or above (much of the code works in Python2, but this +is no longer officially supported; see Dropping support for Python 2.7).

                                                                                                        • NumPy (for PyClaw/VisClaw)

                                                                                                        • matplotlib (for PyClaw/VisClaw)

                                                                                                        -

                                                                                                        The Anaconda Python Distribution -is an easy way to get all of these. -See Python Hints for more information on -installing the required modules and to get started using Python if -you are not familiar with it.

                                                                                                        +

                                                                                                        There are many ways to install the Python scientific stack, e.g. via +apt-get or brew. On MacOS, you might check out +ScipySuperpack for Homebrew.

                                                                                                        pip

                                                                                                        If you are installing via pip install then you need pip. -You may already have it; in particular the Anaconda Python distribution -contains pip. If you need to install it, see -https://pip.pypa.io/en/stable/installing/

                                                                                                        -

                                                                                                        The version of pip install suggested for Quick Installation of all packages requires +If you need to install it, see +https://pip.pypa.io/en/stable/installation/

                                                                                                        +

                                                                                                        The version of pip install suggested for Quick Installation of all packages with pip requires a recent version of pip, so you may need to upgrade if you run into problems.

                                                                                                        Git

                                                                                                        If you are installing via pip using the command in -Quick Installation of all packages, or via git clone, then you need Git. +Quick Installation of all packages with pip, or via git clone, then you need Git. You may already have it; in particular the Xcode tools on Mac OSX contains Git. If you need to install it, see the Git book.

                                                                                                        diff --git a/pyclaw/about.html b/pyclaw/about.html index 372c43c39d..f978d88b51 100644 --- a/pyclaw/about.html +++ b/pyclaw/about.html @@ -73,7 +73,7 @@

                                                                                                        Navigation

                                                                                                        previous |
                                                                                                      • Clawpack 5.8.x documentation »
                                                                                                        • -
                                                                                                      • Pyclaw »
                                                                                                        • +
                                                                                                      • PyClaw »
                                                                                                      @@ -167,7 +167,7 @@

                                                                                                      Table of Contents

                                                                                                      Related Topics

                                                                                                      @@ -129,7 +129,7 @@

                                                                                                      Version 5.8.x

                                                                                                      Related Topics

                                                                                                      • Documentation overview
                                                                                                          -
                                                                                                        • Pyclaw @@ -339,7 +339,7 @@

                                                                                                          Table of Contents

                                                                                                          Related Topics

                                                                                                          • Documentation overview
                                                                                                              -
                                                                                                            • Pyclaw @@ -232,7 +232,7 @@

                                                                                                              Version 5.8.x

                                                                                                              Related Topics

                                                                                                              • Documentation overview
                                                                                                                  -
                                                                                                                • Pyclaw
                                                                                                                    +
                                                                                                                  • PyClaw
                                                                                                                    • Going Further @@ -390,7 +390,7 @@

                                                                                                                      Table of Contents

                                                                                                                      Related Topics

                                                                                                                      • Documentation overview
                                                                                                                          -
                                                                                                                        • Pyclaw @@ -334,7 +334,7 @@

                                                                                                                          Table of Contents

                                                                                                                          Related Topics

                                                                                                                          • Documentation overview
                                                                                                                              -
                                                                                                                            • Pyclaw @@ -134,7 +134,7 @@

                                                                                                                              From the command line

                                                                                                                              Built-in examples

                                                                                                                              -

                                                                                                                              You can see results from many of the examples in the galleries.

                                                                                                                              +

                                                                                                                              You can see results from many of the examples in the Clawpack Gallery.

                                                                                                                              Adding new examples

                                                                                                                              @@ -171,7 +171,7 @@

                                                                                                                              Table of Contents

                                                                                                                              Related Topics

                                                                                                                              @@ -769,7 +769,7 @@

                                                                                                                              Table of Contents

                                                                                                                              Related Topics

                                                                                                                              • Documentation overview
                                                                                                                                  -
                                                                                                                                • Pyclaw @@ -136,7 +136,7 @@

                                                                                                                                  Version 5.8.x

                                                                                                                                  Related Topics

                                                                                                                                  • Documentation overview
                                                                                                                                      -
                                                                                                                                    • Pyclaw
                                                                                                                                        +
                                                                                                                                      • PyClaw
                                                                                                                                        • diff --git a/pyclaw/index.html b/pyclaw/index.html index 20726d7dd6..a3e6589005 100644 --- a/pyclaw/index.html +++ b/pyclaw/index.html @@ -4,7 +4,7 @@ - Pyclaw — Clawpack 5.8.x documentation + PyClaw — Clawpack 5.8.x documentation @@ -82,22 +82,34 @@

                                                                                                                                        Navigation

                                                                                                                                        -

                                                                                                                                        Pyclaw

                                                                                                                                        +

                                                                                                                                        PyClaw

                                                                                                                                        +

                                                                                                                                        In this section of the documentation, PyClaw refers +a Python version of the hyperbolic PDE solvers that allows solving the +problem in Python (e.g. in a Jupyter notebook) without explicitly using +any Fortran code. Versions of the solvers are written in Python. +However, they use Riemann solvers that are converted from the Fortran +versions into Python-callable versions using +f2py, +to facilitate using the same large set of solvers from either Fortran +or Python. Note that +in order for this to work the solvers must be precompiled, as is done +when using pip install, for example (see pip install instructions).

                                                                                                                                        +

                                                                                                                                        See Which Clawpack solver should I use? for more information about the different +capabilities of PyClaw relative to Classic, AMRClaw, and GeoClaw.

                                                                                                                                        +

                                                                                                                                        Note: The clawpack/pyclaw directory also contains some +Python tools that are used many places in +Clawpack, e.g. when plotting with visclaw or when compiling and +running Fortran code using a Makefile and setrun.py file +(when using Classic, AMRClaw, and GeoClaw). +These modules are mostly used “under the hood”. +Other Python tools of use in the Fortran versions +are described elsewhere; see e.g. Plotting with Visclaw or GeoClaw Description and Detailed Contents. +All of these modules are pure Python and should work fine as long +as the top level of Clawpack is on your Python path.

                                                                                                                                        PyClaw installation

                                                                                                                                        -

                                                                                                                                        Just do this:

                                                                                                                                        -
                                                                                                                                        pip install clawpack
-
                                                                                                                                        -
                                                                                                                                        -

                                                                                                                                        Installing with pip requires that you have a Fortran compiler installed.

                                                                                                                                        -

                                                                                                                                        Alternatively, if you use Anaconda or -Conda, you can:

                                                                                                                                        -
                                                                                                                                        conda install -c clawpack -c conda-forge clawpack
-
                                                                                                                                        -
                                                                                                                                        -

                                                                                                                                        This option will also install optional dependencies including PETSc and HDF5, -which are useful for large-scale parallel runs. Installing with Conda does not -require that you have a Fortran compiler.

                                                                                                                                        +

                                                                                                                                        Using pip install is the recommended approach, see +pip install instructions.

                                                                                                                                        Examples

                                                                                                                                        @@ -293,7 +305,7 @@

                                                                                                                                        Version 5.8.x

                                                                                                                                        Table of Contents

                                                                                                                                        @@ -474,7 +474,7 @@

                                                                                                                                        Table of Contents

                                                                                                                                        Related Topics

                                                                                                                                        @@ -336,7 +336,7 @@

                                                                                                                                        Table of Contents

                                                                                                                                        Related Topics

                                                                                                                                        @@ -293,7 +293,7 @@

                                                                                                                                        Table of Contents

                                                                                                                                        Related Topics

                                                                                                                                        • Documentation overview
                                                                                                                                            -
                                                                                                                                          • Pyclaw
                                                                                                                                              +
                                                                                                                                            • PyClaw
                                                                                                                                              • Going Further @@ -150,7 +150,7 @@

                                                                                                                                                Table of Contents

                                                                                                                                                Related Topics

                                                                                                                                                • Documentation overview
                                                                                                                                                    -
                                                                                                                                                  • Pyclaw
                                                                                                                                                      +
                                                                                                                                                    • PyClaw
                                                                                                                                                      • PyClaw Basics @@ -279,7 +279,7 @@

                                                                                                                                                        Table of Contents

                                                                                                                                                        Related Topics

                                                                                                                                                        • Documentation overview
                                                                                                                                                            -
                                                                                                                                                          • Pyclaw
                                                                                                                                                              +
                                                                                                                                                            • PyClaw
                                                                                                                                                              • Going Further @@ -513,7 +513,7 @@

                                                                                                                                                                Table of Contents

                                                                                                                                                                Related Topics

                                                                                                                                                                • Documentation overview
                                                                                                                                                                    -
                                                                                                                                                                  • Pyclaw @@ -336,7 +336,7 @@

                                                                                                                                                                    Table of Contents

                                                                                                                                                                    Related Topics

                                                                                                                                                                    • Documentation overview
                                                                                                                                                                        -
                                                                                                                                                                      • Pyclaw @@ -579,7 +579,7 @@

                                                                                                                                                                        Table of Contents

                                                                                                                                                                        Related Topics

                                                                                                                                                                        • Documentation overview
                                                                                                                                                                            -
                                                                                                                                                                          • Pyclaw
                                                                                                                                                                              +
                                                                                                                                                                            • PyClaw
                                                                                                                                                                              • Going Further @@ -201,7 +201,7 @@

                                                                                                                                                                                Table of Contents

                                                                                                                                                                                Related Topics

                                                                                                                                                                                • Documentation overview
                                                                                                                                                                                    -
                                                                                                                                                                                  • Pyclaw
                                                                                                                                                                                      +
                                                                                                                                                                                    • PyClaw
                                                                                                                                                                                      • PyClaw Basics @@ -451,7 +451,7 @@

                                                                                                                                                                                        Table of Contents

                                                                                                                                                                                        Related Topics

                                                                                                                                                                                        • Documentation overview
                                                                                                                                                                                            -
                                                                                                                                                                                          • Pyclaw @@ -158,7 +158,7 @@

                                                                                                                                                                                            Table of Contents

                                                                                                                                                                                            Related Topics

                                                                                                                                                                                            • Documentation overview
                                                                                                                                                                                                -
                                                                                                                                                                                              • Pyclaw @@ -225,7 +225,7 @@

                                                                                                                                                                                                Table of Contents

                                                                                                                                                                                                Related Topics

                                                                                                                                                                                                • Documentation overview
                                                                                                                                                                                                    -
                                                                                                                                                                                                  • Pyclaw
                                                                                                                                                                                                      +
                                                                                                                                                                                                    • PyClaw
                                                                                                                                                                                                      • PyClaw Basics @@ -321,7 +321,7 @@

                                                                                                                                                                                                        Table of Contents

                                                                                                                                                                                                        Related Topics

                                                                                                                                                                                                        • Documentation overview
                                                                                                                                                                                                            -
                                                                                                                                                                                                          • Pyclaw
                                                                                                                                                                                                              +
                                                                                                                                                                                                            • PyClaw
                                                                                                                                                                                                              • diff --git a/python.html b/python.html index 657b3e15f8..91ed94d888 100644 --- a/python.html +++ b/python.html @@ -82,23 +82,9 @@

                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              -

                                                                                                                                                                                                              Python Hints

                                                                                                                                                                                                              - +

                                                                                                                                                                                                              Python Hints

                                                                                                                                                                                                              -

                                                                                                                                                                                                              Dropping support for Python 2.7

                                                                                                                                                                                                              +

                                                                                                                                                                                                              Dropping support for Python 2.7

                                                                                                                                                                                                              As of Clawpack v5.7.0 we are no longer supporting Python 2.7, and Python 3.x is expected, see v5.7.0 release notes. At this point we believe v5.7.0 still works with Python 2.7, but we are phasing out @@ -118,37 +104,8 @@

                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              https://docs.python.org/3/howto/pyporting.html and other online resources discussing the differences between Python 2 and 3.

                                                                                                                                                                                                              -
                                                                                                                                                                                                              -

                                                                                                                                                                                                              What is Python?

                                                                                                                                                                                                              -

                                                                                                                                                                                                              Python is a powerful object-oriented interpreted scripting/programming -language. Some version of Python is almost certainly on your computer -already (on unix, linux, OSX type:

                                                                                                                                                                                                              -
                                                                                                                                                                                                              $ python --version
-
                                                                                                                                                                                                              -
                                                                                                                                                                                                              -

                                                                                                                                                                                                              to find out which version, or just:

                                                                                                                                                                                                              -
                                                                                                                                                                                                              $ python
-
                                                                                                                                                                                                              -
                                                                                                                                                                                                              -

                                                                                                                                                                                                              to start a python shell with a prompt that looks like:

                                                                                                                                                                                                              -
                                                                                                                                                                                                              >>>
-
                                                                                                                                                                                                              -
                                                                                                                                                                                                              -

                                                                                                                                                                                                              You may prefer to use IPython, which is a nicer shell -than the pure python shell, with things like command completion and history. -See the Quick IPython Tutorial.

                                                                                                                                                                                                              -
                                                                                                                                                                                                              -
                                                                                                                                                                                                              -

                                                                                                                                                                                                              Installation of required modules

                                                                                                                                                                                                              -

                                                                                                                                                                                                              To effectively use the pyclaw and Clawpack plotting routines that are -written in Python, you will need version 2.7 or greater -(but not 3.0 or above, which is not backwards compatible). -some modules that are not included in the standard Python distribution. -Python modules are loaded with the import statement in Python and a wide -variety of specialized modules exist for various purposes since people use -Python for many different purposes.

                                                                                                                                                                                                              -

                                                                                                                                                                                                              An alternative to installing the packages discussed below, you could also use the -Clawpack Virtual Machine, which has all the required Python modules pre-installed.

                                                                                                                                                                                                              +
                                                                                                                                                                                                              +

                                                                                                                                                                                                              References and tutorials

                                                                                                                                                                                                              For use with Clawpack, you will need the Numpy module (Numerical Python) that allows working with arrays in much the same way as in Matlab. This is distributed as part of @@ -156,44 +113,24 @@

                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              See the Installing SciPy page for tips installing SciPy and NumPy on various platforms.

                                                                                                                                                                                                              For plotting you will also need the matplotlib module which provides Matlab-like -plotting commands for 1d and 2d plots (e.g. contour and pcolor plots). -This is generally the hardest thing to get going properly. See the -matplotlib Installation FAQ.

                                                                                                                                                                                                              -

                                                                                                                                                                                                              Often the easiest way to get all the modules you need is to install the

                                                                                                                                                                                                              -

                                                                                                                                                                                                              Anaconda Python Distribution -or the -Enthought Python Distribution, which is free for academic -users. Versions are available for Windows, Mac OS X, and Redhat linux.

                                                                                                                                                                                                              -

                                                                                                                                                                                                              With some versions of Linux (e.g. debian and Ubuntu), you can easily install -what’s needed using apt-get:

                                                                                                                                                                                                              -
                                                                                                                                                                                                              $ apt-get install python-numpy
-$ apt-get install python-scipy
-$ apt-get install python-matplotlib
-
                                                                                                                                                                                                              -
                                                                                                                                                                                                              -

                                                                                                                                                                                                              For OS X, you might also try the Scipy Superpack. -See also these tips on installing matplotlib on OS X.

                                                                                                                                                                                                              -
                                                                                                                                                                                                              -
                                                                                                                                                                                                              -

                                                                                                                                                                                                              Notebooks

                                                                                                                                                                                                              -

                                                                                                                                                                                                              See notebooks.

                                                                                                                                                                                                              +

                                                                                                                                                                                                              Notebooks

                                                                                                                                                                                                              +

                                                                                                                                                                                                              The Clawpack Gallery of Jupyter +Notebooks +contains a number of notebooks with other examples of using Python for +Clawpack.

                                                                                                                                                                                                              @@ -212,8 +149,6 @@

                                                                                                                                                                                                              Table of Contents

                                                                                                                                                                                                              • Python Hints diff --git a/python_path.html b/python_path.html index d4f9957780..6bc2ad1aa4 100644 --- a/python_path.html +++ b/python_path.html @@ -78,10 +78,8 @@

                                                                                                                                                                                                                Navigation

                                                                                                                                                                                                                When using PyClaw or other Python tools from Clawpack (e.g. the visualization tools in VisClaw or Python tools for working with topo and dtopo from GeoClaw), you need to be able to import various modules.

                                                                                                                                                                                                                -

                                                                                                                                                                                                                For a general discussion of importing Python modules, see the tutorial in -the Python documentation: -Python 2, -Python 3.

                                                                                                                                                                                                                +

                                                                                                                                                                                                                For a general discussion of importing Python modules, see the tutorial in the +Python3 documentation.

                                                                                                                                                                                                                Below are some hints in case you run into problems with import statements with modules not being found, or being imported from the wrong version of Clawpack (if you have more than one on your computer).

                                                                                                                                                                                                                @@ -219,13 +217,20 @@

                                                                                                                                                                                                                easy-install.pth

                                                                                                                                                                                                                PYTHONPATH

                                                                                                                                                                                                                -
                                                                                                                                                                                                                -

                                                                                                                                                                                                                Warning

                                                                                                                                                                                                                -

                                                                                                                                                                                                                Setting the environment variable PYTHONPATH is generally +

                                                                                                                                                                                                                If you install Clawpack with pip, then you do not need to include it in +environment variable PYTHONPATH.

                                                                                                                                                                                                                +

                                                                                                                                                                                                                Setting the environment variable PYTHONPATH is often considered bad practice in the Python community and can lead to problems, see for example PYTHONPATH Considered Harmful.

                                                                                                                                                                                                                -
                                                                                                                                                                                                                +

                                                                                                                                                                                                                In spite of the possible drawbacks, some Clawpack developers often +use PYTHONPATH to switch versions without difficulty, particularly +when using one of the Options for installing Clawpack Fortran codes rather than pip.

                                                                                                                                                                                                                +

                                                                                                                                                                                                                If you do wish to use it, you should set PYTHONPATH to point to the top +level of the clawpack directory for the code you wish to use. +Then use the whichclaw.py utility to check that this is where Clawpack +is imported from, and there is not an easy-install.pth file generated by +pip that points to a different location.

                                                                                                                                                                                                                If you have an environment variable PYTHONPATH set, the paths specified here may be searched before or after what is specified in the users’ site-packages/easy-install.pth, depending on how you set PYTHONPATH. @@ -240,13 +245,6 @@

                                                                                                                                                                                                                PYTHONPATHwhichclaw.py utility to report this, along with any other possibly conflicting easy-install.pth files.

                                                                                                                                                                                                                See Set environment variables for information on setting environment variables.

                                                                                                                                                                                                                -

                                                                                                                                                                                                                In spite of the possible drawbacks, some Clawpack developers often -use PYTHONPATH to switch versions without difficulty. If you do -wish to use it, you should set PYTHONPATH to point to the top -level of the clawpack directory for the code you wish to use. -Then use the whichclaw.py utility to check that this is where Clawpack -is imported from, and there is not a easy-install.pth that points to a -different location.

                                                                                                                                                                                                              diff --git a/regression.html b/regression.html index 22fe3dfe1d..10c6ea2246 100644 --- a/regression.html +++ b/regression.html @@ -73,7 +73,7 @@

                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              previous |
                                                                                                                                                                                                            • Clawpack 5.8.x documentation »
                                                                                                                                                                                                              • -
                                                                                                                                                                                                            • Pyclaw »
                                                                                                                                                                                                              • +
                                                                                                                                                                                                            • PyClaw »
                                                                                                                                                                                                            • Developers’ Guide »
                                                                                                                                                                                                            @@ -130,7 +130,7 @@

                                                                                                                                                                                                            Fortran codesgalleries. An attempt at automating this +with those archived in the Clawpack Gallery. An attempt at automating this can be found in the $CLAW/amrclaw/examples directory, which uses the imagediff tool described below. This is still under development.

                                                                                                                                                                                                            @@ -322,7 +322,7 @@

                                                                                                                                                                                                            Table of Contents

                                                                                                                                                                                                            Related Topics

                                                                                                                                                                                                            • Documentation overview
                                                                                                                                                                                                                -
                                                                                                                                                                                                              • Pyclaw
                                                                                                                                                                                                                  +
                                                                                                                                                                                                                • PyClaw
                                                                                                                                                                                                                  • Developers’ Guide
                                                                                                                                                                                                                    • diff --git a/release_5_6_0.html b/release_5_6_0.html index bec7d0eab6..e31e02cfaf 100644 --- a/release_5_6_0.html +++ b/release_5_6_0.html @@ -78,7 +78,7 @@

                                                                                                                                                                                                                    Navigation

                                                                                                                                                                                                                    Clawpack 5.6.0 was released on June 2, 2019. See Installing Clawpack.

                                                                                                                                                                                                                    Changes relative to Clawpack 5.5.0 (Aug 28, 2018) are shown below.

                                                                                                                                                                                                                    To see more recent changes that are in the the master branch but not yet -released, see Changes to master since v5.8.0.

                                                                                                                                                                                                                    +released, see Changes to master since v5.8.1.

                                                                                                                                                                                                                    Changes that are not backward compatible

                                                                                                                                                                                                                    diff --git a/release_5_6_1.html b/release_5_6_1.html index a7aae1568e..9ad558f6ae 100644 --- a/release_5_6_1.html +++ b/release_5_6_1.html @@ -78,7 +78,7 @@

                                                                                                                                                                                                                    Navigation

                                                                                                                                                                                                                    Clawpack 5.6.1 was released on October 28, 2019. See Installing Clawpack.

                                                                                                                                                                                                                    Changes relative to Clawpack 5.6.0 (June 2, 2019) are shown below.

                                                                                                                                                                                                                    To see more recent changes that are in the the master branch but not yet -released, see Changes to master since v5.8.0.

                                                                                                                                                                                                                    +released, see Changes to master since v5.8.1.

                                                                                                                                                                                                                    Changes that are not backward compatible

                                                                                                                                                                                                                    $CLAW/amrclaw/src/2d/amr_module.f90 has changed, so do a make new in diff --git a/release_5_7_0.html b/release_5_7_0.html index dd388cdcb5..efe3f6f481 100644 --- a/release_5_7_0.html +++ b/release_5_7_0.html @@ -80,7 +80,7 @@

                                                                                                                                                                                                                    Navigation

                                                                                                                                                                                                                    [DOI 10.5281/zenodo.3764278].

                                                                                                                                                                                                                    Changes relative to Clawpack 5.6.1 (October 28, 2019) are shown below.

                                                                                                                                                                                                                    To see more recent changes that are in the the master branch but not yet -released, see Changes to master since v5.8.0.

                                                                                                                                                                                                                    +released, see Changes to master since v5.8.1.

                                                                                                                                                                                                                    Python support

                                                                                                                                                                                                                    As of v5.7.0 we are no longer supporting Python 2.7, and Python 3.x is diff --git a/release_5_7_1.html b/release_5_7_1.html index 88ac8b2eef..bc9f4314ea 100644 --- a/release_5_7_1.html +++ b/release_5_7_1.html @@ -80,7 +80,7 @@

                                                                                                                                                                                                                    Navigation

                                                                                                                                                                                                                    [DOI 10.5281/zenodo.4025432].

                                                                                                                                                                                                                    Changes relative to Clawpack 5.7.0 (April 23, 2020) are shown below.

                                                                                                                                                                                                                    To see more recent changes that are in the the master branch but not yet -released, see Changes to master since v5.8.0.

                                                                                                                                                                                                                    +released, see Changes to master since v5.8.1.

                                                                                                                                                                                                                    Changes that are not backward compatible

                                                                                                                                                                                                                      diff --git a/release_5_8_0.html b/release_5_8_0.html index f16b5d18fe..2400985845 100644 --- a/release_5_8_0.html +++ b/release_5_8_0.html @@ -79,7 +79,7 @@

                                                                                                                                                                                                                      Navigation

                                                                                                                                                                                                                      Permanent DOI: http://doi.org/10.5281/zenodo.4503024

                                                                                                                                                                                                                      Changes relative to Clawpack 5.7.1 (Sept. 11, 2020) are shown below.

                                                                                                                                                                                                                      To see more recent changes that are in the the master branch but not yet -released, see Changes to master since v5.8.0.

                                                                                                                                                                                                                      +released, see Changes to master since v5.8.1.

                                                                                                                                                                                                                      Changes that are not backward compatible

                                                                                                                                                                                                                        diff --git a/release_5_8_1.html b/release_5_8_1.html new file mode 100644 index 0000000000..86ae504ffd --- /dev/null +++ b/release_5_8_1.html @@ -0,0 +1,245 @@ + + + + + + + v5.8.1 release notes — Clawpack 5.8.x documentation + + + + + + + + + + + + + + + + +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        + +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        + + + +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        + +
                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        v5.8.1 release notes

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        Clawpack 5.8.1 was released on October 19, 2021. See Installing Clawpack.

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        The installation instructions have been reorganized (once again) +in an attempt to make the different options clearer.

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        Permanent DOI: http://doi.org/10.5281/zenodo.??

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        Changes relative to Clawpack 5.8.0 (February 4, 2021) are shown below.

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        To see more recent changes that are in the the master branch but not yet +released, see Changes to master since v5.8.1.

                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        Changes that are not backward compatible

                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        General changes

                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        Changes to classic

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        No changes.

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        See classic diffs

                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        Changes to clawutil

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        No changes.

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        See clawutil diffs

                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        Changes to visclaw

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        No major changes.

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        See visclaw diffs

                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        Changes to riemann

                                                                                                                                                                                                                        +
                                                                                                                                                                                                                          +

                                                                                                                                                                                                                        • Fix rp1_shallow_hlle.f90 to work better near dry states.

                                                                                                                                                                                                                          • +
                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        See riemann diffs

                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        Changes to amrclaw

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        No changes.

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        See amrclaw diffs

                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        Changes to geoclaw

                                                                                                                                                                                                                        +
                                                                                                                                                                                                                          +

                                                                                                                                                                                                                        • Some improvements to storm tracks

                                                                                                                                                                                                                          • +

                                                                                                                                                                                                                        • Reading (some) geotiff files now supported in topotools

                                                                                                                                                                                                                          • +

                                                                                                                                                                                                                        • Added kmltools.topo2kmz to make Google Earth overlays showing topography

                                                                                                                                                                                                                          • +

                                                                                                                                                                                                                        • Some other bug fixes.

                                                                                                                                                                                                                          • +
                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        See geoclaw diffs

                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        Changes to PyClaw

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        For changes in PyClaw, see the PyClaw changelog.

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        See pyclaw diffs

                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        Other Clawpack Repositories

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        The repositories below are not included in the Clawpack tarfile or pip +install, but changes to these repositories may also be of interest.

                                                                                                                                                                                                                        + +
                                                                                                                                                                                                                        + + +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        + +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        + © Copyright CC-BY 2020, The Clawpack Development Team. + Created using Sphinx. +
                                                                                                                                                                                                                        + + + + \ No newline at end of file diff --git a/releases.html b/releases.html index b52a989f7a..cf9b5ab793 100644 --- a/releases.html +++ b/releases.html @@ -92,7 +92,7 @@

                                                                                                                                                                                                                        Other notes:Citing this work for the suggested way to cite the version of Clawpack that you are using in publications.

                                                                                                                                                                                                                      • For changes in PyClaw, see the PyClaw changelog.

                                                                                                                                                                                                                        • -

                                                                                                                                                                                                                      • See Changes to master since v5.8.0 for changes to the master branch on Github +

                                                                                                                                                                                                                      • See Changes to master since v5.8.1 for changes to the master branch on Github that are not in the most recent release.

                                                                                                                                                                                                                      • The “dev” branch of the documentation (selected under Versions on the menu @@ -109,6 +109,8 @@

                                                                                                                                                                                                                        Releases:10.17605/osf.io/kmw6h. See Citing this work for more information on how best to cite Clawpack.

                                                                                                                                                                                                                          +

                                                                                                                                                                                                                        • v5.8.1 release notes – October 19, 2021 +[DOI 10.5281/zenodo.??]

                                                                                                                                                                                                                        • v5.8.0 release notes – February 4, 2021 [DOI 10.5281/zenodo.4503024]

                                                                                                                                                                                                                        • v5.7.1 release notes – September 11, 2020 diff --git a/searchindex.js b/searchindex.js index 94be04cfc2..794aa99b41 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ 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155],alloc:[20,99,117,126,138],allocat:117,allot:59,allow:[4,6,13,22,27,28,29,32,38,39,44,45,47,50,51,53,54,56,58,64,66,67,70,71,73,76,77,86,92,93,99,101,104,105,106,110,111,113,114,117,118,119,120,121,123,124,126,129,131,137,139,140,141,142,146,150,152,154],almost:105,alon:[16,51],along:[6,14,16,24,27,30,32,39,44,51,54,68,70,106,110,117,128,131,133,140,146,154],alpha:[51,55,99],alphabet:81,alreadi:[0,1,6,12,13,18,28,29,41,55,56,57,58,59,60,66,79,80,94,98,100,103,105,114,122,152],also:[3,4,5,6,7,8,9,11,12,16,17,18,20,22,23,24,25,28,29,30,32,33,35,36,37,38,39,41,42,44,47,48,51,52,53,54,55,56,57,58,59,62,63,66,67,68,70,71,72,73,76,77,79,83,85,86,89,91,93,94,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,135,137,138,139,140,141,142,144,145,146,147,148,149,150,152,153,154,155,157,158],alter:51,altern:[30,35,36,44,47,51,57,60,62,67,76,91,94,105,106,110,117,118,119],although:[30,51,63,67,95,96,98,110,122,152],alwai:[16,22,26,27,28,32,41,53,54,58,67,83,92,109,110,113,114,126,133,139,140,141,150,155],amal:[4,17,81,91],amazon:25,amazonaw:13,amdq:[97,129],ami:25,among:124,amount:[44,48,54],amplitud:[5,119],amr:[4,7,8,16,20,23,25,27,28,32,34,38,44,45,52,59,67,72,73,76,81,89,118,120,121,122,124,126,133,136,137,139,141,149,155],amr_1d:122,amr_2d:[121,122],amr_:[3,7],amr_celledges_show:3,amr_contour_color:3,amr_contour_show:3,amr_data_show:118,amr_level:72,amr_level_max:139,amr_levels_max:[32,110,138,139],amr_modul:[71,110,117,123,124],amrclaw:[4,5,6,12,15,16,19,20,22,23,24,28,36,38,39,41,44,45,46,52,55,56,57,58,60,66,67,68,71,72,73,100,106,107,110,111,128,129,131,134,135,137,140,144,145,148,149,153],amrdata:[5,22,32,110,124,126,138,139,140],amrflag:110,amrlib:117,amrnez:110,an11:54,anaconda:[51,80,91,100,105],anal:17,analog:[137,138],analysi:17,andi:4,angl:[16,30,47,70],ani:[3,4,5,6,8,13,16,18,19,20,22,27,28,29,32,35,36,37,45,48,50,51,54,55,56,58,61,62,64,66,67,69,71,72,73,77,81,87,88,89,91,92,93,94,96,98,100,104,106,109,110,111,117,121,123,128,131,132,133,136,137,138,140,146,155,158],anim:[12,16,42,51,117,124,125,142],animation_tool:[124,125],anisotrop:[6,22],anl:94,annot:[27,59],annual:24,anoth:[3,22,39,44,51,55,57,58,72,76,80,88,99,102,111,121,146,155],answer:24,anyth:[3,6,28,29,56,58,63,111,121],anywher:110,aoml:146,apach:13,apdq:[97,129],api:[47,121],app:[12,13,18,23,26,28,29,32,37,42,70,108,109,116,120,121,122,123,124,125,126,130],appar:[30,32,71],appeal:51,appear:[0,1,3,5,8,13,18,23,32,44,45,51,54,57,59,62,65,77,93,98,101,119,126,140,142,150],append:[5,20,32,38,39,44,51,60,77,86,98,110,118,119,128,129,139],appl:17,appli:[3,4,5,6,13,16,25,30,48,51,53,64,66,70,77,79,87,89,92,99,110,128,137,140,155],applic:[4,6,15,16,19,20,22,23,24,28,29,32,35,36,37,41,42,45,46,55,56,58,63,66,68,71,79,88,89,90,91,93,99,104,107,109,110,111,113,116,117,119,120,121,123,124,129,131,133,134,137,140,144,145,150,152,153,155,156],appreci:81,approach:[5,7,13,28,29,38,44,54,56,69,76,84,94,96,104,110,117,119,120,122,129,130,136,140,155,158],appropri:[4,5,6,13,16,24,28,45,48,49,51,55,56,58,59,60,64,67,68,69,71,83,86,87,88,92,94,95,96,97,98,111,123,129,132,135,137,146,155,158],approv:48,approxim:[6,16,25,33,48,51,70,129],april:[24,124,125,127],apt:[13,105],arbitrari:[32,59,99,113,131,140],arbitrarili:66,arc:132,arcgi:152,architectur:94,archiv:[12,21,36,51,55,111,142,148,152,154],arcminut:[70,150],arcsecond:[45,150],area:[15,22,45,99,108,119,133,134],arg:[89,98],argument:[0,1,2,3,27,30,45,47,50,51,53,77,83,84,88,89,92,96,98,99,101,104,111,121,129,131,136,137,138,146,152,155],argv:[139,141],aris:[61,81],arithmet:64,aron:[4,17,81,91],arora:87,arora_ro:87,around:[6,30,32,39,59,92,108,111,124,138,139,146,152,155],arrai:[0,3,6,15,20,22,27,30,32,33,38,44,45,47,49,53,59,77,83,84,86,87,89,91,92,93,96,97,98,99,101,103,104,105,113,114,115,119,121,124,126,129,130,131,134,137,138,139,140,141,146,150,152,155],arrang:152,arriv:[22,32,34,39,45,119,132,133],arrival_tol:32,articl:[4,17,91,142],artifici:[16,133],arxiv:52,asc:152,ascii:[44,53,67,83,86,93,98,119,128,137,139,141,150,156],ascii_output_format:68,ask:24,ask_us:152,aspect:[12,24,29,48,49,67],assembl:57,assert:[139,141],assess:[4,48,132],assign:[30,32,83,86,92,98],assist:[22,124],associ:[0,1,2,6,22,51,58,71,89,92,93,111],assum:[3,5,20,22,30,32,36,39,47,48,51,53,54,55,59,67,70,76,92,93,95,96,97,103,104,110,117,131,132,137,140,146,147,150,152,154,158],assumpt:[51,54],asteroid:4,astronom:132,atcf:[108,121,146,147],aterrel:4,atmospher:4,attach:[55,92,101],attempt:[5,8,11,20,33,35,36,62,92,104,111,113,146,152,153],attirbut:22,attr:[89,98],attribur:5,attribut:[5,7,22,30,38,44,66,70,76,78,79,83,86,89,92,94,96,98,99,110,113,118,122,128,136,137,138,140,146,152],attributeerror:77,aug:[17,122],aug_glob:97,augment:[66,130],august:[24,121,127],austin:4,author:[17,25,45,48,87,91,92,97,109],auto:[0,44,84],autom:[14,54,84,111],automat:[0,2,3,8,11,16,30,35,36,41,51,55,62,76,77,79,83,88,92,94,100,101,102,104,111,113,124,126,137,138,140,150],au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rown:[81,152],brows:[11,24,42,51,67,142,155],browser:[13,28,29,35,36,51,54,142],bsd:[4,61,81,121],buffer:[30,39,44,110,118,119,138,139,152],buffer_length:152,buffer_s:[30,70],bug:[4,8,12,22,24,41,51,64,71,77,81,116,117,118,119,121,126],build:[4,17,28,29,54,55,67,84,94,104,120,131],buildsystem:94,built:[28,29,64,73,82,91,94,96,98,110,111,144,145],bulk:[19,83,97,103,129,139,155],bull:[17,30],buoi:45,burger:[91,129,155],burgers_1d:97,burgers_1d_pi:97,busi:[61,81],butcher:99,button:[12,13,28,51,59,120],bzip2:124,c210:[17,91],c231:[17,91],c_center:89,c_centers_with_ghost:89,c_l:97,c_node:89,c_nodes_with_ghost:89,c_r:97,cach:[22,47,55,79,81,124,138],cache_dir:47,cada:87,cada_torrilhon_limit:87,cada_torrilhon_limiter_nonlinear:87,cake:74,cal:[129,155,158],calcul:[3,5,6,27,30,33,45,47,67,70,77,89,97,99,114,119,152],calculate_geometri:30,calculate_geometry_triangl:30,calhellev08:17,calhoun:[4,17,51],calhounhelzellevequ:16,call:[1,6,9,20,22,27,30,38,41,44,50,51,63,66,67,70,72,77,79,83,84,86,87,92,93,96,98,99,101,103,104,110,111,113,117,118,120,121,129,131,133,135,137,139,140,141,146,152,155],call_before_step_each_stag:99,call_setplot:77,callabl:104,calucl:97,cambridg:17,came:14,camera:51,can:[0,2,3,4,5,6,7,8,9,11,12,13,14,15,16,19,20,22,24,26,27,28,29,30,32,35,36,37,38,39,40,41,42,44,45,46,47,48,51,52,53,54,55,56,57,58,59,60,62,63,64,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,83,84,85,87,88,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,110,111,113,114,117,118,119,120,121,124,125,126,127,128,129,131,132,133,134,135,136,137,138,139,140,141,142,144,145,146,148,150,152,153,154,155,156,158],cannot:[52,58,92,126,133,146],canopi:100,capa:98,capa_index:[137,139,141],capab:152,capabili:121,capabilit:119,capabilti:121,capabl:[7,12,22,32,34,48,52,66,73,84,113,118,119,121,122,123,124,125,152,154],capac:[15,97,134,137,138,139,141],captur:[32,48,131,150],car_nam:146,care:[32,39,45,94],carefulli:[20,22,64],cartesian:[32,46,59,84,140],cartopi:146,cascad:4,cast:152,cat_nam:146,catalog:154,categor:146,categori:146,category_color:146,caus:[22,48,51,54,61,62,79,81,102,111,118,119,120,122,126,136,138,150,152],caut:87,caution:48,cautionari:[25,45,63,140],cautiou:48,caxi:67,cb_file:59,cb_filenam:59,cb_kwarg:152,cb_name:59,cb_xfrac:59,cb_yfrac:59,cbar:[97,152],cdot:[64,96,131],ceas:105,cell:[3,4,5,7,8,15,16,20,22,25,27,32,33,44,45,51,53,59,66,67,71,72,73,83,89,94,97,99,101,103,110,113,114,118,119,120,121,122,123,124,126,129,132,133,134,137,138,139,140,141,147,149,150,155,158],celledg:3,celledges_show:[3,22],cellgridintegr:113,cellgridintegrate2:113,cellsiz:[39,53,117,150],center:[4,5,27,30,32,33,39,44,51,53,59,70,83,89,96,97,103,110,121,131,133,138,139,140,146,147,150,155],centerlin:30,centers_with_ghost:89,central:[137,146,147],central_pressur:146,centroid:[30,70],certain:[14,32,45,57,66,93,110,118,131,137],certainli:[94,105],certik:[4,81],cf2py:84,cfl:[6,89,93,99,103,113,118,137,139,140,141],cfl_desir:[99,137,139,141],cfl_max:[99,137,139,141],cfl_superbe:87,cfl_superbee_theta:87,challeng:120,chanc:81,chang:[1,6,8,13,15,16,19,20,25,28,29,30,32,40,41,50,51,52,53,54,55,56,58,59,62,63,64,66,67,68,71,72,73,76,79,83,84,90,92,93,101,104,105,108,109,110,111,127,129,133,134,137,138,139,140,141,144,145,150,153,155],changelog:[18,22,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127],changes_to_mast:55,channel:24,chapter:[16,129,137,155],char_decomp:99,charact:47,characterist:99,charg:13,chava:140,cheaper:13,check:[6,14,15,16,20,32,35,36,40,41,50,51,52,54,55,56,58,62,67,77,83,84,86,91,94,98,99,101,103,104,106,107,110,114,123,131,133,134,138,139,144,145,146,152,153,154,155],check_3rd_ord_cond:99,check_diff:[104,111],check_lmm_cond:99,check_valid:86,check_valu:[104,111],checkout:[28,52,54,55],checkpoint:[25,44,118,119,121,123,126,137,139,141],checkpt_interv:[137,139],checkpt_styl:[118,128,137,139],checkpt_tim:[137,139],checksum:92,chen:[30,154],chile2010:[51,109,110,113,116,122,150],chile2010_adjoint:5,chile2010_fgmax:32,chile2010a:[29,109],chile2010b:109,chile:[45,59,70],chile_2010:51,chile_dtopo:70,chk00006:[139,141],chk00100:118,chk:118,chkaaaaa:118,chkbbbbb:118,chknnnnn:[128,137,139,141],choic:[16,45,76,99,137,139,140,141,155],choos:[0,7,70,96,137,140],chose:64,chosen:[3,29,32,38,39,51,53,66,103,110,126,132,138],chri:4,chunk:92,chunksiz:92,circl:[3,47,77],circular:17,cise:17,citat:[4,55],cite:[25,55,57,127],cjvogl:4,clamshel:114,clarifi:22,clariti:38,clash:67,classic4:141,classic:[4,6,12,15,16,19,20,22,23,24,28,41,42,46,55,56,57,58,63,69,71,72,73,81,83,86,88,89,90,91,92,96,106,107,111,128,129,134,135,138,140,145,153,155],classic_1d:63,claw1:[63,104],claw1ez:63,claw:[5,6,8,11,12,13,14,15,16,19,20,22,24,28,30,32,33,35,36,37,38,40,41,44,45,47,49,50,52,54,55,56,57,58,59,62,63,67,69,70,71,78,83,86,88,91,92,93,94,100,102,106,107,108,109,110,111,113,114,116,117,120,121,123,129,133,134,139,140,141,143,144,145,148,149,150,152,153,155,156],claw_1dnoncon:158,claw_git_diff:[28,50,55],claw_git_statu:[28,50,55,125],claw_lib:68,claw_outdir:[62,77],claw_packag:99,claw_pkg:[137,138,139,140,141],claw_topo_download:152,claw_vers:58,clawdata2pyclaw:84,clawdata:[5,38,113,117,128,137,138,139,140,141],clawdev2013:54,clawdev:54,clawgraph:67,clawicon:54,clawlogo:54,clawpack:[1,4,5,6,7,11,16,26,28,30,32,33,34,35,36,37,38,39,41,42,43,44,45,46,47,48,50,51,58,59,60,61,63,66,67,69,70,71,75,76,77,78,79,80,81,82,83,85,86,88,89,90,91,92,93,94,95,96,97,98,101,102,103,104,105,106,109,111,112,113,114,115,116,117,118,119,128,129,131,135,137,138,139,140,142,143,146,148,150,152,153,155,156,158],clawpack_gpu:52,clawpack_src:[56,58,106],clawplotax:[1,2,3,27,77,121,126,136],clawplotdata:[2,3,27,44,51,77,79,86,136],clawplotfigur:[0,1,51,77,136],clawplotitem:[0,1,7,22,27,76,78,118,121,136],clawrundata:[5,44,59,122,128,137,138,139,141],clawsolut:1,clawsolv:[99,129],clawsolver1d:[83,86,89,99,103,129],clawsolver2d:[89,99],clawutil:[5,11,14,19,20,23,28,40,41,50,55,57,62,106,111,135,137,138,139,141,152,153],clean:[22,54,55,104,117,121],cleaner:[28,119],cleanup:120,clear:[1,2,6,67,79],clearer:[123,126],clearfigur:1,clearfram:[1,79],cleargaug:44,clearli:[44,48,51,131],clf:2,clf_each_fram:2,click:[4,12,13,18,28,51,54,111,120,127],clifford:24,clint:17,clobber:[92,118],clockwis:[32,47,70,152],clone:[12,18,23,24,42,52,54,55,56,58,80,94,100,109,153],close:[13,39,51,54,66,67,92,110,124,138,146],closer:[70,139],closest:146,cloud:13,cluster:[6,17,57,110,138,139],clustering_cutoff:[110,138,139],cma:146,cmap:[39,51,59,66,77,131,152],cmap_dri:[39,66],cmap_land:66,cmap_sea:66,cmap_sea_dri:66,cmap_slip:30,cmap_topo:66,cmax:[51,59],cmax_dz:30,cmax_slip:30,cmdline:106,cmin:[51,59],cmin_slip:30,cmmi:4,cname:54,coars:[3,32,51,110,119,126,137,150,155],coarsen:[53,110,121,122,138,150,152],coarsen_method:53,coarser:[3,16,53,119,133,137,138,155],coarsest:[6,51,72,113,128,137],coast:[39,66,110,133,152],coastal:[48,124,132,133,140,150],coastlin:[32,51,66,124,131,140,154],code:[4,5,6,7,8,12,14,16,19,20,21,22,23,24,27,29,32,35,36,38,40,41,42,44,45,48,50,52,53,54,56,57,61,62,63,64,68,69,70,71,72,73,75,77,79,81,83,84,89,91,92,93,94,96,99,100,103,105,106,109,112,113,114,117,118,119,120,121,122,123,124,126,128,129,130,131,137,138,139,140,141,142,146,148,149,150],code_of_conduct:121,coeffici:[5,64,96,97,99,101,102,103,129,140],colella:[6,17],collabor:[51,142],collect:[12,25,26,28,30,32,70,76,83,99,142],collela:120,color:[3,30,39,51,59,66,67,76,131,136,146,152],colorado:24,colorbar:[3,39,59,66,121,124,131,152],colorbar_kwarg:121,colorbar_labels:30,colorbar_shrink:30,colorbar_ticks:30,colormap:[3,30,39,46,51,66,67,76,78,118,124,152],column:[10,30,32,44,48,60,93,97,117,131,152],column_list:30,column_map:30,com:[12,13,23,24,26,28,29,52,54,55,56,57,58,92,94,96,100,116,118,119,120,127,130],combin:[20,54,59,118,154],combinatori:111,come:[3,28,77,79,88,94,99,117,150,155],comfort:[58,96],comm_world:104,command:[0,1,2,3,11,13,14,28,40,50,51,52,55,56,57,58,62,69,76,77,80,83,84,86,91,94,95,99,103,104,105,106,111,129,135,136,137,138,150,152],commenc:128,comment:[5,11,24,49,55,120,128],commit:[25,30,50,54,55,111],common:[3,23,28,35,36,40,41,62,63,73,76,83,97,99,101,102,119,121,124,153,155],common_sourc:63,commonli:[3,67,77,79],commun:[25,51,81,101,104,106,110,121],comot:4,compact:[66,150],compactli:131,compar:[5,22,36,44,48,51,55,77,93,110,111,132,138,140,148,154,158],compare_gaug:117,comparison:52,compat:[28,30,47,51,59,70,76,94,102,105,114,115,119,120,152],compil:[13,25,35,36,40,46,56,58,63,71,73,79,80,84,91,92,96,100,104,113,129,130,135],compile_librari:104,complet:[20,22,28,47,62,79,83,84,94,104,105,111],complevel:92,complex:[12,38,89],compliant:41,complic:[16,77,84,131,136],compon:[3,16,20,22,25,36,44,56,58,67,72,76,96,98,100,101,110,117,126,130,137,138,139,150,155],compos:[30,83],comprehens:111,compress:[30,92,152],compris:[22,91,152],comput:[3,4,5,6,13,16,17,27,29,30,32,33,39,44,47,51,53,56,58,59,60,62,68,70,76,77,79,84,86,89,91,92,93,94,99,103,105,106,108,110,113,114,118,119,123,126,129,133,137,139,140,141,147,150,155,158],computation:[84,99],compute_f:[86,93],compute_gauge_valu:93,compute_p:[83,86],concentr:108,concept:[25,129],concern:[22,45,138],conclus:[4,51],conda:[51,56,80,91],condit:[5,7,20,25,61,63,73,81,82,83,84,86,93,99,107,113,114,117,121,132,137,139,140,141],conduct:121,conf:[54,55],confer:24,config:94,config_fc:153,configur:[77,83,94,152],confirm:48,conflict:[6,28,58,62,67,102,106],conform:[22,28,33,98,121,150],confus:[3,53,58,106,126,129],conjunct:[24,39,66,92,110],conlict:62,connect:[32,54,59,66,124,131],consequenti:[61,81],conserv:[4,5,6,17,93,99,101,122,130,155,158],consid:[6,39,48,57,58,66,84,106,135,142,152],consider:[48,83],consist:[6,25,32,47,51,55,59,94,105,119,129,131,140,150,155],consol:[13,93,140],consolid:117,constant:[30,32,48,59,64,94,97,129,130,131,133,140,152,155],constant_storm_modul:117,constrain:110,constraint:[39,44,131,138,158],construc:59,construct:[22,30,32,53,83,89,104,146,147,150],construct_function_handl:104,constructor:101,consult:102,contact:[12,88,91,100],contain:[1,3,5,12,13,20,23,25,26,30,32,33,35,36,37,40,42,44,45,47,49,50,51,52,53,54,55,57,59,60,62,63,66,67,68,72,73,77,79,80,83,84,86,87,89,92,94,96,97,98,99,101,103,104,106,110,111,113,114,121,122,127,129,131,136,137,140,142,146,150,152,153,155],containing_rect:30,contains:29,containt:128,contamin:137,contan:51,content:[4,6,23,51,55,73,84,140,150,155,156],context:[27,51,155],contigu:[72,92,101,131],continent:[7,66],contingu:22,continu:[13,22,28,30,49,54,81,105,129,137,158],contour:[3,30,44,51,53,67,105,136,152],contour_color:3,contour_kwarg:[3,152],contour_level:[3,152],contour_max:3,contour_min:3,contour_nlevel:3,contour_show:3,contourf:[51,76],contract:[4,61,81],contrast:[53,131],contribut:[4,24,25,57,81,84,91,96,99,108,111],contributor:[4,24,61,91],control:[6,7,23,25,32,41,44,54,56,58,60,67,79,82,87,89,91,92,93,94,96,110,119,124,130,140],conveni:[1,27,32,35,36,39,44,51,79,86,88,91,93,95,103,155,158],convens:150,convent:[3,22,30,46,53,70,97,150],converg:[66,76],convers:[19,25,84,92,110,131,150,154],convert43to46:19,convert46to50:20,convert:[3,22,25,30,33,42,47,51,56,58,59,62,70,84,96,104,105,121,124,137,138,146,150,154],convert_fort_double_to_float:104,convert_readm:11,convert_to_standard_unit:30,convex:[7,32],coodin:30,coord:[47,51],coordin:[4,23,30,32,47,72,76,83,89,93,94,103,110,131,140,152],coordinate_specif:[30,70],coordinate_system:[15,60,134,140],coorind:152,copi:[6,14,15,16,35,36,44,51,54,55,58,67,83,86,96,101,107,108,109,110,114,118,121,125,133,134,138,142,144,145,150,155],copyq1:63,copyright:[61,81],core:[4,12,73,111,121],corioli:[48,140,144,145],coriolis_forc:[48,140],corner:[3,30,32,53,70,72,89,131,137,139,141,150,152],correct:[20,28,41,54,55,63,64,67,77,83,89,94,98,104,113,114,118,133,137,139,140,141],correctli:[28,32,84,90,117,140],correspond:[3,6,12,23,25,27,30,44,47,48,53,54,55,59,67,70,77,83,87,89,92,93,96,98,101,110,111,129,131,132,137,138,139,140,141,146,150,154,155],correspondingli:32,cos:[39,47,49,66,83,96],cosin:83,cost:[13,99],costli:130,could:[5,12,13,27,32,35,36,39,44,53,58,60,66,70,71,77,79,83,89,93,101,102,105,106,117,126,131,133,138,139,140,141,152,155],council:4,count:83,count_from_zero:83,counter:[104,152],counterclockwis:70,coupl:[119,158],courant:[4,6,110,120,137,138,139,141],cours:[13,26,32,44,46,60,70,94,95,103,105,108,140,150],cover:[6,7,27,28,30,32,38,39,51,59,66,70,110,114,119,133,139,150],coverag:[91,111],covert:11,covid:24,cparam:[83,101],cpp:52,cpu:[13,52,118,121,123,149],crash:[118,137,138],creat:[0,1,2,3,5,6,7,19,24,25,28,30,32,33,35,36,38,40,42,44,45,46,50,52,54,57,58,59,62,70,72,76,77,79,84,85,88,89,91,92,95,98,101,102,103,104,110,111,113,117,118,119,121,122,123,126,131,136,137,138,139,142,143,146,152,154,155,156],create_dtopo_xi:[30,70],create_dtopographi:[30,70],create_topo_func:152,creation:[39,77,91,113],criteria:[6,7,22,25,32,66,101],criterion:[32,110,139],critic:[51,93,129],crop:[53,152],cross:28,crucial:[51,150],csdm:24,cse:24,csh:94,csv:[30,70,121],csvfault:[30,70],ctrl:[29,77],cube:67,cultu:66,cumul:121,current:[3,5,13,14,20,22,24,27,28,29,30,32,38,39,41,44,45,48,53,54,55,56,57,58,59,60,67,68,72,77,79,89,92,93,94,99,101,104,106,110,111,118,120,121,128,132,136,137,138,139,140,141,146,147,150,152,154],current_data:[0,3,25,44,76,77],curv:[3,44,76,131],custom:[0,13,16,20,22,25,63,67,73,76,84,90,96,133],custom_bc:96,customari:93,cut:138,cutoff:[6,139],cvf:55,cvs:51,cxx:94,cyber:17,cygwin:86,cython:94,dai:[6,13,51,140],dalcin:81,dam:[51,133],dam_break:130,damag:[6,61,81],damian:57,damiansra:96,dark:131,darker:51,darryl:17,dart:45,dash:[3,94],daspect:67,dat:[30,146],data:[0,1,3,5,25,27,30,32,35,36,38,39,40,42,44,45,46,47,53,54,59,60,61,62,66,67,76,77,78,79,81,83,86,89,92,93,95,97,98,99,101,104,107,108,109,110,113,115,116,118,119,121,122,123,124,126,129,131,132,138,139,141,146,149,151,156],data_break:[39,66,152],data_fil:33,data_limit:[39,66],data_storm:146,data_typ:104,databas:[13,30,70,104,108,121,150],datadir:118,dataset:[150,152,154],date:[5,28,40,47,51,54,55,62,77,146,153],date_tim:47,datetiem:146,datetim:[47,146],datum:[47,48,97,132,140,154],dave:30,davi:[4,17],david:[4,17,81,91,99],davis2018:[5,17],davisleveque2016:[5,17],davisleveque2018:[5,17],dawson:17,daylight:59,dcp:59,deal:[30,48,76,93,94,101,146,152],dealt:[32,39],debian:105,debug:[7,41,62,72,76,93,101,106,111,137,139],debugg:77,decid:[83,99],decim:[47,59],decimc:146,decis:51,declar:[20,22,101,126,155],decompos:[72,129,158],decomposit:137,decor:104,decoupl:54,decreas:[44,133,150],deduc:150,deep:[5,66,140],deep_depth:140,deeper:[131,140,150],deepli:103,def:[0,1,3,44,51,66,77,83,89,93,96,99,139,141,146],default_tfluct:99,defenc:4,defens:4,defin:[0,1,3,5,6,7,22,27,30,32,38,39,41,51,59,60,62,66,67,70,77,79,83,86,89,95,96,98,99,101,103,104,110,113,121,126,129,139,141,146,150,152,153,155,158],definit:[30,67,83,110,116],deform:[17,30,33,45,70,154],deg2dm:59,degener:131,degre:[30,47,51,59,70],delet:[20,28,56,58],delimit:30,delin:140,delta:[87,89,96,99,129,152,155,158],delta_h:97,delta_hu:97,delta_i:152,delta_limit:152,delta_x:152,dem:[32,45,53,121,150,152,154],demo:94,demonstr:[12,25,88,94],denot:[6,22,44,53,129,152],dens:147,densiti:[86,93,97,101,103,138,139,155],depart:[4,146],depdend:87,depend:[3,13,16,28,29,30,32,35,36,40,41,46,48,51,56,57,62,64,67,70,77,82,91,92,97,98,99,104,106,110,121,133,138,140,152,153,155,158],deprec:[7,30,34,54,117,121,140,150,152],depress:32,depth:[4,5,16,17,22,30,32,33,39,44,45,48,64,70,76,78,130,132,133,140,150],deriv:[61,70,81,86,90,91,101,111],describ:[3,4,5,6,7,13,14,16,19,26,28,30,31,32,35,36,38,39,44,46,47,48,51,52,54,55,59,60,62,63,66,67,70,72,73,76,77,78,89,92,98,104,108,110,111,119,122,123,129,131,132,136,137,138,140,146,147,150,152,154,155,158],descript:[3,4,6,9,22,23,25,30,59,67,70,73,76,92,104,108,110,129,130,140,146,150,158],design:[4,27,28,51,81,83,103,131,154],desir:[0,1,2,3,6,7,16,22,25,26,30,32,33,39,42,44,55,56,58,59,60,66,70,75,76,77,79,83,84,86,93,98,99,107,119,121,124,133,135,137,138,139,141,146,150,152,153],desktop:94,destin:51,detail:[4,5,10,16,22,23,25,26,28,29,30,32,35,36,38,41,46,48,51,54,56,57,58,61,62,66,67,70,73,77,81,86,87,88,89,92,93,94,95,96,97,99,109,110,111,114,119,121,126,129,131,136,137,140,142,146,150,153,154,155,158],detect:[51,62,92,100,104,153],deterimin:[140,152],determin:[3,5,6,30,32,39,44,45,48,50,51,54,59,70,77,87,89,92,97,101,106,110,114,118,119,128,131,132,136,137,138,140,152,155],determine_topo_typ:152,dev:[18,24,28,54,55,94,121,122,127],develop:[4,6,7,12,13,18,22,23,48,52,54,57,58,61,66,67,76,80,81,84,91,96,99,100,106,108,111,121,122,124,126,129,132,133,139],dict:[30,86,92,97,98,101,146,152],dictionari:[0,1,2,3,30,44,60,77,83,86,92,97,98,101,103,106,146,150,152],dicuss:30,did:[121,126,131,150],didn:116,died:113,diff:[18,50,55,113,114,115,116,117,118,119,120,121,122,123,124,125,126],differ:[1,3,6,7,12,15,16,22,28,30,31,35,36,39,44,46,48,50,53,56,59,62,64,66,67,70,71,76,79,83,84,86,88,89,92,97,99,104,105,106,107,110,111,117,118,119,120,121,124,126,129,132,133,134,137,138,139,140,144,145,150,152,153,154,155,158],differenti:[17,30],difficult:44,difficulti:[100,102,106],diffus:96,digit:[32,39,53,59,60,77,119,120,121,152],dike:[39,66,124],dim:[96,97,99],dimens:[5,6,7,16,20,22,25,44,47,53,59,67,83,84,86,92,94,96,97,98,101,103,110,121,124,129,137,138,139,141,152,155],dimension:[3,7,8,17,22,25,30,32,35,36,44,48,52,67,89,96,117,118,120,123,139,140,141,152,155],dimensional_split:[89,117,137,139,141],dip:[30,70],dir:[55,94,156],direct:[6,8,16,22,30,32,35,36,44,47,51,55,59,61,62,67,70,71,77,81,86,96,103,110,120,129,137,138,140,152],directli:[8,19,23,32,48,56,67,70,77,79,83,84,87,91,101,104,106,121,152,156],directori:[1,3,5,6,11,12,13,14,15,16,19,20,22,23,25,28,29,31,32,35,36,37,40,42,44,45,47,50,51,54,55,56,57,59,63,67,68,71,75,76,79,86,88,89,91,92,93,96,103,106,107,108,110,111,113,118,119,120,121,123,128,129,133,134,135,136,137,138,142,144,145,148,149,150,153,155,156],directorti:108,disabl:[49,100,140],disable_petsc:104,discard:[32,99],disclaim:[61,81],discontinu:[4,99,158],discov:64,discoveri:111,discret:99,discrib:4,discuss:[5,24,28,30,48,53,56,66,70,92,103,105,106,110,119,121,129,140,158],disk:[13,44,83,92,93,111,119],dispers:48,displac:[30,45,48,70,133,140,154],displai:[1,13,35,36,40,44,51,59,77,93,111,140],display_format:[44,60],display_landfall_tim:140,dist:55,dist_latlong2met:47,dist_meters2latlong:47,distanc:[30,47,51,70,140,150,152],distant:[108,110],distinct:[44,119],distinguish:39,distribut:[4,12,13,29,30,54,61,70,73,80,81,99,105,124],disturb:51,distutil:84,dive:105,divid:[110,137],divis:[4,51],dlgeorg:4,dms2decim:47,dnetcdf:[41,150],doc:[18,23,24,28,30,51,55,87,104,105,106,120,121,122,123,124,125,126,143],docker:[18,25,55,56,120,121,122,123,124,125,126,157],docker_disk:29,docker_imag:55,dockerfile_v5:29,dockerhub:[29,55],dockeril:29,docstr:[84,88,111],doctest:89,documen:54,document:[0,1,2,3,6,7,18,21,22,23,24,25,28,29,32,45,48,53,58,61,70,76,77,78,79,81,87,89,92,93,94,95,99,101,104,106,114,127,136,139,156,157],dodsc:[39,66],doe:[4,5,11,16,20,27,28,39,40,48,51,53,54,56,67,73,77,80,89,91,98,101,104,110,111,114,119,123,126,128,129,130,133,146,152,153,155],doesn:[28,32,58,63,101],doflag:110,doi:[4,17,52,55,57,124,125,126,127],doing:[6,11,19,25,28,33,39,44,48,50,52,54,58,63,77,79,89,91,110,111,118,119,120,121],domain:[5,6,16,17,33,38,39,48,51,54,59,70,72,82,83,84,86,94,96,98,101,108,110,138,139,141,150],don:[13,27,28,54,55,77,93,94,100,111,139,153],done:[1,6,7,8,11,13,16,19,20,28,35,36,39,44,46,51,53,54,58,59,62,66,67,70,76,77,79,83,87,88,104,110,114,118,119,123,128,129,131,136,138,140,149,152,153,154],donna:[4,17],donnabois:4,donor:[137,139,141],dontflag:110,dot:[40,44,51,57,58,59,62,153],doubl:[67,84,89,104,129,138],down:[13,30,93,118,146,150,152],download:[12,13,28,29,30,36,37,39,45,51,55,56,57,58,68,88,94,100,121,122,127,148,152,153,154],downward:70,doxygen:[6,7,25,120],dpc:59,dpi:[51,59],dpng:67,dprint:[138,139],dq_src:[96,99],dqdt:99,draft:55,drag:140,drag_law:140,draw:3,drawback:106,drawcontourlin:67,drawn:[30,51,136],driver:[20,63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106,108,110,119,134,142,144,145,153],within:[6,16,28,29,54,56,58,66,73,77,95,104,106,110,129,131,136,142,152],without:[16,22,40,44,48,57,59,61,62,63,66,67,77,79,80,81,87,92,93,104,106,111,131,139,141,146,153,155],wkt:51,wmo:146,wmo_:146,wmo_ag:146,won:[12,13,66,84,152],woodward:120,word:[93,121,146],work:[3,5,8,13,16,19,20,22,24,25,26,28,29,32,35,36,40,45,48,51,52,53,54,55,56,57,58,59,66,67,69,70,71,77,80,81,82,83,85,86,87,91,92,93,94,97,99,100,105,106,108,109,110,111,115,116,117,118,119,120,121,124,126,127,129,136,137,138,140,142,147,150,153,157],workflow:[108,142,146],workshop:[108,124],workspac:[24,67,101],world:[48,64,91,94,146],worst:132,worth:101,worthwhil:96,would:[2,3,12,13,16,24,27,28,32,38,41,51,53,55,56,58,60,62,63,66,70,72,77,81,83,86,89,93,104,111,119,131,132,133,136,137,140,146,150,155],wouldn:63,wpalg:17,wrap:[59,81,84,89,99,104,146],wrapper:152,write:[7,28,30,38,39,44,45,50,53,54,64,70,72,73,76,83,86,89,90,92,93,94,98,119,121,139,141,146,150,152],write_:92,write_arrai:92,write_atcf:146,write_aux:[92,98],write_aux_alwai:[83,86,93],write_aux_init:[83,86],write_aux_int:93,write_geoclaw:146,write_hurdat:146,write_imd:146,write_jma:146,write_p:[92,98],write_tcvit:146,written:[6,11,25,30,32,40,44,58,59,60,61,70,72,73,77,81,90,92,96,105,119,129,137,138,139,140,141,146,152,155],wrong:[58,63,67,93,106],www:[4,13,17,30,39,43,45,54,60,61,66,68,81,84,89,92,94,120,122,146,152],x1_desir:33,x1_domain:33,x1_new:33,x2_desir:33,x2_new:33,x_1:[5,131],x_2:[5,131],x_c:131,x_cell:59,x_center:131,x_edg:[59,131],x_i:[129,155,158],x_inch:59,x_mask:152,xarr:89,xarrai:152,xarray_d:152,xclaw:[35,36,86],xclawcmd:86,xclawerr:86,xclawout:86,xcode:80,xdir:86,xiaom:30,xinsheng:[4,52],xinshengqin:[4,52],xleft:[138,139],xlf:100,xlimit:[0,44,51,124],xllcenter:[53,121,150],xllcorner:[53,150],xllower:121,xlow:72,xlower:[0,3,16,22,27,39,84,121,139,141,150,152,155],xlowerg:84,xmax:0,xmin:0,xpoint:140,xrang:96,xtick:[39,49],xupper:[0,22,139,141,152],xxdiff:111,xxx:150,xxxx:67,xy_fil:32,xy_fnam:33,xylim:30,xzf:57,y_c:131,y_cell:59,y_center:131,y_edg:[59,131],y_inch:59,year:[4,17,22,51,59,91,112,122,146],yellow:[59,77,146],yellow_red_blu:77,yes:67,yet:[1,13,20,25,48,52,54,57,59,76,99,119,120,121,122,123,124,125,126,127,129,137,139,157],yianni:[4,17,81],yield:3,yleft:[138,139],ylimit:[0,44,51,124,136],yllcenter:[53,121,150],yllcorner:[53,150],yllower:121,ylow:72,ylower:[3,22,27,39,84,121,139,150,152],ylowerg:84,ymax:0,ymin:0,yml:111,yong:17,you:[0,3,4,5,12,13,14,15,16,18,19,20,22,23,24,25,26,27,28,29,32,35,36,37,38,40,41,42,44,47,50,51,52,53,54,55,56,57,58,59,62,63,66,67,68,69,70,71,72,73,75,76,77,79,80,81,83,84,85,86,88,91,92,93,94,95,96,97,99,100,101,102,103,105,106,107,108,109,111,113,118,119,120,121,124,126,127,128,129,130,131,132,133,134,135,136,138,139,140,141,142,143,144,145,146,148,150,153,154,155,157],your:[4,6,15,16,19,20,24,25,26,35,37,41,44,53,54,55,56,57,58,68,71,76,77,79,81,82,83,84,85,88,90,91,93,102,103,105,106,107,108,110,111,113,121,129,134,135,144,145,150,153,155],yourself:[41,44,57],youtub:[24,108,124],ypoint:140,yupper:[22,139,152],z_allow_wet:39,z_dry:39,z_format:[39,66,152],zdry:[39,66],zenodo:[4,57,124,125,126,127],zero:[3,16,30,32,39,41,59,67,83,96,97,101,103,126,131,132],zip:[12,51,55],zipinfo:51,zlib:92,zlower:22,zmask:66,zmax:[39,66],zmin:[39,66],znearshor:66,zone:[48,51,59,138,139],zoom:[24,51],zsh:94,zshallow:66,ztopo:66,zupper:22,zvar:152},titles:["ClawPlotAxes","ClawPlotData","ClawPlotFigure","ClawPlotItem","About this software","Guiding AMR with adjoint flagging","Adaptive mesh refinement (AMR) algorithms","AMRClaw Description and Detailed Contents","AMRClaw for 1d problems","Doxygen documentation of AMRClaw","AMRClaw Flowcharts","Application documentation","Clawpack Applications repository","Amazon Web Services EC2 Clawpack AMI","b4run function","b4step default routines","Boundary conditions","Bibliography","Changes to master since v5.8.0","Converting from Clawpack 4.3 to 4.6","Converting from Clawpack 4.6 to 5.0","Clawpack 4.x links","Changes in Clawpack 5.0","Clawpack components","Clawpack Community","Full Table of Contents","Contributing examples and applications","current_data","Developers\u2019 Guide","Docker for Clawpack","dtopotools module for moving topography","Fortran 77 vs. Fortran 90 files","Fixed grid monitoring","fgmax_tools module for working with topography data","Fixed grid output","Running an example","Testing your Fortran installation and running an example","Testing a PyClaw installation and running an example","Specifying flagregions for adaptive refinement","Force Cells to be Dry Initially","Fortran version","Fortran Compilers","Examples from the book FVMHP","<no title>","Gauges","GeoClaw Description and Detailed Contents","Getting started with GeoClaw","geoclaw.util module of utility functions","Cautionary Hints on using GeoClaw","GeoClaw plotting tools","Keeping track of repository versions with Git","Visualizing GeoClaw results in Google Earth","Using the GPU version of Clawpack","Grid registration","Guide for updating this documentation","Guide for doing a Clawpack release","Installing Clawpack","Additional options for installing Clawpack","pip install instructions","kmltools module of utility functions","Lagrangian gauges for particle tracking","License","Clawpack Makefiles","Library routines in Makefiles","Manning friction term","The mapc2p function","Marching Front algorithm","Plotting using Matlab","Using NetCDF output","Creating a new application directory","Earthquake sources: Fault slip and the Okada model","Using OpenMP","Output data formats","Which Clawpack solver should I use?","Clawpack Community Photos","Plotting examples","Plotting with Visclaw","Plotting hints and FAQ","Plotting routines for GeoClaw","Plotting options in Python","Installation Prerequisites","About PyClaw","PyClaw Basics","Understanding Pyclaw Classes","Porting a problem from Clawpack 4.6.x to PyClaw","Running PyClaw in the cloud","Pyclaw Controller Class","Pyclaw Limiters","Working with PyClaw\u2019s built-in examples","PyClaw Geometry","Going Further","Pyclaw","Pyclaw Input/Output Package","PyClaw output","Running in parallel","Plotting PyClaw results","Setting up your own problem","Riemann Solver Package","PyClaw Solutions","Using PyClaw\u2019s solvers: Classic and SharpClaw","Installing PyClaw","PyClaw State","Troubleshooting","PyClaw tutorial: Solve the acoustics equations","Pyclaw Utility Module","Python Hints","Python path","qinit 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,allocat:117,allot:59,allow:[4,6,13,22,27,28,29,32,38,39,44,45,47,50,51,53,54,58,64,66,67,70,71,73,76,77,86,91,92,93,99,101,104,105,106,110,111,113,114,117,118,119,120,121,123,124,126,130,132,138,140,141,142,143,147,151,153,155],alon:[16,51],along:[6,14,16,24,27,30,32,39,44,51,54,57,68,70,106,110,117,129,132,134,141,147,155],alpha:[51,55,99],alphabet:81,alreadi:[0,1,6,12,13,18,28,29,41,55,56,58,59,60,66,79,80,94,98,100,103,105,114,122,136,153],also:[3,4,5,6,7,8,9,11,12,16,17,18,20,22,23,24,25,28,29,30,32,33,35,36,37,38,39,41,42,43,44,47,48,51,52,53,54,55,56,57,58,59,62,63,66,67,68,70,71,72,73,76,77,79,83,85,86,89,91,93,94,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,138,139,140,141,142,143,145,146,147,148,149,150,151,153,154,155,156,158,159],alter:51,altern:[30,35,36,44,47,51,56,60,62,67,76,91,94,106,110,117,118,119],although:[30,51,63,67,95,96,98,110,122,153],alwai:[16,22,26,27,28,32,41,53,54,58,67,83,92,109,110,113,114,126,134,140,141,142,151,156],amal:[4,17,81,91],amazon:25,amazonaw:13,amdq:[97,130],ami:25,among:124,amount:[44,48,54],amplitud:[5,119],amr:[4,7,8,16,20,23,25,27,28,32,34,38,44,45,52,59,67,72,73,76,81,89,118,120,121,122,124,126,134,137,138,140,142,150,156],amr_1d:122,amr_2d:[121,122],amr_:[3,7],amr_celledges_show:3,amr_contour_color:3,amr_contour_show:3,amr_data_show:118,amr_level:72,amr_level_max:140,amr_levels_max:[32,110,139,140],amr_modul:[71,110,117,123,124],amrclaw:[4,5,6,12,15,16,19,20,22,23,24,28,36,38,39,41,43,44,45,46,52,55,56,57,58,60,66,67,68,71,72,73,80,91,100,106,107,110,111,129,130,132,135,136,138,141,145,146,149,150,154],amrdata:[5,22,32,110,124,126,139,140,141],amrflag:110,amrlib:117,amrnez:110,an11:54,anaconda:[51,100],anal:17,analog:[138,139],analysi:17,andi:4,angl:[16,30,47,70],ani:[3,4,5,6,8,13,16,18,19,20,22,27,28,29,32,35,36,37,45,48,50,51,54,55,57,58,61,62,64,66,67,69,71,72,73,77,81,87,88,89,91,92,93,94,96,98,100,104,106,109,110,111,117,121,123,129,132,133,134,137,138,139,141,147,156,159],anim:[12,16,42,51,117,124,125,143],animation_tool:[124,125],anisotrop:[6,22],anl:94,annot:[27,59],annual:24,anoth:[3,22,39,44,51,55,58,59,72,76,80,88,99,102,111,121,147,156],answer:24,anyth:[3,6,28,29,58,63,111,121],anywher:110,aoml:147,apach:13,apdq:[97,130],api:[47,121],app:[12,13,18,23,26,28,29,32,37,42,43,70,108,109,116,120,121,122,123,124,125,126,127,131],appar:[30,32,71],appeal:51,appear:[0,1,3,5,8,13,18,23,32,44,45,51,54,59,62,65,77,93,98,101,119,126,141,143,151],append:[5,20,32,38,39,44,51,60,77,86,98,110,118,119,129,130,140],appl:17,appli:[3,4,5,6,13,16,25,30,48,51,53,64,66,70,77,79,87,89,92,99,110,129,138,141,156],applic:[4,6,15,16,19,20,22,23,24,28,29,32,35,36,37,41,42,43,45,46,55,57,58,63,66,68,71,79,88,89,90,91,93,99,104,107,109,110,111,113,116,117,119,120,121,123,124,130,132,134,135,138,141,145,146,151,153,154,156,157],appreci:81,approach:[5,7,13,28,29,38,44,54,57,69,76,84,91,94,96,104,110,117,119,120,122,130,131,137,141,156,159],appropri:[4,5,6,13,16,24,28,45,48,49,51,55,57,59,60,64,67,68,69,71,83,86,87,88,92,94,95,96,97,98,111,123,130,133,138,147,156,159],approv:48,approxim:[6,16,25,33,48,51,70,130],april:[24,124,125,128],apt:[13,80],arbitrari:[32,59,99,113,132,141],arbitrarili:66,arc:133,arcgi:153,architectur:94,archiv:[12,21,36,51,55,111,143,149,153,155],arcminut:[70,151],arcsecond:[45,151],area:[15,22,45,99,108,119,134,135],arg:[89,98],argument:[0,1,2,3,27,30,45,47,50,51,53,77,83,84,88,89,92,96,98,99,101,104,111,121,130,132,137,138,139,147,153,156],argv:[140,142],aris:[61,81],arithmet:64,aron:[4,17,81,91],arora:87,arora_ro:87,around:[6,30,32,39,59,92,108,111,124,139,140,147,153,156],arrai:[0,3,6,15,20,22,27,30,32,33,38,44,45,47,49,53,59,77,83,84,86,87,89,91,92,93,96,97,98,99,101,103,104,105,113,114,115,119,121,124,126,130,131,132,135,138,139,140,141,142,147,151,153,156],arrang:153,arriv:[22,32,34,39,45,119,133,134],arrival_tol:32,articl:[4,17,91,143],artifici:[16,134],arxiv:52,asc:153,ascii:[44,53,67,83,86,93,98,119,129,138,140,142,151,157],ascii_output_format:68,ask:24,ask_us:153,aspect:[12,24,29,43,48,49,67,153],assert:[140,142],assess:[4,48,133],assign:[30,32,83,86,92,98],assist:[22,124],associ:[0,1,2,6,22,51,58,71,89,92,93,111],assum:[3,5,20,22,30,32,36,39,47,48,51,53,54,55,59,67,70,76,92,93,95,96,97,103,104,110,117,132,133,138,141,147,148,151,153,155,159],assumpt:[51,54],asteroid:4,astronom:133,atcf:[108,121,147,148],aterrel:4,atmospher:4,attach:[55,92,101],attempt:[5,8,11,20,33,35,36,62,92,104,111,113,127,147,153,154],attirbut:22,attr:[89,98],attribur:5,attribut:[5,7,22,30,38,44,66,70,76,78,79,83,86,89,92,94,96,98,99,110,113,118,122,129,137,138,139,141,147,153],attributeerror:77,aug:[17,122],aug_glob:97,augment:[66,131],august:[24,121,128],austin:4,author:[17,25,45,48,87,91,92,97,109],auto:[0,44,84],autom:[14,54,84,111],automat:[0,2,3,8,11,16,30,35,36,41,51,55,62,76,77,79,83,88,92,94,100,101,102,104,111,113,124,126,138,139,141,151],autonom:5,aux1:32,aux1d:156,aux:[5,6,1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,23,25,26,30,32,33,35,36,37,40,42,43,44,45,47,49,50,51,52,53,54,55,59,60,62,63,66,67,68,72,73,77,79,80,83,84,86,87,89,91,92,94,96,97,98,99,101,103,104,105,106,110,111,113,114,121,122,128,130,132,137,138,141,143,147,151,153,154,156],containing_rect:30,contains:29,containt:129,contamin:138,contan:51,content:[4,6,23,51,55,73,84,91,141,151,156,157],context:[27,51,156],contigu:[72,92,101,132],continent:[7,66],contingu:22,continu:[13,22,28,30,49,54,81,105,130,138,159],contour:[3,30,44,51,53,67,105,137,153],contour_color:3,contour_kwarg:[3,153],contour_level:[3,153],contour_max:3,contour_min:3,contour_nlevel:3,contour_show:3,contourf:[51,76],contract:[4,61,81],contrast:[53,132],contribut:[4,24,25,57,81,84,91,96,99,108,111],contributor:[4,24,61,91],control:[6,7,23,25,32,41,44,54,58,60,67,79,82,87,89,91,92,93,94,96,110,119,124,131,141],conveni:[1,27,32,35,36,39,44,51,79,86,88,91,93,95,103,156,159],convens:151,convent:[3,22,30,46,53,70,97,151],converg:[66,76],convers:[19,25,84,92,110,132,151,155],convert43to46:19,convert46to50:20,convert:[3,22,25,30,33,42,47,51,58,59,62,70,73,84,91,96,104,105,121,124,138,139,147,151,155],convert_fort_double_to_float:104,convert_readm:11,convert_to_standard_unit:30,convex:[7,32],coodin:30,coord:[47,51],coordin:[4,23,30,32,47,72,76,83,89,93,94,103,110,132,141,153],coordinate_specif:[30,70],coordinate_system:[15,60,135,141],coorind:153,copi:[6,14,15,16,35,36,44,51,54,55,58,67,83,86,96,101,107,108,109,110,114,118,121,125,134,135,139,143,145,146,151,156],copyq1:63,copyright:[61,81],core:[4,12,73,111,121],corioli:[48,141,145,146],coriolis_forc:[48,141],corner:[3,30,32,53,70,72,89,132,138,140,142,151,153],correct:[20,28,41,54,55,63,64,67,77,83,89,94,98,104,113,114,118,134,138,140,141,142],correctli:[28,32,84,90,117,141],correspond:[3,6,12,23,25,27,30,44,47,48,53,54,55,59,67,70,77,83,87,89,92,93,96,98,101,110,111,130,132,133,138,139,140,141,142,147,151,155,156],correspondingli:32,cos:[39,47,49,66,83,96],cosin:83,cost:[13,99],costli:131,could:[5,12,13,27,32,35,36,39,44,53,60,66,70,71,77,79,83,89,93,101,102,106,117,126,132,134,139,140,141,142,153,156],council:4,count:83,count_from_zero:83,counter:[104,153],counterclockwis:70,coupl:[119,159],courant:[4,6,110,120,138,139,140,142],cours:[13,26,32,44,46,60,70,94,95,103,105,108,141,151],cover:[6,7,27,28,30,32,38,39,51,59,66,70,110,114,119,134,140,151],coverag:[91,111],covert:11,covid:24,cparam:[83,101],cpp:52,cpu:[13,52,118,121,123,150],crash:[118,138,139],creat:[0,1,2,3,5,6,7,19,24,25,28,30,32,33,35,36,38,40,42,44,45,46,50,52,54,58,59,62,70,72,76,77,79,84,85,88,89,91,92,95,98,101,102,103,104,110,111,113,117,118,119,121,122,123,126,132,137,138,139,140,143,144,147,153,155,156,157],create_dtopo_xi:[30,70],create_dtopographi:[30,70],create_topo_func:153,creation:[39,77,91,113],criteria:[6,7,22,25,32,66,101],criterion:[32,110,140],critic:[51,93,130],crop:[53,153],cross:28,crucial:[51,151],csdm:24,cse:24,csh:94,csv:[30,70,121],csvfault:[30,70],ctrl:[29,77],cube:67,cultu:66,cumul:121,current:[3,5,13,14,20,22,24,27,28,29,30,32,38,39,41,44,45,48,53,54,55,57,58,59,60,67,68,72,77,79,89,92,93,94,99,101,104,106,110,111,118,120,121,129,133,137,138,139,140,141,142,147,148,151,153,155],current_data:[0,3,25,44,76,77],curv:[3,44,76,132],custom:[0,13,16,20,22,25,63,67,73,76,84,90,96,134],custom_bc:96,customari:93,cut:139,cutoff:[6,140],cvf:55,cvs:51,cxx:94,cyber:17,cygwin:86,cython:94,dai:[6,13,51,141],dalcin:81,dam:[51,134],dam_break:131,damag:[6,61,81],damiansra:96,dark:132,darker:51,darryl:17,dart:45,dash:[3,94],daspect:67,dat:[30,147],data:[0,1,3,5,25,27,30,32,35,36,38,39,40,42,44,45,46,47,53,54,59,60,61,62,66,67,76,77,78,79,81,83,86,89,92,93,95,97,98,99,101,104,107,108,109,110,113,115,116,118,119,121,122,123,124,126,130,132,133,139,140,142,147,150,152,157],data_break:[39,66,153],data_fil:33,data_limit:[39,66],data_storm:147,data_typ:104,databas:[13,30,70,104,108,121,151],datadir:118,dataset:[151,153,155],date:[5,28,40,47,51,54,55,62,77,147,154],date_tim:47,datetiem:147,datetim:[47,147],datum:[47,48,97,133,141,155],dave:30,davi:[4,17],david:[4,17,81,91,99],davis2018:[5,17],davisleveque2016:[5,17],davisleveque2018:[5,17],dawson:17,daylight:59,dcp:59,deal:[30,48,76,93,94,101,147,153],dealt:[32,39],debug:[7,41,62,72,76,93,101,106,111,138,140],debugg:77,decid:[83,99],decim:[47,59],decimc:147,decis:51,declar:[20,22,101,126,156],decompos:[72,130,159],decomposit:138,decor:104,decoupl:54,decreas:[44,134,151],deduc:151,deep:[5,66],deeper:[132,141,151],deepli:103,def:[0,1,3,44,51,66,77,83,89,93,96,99,140,142,147],default_tfluct:99,defenc:4,defens:4,defin:[0,1,3,5,6,7,22,27,30,32,38,39,41,51,59,60,62,66,67,70,77,79,83,86,89,95,96,98,99,101,103,104,110,113,121,126,130,140,142,147,151,153,154,156,159],definit:[30,67,83,110,116],deform:[17,30,33,45,70,155],deg2dm:59,degener:132,degre:[30,47,51,59,70],delet:[20,28,58],delimit:30,delin:141,delta:[87,89,96,99,130,153,156,159],delta_h:97,delta_hu:97,delta_i:153,delta_limit:153,delta_x:153,dem:[32,45,53,59,121,151,153,155],demo:94,demonstr:[12,25,88,94],denot:[6,22,44,53,130,153],dens:148,densiti:[86,93,97,101,103,139,140,156],depart:[4,147],depdend:87,depend:[3,13,16,28,29,30,32,35,36,40,41,46,48,51,62,64,67,70,77,82,92,97,98,99,104,106,110,121,134,139,141,153,154,156,159],deprec:[7,30,34,54,58,117,121,141,151,153],depress:32,depth:[4,5,16,17,22,30,32,33,39,44,45,48,64,70,76,78,131,133,134,141,151],deriv:[61,70,81,86,90,91,101,111],describ:[3,4,5,6,7,13,14,16,19,26,28,30,31,32,35,36,38,39,44,46,47,48,51,52,54,55,57,59,60,62,63,66,67,70,72,73,76,77,78,89,91,92,98,104,108,110,111,119,122,123,130,132,133,137,138,139,141,147,148,151,153,155,156,159],descript:[3,4,6,9,22,23,25,30,59,67,70,73,76,91,92,104,108,110,130,131,141,147,151,159],design:[4,27,28,51,81,83,103,132,155],desir:[0,1,2,3,6,7,16,22,25,26,30,32,33,39,42,44,55,58,59,60,66,70,75,76,77,79,83,84,86,93,98,99,107,119,121,124,134,136,138,139,140,142,147,151,153,154],desktop:94,destin:51,detail:[4,5,10,16,22,23,25,26,28,29,30,32,35,36,38,41,46,48,51,54,57,58,61,62,66,67,70,73,77,81,86,87,88,89,91,92,93,94,95,96,97,99,109,110,111,114,119,121,126,130,132,137,138,141,143,147,151,154,155,156,159],detect:[51,62,92,100,104,154],deterimin:[141,153],determin:[3,5,6,30,32,39,44,45,48,50,51,54,59,70,77,87,89,92,97,101,106,110,114,118,119,129,132,133,137,138,139,141,153,156],determine_topo_typ:153,dev:[18,24,28,54,55,94,121,122,127,128],develop:[4,6,7,12,13,18,22,23,48,52,54,57,58,61,66,67,76,80,81,84,91,96,99,100,106,108,111,121,122,124,126,130,133,134,140],dict:[30,86,92,97,98,101,147,153],dictionari:[0,1,2,3,30,44,60,77,83,86,92,97,98,101,103,106,147,151,153],dicuss:30,did:[121,126,132,151],didn:116,died:113,diff:[18,50,55,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127],differ:[1,3,6,7,12,15,16,22,28,30,31,35,36,39,44,46,48,50,53,57,59,62,64,66,67,70,71,76,79,83,84,86,88,89,91,92,97,99,104,105,106,107,110,111,117,118,119,120,121,124,126,127,130,133,134,135,136,138,139,140,141,145,146,151,153,154,155,156,159],differenti:[17,30],difficult:44,difficulti:[100,102,106],diffus:96,digit:[32,39,53,59,60,77,119,120,121,153],dike:[39,66,124],dim:[96,97,99],dimens:[5,6,7,16,20,22,25,44,47,53,59,67,83,84,86,92,94,96,97,98,101,103,110,121,124,130,138,139,140,142,153,156],dimension:[3,7,8,17,22,25,30,32,35,36,44,48,52,67,89,96,117,118,120,123,140,141,142,153,156],dimensional_split:[89,117,138,140,142],dip:[30,70],dir:[55,94,157],direct:[6,8,16,22,30,32,35,36,44,47,51,55,59,61,62,67,70,71,77,81,86,96,103,110,120,130,138,139,141,153],directli:[8,19,23,32,48,57,67,70,77,79,83,84,87,91,101,104,106,121,153,157],directori:[1,3,5,6,11,12,13,14,15,16,19,20,22,23,25,28,29,31,32,35,36,37,40,42,43,44,45,47,50,51,54,55,57,59,63,67,68,71,75,76,79,86,88,89,91,92,93,96,103,106,107,108,110,111,113,118,119,120,121,123,129,130,134,135,136,137,138,139,143,145,146,149,150,151,154,156,157],directorti:108,disabl:[49,100,141],disable_petsc:104,discard:[32,99],disclaim:[61,81],discontinu:[4,99,159],discov:64,discoveri:111,discret:99,discrib:4,discuss:[5,24,28,30,48,53,66,70,92,103,105,106,110,119,121,130,141,159],disk:[13,44,83,92,93,111,119],dispers:48,displac:[30,45,48,70,134,141,155],displai:[1,13,35,36,40,44,51,59,77,93,111,141],display_format:[44,60],display_landfall_tim:141,dist:55,dist_latlong2met:47,dist_meters2latlong:47,distanc:[30,47,51,70,141,151,153],distant:[108,110],distinct:[44,119],distinguish:39,distribut:[4,12,13,29,30,54,61,70,73,81,99,105,124],disturb:51,distutil:84,divid:[110,138],divis:[4,51],dlgeorg:4,dms2decim:47,dnetcdf:[41,151],doc:[18,23,24,28,30,51,55,87,104,105,106,120,121,122,123,124,125,126,127,144],docker:[18,25,55,56,120,121,122,123,124,125,126,127,158],docker_disk:29,docker_imag:55,dockerfile_v5:29,dockerhub:[29,55],dockeril:29,docstr:[84,88,111],doctest:89,documen:54,document:[0,1,2,3,6,7,18,21,22,23,24,25,28,29,32,45,48,53,58,61,70,76,77,78,79,81,87,89,92,93,94,95,99,101,104,106,114,127,128,137,140,157,158],dodsc:[39,66],doe:[4,5,11,16,20,27,28,39,40,48,51,53,54,58,67,73,77,80,89,98,101,104,110,111,114,119,123,126,129,130,131,134,147,153,154,156],doesn:[28,32,58,63,101],doflag:110,doi:[4,17,52,55,57,124,125,126,127,128],doing:[6,11,19,25,28,33,39,44,48,50,52,54,58,63,77,79,89,91,110,111,118,119,120,121],domain:[5,6,16,17,33,38,39,48,51,54,59,70,72,82,83,84,86,94,96,98,101,108,110,139,140,142,151],don:[13,27,28,54,55,77,93,94,100,111,140,154],done:[1,6,7,8,11,13,16,19,20,28,35,36,39,44,46,51,53,54,56,59,62,66,67,70,76,77,79,83,87,88,91,104,110,114,118,119,123,129,130,132,137,139,141,150,153,154,155],donna:[4,17],donnabois:4,donor:[138,140,142],dontflag:110,dot:[40,44,51,58,59,62,154],doubl:[67,84,89,104,130,139],down:[13,30,93,118,147,151,153],download:[12,13,28,29,30,36,37,39,45,51,55,57,58,68,88,94,100,121,122,128,149,153,154,155],downward:70,doxygen:[6,7,25,120],dpc:59,dpi:[51,59],dpng:67,dprint:[139,140],dq_src:[96,99],dqdt:99,draft:55,drag:141,drag_law:141,draw:3,drawback:106,drawcontourlin:67,drawn:[30,51,137],driver:[20,63],drop:[13,54,80,124,126,134,138],dry:[16,17,25,32,45,97,124,127,131,134],dry_point:39,dry_points_sum:39,dry_toler:97,ds824:147,dst:59,dt_check:32,dt_initi:[113,138,140,141,142],dt_max:[138,140,142],dt_max_dtopo:[113,141],dt_variabl:[138,140,142],dtdtopo:116,dtdx1d:115,dtdx:87,dtdy1d:115,dtfe:99,dtopo2kml:59,dtopo:[25,30,33,45,48,53,59,70,106,113,115,116,124,126,134,141,151,153,155],dtopo_data:[113,141],dtopo_file_nam:59,dtopo_modul:113,dtopo_path:33,dtopo_typ:[30,33,59,70],dtopofil:[59,70,141],dtopographi:[30,70],dtopotool:[45,70,115,116,118,121,122,151,152],dtopotools_exampl:[30,70,109],dtopotyp:[141,151],due:[17,24,30,39,47,70,111,120,121,126,134,154],dummi:[84,99,156],dump:[72,138],dumpgaug:117,duplic:[77,116,129],durat:[30,126,133],dure:[5,22,32,39,44,59,70,73,113,133,134,140,141,142,151],dxc:84,dyc:84,dylib:51,dynam:[6,20,30,48,70,73,139],dynamic_slip:[30,122],dz_at_t:30,dz_interv:30,dz_max:30,e10:32,e15:44,e26:44,e68:[4,17],e_format_bst:147,e_l:97,e_r:97,each:[1,2,3,5,6,7,12,16,18,22,30,32,34,44,47,51,53,54,55,59,60,63,66,67,70,71,72,75,76,77,79,83,84,87,89,92,93,94,96,97,98,99,101,103,110,111,113,114,118,119,121,122,124,129,130,131,132,134,137,138,139,140,141,142,147,150,151,153,155,159],each_fram:44,each_gaug:44,ear:4,earli:[6,20,134],earlier:[5,20,22,30,32,38,53,70,83,96,113,120,151,153],earth:[25,39,45,52,59,66,70,117,119,127,132,141],earth_radiu:141,earthquak:[25,30,45,48,109,134,141,148,151],eas:59,easi:[4,6,11,29,38,58,67,84,93,94,95,132,143,156],easier:[58,76,119,121,132,156],easiest:[19,28,41,73,77,79,110,156],easili:[3,13,28,32,51,54,67,77,84,89,100,104,111,124,143,147],east:[13,151],easy_instal:94,ec2:25,echo:106,ecosystem:[4,17],edebug:[139,140],edg:[3,6,15,16,27,30,32,33,38,59,70,89,97,130,132,135,139,140,142,156],edgecolor:132,edit:[51,54,55,58,79],editabl:28,editor:72,edu:[30,51,68,92,123],effect:[44,51,64,67,89,93,110,111,133,141,153],effici:[48,52,81,91,92,93,101,110,132,139],effort:92,efix:[97,131],egg:[29,58],eigenvalu:5,eigenvector:[5,130,159],either:[12,16,20,30,32,39,45,46,51,60,62,66,67,70,77,79,83,89,91,92,93,99,104,106,110,111,117,118,119,121,130,132,134,139,141,147,151,153,156,159],elast:[13,70],element:[0,3,22,59,97,99,101,138,139,140,141],elementwis:93,elev:[22,25,32,39,45,46,48,51,53,59,76,107,110,124,132,133,141,151,153,155],elif:[140,142],elimin:[8,22,66,84,106,121,141],ell:130,els:[27,28,58,66,101,121,132,134,142],elsewher:[5,24,39,91,132],emerg:4,emmanuel:141,emmett:[17,81,91],empir:[48,64],empti:[12,44,98,101,104,106,138,147,153],empyclaw:96,enabl:[89,93,100,104,119],encapsul:48,encount:[40,51,77,100,102],encourag:67,end:[13,29,30,32,44,47,51,55,59,86,93,97,103,105,108,110,118,119,121,129,131,132,140,142,147,150],end_dat:47,enddo:156,endian:92,endors:[61,81],energi:[93,97],enforc:132,eng:147,engin:[17,51],enhanc:[64,81,121],enlarg:119,enough:[5,54,66,139,148,150,151],ensembl:147,ensur:[35,36,37,67,108],enter:[67,92,94,100],enthought:[100,102],entir:[5,6,38,48,51,59,66,70,71,73,83,93,98,108,110,114,132,153],entireti:86,entri:[51,60,83,93,104,147],entropi:[97,131],enumer:[89,99],environ:[14,25,28,35,36,37,40,50,51,54,57,58,67,69,71,73,95,102,104,106,119,153,154],envis:16,epd:102,eprint:[139,140],epsg:51,epsilon:87,eqn:159,eqnarrai:103,equal:[16,30,32,51,70,94,96,110,129,132,138,140,142,151,153],equat:[4,5,16,17,25,35,36,45,48,60,64,77,82,83,84,86,91,92,93,96,99,100,101,114,117,119,121,122,130,138,140,141,142,151,156,159],equiv:159,equival:[6,44,52,53,59,60,123,151],err:140,errest:110,erron:[30,70],error:[5,16,20,35,36,40,51,58,67,71,77,86,91,92,93,104,110,111,122,126,139,140,147,154],escap:[110,140],escienc:13,especi:[28,51,84,96],esri:[53,151],essenti:[5,53,67,99,141,151],est:140,establis:121,establish:4,estim:[5,64,110,139,141],estimat:[5,140],eta:[25,30,32,39,44,45,110,117,124,133],eta_init:134,eta_tild:32,etc:[0,2,16,19,20,24,27,28,32,33,48,51,54,57,59,63,72,76,84,130,137,138,141,147,156],etopo1:[121,132,133,151,153,155],etopo_sample_2min:153,etopotool:[121,151],euler:[60,91,99,115,117,120,122,130,156],euler_1d_pi:97,euler_2d:[35,37,91,96],euler_exact_1d:97,euler_hll_1d:97,euler_hllc_1d:97,euler_roe_1d:97,evalu:[17,27,30,64,83,89,99,153,156],even:[39,48,51,58,61,70,81,104,110,124,139,140,151,154,156],evenli:[51,93],event:[33,45,48,59,61,70,81,133,134,138],event_tim:59,eventu:[13,45,124],ever:[137,141],everi:[6,12,28,32,44,60,62,63,83,86,88,92,93,101,110,111,119,120,130,134,136,138,140,142,147,151,153,156],everyth:[32,55,58,71,94,103,104,111,121],everywher:[38,39,47,64,101,134],evolv:[22,83,86,99],evolve_to_tim:[83,99],exact:97,exactli:[28,50,52,101,132,138],exam:77,examin:[16,35,36,44,66,106],exampl:[0,1,2,3,4,5,6,7,8,9,13,14,16,20,22,24,27,28,29,30,38,40,41,43,45,47,53,54,55,56,57,59,60,62,63,64,68,70,71,72,76,77,79,81,82,83,84,86,89,90,92,93,96,97,98,99,100,103,104,105,106,108,109,110,111,113,115,116,117,118,119,120,121,122,123,124,125,129,130,131,133,134,136,137,138,139,140,141,142,143,147,149,150,151,153,154,155,156],exce:[32,51,110,139],exceed:[110,121],except:[22,27,30,39,92,97,104,124,138,141,147,151],ex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this software","Guiding AMR with adjoint flagging","Adaptive mesh refinement (AMR) algorithms","AMRClaw Description and Detailed Contents","AMRClaw for 1d problems","Doxygen documentation of AMRClaw","AMRClaw Flowcharts","Application documentation","Clawpack Applications repository","Amazon Web Services EC2 Clawpack AMI","b4run function","b4step default routines","Boundary conditions","Bibliography","Changes to master since v5.8.1","Converting from Clawpack 4.3 to 4.6","Converting from Clawpack 4.6 to 5.0","Clawpack 4.x links","Changes in Clawpack 5.0","Clawpack components","Clawpack Community","Full Table of Contents","Contributing examples and applications","current_data","Developers\u2019 Guide","Docker for Clawpack","dtopotools module for moving topography","Fortran 77 vs. Fortran 90 files","Fixed grid monitoring","fgmax_tools module for working with topography data","Fixed grid output","Running an example","Testing your Fortran installation and running an example","Testing a PyClaw installation and running an example","Specifying flagregions for adaptive refinement","Force Cells to be Dry Initially","Fortran version","Fortran Compilers","Examples from the book FVMHP","Clawpack Gallery","Gauges","GeoClaw Description and Detailed Contents","Getting started with GeoClaw","geoclaw.util module of utility functions","Cautionary Hints on using GeoClaw","GeoClaw plotting tools","Keeping track of repository versions with Git","Visualizing GeoClaw results in Google Earth","Using the GPU version of Clawpack","Grid registration","Guide for updating this documentation","Guide for doing a Clawpack release","Installing Clawpack","Options for installing Clawpack Fortran codes","pip install instructions","kmltools module of utility functions","Lagrangian gauges for particle tracking","License","Clawpack Makefiles","Library routines in Makefiles","Manning friction term","The mapc2p function","Marching Front algorithm","Plotting using Matlab","Using NetCDF output","Creating a new application directory","Earthquake sources: Fault slip and the Okada model","Using OpenMP","Output data formats","Which Clawpack solver should I use?","Clawpack Community Photos","Plotting examples","Plotting with Visclaw","Plotting hints and FAQ","Plotting routines for GeoClaw","Plotting options in Python","Installation Prerequisites","About PyClaw","PyClaw Basics","Understanding Pyclaw Classes","Porting a problem from Clawpack 4.6.x to PyClaw","Running PyClaw in the cloud","Pyclaw Controller Class","Pyclaw Limiters","Working with PyClaw\u2019s built-in examples","PyClaw Geometry","Going Further","PyClaw","Pyclaw Input/Output Package","PyClaw output","Running in parallel","Plotting PyClaw results","Setting up your own problem","Riemann Solver Package","PyClaw Solutions","Using PyClaw\u2019s solvers: Classic and SharpClaw","Installing PyClaw","PyClaw State","Troubleshooting","PyClaw tutorial: Solve the acoustics equations","Pyclaw Utility Module","Python Hints","Python path","qinit default routines","Quick start guide for storm surge modeling","Quick start guide for tsunami modeling","AMR refinement criteria","Regression testing","v5.0.0 release notes","v5.1.0 release notes","v5.2.0 release notes","v5.2.1 release notes","v5.2.2 release notes","v5.3.0 release notes","v5.3.1 release notes","v5.4.0 release notes","v5.4.1 release notes","v5.5.0 release notes","v5.6.0 release notes","v5.6.1 release notes","v5.7.0 release notes","v5.7.1 release notes","v5.8.0 release notes","v5.8.1 release notes","Releases of Clawpack and release notes","Checkpointing and restarting","Riemann solvers","Shallow water Riemann solvers in Clawpack","Ruled Rectangles","Setting sealevel","Set Eta Init \u2013 spatially varying initial surface elevation","setaux default routines","Set environment variables","Using setplot.py to specify the desired plots","Specifying classic run-time parameters in setrun.py","Specifying AMRClaw run-time parameters in setrun.py","Sample setrun.py module for AMRClaw","Specifying GeoClaw parameters in setrun.py","Sample setrun.py module for classic Clawpack","Saving and sharing results","Compiling the Sphinx documentation locally","src1d default routines","src default routines","Storm Specification Class and Tools","Sources for Storm Surge Data","Testing your installation","Timing Statistics","Topography data","Python tools for working with topo and dtopo","topotools module for working with topography data","Troubleshooting","Some sources of tsunami data","User files required for the Fortran code","Plotting with VisIt","Clawpack Virtual Machine","Wave-propagation algorithms"],titleterms:{"1d_fill_between":3,"1d_from_2d_data":3,"1d_plot":3,"2d_contour":3,"2d_pcolor":3,"case":134,"catch":28,"class":[83,86,147],"default":[15,107,134,135,145,146],"final":55,"function":[14,47,59,65,66,79,93,99,159],"import":106,"new":[46,54,69,88,111],"switch":67,"true":77,Adding:[28,51,88,96,130],For:6,Going:90,One:[130,131,159],The:[51,65,66,67,103],Use:102,Using:[5,13,25,29,38,52,58,63,68,71,93,96,99,130,137,156],about:[4,81],abov:29,access:79,acoust:[97,103],adapt:[6,16,25,38],add:77,addit:[51,139,141],adjoint:5,adjust:134,advect:97,after:129,afterfram:67,algorithm:[6,17,66,73,159],alias:51,all:[3,58,66],along:66,amazon:13,ami:13,amr:[3,5,6,22,66,71,110,132,139,141],amrclaw:[7,8,9,10,18,25,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,139,140,156],anoth:77,app:55,applic:[11,12,17,25,26,62,69,94],approach:8,arcsecond:[39,66],area:66,argument:66,arrai:[39,66,72,102],arriv:141,artifact:51,ascii:[72,92],attribut:[0,1,2,3,27,32,51,77,132],author:4,auto:[30,33,47,59,153],aux:[72,83],auxiliari:96,avail:[24,42],axes:49,b4run:14,b4step:[15,156],background:77,backward:[18,121,122,123,124,125,126,127],base:62,basic:[51,82,95],bathymetri:155,befor:156,behavior:134,below:66,better:29,between:[29,77],bibliographi:17,binari:72,binder:29,book:42,boundari:[6,16,96,156,159],bounding_box:132,branch:[28,54],buffer:66,bug:28,built:[54,88],buoi:155,burger:97,candid:55,capac:159,cautionari:48,cell:[6,39,132],cfl:87,chang:[18,22,77,99,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127],chardiff:111,check:[28,111],checkpoint:129,chile:51,choic:32,choos:[6,66],cite:[4,91],clamshel:16,classic:[18,25,35,36,99,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,138,142,149],claw:[74,136],clawcode2html:11,clawpack:[12,13,17,18,19,20,21,22,23,24,25,29,43,52,54,55,56,57,62,73,74,84,87,99,100,120,121,122,123,124,125,126,127,128,131,142,158],clawplotax:0,clawplotdata:1,clawplotfigur:2,clawplotitem:[3,77],clawutil:[18,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127],clinic:24,clone:[28,57],cloud:85,code:[11,25,28,39,46,57,58,74,111,154,156],color:77,colorbar:51,colormap:77,command:[29,37,67,79,88,154],commit:28,commun:[24,28,74],comparison:111,compat:[18,121,122,123,124,125,126,127],compil:[41,62,68,102,144,154],compon:[23,77],comput:[73,129],condit:[6,16,96,103,156,159],configur:54,contain:29,content:[7,25,28,39,45,66,77,83,93,99,111,132],continent:132,continu:111,contourf:77,contribut:[26,28,131],contributor:81,control:[83,86,103],convers:20,convert:[11,19,20],convex:132,coordin:[49,51],copi:69,correctli:94,cover:132,coverag:28,creat:[13,29,39,51,55,66,67,69,83],creation:83,criteria:110,current_data:[27,79],curv:77,custom:[99,130],dart:155,data:[33,51,72,137,141,148,151,153,154,155,156],debug:[77,139],defin:[16,132],deform:134,dem:[39,66],demonstr:131,depend:[87,100],deprec:8,depth:49,deriv:[83,93],describ:17,descript:[7,45],desir:137,detail:[6,7,45],determin:66,dev:74,develop:[24,25,28,74],diff:111,differ:[32,51,58,63,73,77],dimens:[89,131,159],dimension:130,directli:13,directori:[58,62,69,77],displac:151,doc:54,docker:29,dockerfil:[29,55],docstr:[30,33,47,59,153],doctest:111,document:[9,11,30,33,47,54,55,59,91,120,121,144,153],doing:55,domain:[89,103],done:156,download:151,doxygen:9,drop:105,dry:[39,66],dtopo:152,dtopotool:30,duplic:62,each:[28,156],earth:51,earthquak:[70,155],easi:106,ec2:13,elev:[49,66,134],environ:[41,136],equat:[97,103,131],error:[28,102],eta:134,euler:97,event:[24,51],exampl:[12,25,26,32,35,36,37,39,42,44,46,51,58,66,67,69,75,88,91,94,132],exe:154,exist:69,experi:58,extra:54,extrapol:110,f2py:154,faq:77,faster:51,fault:70,featur:91,fflag:41,fgmax:[32,66],fgmax_tool:33,figur:[51,77],file:[13,29,31,32,39,51,53,54,55,57,63,67,77,79,111,129,132,141,151,156],fileio:92,find:[13,66,77],finer:6,fix:[28,32,34,71,141],flag2refin:110,flag:[5,6,62,66,110,132,139],flagregion:38,flow:[25,83],flowchart:10,fly:76,forc:39,force_dry_init:39,fork:28,format:[32,72,151],formul:159,fort:[72,77],fortran:[22,25,31,36,39,40,41,57,80,102,111,154,156],found:67,frame:93,framework:55,friction:64,from:[13,19,20,22,25,28,30,33,37,39,42,47,54,59,66,79,84,88,95,132,153],front:66,full:25,fund:[4,81],further:90,fvmhp:42,galleri:[43,54,67],gaug:[44,51,60,93,155],gdal:51,gener:[18,22,30,33,47,54,59,121,122,123,124,125,126,127,141,153],geo:141,geoclaw:[5,15,16,18,22,25,29,39,45,46,47,48,49,51,71,74,78,107,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,132,135,141,145,146],geometri:89,geophys:25,get:[25,29,46,67],gfortran:[41,100],ghost:6,git:[28,50,54,57,80],github:[28,55],given:66,global:119,godunov:159,googl:51,gpu:52,grid:[6,16,32,34,53,71,89,141],guid:[5,28,54,55,108,109],guidelin:28,hack:74,hazard:48,hdf5:92,help:67,high:159,hint:[48,77,105],hll:131,host:29,how:[77,79,93],hpc3:74,html:[11,79],imag:[29,51],imagediff:111,implement:110,includ:[12,54],independ:87,indic:[66,91],init:134,initi:[6,39,66,96,103,134,156],input:[22,32,92,138,139],instal:[28,36,37,56,57,58,68,73,80,91,94,100,102,106,149,154],instanc:13,instanti:132,instruct:[28,58],integr:111,intel:41,interact:[79,88],interfac:73,intern:39,interpol:32,interpret:37,iplotclaw:79,ipython:[37,88],issu:28,item:77,jupyt:[12,29,37,143],kaust:74,keep:50,kinemat:70,kml:51,kmltool:59,kmz:51,lagrangian:60,latest:28,latex:79,latitud:[49,51],launch:13,layer:131,level:[28,134],lflag:41,librari:[51,63],licens:[4,61,81],limit:87,line:[37,79,88,111,154],link:21,load:51,local:144,locat:44,log:[13,93],longitud:[49,51],machin:[29,158],make:[77,94,143,154],make_kml:132,makefil:[40,62,63,96,129],man:64,map:51,mapc2p:65,march:66,mask:66,mask_outsid:132,master:[18,28],math:85,matlab:67,matplotlib:100,maxfram:67,maximum:141,mesh:[6,25],method:[0,1,2,3,132,159],mhw:66,migrat:25,miss:131,model:[48,70,108,109,155],modif:39,modifi:[28,63,129],modul:[30,33,47,59,91,104,140,142,153],monitor:[32,141],more:[6,36,40],most:28,move:[29,30],multipl:51,name:[62,63],need:51,netcdf:[53,68,72,92,151],never:28,next:[56,57,58,100],nose:100,note:[112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128],notebook:[12,29,37,105,143],number:55,numpi:100,object:[89,137],obtain:100,okada:70,old:8,older:25,onli:66,open:55,openmp:71,oper:80,option:[51,57,79,94,96],order:102,osf:55,other:[17,18,23,24,29,32,54,77,120,121,122,123,124,125,126,127,128,132,134],out:[28,66],outdir:77,output:[32,34,62,66,67,68,71,72,83,92,93,111,129,138,139,141,154],overlai:51,overview:[25,137],own:[13,29,96],packag:[22,58,92,97],page:54,paper:17,parallel:[73,89,94,95,101],paramet:[22,44,77,79,103,138,139,141],particl:60,pass:94,patch:89,path:[67,106],pcolor:77,petclaw:[89,101],petsc:94,photo:74,pip:[58,80,154],pixel:111,plot:[3,13,22,25,32,44,46,49,51,60,62,67,68,75,76,77,78,79,88,94,95,111,137,143,154,157],plot_typ:3,plotax:51,plotclaw:67,plotdata:51,plotfigur:51,plotitem:51,point:[32,66],pointwis:130,polygon:132,port:84,post:76,potenti:131,ppflag:41,pre:41,prepar:55,prerequisit:80,previou:[24,54],previous_pts_chosen:66,print:139,printfram:79,problem:[8,84,96,103,156],procedur:32,process:[32,76],processor:41,produc:79,propag:159,provid:77,pth:106,publish:51,pull:28,pyclaw:[18,22,25,35,37,58,81,82,83,84,85,86,87,88,89,91,92,93,95,98,99,100,101,103,104,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,149],pyflak:28,pylint:28,pypi:55,python:[20,79,80,100,105,106,124,152],pythonpath:[106,136],q0002:72,qinit:[107,141,151],quantiti:[83,93],quick:[58,108,109],raw:72,read:[39,132],readm:11,recent:[24,28],rectangl:[38,132],rectangular:70,refer:[17,25,52,91,105],refin:[6,16,25,38,110,141],region:[66,110,132,141],registr:53,regress:111,relat:132,releas:[54,55,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128],remot:28,remov:51,replac:63,report:28,repositori:[12,18,23,28,50,54,55,120,121,122,123,124,125,126,127,130],request:28,requir:[51,156],resolut:[51,159],resourc:25,restart:[29,83,129],result:[13,46,51,68,95,143],richardson:110,riemann:[18,25,91,96,97,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,130,131,156],roe:131,routin:[15,22,63,78,107,135,145,146],rst:11,rule:[38,132],run:[29,35,36,37,46,83,85,88,94,95,111,138,139,154],ruptur:70,sage:85,same:63,sampl:[39,66,140,142],save:[93,143],scienc:55,script:96,sea:134,sealevel:133,search:67,seismic:134,select:132,serial:[89,101,111],servic:13,session:24,set:[46,67,77,79,96,133,134,136,154],setaux:[135,156],setplot:[67,77,79,137],setrun:[22,44,138,139,140,141,142],shallow:[97,131],share:143,sharpclaw:99,shelf:132,shoot:[28,67],shore:66,should:73,signatur:99,simpl:[32,132],simul:83,simultan:111,sinc:18,size:77,slip:70,slu:132,softwar:[4,17],solut:[77,83,98],solv:103,solver:[73,83,91,96,97,99,103,130,131,156],some:[29,77,155],someth:77,sourc:[62,70,96,148,155,156,159],space:159,spatial:[134,156],special:[3,139],specif:[32,103,111,141,147,156],specifi:[38,60,77,79,110,137,138,139,141,156],sphere:16,sphinx:[54,144],sprint:[24,74],src1d:[145,156],src:[146,156],start:[25,29,46,108,109],state:101,statist:150,step:[56,57,58,100,156],stop:[13,29],storm:[108,141,147,148],stream:24,style:[32,54],subfault:70,submodul:12,support:[105,124],surfac:[49,134],surg:[108,148],sys:106,system:80,t0002:72,tabl:[25,91],tag:54,tar:[55,57],term:[64,96,156,159],test:[28,36,37,94,100,111,149],than:77,thi:[4,54],tide:155,tile:51,time:[138,139,141,150,156],tip:[28,40,49,51,94],titl:77,tool:[20,25,44,49,60,111,147,152],top:28,topo:152,topofil:66,topographi:[30,33,39,46,51,66,141,151,153,155],topotool:153,track:[50,60],transfer:13,travi:111,triangular:70,troubl:[28,67,154],troubleshoot:[58,102,154],tsunami:[48,51,109,155],tutori:[24,103,105],tvd:87,two:131,understand:83,univers:74,upcom:24,updat:[28,54,55],usag:39,use:[73,134],used:154,useful:[29,131],user:[16,24,29,73,156],using:[48,67,156],utah:74,util:[47,59,104],valu:[32,83],vari:[134,156],variabl:[41,62,96,136],version:[25,29,40,50,52,54,55,58,106],view:13,virtual:158,visclaw:[18,25,60,76,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127],visit:157,visual:[25,51],washington:74,water:[49,97,131],wave:[130,159],web:13,webpag:[13,54,143],what:[77,79,93,131],when:93,where:93,which:[73,106],whichclaw:106,work:[4,33,88,152,153,156],workflow:28,workshop:[24,74],write:[66,96,111,132],written:93,your:[13,28,29,36,51,94,96,100,143,149],zenodo:55,zone:66}}) \ No newline at end of file diff --git a/setenv.html b/setenv.html index d2705f818e..96f5595f66 100644 --- a/setenv.html +++ b/setenv.html @@ -21,7 +21,7 @@ - +

                                                                                                                                                                                                                          @@ -70,7 +70,7 @@

                                                                                                                                                                                                                          Navigation

                                                                                                                                                                                                                          next |
                                                                                                                                                                                                                        • - previous |
                                                                                                                                                                                                                        • Clawpack 5.8.x documentation »
                                                                                                                                                                                                                        @@ -83,6 +83,8 @@

                                                                                                                                                                                                                        Navigation

                                                                                                                                                                                                                        Set environment variables

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        The export commands below work in the bash shell. The syntax may +be different in other shells.

                                                                                                                                                                                                                        CLAW

                                                                                                                                                                                                                        To use the Fortran versions of Clawpack you will need to set the @@ -117,9 +119,15 @@

                                                                                                                                                                                                                        FC

                                                                                                                                                                                                                        PYTHONPATH

                                                                                                                                                                                                                        -

                                                                                                                                                                                                                        We do not recommend setting this environment variable. See -Python path for more information. Instead we recommend using pip -install to set the Python path appropriately, see pip install instructions.

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        If you used pip to install Clawpack then you should not set this +environment variable. But if you installed without pip, e.g. following +Options for installing Clawpack Fortran codes, then you need to set PYTHONPATH to include +the directory $CLAW. If PYTHONPATH is already set, then you may want to +insert $CLAW into the list of directories searched by Python via:

                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        export PYTHONPATH=$CLAW:$PYTHONPATH
+
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        See Python path for more information.

                                                                                                                                                                                                                        @@ -146,7 +154,7 @@

                                                                                                                                                                                                                        Table of Contents

                                                                                                                                                                                                                        Related Topics

                                                                                                                                                                                                                        diff --git a/setrun_geoclaw.html b/setrun_geoclaw.html index d35bf5b9c9..b5b5fe38e4 100644 --- a/setrun_geoclaw.html +++ b/setrun_geoclaw.html @@ -142,23 +142,6 @@

                                                                                                                                                                                                                        Additional AMR parameters -
                                                                                                                                                                                                                        -rundata.refinement_data.max_level_deep : int
                                                                                                                                                                                                                        -

                                                                                                                                                                                                                        For simulations over the ocean, it is often useful to specify -a maximum refinement level allowed in deep parts of the ocean. This is -useful if a high level of refinement is specified on some rectangular -region but only the parts of this region near the shore actually need to -be refined.

                                                                                                                                                                                                                        -
                                                                                                                                                                                                                        - -
                                                                                                                                                                                                                        -
                                                                                                                                                                                                                        -rundata.refinement_data.deep_depth : float
                                                                                                                                                                                                                        -

                                                                                                                                                                                                                        The deepness that triggers the refinement limitation imposed by -max_level_deep above.

                                                                                                                                                                                                                        -
                                                                                                                                                                                                                        -

                                                                                                                                                                                                                        • General geo parameters

                                                                                                                                                                                                                        diff --git a/sharing.html b/sharing.html index 77625870ff..d25c85402d 100644 --- a/sharing.html +++ b/sharing.html @@ -87,7 +87,7 @@

                                                                                                                                                                                                                        Navigation

                                                                                                                                                                                                                        results that you have obtained with this software. These make it relatively easy to generate a set of webpages such as those seen when browsing the examples collected in -galleries.

                                                                                                                                                                                                                        +Clawpack Gallery.

                                                                                                                                                                                                                        These webpages can easily be posted on your own website to be viewed by others if you wish, for example to share on-going work with collaborators or to supplement a journal article.

                                                                                                                                                                                                                        @@ -106,11 +106,13 @@

                                                                                                                                                                                                                        Sharing your results

                                                                                                                                                                                                                        -
                                                                                                                                                                                                                        -

                                                                                                                                                                                                                        IPython notebooks

                                                                                                                                                                                                                        -

                                                                                                                                                                                                                        You should also consider creating an IPython notebook to explain your +

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        Jupyter notebooks

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        You should also consider creating an Jupyter notebook to explain your problem, illustrate your workflow, and present plots and animations all in -one. See notebooks for some examples.

                                                                                                                                                                                                                        +one. See the +Gallery of Notebooks +for some examples.

                                                                                                                                                                                                                        @@ -130,7 +132,7 @@

                                                                                                                                                                                                                        Table of Contents

                                                                                                                                                                                                                      • Saving and sharing results
                                                                                                                                                                                                                      diff --git a/storm_module.html b/storm_module.html index 609a2938c7..75fa6c81c4 100644 --- a/storm_module.html +++ b/storm_module.html @@ -586,7 +586,7 @@

                                                                                                                                                                                                                      Navigation

                                                                                                                                                                                                                      -

                                                                                                                                                                                                                      System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/surge/storm.py:docstring of clawpack.geoclaw.surge.storm.fill_rad_w_other_source, line 15)

                                                                                                                                                                                                                      +

                                                                                                                                                                                                                      System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/surge/storm.py:docstring of clawpack.geoclaw.surge.storm.fill_rad_w_other_source, line 15)

                                                                                                                                                                                                                      Field list ends without a blank line; unexpected unindent.

                                                                                                                                                                                                                        @@ -617,7 +617,7 @@

                                                                                                                                                                                                                        Navigation

                                                                                                                                                                                                                        -

                                                                                                                                                                                                                        System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/surge/storm.py:docstring of clawpack.geoclaw.surge.storm.fill_rad_w_other_source, line 26)

                                                                                                                                                                                                                        +

                                                                                                                                                                                                                        System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/surge/storm.py:docstring of clawpack.geoclaw.surge.storm.fill_rad_w_other_source, line 26)

                                                                                                                                                                                                                        Field list ends without a blank line; unexpected unindent.

                                                                                                                                                                                                                          diff --git a/testing.html b/testing.html index caaad02d3e..6cfef2f205 100644 --- a/testing.html +++ b/testing.html @@ -85,7 +85,7 @@

                                                                                                                                                                                                                          Navigation

                                                                                                                                                                                                                          Testing your installation

                                                                                                                                                                                                                          PyClaw

                                                                                                                                                                                                                          -

                                                                                                                                                                                                                          If you downloaded Clawpack manually, you can test your Pyclaw +

                                                                                                                                                                                                                          If you downloaded Clawpack manually, you can test your PyClaw installation as follows (starting from your clawpack directory):

                                                                                                                                                                                                                          cd pyclaw
 nosetests
@@ -118,7 +118,7 @@ 
                                                                                                                                                                                                                          Classicgalleries.  See also Regression testing.
                                                                                                                                                                                                                          
+archived in the Clawpack Gallery.  See also Regression testing.
                                                                                                                                                                                                                          diff --git a/topo.html b/topo.html index b40e02e3f8..4b8f7493be 100644 --- a/topo.html +++ b/topo.html @@ -147,8 +147,10 @@

                                                                                                                                                                                                                          Navigation

                                                                                                                                                                                                                          These files are larger than necessary since they store the x,y values at each point even though the points are required to be equally spaced. Many data sets come this way, but note that you can convert a file of -this type to one of the more compact types below using:

                                                                                                                                                                                                                          -
                                                                                                                                                                                                                          [insert python code]
+this type to one of the more compact types below using e.g.:
                                                                                                                                                                                                                          
+
                                                                                                                                                                                                                          from clawpack.geoclaw import topotools
+topo = topotools.Topography(input_path, topo_type=1)
+topo.write(output_path, topo_type=3)
                                                                                                                                                                                                                    diff --git a/topotools_module.html b/topotools_module.html index f7e04b11e6..31b90c7321 100644 --- a/topotools_module.html +++ b/topotools_module.html @@ -314,7 +314,7 @@

                                                                                                                                                                                                                    Navigation

                                                                                                                                                                                                                    -plot(axes=None, contour_levels=None, contour_kwargs={}, limits=None, cmap=None, add_colorbar=True, plot_box=False, fig_kwargs={}, data_break=0.0, cb_kwargs={})
                                                                                                                                                                                                                    +plot(axes=None, contour_levels=None, contour_kwargs={}, limits=None, cmap=None, add_colorbar=True, plot_box=False, long_lat=True, fig_kwargs={}, data_break=0.0, cb_kwargs={})

                                                                                                                                                                                                                    Plot the topography.

                                                                                                                                                                                                                    Input
                                                                                                                                                                                                                    @@ -334,6 +334,9 @@

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                                                                                                                                                                                                                  • fig_kwargs (dict) - keyword arguments to be passed to figure.

                                                                                                                                                                                                                  • plot_box (bool or color specifier) - If evaluates to True, plot a box around limits of this topo.

                                                                                                                                                                                                                    • +

                                                                                                                                                                                                                  • long_lat (bool) - If this is a longitude-latitude plot then set the +aspect of the plot to compensate for stretching. If not then the +aspect is set to “equal”.

                                                                                                                                                                                                                  • data_break (float) - when default cmap is used, the value to use to break between water and land colormaps. Defaults to 0., but for some topo files may need to use e.g. 0.01 diff --git a/user_routines.html b/user_routines.html index 2a26d8ae19..ea2693abeb 100644 --- a/user_routines.html +++ b/user_routines.html @@ -101,7 +101,7 @@

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                                                                                                                                                                                                                  • $CLAW/amrclaw/examples

                                                                                                                                                                                                                  • $CLAW/geoclaw/examples

                                                                                                                                                                                                                  -

                                                                                                                                                                                                                  You can also browse from the galleries to the README file for an +

                                                                                                                                                                                                                  You can also browse from the Clawpack Gallery to the README file for an example and then to the source code for the application-specific codes.

                                                                                                                                                                                                                  Specifying the initial conditions

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                                                                                                                                                                                                                  Galleries of all Clawpack applications

                                                                                                                                                                                                                  See also IPython notebook examples.

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                                                                                                                                                                                                                From the command lineList of built-in examples

                                                                                                                                                                                                                You can see results from many of the examples in the Galleries of all Clawpack applications.

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                                                                                                                                                                                                                PyClaw is:

                                                                                                                                                                                                                PyClaw Documentation

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                                                                                                                                                                                                                References and tutorialsMatplotlib gallery

                                                                                                                                                                                                              • `LeVeque’s class notes

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                                                                                                                                                                                                                the initial conditions as desired.

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lim:94,xlimit:[0,32,94],xll:94,xllcenter:94,xllcorner:115,xlow:50,xlower:[0,3,12,19,22,61,94,106,108,115,118],xlowerg:61,xmax:0,xmin:0,xpoint:107,xrang:82,xtick:35,xupper:[0,19,94,106,108],xxdiff:96,xxxx:44,xyz03:94,xzvf:39,year:[4,13,19,77,97],yellow:[54,65],yellow_red_blu:54,yes:44,yet:[1,10,17,34,53,86,104,106,120],yianni:58,yield:3,yleft:[105,106],ylim:94,ylimit:[0,32,94,103],yllcenter:94,yllcorner:115,ylow:50,ylower:[3,19,22,61,94,106,115],ylowerg:61,ymax:0,ymin:0,yml:96,yong:13,you:[0,3,4,10,11,12,14,16,17,19,20,22,23,26,28,29,32,36,37,38,39,41,44,45,46,47,48,49,50,51,52,53,54,56,58,60,61,62,63,65,66,67,68,69,71,72,74,77,78,80,81,82,83,86,87,88,89,90,92,94,98,99,101,102,103,106,107,108,109,110,111,112,115,116,117,118,120],your:[5,11,12,16,17,21,26,29,32,36,38,45,46,49,53,54,56,58,59,60,61,62,65,66,67,69,71,72,76,77,84,89,90,92,93,94,95,98,102,111,112,115,116,118],yourdomain:[65,68],yourself:[29,32,47,64,68],ypoint:107,yum:65,yupper:[19,94,106],yuri:65,zaytsev:65,zero:[3,12,29,44,60,82,83,88,90,101],zip:9,zlower:19,zone:[34,105,106],zoom:94,zsh:80,zupper:19,zxvf:94},titles:["ClawPlotAxes","ClawPlotData","ClawPlotFigure","ClawPlotItem","About this software","Adaptive mesh refinement (AMR) algorithms","AMRClaw","AMRClaw for 1d problems","Application documentation","Clawpack Applications repository","Amazon Web Services EC2 Clawpack AMI","b4step default routines","Boundary conditions","Bibliography","Examples from the book FVMHP","Recent changes \u2014 release notes","Converting from Clawpack 4.3 to 4.6","Converting from Clawpack 4.6 to 5.0","Clawpack 4.x links","Changes in Clawpack 5.0","Clawpack components","Full Table of Contents","current_data","Developers\u2019 Guide","Fixed grid monitoring","Fixed grid output","Running an example","Flagging cells for adaptive refinement","Fortran version","Fortran Compilers","FVMHP book","Galleries of all Clawpack applications","Gauges","GeoClaw","Cautionary Hints on using GeoClaw","GeoClaw plotting tools","git resources","Keeping track of git versions","Guide for updating this documentation","Installation instructions","License","Clawpack Makefiles","Manning friction term","The mapc2p function","Plotting using Matlab","Using NetCDF output","Creating a new application directory","IPython notebook examples","Earthquake sources: Fault slip and the Okada model","Using OpenMP","Output data formats","Which Clawpack solver should I use?","Plotting examples","Visclaw Plotting options","Plotting hints and FAQ","Plotting routines for GeoClaw","Plotting options in Python","Previous versions of Clawpack","About PyClaw","PyClaw Basics","Understanding Pyclaw Classes","Porting a problem from Clawpack 4.6.x to PyClaw","Running PyClaw in the cloud","Pyclaw Controller Class","Development workflow","Installing and configuring git","git resources","Maintainer workflow","Contributing to PyClaw code development","General information for developers","Pyclaw Limiters","Working with PyClaw\u2019s built-in examples","Information for developers","Future work","Building the PyClaw gallery locally","PyClaw Geometry","Going Further","Pyclaw","Pyclaw Input/Output Package","Advanced output options","Running in parallel","Plotting PyClaw results","Setting up your own problem","Riemann Solver Package","Conventions for coding and documenting PyClaw","PyClaw Solutions","Using PyClaw\u2019s solvers: Classic and SharpClaw","Installing PyClaw","PyClaw State","Troubleshooting","PyClaw tutorial: Solve the acoustics equations","Pyclaw Utility Module","Python Hints","qinit default routines","Quick start guide for tsunami modeling","AMR refinement criteria","Regression testing","Release 5.0.0","Release 5.1.0","Checkpointing and restarting","Riemann solvers","Setting sealevel","setaux default routines","Using setplot.py to specify the desired plots","Specifying classic run-time parameters in setrun.py","Specifying AMRClaw run-time parameters in setrun.py","Sample setrun.py module for AMRClaw","Specifying GeoClaw parameters in setrun.py","Sample setrun.py module for classic Clawpack","Saving and sharing results","Compiling the Sphinx documentation locally","src1d default routines","src default routines","Testing your installation","Condensed Table of Contents","Topography data","Troubleshooting","Some sources of tsunami data","User files required for the Fortran code","Plotting with VisIt","Clawpack Virtual Machine","Wave-propagation 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lim:94,xlimit:[0,32,94],xll:94,xllcenter:94,xllcorner:115,xlow:50,xlower:[0,3,12,19,22,61,94,106,108,115,118],xlowerg:61,xmax:0,xmin:0,xpoint:107,xrang:82,xtick:35,xupper:[0,19,94,106,108],xxdiff:96,xxxx:44,xyz03:94,xzvf:39,year:[4,13,19,77,97],yellow:[54,65],yellow_red_blu:54,yes:44,yet:[1,10,17,34,53,86,104,106,120],yianni:58,yield:3,yleft:[105,106],ylim:94,ylimit:[0,32,94,103],yllcenter:94,yllcorner:115,ylow:50,ylower:[3,19,22,61,94,106,115],ylowerg:61,ymax:0,ymin:0,yml:96,yong:13,you:[0,3,4,10,11,12,14,16,17,19,20,22,23,26,28,29,32,36,37,38,39,41,44,45,46,47,48,49,50,51,52,53,54,56,58,60,61,62,63,65,66,67,68,69,71,72,74,77,78,80,81,82,83,86,87,88,89,90,92,94,98,99,101,102,103,106,107,108,109,110,111,112,115,116,117,118,120],your:[5,11,12,16,17,21,26,29,32,36,38,45,46,49,53,54,56,58,59,60,61,62,65,66,67,69,71,72,76,77,84,89,90,92,93,94,95,98,102,111,112,115,116,118],yourdomain:[65,68],yourself:[29,32,47,64,68],ypoint:107,yum:65,yupper:[19,94,106],yuri:65,zaytsev:65,zero:[3,12,29,44,60,82,83,88,90,101],zip:9,zlower:19,zone:[34,105,106],zoom:94,zsh:80,zupper:19,zxvf:94},titles:["ClawPlotAxes","ClawPlotData","ClawPlotFigure","ClawPlotItem","About this software","Adaptive mesh refinement (AMR) algorithms","AMRClaw","AMRClaw for 1d problems","Application documentation","Clawpack Applications repository","Amazon Web Services EC2 Clawpack AMI","b4step default routines","Boundary conditions","Bibliography","Examples from the book FVMHP","Recent changes \u2014 release notes","Converting from Clawpack 4.3 to 4.6","Converting from Clawpack 4.6 to 5.0","Clawpack 4.x links","Changes in Clawpack 5.0","Clawpack components","Full Table of Contents","current_data","Developers\u2019 Guide","Fixed grid monitoring","Fixed grid output","Running an example","Flagging cells for adaptive refinement","Fortran version","Fortran Compilers","FVMHP book","Galleries of all Clawpack applications","Gauges","GeoClaw","Cautionary Hints on using GeoClaw","GeoClaw plotting tools","git resources","Keeping track of git versions","Guide for updating this documentation","Installation instructions","License","Clawpack Makefiles","Manning friction term","The mapc2p function","Plotting using Matlab","Using NetCDF output","Creating a new application directory","IPython notebook examples","Earthquake sources: Fault slip and the Okada model","Using OpenMP","Output data formats","Which Clawpack solver should I use?","Plotting examples","Visclaw Plotting options","Plotting hints and FAQ","Plotting routines for GeoClaw","Plotting options in Python","Previous versions of Clawpack","About PyClaw","PyClaw Basics","Understanding Pyclaw Classes","Porting a problem from Clawpack 4.6.x to PyClaw","Running PyClaw in the cloud","Pyclaw Controller Class","Development workflow","Installing and configuring git","git resources","Maintainer workflow","Contributing to PyClaw code development","General information for developers","Pyclaw Limiters","Working with PyClaw\u2019s built-in examples","Information for developers","Future work","Building the PyClaw gallery locally","PyClaw Geometry","Going Further","Pyclaw","Pyclaw Input/Output Package","Advanced output options","Running in parallel","Plotting PyClaw results","Setting up your own problem","Riemann Solver Package","Conventions for coding and documenting PyClaw","PyClaw Solutions","Using PyClaw\u2019s solvers: Classic and SharpClaw","Installing PyClaw","PyClaw State","Troubleshooting","PyClaw tutorial: Solve the acoustics equations","Pyclaw Utility Module","Python Hints","qinit default routines","Quick start guide for tsunami modeling","AMR refinement criteria","Regression testing","Release 5.0.0","Release 5.1.0","Checkpointing and restarting","Riemann solvers","Setting sealevel","setaux default routines","Using setplot.py to specify the desired plots","Specifying classic run-time parameters in setrun.py","Specifying AMRClaw run-time parameters in setrun.py","Sample setrun.py module for AMRClaw","Specifying GeoClaw parameters in setrun.py","Sample setrun.py module for classic Clawpack","Saving and sharing results","Compiling the Sphinx documentation locally","src1d default routines","src default routines","Testing your installation","Condensed Table of Contents","Topography data","Troubleshooting","Some sources of tsunami data","User files required for the Fortran code","Plotting with VisIt","Clawpack Virtual Machine","Wave-propagation algorithms"],titleterms:{"1d_fill_between":3,"1d_from_2d_data":3,"1d_plot":3,"2d_contour":3,"2d_pcolor":3,"case":84,"catch":69,"class":[60,63],"default":[11,93,102,111,112],"function":[43,56,79,121],"long":67,"new":[33,46,64,69,71,84],"switch":44,"true":54,Adding:[71,82],For:21,Going:76,One:[100,121],The:[43,44,64,90,94],Use:89,Using:[10,45,49,79,82,86,103,118],about:[4,58],access:56,account:68,acoust:[83,90],adapt:[5,12,21,27],add:[54,84],added:84,addit:[105,107],advanc:[36,66,79],advect:83,after:99,afterfram:44,algorithm:[5,13,51,121],all:[3,31,39],altern:39,amazon:10,ami:10,amr:[3,5,19,49,95,105,107],amrclaw:[6,7,21,97,98,105,106,118],anoth:54,applic:[8,9,13,21,31,41,46,80],arrai:[50,89],arriv:107,ascii:[50,78],ask:64,attribut:[0,1,2,3,22,54],author:4,aux:[50,60],auxiliari:82,avail:14,axes:35,b4step:[11,118],background:54,basic:[59,81],bathymetri:[94,117],befor:118,between:54,bibliographi:[13,21],binari:50,book:[14,30],boundari:[5,12,82,118,121],branch:64,bug:69,build:74,built:71,buoi:117,burger:83,capac:121,cautionari:34,cell:[5,27],cfl:70,chang:[15,19,54,64,67,97,98],chardiff:96,check:[67,69,84],checkpoint:99,choos:5,cite:[4,77],clamshel:12,classic:[86,97,98,104,108],clawcode2html:8,clawpack:[9,10,13,15,16,17,18,19,20,31,39,41,51,57,61,86,87,108,120],clawplotax:0,clawplotdata:1,clawplotfigur:2,clawplotitem:[3,54],clawutil:98,clone:[23,68],cloud:62,code:[8,21,23,33,68,84,96,113,118],color:54,colormap:54,command:[44,56,71],comment:84,commit:[64,67],commun:69,comparison:96,compil:[29,39,41,45,89,110],compon:[20,54],comput:[51,99],condens:114,condit:[5,12,82,90,118,121],configur:[65,68],consid:64,content:[21,54,60,86,92,114],continu:96,contourf:54,contribut:[68,69],contributor:58,control:[60,63,90],convent:84,convers:17,convert:[8,16,17],coordin:35,copi:[46,68],correctli:80,coverag:69,creat:[10,44,46,60,68],creation:60,criteria:95,current_data:[22,56],curv:54,dart:117,data:[50,103,107,115,116,117,118],debug:[54,105],defin:12,delet:64,depend:[69,70,87],depth:35,deriv:[60,79],describ:13,desir:103,detail:[64,65],develop:[21,23,39,64,68,69,72],differ:[51,54],dimens:[75,121],dimension:100,directli:10,directori:[41,46,54],displac:115,docstr:84,doctest:69,document:[8,38,77,84,110],domain:[75,90],done:118,download:115,dtopo:94,each:118,earthquak:[48,94,117],ec2:10,edit:64,elev:35,environ:[29,39],equat:[83,90],error:[69,89],euler:83,exampl:[9,14,21,26,32,33,44,46,47,52,71,80],exe:116,exist:46,explor:64,extrapol:95,faq:54,fault:48,featur:64,few:67,fflag:29,fgmax:24,figur:54,file:[10,24,44,54,56,96,99,107,115,118],find:[10,54],finer:5,fix:[24,25,49,68,107],flag2refin:95,flag:[5,27,41,95,105],flow:[21,60],fly:53,fork:[23,68],format:50,formul:121,fort:[50,54],fortran:[19,21,28,29,84,89,96,113,118],found:44,friction:42,from:[10,14,16,17,19,23,56,61,64,68,71,81,94],full:21,fund:[4,58],further:76,futur:73,fvmhp:[14,30],galleri:[31,44,74],gaug:[32,79,94,117],gener:[19,69,107],geo:107,geoclaw:[11,12,19,21,33,34,35,49,55,93,95,97,98,102,107,111,112],geometri:75,geophys:21,get:[21,44,68,94],gfortran:[29,87],ghost:5,git:[23,36,37,65,66],github:[23,64,68],godunov:121,grid:[5,12,24,25,49,75,107],guid:[23,38,94],guidelin:69,hazard:34,hdf5:78,help:44,high:[21,121],hint:[34,54,92],histori:[64,67],how:[54,56],html:[8,56],imagediff:96,includ:9,independ:70,indic:77,inform:[69,72],initi:[5,82,90,118],input:[19,24,78,104,105],instal:[23,39,45,51,65,80,87,89,92,113,116],instanc:10,instruct:[23,39,84],integr:[67,96],intel:29,interact:[56,71],interfac:51,iplotclaw:56,ipython:[47,71],item:54,keep:37,latest:39,latex:56,latitud:35,launch:10,layout:84,level:23,licens:[4,40,58],limit:70,line:[56,71,96],link:18,list:71,local:[68,74,110],locat:32,log:10,longitud:35,machin:120,main:68,maintain:67,make:[54,64,68,80,109,116],makefil:[28,41,82,99],man:42,manual:[36,66],mapc2p:43,master:64,math:62,matlab:44,matplotlib:87,maxfram:44,maximum:107,merg:64,mesh:[5,21],mess:64,method:[0,1,2,3,21,121],might:64,mirror:64,model:[34,48,94,117],modifi:[23,99],modul:[77,91,92,106,108],monitor:[24,107],more:[28,64],most:23,motion:94,name:84,netcdf:[45,50,78],next:87,nose:87,note:15,notebook:[47,92],numpi:87,object:[75,103],obtain:87,okada:[48,94],onli:39,onlin:[36,66],openmp:49,option:[53,56,79,80,82],order:[21,84,89],other:[20,54,64,94],out:23,outdir:54,output:[24,25,41,44,45,49,50,60,78,79,96,99,104,105,107,116],overview:[21,33,64,65,103],own:[10,68,82],packag:[19,39,78,83],page:[36,66],paper:13,parallel:[51,75,80,81,88],paramet:[19,32,54,56,90,94,104,105,107],pass:80,patch:[68,75],path:44,pcolor:54,peopl:64,petclaw:[75,88],petsc:80,piec:84,pixel:96,plot:[3,10,19,21,24,32,33,35,41,44,45,52,53,54,55,56,71,80,81,96,103,109,116,119],plot_typ:3,plotclaw:44,point:[23,68],port:61,post:53,prerequisit:39,previou:57,print:105,printfram:56,problem:[7,61,82,90,118],process:[24,53],produc:56,propag:121,provid:54,pull:23,push:67,pyclaw:[19,21,39,58,59,60,61,62,63,68,70,71,74,75,77,78,81,84,85,86,87,88,90,91,96,97,98,113],pyflak:69,pylint:69,python:[17,21,56,87,92],q0002:50,qinit:[93,107,115],quantiti:[60,79],quick:[68,94],raw:50,readm:8,rebas:64,recent:[15,23],recov:64,refer:[77,92],refin:[5,12,21,27,95,107],region:[27,95,107],regress:[84,96],releas:[15,97,98],remot:23,repositori:[9,20,64,68],request:23,requir:[92,118],resolut:121,resourc:[21,36,66],restart:[60,99],result:[10,33,45,81,109],review:64,rewrit:64,richardson:95,riemann:[77,82,83,97,98,100,118],routin:[11,19,55,93,102,111,112],rst:8,run:[26,33,39,60,62,69,71,80,81,104,105,116],sage:[62,92],sampl:[106,108],save:109,script:82,seafloor:94,sealevel:101,search:44,seri:67,serial:[69,75,88],servic:10,set:[23,33,39,44,54,56,68,82,94,101],setaux:[102,118],setplot:[44,54,56,103],setrun:[19,32,94,104,105,106,107,108],sever:64,shallow:83,share:[64,109],sharpclaw:[21,86],shoot:44,should:51,simul:60,simultan:69,singl:64,size:54,slip:48,softwar:[4,13],solut:[54,60,85],solv:90,solver:[51,60,77,82,83,86,90,100,118],some:[54,64,84,117],someth:54,sourc:[48,82,94,117,118,121],space:121,spatial:118,special:[3,105],specif:[24,69,90,118],specifi:[54,56,94,95,103,104,105,107,118],sphere:12,sphinx:110,src1d:[111,118],src:[112,118],start:[21,94],state:88,step:[87,118],stop:10,substanti:68,summari:[36,64,66],surfac:35,t0002:50,tabl:[21,77,114],term:[42,82,118,121],test:[23,39,69,80,84,87,96,113],than:54,thi:[4,38],thing:64,tide:117,time:[104,105,107,118],tip:[28,35,80,84],titl:54,tool:[17,21,32,35,96],top:23,topo:94,topographi:[33,94,107,115,117],track:37,transfer:10,travi:96,troubl:[44,116],troubleshoot:[89,116],trunk:[64,67],tsunami:[34,94,117],tutori:[36,66,90,92],tvd:70,understand:60,updat:[38,64],ups:64,use:51,user:[12,51,118],using:[34,44,118],util:91,valu:[24,60],vari:118,variabl:[29,39,41,82],version:[28,37,39,57],view:10,virtual:120,visclaw:[21,53,97,98],visit:119,visual:21,wai:39,wakari:62,want:64,water:[35,83],wave:[100,121],web:10,webpag:[10,38,109],what:[54,56],when:84,which:51,without:39,work:[4,71,73,118],workflow:[23,36,64,66,67],write:[69,82,84],you:[64,84],your:[10,23,39,64,68,80,82,87,109,113]}}) 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                                                                                                                                                                                                                with latitude when coordinate_system == 2).

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                                                                                                                                                                                                                (an ocean at rest remains at rest).

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                                                                                                                                                                                                                see Using src1d for source terms with AMRClaw.

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                                                                                                                                                                                                                diff --git a/v5.2.x/.buildinfo b/v5.2.x/.buildinfo index 0aead167dd..3ddaa44802 100644 --- a/v5.2.x/.buildinfo +++ b/v5.2.x/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. 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c4ff7ad89bb4d9aa94512b02a26dc282526e86cb..0c396cd4c379d0d90c59f2dba463a7ce6fae4a1c 100644 GIT binary patch delta 23 fcmaEHg89V><_&g?97*Yw*;T1oWt-g?l^z2CeWwY@ delta 23 fcmaEHg89V><_&g?99iWRX1Ru0S)1J$l^z2CdQ}Nt diff --git a/v5.2.x/.doctrees/visit_plotting.doctree b/v5.2.x/.doctrees/visit_plotting.doctree index 8d9219bd7e6d24db6da39399e26ad23f29ff00d5..369a7269ca650e449f02e5beb453924d115f2755 100644 GIT binary patch delta 21 ccmZp7YIoY;z{ru5UYT8$npL*hgK@t+09CRF(f|Me delta 21 ccmZp7YIoY;z{rtRUSXDNn3c8JgK@t+08(HFX8-^I diff --git a/v5.2.x/.doctrees/vm.doctree b/v5.2.x/.doctrees/vm.doctree index b778f715626396dd5b5bed1004d77c11b77a127d..84a1a3bc743853a107fad1b6a01f4dab5b8431eb 100644 GIT binary patch delta 21 ccmX@8bWmx71|vsOdS!N1YF62114cms09LmL82|tP delta 21 ccmX@8bWmx71|vsSd4*Z7VOG{=14cms08?cKt^fc4 diff --git a/v5.2.x/.doctrees/wp_algorithms.doctree b/v5.2.x/.doctrees/wp_algorithms.doctree index 45706a3c00f2c6663c0b9ad41f4a7e9fad584097..30b3ca6e57000da28a8895c34e3c065e73ba7fba 100644 GIT binary patch delta 23 fcmdn^j&b8V#tn9i97*Yw*;T1oWt-g?UzY*^dsYel delta 23 fcmdn^j&b8V#tn9i99iWRX1Ru0S)1J$UzY*^cmxTP diff --git a/v5.2.x/b4step_defaults.html b/v5.2.x/b4step_defaults.html index bf8ea55cd0..257cae3da0 100644 --- a/v5.2.x/b4step_defaults.html +++ b/v5.2.x/b4step_defaults.html @@ -82,17 +82,17 @@

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                                                                                                                                                                                                                  as needed. Remember to change to Makefile to point to the proper version.

                                                                                                                                                                                                                  $CLAW/classic/src/1d/b4step1.f90:

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                                                                                                                                                                                                                  +

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                                                                                                                                                                                                                  $CLAW/classic/src/2d/b4step2.f90:

                                                                                                                                                                                                                  -

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                                                                                                                                                                                                                  $CLAW/classic/src/3d/b4step3.f90:

                                                                                                                                                                                                                  -

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                                                                                                                                                                                                                  with latitude when coordinate_system == 2).

                                                                                                                                                                                                                  $CLAW/geoclaw/src/2d/shallow/b4step2.f90:

                                                                                                                                                                                                                  -

                                                                                                                                                                                                                  System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpjwx6m1jj/5fcd911597685d99d94bee49a3dcea97a4bab85a/b4step_defaults.rst, line 48)

                                                                                                                                                                                                                  +

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                                                                                                                                                                                                                  Include file ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/geoclaw/src/2d/shallow/b4step2.f90’ not found or reading it failed

                                                                                                                                                                                                                  diff --git a/v5.2.x/galleries.html b/v5.2.x/galleries.html index 541733c02b..43f722bb5a 100644 --- a/v5.2.x/galleries.html +++ b/v5.2.x/galleries.html @@ -85,19 +85,19 @@

                                                                                                                                                                                                                  Navigation

                                                                                                                                                                                                                  See also IPython notebook examples.

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                                                                                                                                                                                                                  -

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                                                                                                                                                                                                                  diff --git a/v5.2.x/genindex.html b/v5.2.x/genindex.html index 41c7be6516..4be04f29bf 100644 --- a/v5.2.x/genindex.html +++ b/v5.2.x/genindex.html @@ -970,15 +970,17 @@

                                                                                                                                                                                                                  T

                                                                                                                                                                                                                1. tfluct_solver (pyclaw.sharpclaw.solver.SharpClawSolver attribute)
                                                                                                                                                                                                                  2. -

                                                                                                                                                                                                                  Galleries of all Clawpack applications

                                                                                                                                                                                                              - +
                                                                                                                                                                                                              -

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                                                                                                                                                                                                              Problems with “include” directive path: -InputError: [Errno 2] No such file or directory: ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpjwx6m1jj/5fcd911597685d99d94bee49a3dcea97a4bab85a/git_links.inc’.

                                                                                                                                                                                                              +InputError: [Errno 2] No such file or directory: ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/5fcd911597685d99d94bee49a3dcea97a4bab85a/git_links.inc’.

                                                                                                                                                                                                              .. include:: git_links.inc
                                                                                                                                                                                                              diff --git a/v5.2.x/kmltools_module.html b/v5.2.x/kmltools_module.html index ef62a33b10..783784f9dc 100644 --- a/v5.2.x/kmltools_module.html +++ b/v5.2.x/kmltools_module.html @@ -107,6 +107,7 @@

                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                            • pcolorcells_for_kml - version of pcolormesh with appropriate dpi and size

                                                                                                                                                                                                            • png2kml - create kml file wrapping a png figure to be viewed on GE

                                                                                                                                                                                                            • kml_build_colorbar - create a colorbar to display on GE

                                                                                                                                                                                                              • +

                                                                                                                                                                                                            • topo2kmz - create kmz file showing onshore and offshore topography

                                                                                                                                                                                                            • kml_header - used internally

                                                                                                                                                                                                            • kml_footer - used internally

                                                                                                                                                                                                            • kml_region - used internally

                                                                                                                                                                                                              • @@ -216,7 +217,7 @@

                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              -clawpack.geoclaw.kmltools.kml_build_colorbar(cb_filename, cmap, cmin=None, cmax=None, norm=None, label=None, title=None, extend='neither')
                                                                                                                                                                                                              +clawpack.geoclaw.kmltools.kml_build_colorbar(cb_filename, cmap, cmin=None, cmax=None, norm=None, label=None, title=None, extend='neither', close_figs=True)

                                                                                                                                                                                                              Make a png file with a colorbar corresponding to cmap, norm. cmin, cmax are used only if nrm is not provided.

                                                                                                                                                                                                              @@ -328,7 +329,7 @@

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                                                                                                                                                                                                              Internally the value dpi (dots per inch) for the png file is determined so that it is at least 16 and so that:

                                                                                                                                                                                                              -

                                                                                                                                                                                                              System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

                                                                                                                                                                                                              +

                                                                                                                                                                                                              System Message: ERROR/3 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

                                                                                                                                                                                                              Unexpected indentation.

                                                                                                                                                                                                              @@ -336,7 +337,7 @@

                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              dpi * y_inches = dcp * y_cells

                                                                                                                                                                                                              -

                                                                                                                                                                                                              System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 38)

                                                                                                                                                                                                              +

                                                                                                                                                                                                              System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 38)

                                                                                                                                                                                                              Block quote ends without a blank line; unexpected unindent.

                                                                                                                                                                                                              where x_cells, y_cells are the number of cells in each direction.

                                                                                                                                                                                                              @@ -346,14 +347,14 @@

                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              annotate the figure befor saving it as a png file, which should then be done with:

                                                                                                                                                                                                              -

                                                                                                                                                                                                              System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

                                                                                                                                                                                                              +

                                                                                                                                                                                                              System Message: ERROR/3 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

                                                                                                                                                                                                              Unexpected indentation.

                                                                                                                                                                                                              plt.savefig(png_filename, transparent=True, dpi=kml_dpi)

                                                                                                                                                                                                              -

                                                                                                                                                                                                              System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

                                                                                                                                                                                                              +

                                                                                                                                                                                                              System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

                                                                                                                                                                                                              Block quote ends without a blank line; unexpected unindent.

                                                                                                                                                                                                              The png_extent is needed in construcing a kml file to display the @@ -464,6 +465,39 @@

                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              Color is green by default.

                                                                                                                                                                                                              +
                                                                                                                                                                                                              +
                                                                                                                                                                                                              +clawpack.geoclaw.kmltools.topo2kmz(topo, zlim=(-20, 20), mask_outside_zlim=True, sea_level=0.0, name='topo', force_dry=None, close_figs=True)
                                                                                                                                                                                                              +

                                                                                                                                                                                                              Create kmz file showing onshore and offshore topography as separate layers. +Currently not very flexible but is useful in quickly creating kmz files +to open on Google Earth showing the onshore topography and offshore +bathymetry as two separate layers. Constant colors on rectangular grid +cells should be properly rendered to ease exploration of DEMs. +A colorbar png file is also created and included in the kmz file.

                                                                                                                                                                                                              +
                                                                                                                                                                                                              +
                                                                                                                                                                                                              Input
                                                                                                                                                                                                              +
                                                                                                                                                                                                                +

                                                                                                                                                                                                              • topo should be a topotools.Topography object,

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • zlim is the elevation z limits for choosing the color map

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • mask_outside_zlim if True, suppress plotting outsize zlim

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • sea_level is the break between water and land colors

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • name is used in the kml menu and file name

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • force_dry is currently not used

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • close_figs to close the pyplot figures after making png files

                                                                                                                                                                                                                • +
                                                                                                                                                                                                              +
                                                                                                                                                                                                              +
                                                                                                                                                                                                              Future
                                                                                                                                                                                                              +

                                                                                                                                                                                                              +
                                                                                                                                                                                                              +
                                                                                                                                                                                                              +

                                                                                                                                                                                                              System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.topo2kmz, line 18)

                                                                                                                                                                                                              +

                                                                                                                                                                                                              Field list ends without a blank line; unexpected unindent.

                                                                                                                                                                                                              +
                                                                                                                                                                                                              +

                                                                                                                                                                                                              If force_dry is an array of the same shape as topo.Z then another png +and kml file are created for land that is below sea_level but where +force_dry = True.

                                                                                                                                                                                                              +
                                                                                                                                                                                                              + diff --git a/v5.2.x/objects.inv b/v5.2.x/objects.inv index 6f57fa1ec2523e4078b7270b201188d34f2279ef..048d736b9d44bb228d8644eeeb229977b8015d45 100644 GIT binary patch delta 9624 zcmV;JC1=|EOo2_1h8M^IqV~?%>l_;hg7w(5S>$YX&(7LT&XJwCe}9Qs6E&WNMA!p+ z_KjLX(}(~%F0!JkUk*KQiq=2=3p9rHQZHE04r~tJ( zzA${$R4L1M8L$0j#Pfz%o-vF3kyoHn6j9xg@ZlqNn0og{rs6P|p`Sk66aR|D8}trC5Fx6eGUi|S(q zEU`D$^_ScGe;>VLd9zA}OB~A;f7imsa#R|O8D+3In*A2urmC}w7u~l&vtiUp6Uqn!yT{vV8M@Q)23M> zdenwhelX*WADmK5`pbcEimywSFGtJLocpQ#1L%2Cf0~yq3_q-45xnrw(n|W0G0%W& zTU3!3QQ7Zt||tH0^86diSDuYdys!3SWphd;dXj9X?b z=22dVN&Asyt>?C^vUmY#Tse3?`W@8jLs2w)stvEW!yTffh|gZp{Pw8dm!rweP}*cg zg`uZ7T!fi$7^V(5f)K1)%~}e(4d@R{0{r7qit?BwlYgtI~lHIf^$9l%#bNWvs!SiJJpg z8-pG|1=x+m_5gaQZxSA-2bL`d6CE`#7y}bJ;d+!`hPr2uP-GZYmP4iaW3&veJQ5mN 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zSJG!?A!&{JsKHoH(Yy$i#~O9TRxN1*xy}Zi{b%Px#70K?G@^|7FM6$ju4cA9B$SKo z@QXr%i%yCWd}From the command lineList of built-in examples

                                                                                                                                                                                                              You can see results from many of the examples in the Galleries of all Clawpack applications.

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                                                                                                                                                                                                              PyClaw is:

                                                                                                                                                                                                              PyClaw Documentation

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                                                                                                                                                                                                              References and tutorialsMatplotlib gallery

                                                                                                                                                                                                            • `LeVeque’s class notes

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                                                                                                                                                                                                              the initial conditions as desired.

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                                                                                                                                                                                                              qinit data file parameters.

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86,87,88,89,90,91,93,94,95,96,98,99,100,102,103,105,107,110,111,112,113,121,123,125,126,129],white:43,whith:65,who:[17,20,26,31,37,42,69,71,72],whole:[73,83,84,88],whose:[3,58,65,86,87,88,110,111,123],why:[68,72,88],wide:96,wider:58,width:[25,43,52,54,79,86,88,92,98,99,112,114],wiki:91,wikipedia:88,wind:123,window:[10,25,42,48,60,69,96],wisdom:43,wise:[73,90],wish:[4,10,11,20,24,28,34,37,42,48,56,57,73,81,86,90,91,93,98,105,108,115,117,118],within:[5,12,29,55,58,66,85,88,95,99,106,109,115,123],without:[12,20,22,24,30,34,37,43,44,45,48,58,60,62,68,73,74,82,83,95,96,112,114,124,126],won:[10,65,88,123],word:[68,69,83,88,98],work:[3,7,10,12,17,18,20,22,24,26,28,29,30,35,37,39,41,42,43,48,50,52,53,58,62,63,64,67,68,70,72,73,74,81,82,83,84,87,90,91,96,98,99,100,104,106,109,110,111,113,115,121,128],workflow:[72,76,81],workspac:[48,92],world:[37,46,81,84],worri:68,worst:107,worth:92,worthwhil:86,would:[2,3,10,12,23,24,26,45,54,58,62,64,67,68,73,79,83,88,95,98,107,109,110,121,126],wpalg:13,wrap:[43,62,65,79,90,95],wrapper:123,write:[25,40,46,54,55,57,64,67,68,69,71,72,76,79,80,83,84,89,98,112,114,123],write_:82,write_aux:[82,89],write_aux_alwai:[64,67],write_aux_init:[64,67],write_input_data:26,write_p:89,written:[5,8,25,30,43,44,54,55,58,62,68,82,83,86,96,110,111,112,113,114,123,126],wrong:[48,68,83],www:[4,10,13,25,41,44,49,62,65,66,79,81,84,98,123],x_cell:43,x_edg:43,x_i:[106,126,129],x_inch:43,x_mask:123,xarr:79,xarrai:123,xarray_d:123,xclaw:[28,67],xclawcmd:67,xclawerr:67,xclawout:67,xcode:42,xdir:67,xiaom:25,xleft:[111,112],xlf:91,xlimit:[0,34],xllcenter:98,xllcorner:121,xlow:54,xlower:[0,3,12,20,23,65,98,112,114,121,123,126],xlowerg:65,xmax:0,xmin:0,xpoint:113,xrang:86,xtick:38,xupper:[0,20,98,112,114,123],xxdiff:100,xxxx:48,xylim:25,xzvf:42,y_cell:43,y_edg:43,y_inch:43,year:[4,13,20,43,81,101],yellow:[43,58,69],yellow_red_blu:58,yes:48,yet:[1,10,18,37,43,57,90,110,112,128],yianni:62,yield:3,yleft:[111,112],ylimit:[0,34,109],yllcenter:98,yllcorner:121,ylow:54,ylower:[3,20,23,65,98,112,121,123],ylowerg:65,ymax:0,ymin:0,yml:100,yong:13,you:[0,3,4,10,11,12,14,16,17,18,20,21,23,24,26,28,30,31,34,36,39,40,41,42,43,45,48,49,50,51,52,53,54,55,56,57,58,60,62,64,65,66,67,69,70,71,72,73,75,76,78,81,82,83,84,85,86,87,90,91,92,93,94,96,98,102,105,107,108,109,112,113,114,115,116,117,118,121,124,125,126,128],your:[5,11,12,17,18,22,28,31,34,39,41,49,50,53,57,58,60,62,63,64,65,66,69,70,71,73,75,76,80,81,83,88,93,94,96,97,98,99,102,108,117,118,121,124,126],yourdomain:[69,72],yourself:[31,34,51,68,72],ypoint:113,yum:69,yupper:[20,98,112,123],yuri:69,z_format:123,zaytsev:69,zero:[3,12,25,31,43,48,64,86,87,92,94,107],zip:[9,98],zlower:20,zone:[37,43,111,112],zoom:98,zsh:84,zupper:20,zvar:123},titles:["ClawPlotAxes","ClawPlotData","ClawPlotFigure","ClawPlotItem","About this software","Adaptive mesh refinement (AMR) algorithms","AMRClaw","AMRClaw for 1d problems","Application documentation","Clawpack Applications repository","Amazon Web Services EC2 Clawpack AMI","b4step default routines","Boundary conditions","Bibliography","Examples from the book FVMHP","Recent changes \u2014 release notes","Changes to master since v5.2.1","Converting from Clawpack 4.3 to 4.6","Converting from Clawpack 4.6 to 5.0","Clawpack 4.x links","Changes in Clawpack 5.0","Clawpack components","Full Table of Contents","current_data","Developers\u2019 Guide","dtopotools module for moving topography","Fixed grid monitoring","Fixed grid output","Running an example","Flagging cells for adaptive refinement","Fortran version","Fortran Compilers","FVMHP book","Galleries of all Clawpack applications","Gauges","GeoClaw","geoclaw.util module of utility functions","Cautionary Hints on using GeoClaw","GeoClaw plotting tools","git resources","Keeping track of git versions","Guide for updating this documentation","Installation instructions","kmltools module of utility functions","License","Clawpack Makefiles","Manning friction term","The mapc2p function","Plotting using Matlab","Using NetCDF output","Creating a new application directory","IPython notebook examples","Earthquake sources: Fault slip and the Okada model","Using OpenMP","Output data formats","Which Clawpack solver should I use?","Plotting examples","Visclaw Plotting options","Plotting hints and FAQ","Plotting routines for GeoClaw","Plotting options in Python","Previous versions of Clawpack","About PyClaw","PyClaw Basics","Understanding Pyclaw Classes","Porting a problem from Clawpack 4.6.x to PyClaw","Running PyClaw in the cloud","Pyclaw Controller Class","Development workflow","Installing and configuring git","git resources","Maintainer workflow","Contributing to PyClaw code development","General information for developers","Pyclaw Limiters","Working with PyClaw\u2019s built-in examples","Information for developers","Future work","Building the PyClaw gallery locally","PyClaw Geometry","Going Further","Pyclaw","Pyclaw Input/Output Package","PyClaw output","Running in parallel","Plotting PyClaw results","Setting up your own problem","Riemann Solver Package","Conventions for coding and documenting PyClaw","PyClaw Solutions","Using PyClaw\u2019s solvers: Classic and SharpClaw","Installing PyClaw","PyClaw State","Troubleshooting","PyClaw tutorial: Solve the acoustics equations","Pyclaw Utility Module","Python Hints","qinit default routines","Quick start guide for tsunami modeling","AMR refinement criteria","Regression testing","Release 5.0.0","Release 5.1.0","Release 5.2.0","Release 5.2.1","Checkpointing and restarting","Riemann solvers","Setting sealevel","setaux default routines","Using setplot.py to specify the desired plots","Specifying classic run-time parameters in setrun.py","Specifying AMRClaw run-time parameters in setrun.py","Sample setrun.py module for AMRClaw","Specifying GeoClaw parameters in setrun.py","Sample setrun.py module for classic Clawpack","Saving and sharing results","Compiling the Sphinx documentation locally","src1d default routines","src default routines","Testing your installation","Condensed Table of Contents","Topography data","Python tools for working with topo and dtopo","topotools module for working with topography data","Troubleshooting","Some sources of tsunami data","User files required for the Fortran code","Plotting with VisIt","Clawpack Virtual Machine","Wave-propagation 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this software","Adaptive mesh refinement (AMR) algorithms","AMRClaw","AMRClaw for 1d problems","Application documentation","Clawpack Applications repository","Amazon Web Services EC2 Clawpack AMI","b4step default routines","Boundary conditions","Bibliography","Examples from the book FVMHP","Recent changes \u2014 release notes","Changes to master since v5.2.1","Converting from Clawpack 4.3 to 4.6","Converting from Clawpack 4.6 to 5.0","Clawpack 4.x links","Changes in Clawpack 5.0","Clawpack components","Full Table of Contents","current_data","Developers\u2019 Guide","dtopotools module for moving topography","Fixed grid monitoring","Fixed grid output","Running an example","Flagging cells for adaptive refinement","Fortran version","Fortran Compilers","FVMHP book","Galleries of all Clawpack applications","Gauges","GeoClaw","geoclaw.util module of utility functions","Cautionary Hints on using GeoClaw","GeoClaw plotting tools","git resources","Keeping track of git versions","Guide for updating this documentation","Installation instructions","kmltools module of utility functions","License","Clawpack Makefiles","Manning friction term","The mapc2p function","Plotting using Matlab","Using NetCDF output","Creating a new application directory","IPython notebook examples","Earthquake sources: Fault slip and the Okada model","Using OpenMP","Output data formats","Which Clawpack solver should I use?","Plotting examples","Visclaw Plotting options","Plotting hints and FAQ","Plotting routines for GeoClaw","Plotting options in Python","Previous versions of Clawpack","About PyClaw","PyClaw Basics","Understanding Pyclaw Classes","Porting a problem from Clawpack 4.6.x to PyClaw","Running PyClaw in the cloud","Pyclaw Controller Class","Development workflow","Installing and configuring git","git resources","Maintainer workflow","Contributing to PyClaw code development","General information for developers","Pyclaw Limiters","Working with PyClaw\u2019s built-in examples","Information for developers","Future work","Building the PyClaw gallery locally","PyClaw Geometry","Going Further","Pyclaw","Pyclaw Input/Output Package","PyClaw output","Running in parallel","Plotting PyClaw results","Setting up your own problem","Riemann Solver Package","Conventions for coding and documenting PyClaw","PyClaw Solutions","Using PyClaw\u2019s solvers: Classic and SharpClaw","Installing PyClaw","PyClaw State","Troubleshooting","PyClaw tutorial: Solve the acoustics equations","Pyclaw Utility Module","Python Hints","qinit default routines","Quick start guide for tsunami modeling","AMR refinement criteria","Regression testing","Release 5.0.0","Release 5.1.0","Release 5.2.0","Release 5.2.1","Checkpointing and restarting","Riemann solvers","Setting sealevel","setaux default routines","Using setplot.py to specify the desired plots","Specifying classic run-time parameters in setrun.py","Specifying AMRClaw run-time parameters in setrun.py","Sample setrun.py module for AMRClaw","Specifying GeoClaw parameters in setrun.py","Sample setrun.py module for classic Clawpack","Saving and sharing results","Compiling the Sphinx documentation locally","src1d default routines","src default routines","Testing your installation","Condensed Table of Contents","Topography data","Python tools for working with topo and dtopo","topotools module for working with topography data","Troubleshooting","Some sources of tsunami data","User files required for the Fortran code","Plotting with VisIt","Clawpack Virtual Machine","Wave-propagation 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                                                                                                                                                                                                              see Using src1d for source terms with AMRClaw.

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                                                                                                                                                                                                              -plot(axes=None, contour_levels=None, contour_kwargs={}, limits=None, cmap=None, add_colorbar=True, plot_box=False, fig_kwargs={}, data_break=0.0, cb_kwargs={})
                                                                                                                                                                                                              +plot(axes=None, contour_levels=None, contour_kwargs={}, limits=None, cmap=None, add_colorbar=True, plot_box=False, long_lat=True, fig_kwargs={}, data_break=0.0, cb_kwargs={})

                                                                                                                                                                                                              Plot the topography.

                                                                                                                                                                                                              Input
                                                                                                                                                                                                              @@ -320,6 +320,9 @@

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                                                                                                                                                                                                            • fig_kwargs (dict) - keyword arguments to be passed to figure.

                                                                                                                                                                                                            • plot_box (bool or color specifier) - If evaluates to True, plot a box around limits of this topo.

                                                                                                                                                                                                              • +

                                                                                                                                                                                                            • long_lat (bool) - If this is a longitude-latitude plot then set the +aspect of the plot to compensate for stretching. If not then the +aspect is set to “equal”.

                                                                                                                                                                                                            • data_break (float) - when default cmap is used, the value to use to break between water and land colormaps. Defaults to 0., but for some topo files may need to use e.g. 0.01 diff --git a/v5.3.x/.buildinfo b/v5.3.x/.buildinfo index bcc87ab689..d669449c26 100644 --- a/v5.3.x/.buildinfo +++ b/v5.3.x/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. 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b/v5.3.x/.doctrees/visit_plotting.doctree index d17e668e4c2b3dac69b4cd2dfb4593c131059dc7..a17ab173dbd8c128a0716bda166b013d2b6ee9ee 100644 GIT binary patch delta 21 ccmZp7YIoY;z{ru5UYT8$npL*hgK@t+09CRF(f|Me delta 21 ccmZp7YIoY;z{rtRUSXDNn3c8JgK@t+08(HFX8-^I diff --git a/v5.3.x/.doctrees/vm.doctree b/v5.3.x/.doctrees/vm.doctree index 4c1fec96cd8f47de87df7a565144eb757fea81b0..332bb2508b960142181b3f431cd3940bdd2a2680 100644 GIT binary patch delta 21 ccmX@8bWmx71|vsOdS!N1YF62114cms09LmL82|tP delta 21 ccmX@8bWmx71|vsSd4*Z7VOG{=14cms08?cKt^fc4 diff --git a/v5.3.x/.doctrees/wp_algorithms.doctree b/v5.3.x/.doctrees/wp_algorithms.doctree index 96414306e0ad2a38d6e5bddb1be1f250ecededcc..b90444e3ac259939311ae8d44db81fef316633d2 100644 GIT binary patch delta 23 fcmdn^j&b8V#tn9i97*Yw*;T1oWt-g?UzY*^dsYel delta 23 fcmdn^j&b8V#tn9i99iWRX1Ru0S)1J$UzY*^cmxTP diff --git a/v5.3.x/b4step_defaults.html b/v5.3.x/b4step_defaults.html index 736ecf6ad7..199b2b0e1c 100644 --- a/v5.3.x/b4step_defaults.html +++ b/v5.3.x/b4step_defaults.html @@ -82,17 +82,17 @@

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                                                                                                                                                                                                              as needed. Remember to change to Makefile to point to the proper version.

                                                                                                                                                                                                              $CLAW/classic/src/1d/b4step1.f90:

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                                                                                                                                                                                                              $CLAW/classic/src/2d/b4step2.f90:

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                                                                                                                                                                                                              $CLAW/classic/src/3d/b4step3.f90:

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                                                                                                                                                                                                              with latitude when coordinate_system == 2).

                                                                                                                                                                                                              $CLAW/geoclaw/src/2d/shallow/b4step2.f90:

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                                                                                                                                                                                                              diff --git a/v5.3.x/galleries.html b/v5.3.x/galleries.html index 5476b40caa..b40cdca6a1 100644 --- a/v5.3.x/galleries.html +++ b/v5.3.x/galleries.html @@ -85,19 +85,19 @@

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                                                                                                                                                                                                              Galleries of all Clawpack applications

                                                                                                                                                                                                              See also IPython notebook examples.

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                                                                                                                                                                                                              diff --git a/v5.3.x/genindex.html b/v5.3.x/genindex.html index 42b10903eb..8e21fbd70e 100644 --- a/v5.3.x/genindex.html +++ b/v5.3.x/genindex.html @@ -970,15 +970,17 @@

                                                                                                                                                                                                              T

                                                                                                                                                                                                            • tfluct_solver (pyclaw.sharpclaw.solver.SharpClawSolver attribute)
                                                                                                                                                                                                              • -

                                                                                                                                                                                                            - +
                                                                                                                                                                                                            • time_integrator (pyclaw.sharpclaw.solver.SharpClawSolver attribute)
                                                                                                                                                                                                            • topo1writer() (in module clawpack.geoclaw.topotools)
                                                                                                                                                                                                            • topo2kml() (in module clawpack.geoclaw.kmltools) +
                                                                                                                                                                                                              • +
                                                                                                                                                                                                            • topo2kmz() (in module clawpack.geoclaw.kmltools)
                                                                                                                                                                                                            • topo2writer() (in module clawpack.geoclaw.topotools)
                                                                                                                                                                                                              • diff --git a/v5.3.x/geoclaw_util_module.html b/v5.3.x/geoclaw_util_module.html index d7df70b485..27829d965a 100644 --- a/v5.3.x/geoclaw_util_module.html +++ b/v5.3.x/geoclaw_util_module.html @@ -102,7 +102,7 @@

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                                                                                                                                                                                                              Note: If using this to initialize a radially-symmetric 2d velocity on the sphere based on a radial velocity U(r), symmetric about (x0, y0), set:

                                                                                                                                                                                                              -

                                                                                                                                                                                                              System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/util.py:docstring of clawpack.geoclaw.util.bearing, line 9)

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                                                                                                                                                                                                              System Message: ERROR/3 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/util.py:docstring of clawpack.geoclaw.util.bearing, line 9)

                                                                                                                                                                                                              Unexpected indentation.

                                                                                                                                                                                                              diff --git a/v5.3.x/kmltools_module.html b/v5.3.x/kmltools_module.html index 6d1c4ae480..74db7d39b8 100644 --- a/v5.3.x/kmltools_module.html +++ b/v5.3.x/kmltools_module.html @@ -104,6 +104,7 @@

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                                                                                                                                                                                                            • pcolorcells_for_kml - version of pcolormesh with appropriate dpi and size

                                                                                                                                                                                                            • png2kml - create kml file wrapping a png figure to be viewed on GE

                                                                                                                                                                                                            • kml_build_colorbar - create a colorbar to display on GE

                                                                                                                                                                                                              • +

                                                                                                                                                                                                            • topo2kmz - create kmz file showing onshore and offshore topography

                                                                                                                                                                                                            • kml_header - used internally

                                                                                                                                                                                                            • kml_footer - used internally

                                                                                                                                                                                                            • kml_region - used internally

                                                                                                                                                                                                              • @@ -213,7 +214,7 @@

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                                                                                                                                                                                                              -clawpack.geoclaw.kmltools.kml_build_colorbar(cb_filename, cmap, cmin=None, cmax=None, norm=None, label=None, title=None, extend='neither')
                                                                                                                                                                                                              +clawpack.geoclaw.kmltools.kml_build_colorbar(cb_filename, cmap, cmin=None, cmax=None, norm=None, label=None, title=None, extend='neither', close_figs=True)

                                                                                                                                                                                                              Make a png file with a colorbar corresponding to cmap, norm. cmin, cmax are used only if nrm is not provided.

                                                                                                                                                                                                              @@ -325,7 +326,7 @@

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                                                                                                                                                                                                              Internally the value dpi (dots per inch) for the png file is determined so that it is at least 16 and so that:

                                                                                                                                                                                                              -

                                                                                                                                                                                                              System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

                                                                                                                                                                                                              +

                                                                                                                                                                                                              System Message: ERROR/3 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

                                                                                                                                                                                                              Unexpected indentation.

                                                                                                                                                                                                              @@ -333,7 +334,7 @@

                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              dpi * y_inches = dcp * y_cells

                                                                                                                                                                                                              -

                                                                                                                                                                                                              System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 38)

                                                                                                                                                                                                              +

                                                                                                                                                                                                              System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 38)

                                                                                                                                                                                                              Block quote ends without a blank line; unexpected unindent.

                                                                                                                                                                                                              where x_cells, y_cells are the number of cells in each direction.

                                                                                                                                                                                                              @@ -343,14 +344,14 @@

                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              annotate the figure befor saving it as a png file, which should then be done with:

                                                                                                                                                                                                              -

                                                                                                                                                                                                              System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

                                                                                                                                                                                                              +

                                                                                                                                                                                                              System Message: ERROR/3 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

                                                                                                                                                                                                              Unexpected indentation.

                                                                                                                                                                                                              plt.savefig(png_filename, transparent=True, dpi=kml_dpi)

                                                                                                                                                                                                              -

                                                                                                                                                                                                              System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

                                                                                                                                                                                                              +

                                                                                                                                                                                                              System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

                                                                                                                                                                                                              Block quote ends without a blank line; unexpected unindent.

                                                                                                                                                                                                              The png_extent is needed in construcing a kml file to display the @@ -461,6 +462,39 @@

                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              Color is green by default.

                                                                                                                                                                                                              +
                                                                                                                                                                                                              +
                                                                                                                                                                                                              +clawpack.geoclaw.kmltools.topo2kmz(topo, zlim=(-20, 20), mask_outside_zlim=True, sea_level=0.0, name='topo', force_dry=None, close_figs=True)
                                                                                                                                                                                                              +

                                                                                                                                                                                                              Create kmz file showing onshore and offshore topography as separate layers. +Currently not very flexible but is useful in quickly creating kmz files +to open on Google Earth showing the onshore topography and offshore +bathymetry as two separate layers. Constant colors on rectangular grid +cells should be properly rendered to ease exploration of DEMs. +A colorbar png file is also created and included in the kmz file.

                                                                                                                                                                                                              +
                                                                                                                                                                                                              +
                                                                                                                                                                                                              Input
                                                                                                                                                                                                              +
                                                                                                                                                                                                                +

                                                                                                                                                                                                              • topo should be a topotools.Topography object,

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • zlim is the elevation z limits for choosing the color map

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • mask_outside_zlim if True, suppress plotting outsize zlim

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • sea_level is the break between water and land colors

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • name is used in the kml menu and file name

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • force_dry is currently not used

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • close_figs to close the pyplot figures after making png files

                                                                                                                                                                                                                • +
                                                                                                                                                                                                              +
                                                                                                                                                                                                              +
                                                                                                                                                                                                              Future
                                                                                                                                                                                                              +

                                                                                                                                                                                                              +
                                                                                                                                                                                                              +
                                                                                                                                                                                                              +

                                                                                                                                                                                                              System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.topo2kmz, line 18)

                                                                                                                                                                                                              +

                                                                                                                                                                                                              Field list ends without a blank line; unexpected unindent.

                                                                                                                                                                                                              +
                                                                                                                                                                                                              +

                                                                                                                                                                                                              If force_dry is an array of the same shape as topo.Z then another png +and kml file are created for land that is below sea_level but where +force_dry = True.

                                                                                                                                                                                                              +
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zxZd-KF=R>XU_1Nv7Pr~BhOq3LP~xygx#=)}4uHK=F+?-!0X?pNt)xCph}iy~B|^{| z_0hr#H^((WES=9-@95<|G>|JX=(j&x4kI=Msashha5e8p9J-m=_K;BQki##m647rk zdP=Ln+z%>FzyYZOyv_!Y>h3?YwD%Z%%Nw7>&T;NfFpOXG_I>9=P+EF0u2`DKh1G<# zu3+qU&MoR+^QP-{35Kdkx9DNBcfKdG-wiHLyDT_}z&Jeoj)n7GkKYs>TMn~(ez5Fl zdDOzkdhnr3NYWoa>T{ cBl;NBM{qsooqkB`z!Puh_rg^9f5mt-From the command lineList of built-in examples

                                                                                                                                                                                                              You can see results from many of the examples in the Galleries of all Clawpack applications.

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                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              PyClaw Documentation

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                                                                                                                                                                                                              References and tutorialsMatplotlib gallery

                                                                                                                                                                                                            • `LeVeque’s class notes

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:[27,93,109],critic:[41,77,103],crop:120,cross:25,crucial:118,cse:21,csh:78,csv:26,csvfault:26,ctrl:60,cube:49,current:[3,10,17,19,24,25,26,27,30,32,35,36,38,44,49,50,52,55,60,62,73,77,78,84,86,89,92,93,94,101,102,104,106,107,109,110,111,118,120,122],current_data:[0,3,22,35,60],curv:[3,22,35],custom:[0,10,12,17,19,49,56,59,67,74,80],custom_bc:80,cut:108,cutoff:[5,109],cvs:41,cxx:78,cyber:13,cygwin:[43,69],cython:78,dai:[5,10,41],dalcin:[64,82],dam:71,damag:[5,45,64],damian:43,damiansra:80,danger:25,darker:41,darryl:13,dart:[22,92],dash:[3,78],daspect:49,dat:26,data:[0,1,3,22,24,26,27,29,31,33,35,36,37,41,42,44,45,46,49,59,60,61,62,64,66,69,73,77,79,81,83,84,86,89,91,92,93,96,98,99,101,103,104,109,111,117,119,124],data_break:120,data_typ:89,databas:[10,26,89,92,118],datadir:101,dataset:[120,122],date:[21,25,31,37,41,42,46,60,121],date_tim:37,datetim:37,datum:[37,38,81,104,110,122],dave:26,david:[4,13,64,75,82,84],dawson:13,daylight:44,dcp:44,deal:[26,38,59,77,78,86,120],dealloc:82,dealt:27,debian:90,debug:[22,32,46,55,77,86,94,107,109],debugg:60,decid:[66,84],decim:[37,44],decis:41,declar:[17,19,86,123],decompos:[55,103,126],decomposit:107,decor:89,deduc:118,deep:110,deeper:110,deepli:88,def:[0,1,3,35,41,60,66,73,77,80,82,84,109,111],default_tfluct:84,defenc:4,defin:[0,1,3,5,19,22,24,26,27,30,32,44,46,49,53,60,62,66,69,73,79,80,82,83,84,86,88,89,93,96,103,109,111,120,121,123,126],definit:[26,49,66,82,93,99],deform:[13,26,53,122],deg2dm:44,degre:[26,37,41,44,53,92],delet:[17,25,35,92,102],delimit:[26,82],delin:110,delta:[70,73,80,82,84,103,120,123,126],delta_h:81,delta_hu:81,delta_i:120,delta_limit:120,delta_x:120,dem:120,demo:[52,78],demonstr:[9,52,71,78],denot:[5,19,35,103,120],densiti:[69,77,81,86,88,108,109,123],depart:4,depdend:70,depend:[3,10,12,25,26,27,29,30,31,32,36,38,41,46,47,49,60,65,81,83,84,89,92,93,110,120,121,123,126],deprec:[26,28,100,110,120],depth:[4,12,13,19,22,26,27,36,38,47,53,61,92,104,110,118],deriv:[45,53,64,69,74,75,86,94],describ:[3,4,5,6,10,12,16,20,23,25,26,27,29,30,36,37,38,41,42,43,44,46,49,53,55,56,59,60,61,73,83,89,92,93,94,103,104,106,107,108,110,118,119,120,122,123,126],descript:[3,4,19,30,44,49,59,82,89,92,93,103,110,118,126],design:[4,24,25,41,64,66,88,92,104,122],desir:[0,1,2,3,5,6,12,19,22,23,26,27,33,35,43,44,58,59,60,62,66,67,69,77,83,84,91,107,109,111,118,120,121],desktop:78,destin:41,detach:25,detail:[4,5,12,19,23,25,26,27,29,30,32,36,38,41,45,49,60,64,69,70,71,73,76,77,78,79,80,81,82,84,92,94,97,103,106,107,110,112,121,123,126],detect:[41,46,76,85,89,121],deterimin:120,determin:[3,5,26,27,30,35,38,40,41,42,44,60,70,73,81,86,92,93,97,101,102,104,106,107,108,110,116,120,123],determine_topo_typ:120,dev:[21,25,78],develop:[4,5,6,10,15,19,20,21,38,42,45,49,52,59,63,64,67,75,80,82,84,85,94,104,109,118],dict:[26,69,76,81,83,86,120],dictionari:[0,1,2,3,26,60,66,69,76,81,83,86,88,120],dicuss:26,didn:[71,99],died:96,diff:[15,40,96,97,98,99,100,101],differ:[1,3,5,6,9,12,19,22,25,26,27,29,35,36,38,40,44,47,49,52,53,54,62,66,67,69,71,73,81,82,84,89,90,92,93,94,100,101,103,104,107,108,109,110,118,120,121,122,123,126],differenti:[13,26],difficult:35,difficulti:[85,87],diffus:80,digit:[44,60,120],dim:[80,81,84],dimens:[5,6,12,17,19,35,37,44,49,66,67,69,78,80,81,83,86,88,93,103,107,108,109,111,120,123],dimension:[3,6,7,13,19,26,27,29,35,38,49,73,80,92,100,101,109,110,111,120,123],dimensional_split:[73,100,107,109,111],dip:[26,53,92],dir:[78,124],direct:[5,7,12,19,26,27,29,37,41,44,45,46,49,53,54,60,64,69,80,88,92,107,108,110,120],directli:[16,20,22,25,38,49,60,62,66,67,70,86,89,90,120,124],directori:[1,3,5,8,9,10,11,12,16,17,19,20,22,25,27,29,31,33,35,36,37,40,41,42,43,44,49,50,54,58,62,69,71,73,77,80,82,88,91,92,93,94,96,101,102,103,105,106,107,108,112,114,115,116,117,118,121,123,124],disabl:[39,85],disable_petsc:89,disallow:82,disappear:[92,122],discard:84,disclaim:[45,64],discontinu:[4,84,126],discov:47,discoveri:94,discret:84,discrib:4,discuss:[21,25,26,38,82,88,90,92,93,103,110,126],disk:[10,66,94],disloc:92,dispers:[38,52],displac:[22,26,38,53,92,110,122],displai:[1,10,29,31,41,44,60,77,82,94],dist_latlong2met:37,dist_meters2latlong:37,distanc:[26,37,53,92,118,120],distribut:[4,10,26,45,53,56,64,84,90],disturb:41,distutil:67,dive:90,divid:[93,107],divis:[4,41],dlgeorg:4,dms2decim:37,dnetcdf:32,doc:[20,21,25,26,41,42,70,72,89,113],docstr:[67,71,94],doctest:73,document:[0,1,2,3,14,18,19,20,21,22,25,27,34,36,38,45,53,59,60,61,62,64,70,71,72,73,76,78,79,84,86,89,92,97,106,109,124,125],doe:[4,8,12,17,24,25,27,31,38,41,43,49,56,60,73,82,83,86,89,94,97,103,118,120,121,123],doesn:[25,86,92],doing:[5,8,16,25,27,35,38,40,42,43,60,62,73,82,92,94,101,102],domain:[5,12,13,30,38,41,42,44,55,65,66,67,69,78,80,83,86,92,93,108,109,111,118],don:[10,24,25,60,77,78,82,85,94,109],done:[1,5,6,7,8,10,12,16,17,22,25,29,35,36,41,43,44,46,49,53,59,60,62,66,70,71,89,92,93,97,101,102,103,106,108,110,117,120,122],donna:4,donnabois:4,donor:[107,109,111],dot:[31,35,41,44,46,121],doubl:[49,67,73,89,103,108],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86,88,90,92,93,94,101,104,106,107,109,110,111,112,118,120,122,123],whatev:[50,66,83],when:[11,12,17,25,26,27,31,32,35,39,40,41,42,43,47,49,53,54,55,56,59,60,62,66,77,78,79,84,87,94,96,97,99,101,103,104,105,106,107,108,109,110,111,112,118,120,121,122,123,124,126],whenc:77,whenev:[25,101,123],where:[1,3,5,10,12,19,24,26,27,29,30,31,35,36,38,41,43,44,46,47,49,50,52,55,56,62,69,73,76,78,81,92,93,96,97,100,101,102,104,106,107,109,110,111,117,118,120,123,126],wherea:[35,41,59,78],whereev:92,wherev:[82,121],whether:[3,5,10,12,19,30,37,45,49,64,73,76,77,81,82,83,84,93,94,107,108,110,120],which:[0,1,3,4,5,6,8,10,12,17,19,22,25,26,27,29,30,35,36,38,41,42,43,44,46,47,49,53,54,55,60,62,66,67,69,70,71,73,76,77,78,79,80,81,82,83,84,85,87,88,89,90,92,93,94,96,97,100,102,104,107,108,109,110,118,120,122,123,126],white:44,whith:67,who:[16,19,21,27,32,38,43],whole:[25,41,77,78,82],whose:[3,60,67,80,81,82,107,108,120],why:82,wide:90,wider:60,width:[26,41,44,53,55,73,80,82,86,92,93,109,111],wiki:85,wikipedia:82,wind:120,window:[10,26,43,49,62,90],wisdom:44,wise:[25,84],wish:[4,10,11,19,25,29,35,38,41,43,49,58,59,75,80,84,85,87,92,102,105,112,114,115,121],within:[5,12,25,30,56,60,79,82,89,93,103,106,112,120],without:[12,19,22,25,31,35,38,44,45,46,49,60,62,64,70,76,77,89,90,94,109,111,121,123],wkt:41,won:[10,67,82,120],word:[77,82,92],work:[3,7,10,12,16,17,19,21,22,23,25,27,29,30,31,36,38,41,42,43,44,49,51,52,53,54,60,64,65,66,68,69,70,75,76,77,78,81,84,85,90,92,93,94,98,99,100,101,103,106,107,108,110,112,118,121,125],workflow:112,workspac:[49,86],world:[38,47,75,78],worst:104,worth:86,worthwhil:80,would:[2,3,10,12,24,25,27,32,41,46,55,60,64,66,69,73,77,82,89,92,94,104,106,107,118,123],wpalg:13,wrap:[44,64,67,73,84,89],wrapper:120,write:[25,26,40,47,55,56,59,66,69,73,74,77,78,83,92,109,111,120],write_:76,write_aux:[76,83],write_aux_alwai:[66,69],write_aux_init:[66,69],write_input_data:27,write_p:83,written:[5,8,26,31,44,45,55,56,60,64,76,77,80,90,107,108,109,110,111,120,123],wrong:[49,77,93],www:[4,10,13,26,36,42,45,50,64,67,68,73,75,78,92,120],x_cell:44,x_edg:44,x_i:[103,123,126],x_inch:44,x_mask:120,xarr:73,xarrai:120,xarray_d:120,xclaw:[29,69],xclawcmd:69,xclawerr:69,xclawout:69,xcode:43,xdir:69,xiaom:26,xleft:[108,109],xlf:85,xlimit:[0,35,41],xllcenter:92,xllcorner:118,xlow:55,xlower:[0,3,12,19,24,67,92,109,111,118,120,123],xlowerg:67,xmax:0,xmin:0,xpoint:110,xrang:80,xtick:39,xupper:[0,19,92,109,111,120],xxdiff:94,xxxx:49,xylim:26,xzvf:43,y_cell:44,y_edg:44,y_inch:44,year:[4,13,19,41,44,75,95],yellow:[44,60],yellow_red_blu:60,yes:49,yet:[1,10,17,38,44,59,84,107,109,125],yianni:64,yield:3,yleft:[108,109],ylimit:[0,35,41,106],yllcenter:92,yllcorner:118,ylow:55,ylower:[3,19,24,67,92,109,118,120],ylowerg:67,ymax:0,ymin:0,yml:94,yong:13,you:[0,3,4,10,11,12,15,16,17,19,20,21,23,24,25,27,29,31,32,33,35,37,40,41,42,43,44,46,49,50,51,52,53,54,55,56,58,59,60,62,64,66,67,68,69,71,72,75,76,77,78,79,80,81,84,85,86,87,88,90,92,94,96,101,102,104,105,106,109,110,111,112,113,114,115,118,121,122,123,125],your:[5,11,12,16,17,21,22,23,29,32,35,42,50,51,54,59,60,62,64,65,66,67,68,71,74,75,77,82,87,88,90,91,92,93,94,96,105,114,115,118,121,123],yourself:[32,35,52],ypoint:110,yupper:[19,92,109,120],z_format:120,zero:[3,12,26,32,44,49,66,80,81,86,88,104],zip:[9,41,92],zipinfo:41,zlower:19,zone:[38,41,44,108,109],zoom:[41,92],zsh:78,zupper:19,zvar:120},titles:["ClawPlotAxes","ClawPlotData","ClawPlotFigure","ClawPlotItem","About this software","Adaptive mesh refinement (AMR) algorithms","AMRClaw","AMRClaw for 1d problems","Application documentation","Clawpack Applications repository","Amazon Web Services EC2 Clawpack AMI","b4step default routines","Boundary conditions","Bibliography","Recent changes \u2014 release notes","Changes to master since v5.3.1","Converting from Clawpack 4.3 to 4.6","Converting from Clawpack 4.6 to 5.0","Clawpack 4.x links","Changes in Clawpack 5.0","Clawpack components","Clawpack Community","Full Table of Contents","Contributing examples and applications","current_data","Developers\u2019 Guide","dtopotools module for moving topography","Fixed grid monitoring","Fixed grid output","Running an example","Flagging cells for adaptive refinement","Fortran version","Fortran Compilers","Examples from the book FVMHP","Galleries of all Clawpack applications","Gauges","GeoClaw","geoclaw.util module of utility functions","Cautionary Hints on using GeoClaw","GeoClaw plotting tools","Keeping track of git versions","Visualizing GeoClaw results in Google Earth","Guide for updating this documentation","Installation instructions","kmltools module of utility functions","License","Clawpack Makefiles","Manning friction term","The mapc2p function","Plotting using Matlab","Using NetCDF output","Creating a new application directory","IPython notebook examples","Earthquake sources: Fault slip and the Okada model","Using OpenMP","Output data formats","Which Clawpack solver should I use?","Clawpack Community Photos","Plotting examples","Visclaw Plotting options","Plotting hints and FAQ","Plotting routines for GeoClaw","Plotting options in Python","Previous versions of Clawpack","About PyClaw","PyClaw Basics","Understanding Pyclaw Classes","Porting a problem from Clawpack 4.6.x to PyClaw","Running PyClaw in the cloud","Pyclaw Controller Class","Pyclaw Limiters","Working with PyClaw\u2019s built-in examples","Building the PyClaw gallery locally","PyClaw Geometry","Going 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,114,115,118,123,126],wendroff:[73,84,107,109,111,126],weno:[56,75,84],weno_ord:84,were:[4,5,17,43,49,50,67,93,96],west:[92,118],western:[92,120],wet:36,what:[5,10,19,22,25,26,35,38,40,41,42,43,44,46,49,50,55,66,69,82,83,86,88,90,92,93,94,101,104,106,107,109,110,111,112,118,120,122,123],whatev:[50,66,83],when:[11,12,17,25,26,27,31,32,35,39,40,41,42,43,47,49,53,54,55,56,59,60,62,66,77,78,79,84,87,94,96,97,99,101,103,104,105,106,107,108,109,110,111,112,118,120,121,122,123,124,126],whenc:77,whenev:[25,101,123],where:[1,3,5,10,12,19,24,26,27,29,30,31,35,36,38,41,43,44,46,47,49,50,52,55,56,62,69,73,76,78,81,92,93,96,97,100,101,102,104,106,107,109,110,111,117,118,120,123,126],wherea:[35,41,59,78],whereev:92,wherev:[82,121],whether:[3,5,10,12,19,30,37,45,49,64,73,76,77,81,82,83,84,93,94,107,108,110,120],which:[0,1,3,4,5,6,8,10,12,17,19,22,25,26,27,29,30,35,36,38,41,42,43,44,46,47,49,53,54,55,60,62,66,67,69,70,71,73,76,77,78,79,80,81,82,83,84,85,87,88,89,90,92,93,94,96,97,100,102,104,107,108,109,110,118,120,122,123,126],white:44,whith:67,who:[16,19,21,27,32,38,43],whole:[25,41,77,78,82],whose:[3,60,67,80,81,82,107,108,120],why:82,wide:90,wider:60,width:[26,41,44,53,55,73,80,82,86,92,93,109,111],wiki:85,wikipedia:82,wind:120,window:[10,26,43,49,62,90],wisdom:44,wise:[25,84],wish:[4,10,11,19,25,29,35,38,41,43,49,58,59,75,80,84,85,87,92,102,105,112,114,115,121],within:[5,12,25,30,56,60,79,82,89,93,103,106,112,120],without:[12,19,22,25,31,35,38,44,45,46,49,60,62,64,70,76,77,89,90,94,109,111,121,123],wkt:41,won:[10,67,82,120],word:[77,82,92],work:[3,7,10,12,16,17,19,21,22,23,25,27,29,30,31,36,38,41,42,43,44,49,51,52,53,54,60,64,65,66,68,69,70,75,76,77,78,81,84,85,90,92,93,94,98,99,100,101,103,106,107,108,110,112,118,121,125],workflow:112,workspac:[49,86],world:[38,47,75,78],worst:104,worth:86,worthwhil:80,would:[2,3,10,12,24,25,27,32,41,46,55,60,64,66,69,73,77,82,89,92,94,104,106,107,118,123],wpalg:13,wrap:[44,64,67,73,84,89],wrapper:120,write:[25,26,40,47,55,56,59,66,69,73,74,77,78,83,92,109,111,120],write_:76,write_aux:[76,83],write_aux_alwai:[66,69],write_aux_init:[66,69],write_input_data:27,write_p:83,written:[5,8,26,31,44,45,55,56,60,64,76,77,80,90,107,108,109,110,111,120,123],wrong:[49,77,93],www:[4,10,13,26,36,42,45,50,64,67,68,73,75,78,92,120],x_cell:44,x_edg:44,x_i:[103,123,126],x_inch:44,x_mask:120,xarr:73,xarrai:120,xarray_d:120,xclaw:[29,69],xclawcmd:69,xclawerr:69,xclawout:69,xcode:43,xdir:69,xiaom:26,xleft:[108,109],xlf:85,xlimit:[0,35,41],xllcenter:92,xllcorner:118,xlow:55,xlower:[0,3,12,19,24,67,92,109,111,118,120,123],xlowerg:67,xmax:0,xmin:0,xpoint:110,xrang:80,xtick:39,xupper:[0,19,92,109,111,120],xxdiff:94,xxxx:49,xylim:26,xzvf:43,y_cell:44,y_edg:44,y_inch:44,year:[4,13,19,41,44,75,95],yellow:[44,60],yellow_red_blu:60,yes:49,yet:[1,10,17,38,44,59,84,107,109,125],yianni:64,yield:3,yleft:[108,109],ylimit:[0,35,41,106],yllcenter:92,yllcorner:118,ylow:55,ylower:[3,19,24,67,92,109,118,120],ylowerg:67,ymax:0,ymin:0,yml:94,yong:13,you:[0,3,4,10,11,12,15,16,17,19,20,21,23,24,25,27,29,31,32,33,35,37,40,41,42,43,44,46,49,50,51,52,53,54,55,56,58,59,60,62,64,66,67,68,69,71,72,75,76,77,78,79,80,81,84,85,86,87,88,90,92,94,96,101,102,104,105,106,109,110,111,112,113,114,115,118,121,122,123,125],your:[5,11,12,16,17,21,22,23,29,32,35,42,50,51,54,59,60,62,64,65,66,67,68,71,74,75,77,82,87,88,90,91,92,93,94,96,105,114,115,118,121,123],yourself:[32,35,52],ypoint:110,yupper:[19,92,109,120],z_format:120,zero:[3,12,26,32,44,49,66,80,81,86,88,104],zip:[9,41,92],zipinfo:41,zlim:44,zlower:19,zone:[38,41,44,108,109],zoom:[41,92],zsh:78,zupper:19,zvar:120},titles:["ClawPlotAxes","ClawPlotData","ClawPlotFigure","ClawPlotItem","About this software","Adaptive mesh refinement (AMR) algorithms","AMRClaw","AMRClaw for 1d problems","Application documentation","Clawpack Applications repository","Amazon Web Services EC2 Clawpack AMI","b4step default routines","Boundary conditions","Bibliography","Recent changes \u2014 release notes","Changes to master since v5.3.1","Converting from Clawpack 4.3 to 4.6","Converting from Clawpack 4.6 to 5.0","Clawpack 4.x links","Changes in Clawpack 5.0","Clawpack components","Clawpack Community","Full Table of Contents","Contributing examples and applications","current_data","Developers\u2019 Guide","dtopotools module for moving topography","Fixed grid monitoring","Fixed grid output","Running an example","Flagging cells for adaptive refinement","Fortran version","Fortran Compilers","Examples from the book FVMHP","Galleries of all Clawpack applications","Gauges","GeoClaw","geoclaw.util module of utility functions","Cautionary Hints on using GeoClaw","GeoClaw plotting tools","Keeping track of git versions","Visualizing GeoClaw results in Google Earth","Guide for updating this documentation","Installation instructions","kmltools module of utility functions","License","Clawpack Makefiles","Manning friction term","The mapc2p function","Plotting using Matlab","Using NetCDF output","Creating a new application directory","IPython notebook examples","Earthquake sources: Fault slip and the Okada model","Using OpenMP","Output data formats","Which Clawpack solver should I use?","Clawpack Community Photos","Plotting examples","Visclaw Plotting options","Plotting hints and FAQ","Plotting routines for GeoClaw","Plotting options in Python","Previous versions of Clawpack","About PyClaw","PyClaw Basics","Understanding Pyclaw Classes","Porting a problem from Clawpack 4.6.x to PyClaw","Running PyClaw in the cloud","Pyclaw Controller Class","Pyclaw Limiters","Working with PyClaw\u2019s built-in examples","Building the PyClaw gallery locally","PyClaw Geometry","Going Further","Pyclaw","Pyclaw Input/Output Package","PyClaw output","Running in parallel","Plotting PyClaw results","Setting up your own problem","Riemann Solver Package","Conventions for coding and documenting PyClaw","PyClaw Solutions","Using PyClaw\u2019s solvers: Classic and SharpClaw","Installing PyClaw","PyClaw State","Troubleshooting","PyClaw tutorial: Solve the acoustics equations","Pyclaw Utility Module","Python Hints","qinit default routines","Quick start guide for tsunami modeling","AMR refinement criteria","Regression testing","Release 5.0.0","Release 5.1.0","Release 5.2.0","Release 5.2.1","Release 5.2.2","Release 5.3.0","Release 5.3.1","Checkpointing and restarting","Riemann solvers","Setting sealevel","setaux default routines","Using setplot.py to specify the desired plots","Specifying classic run-time parameters in setrun.py","Specifying AMRClaw run-time parameters in setrun.py","Sample setrun.py module for AMRClaw","Specifying GeoClaw parameters in setrun.py","Sample setrun.py module for classic Clawpack","Saving and sharing results","Compiling the Sphinx documentation locally","src1d default routines","src default routines","Testing your installation","Timing Statistics","Topography data","Python tools for working with topo and dtopo","topotools module for working with topography data","Troubleshooting","Some sources of tsunami data","User files required for the Fortran code","Plotting with VisIt","Clawpack Virtual Machine","Wave-propagation algorithms"],titleterms:{"1d_fill_between":3,"1d_from_2d_data":3,"1d_plot":3,"2d_contour":3,"2d_pcolor":3,"case":82,"catch":25,"class":[66,69],"default":[11,91,105,114,115],"function":[37,44,48,62,77,84,126],"new":[36,51,71,82,94],"switch":49,"true":60,Adding:[25,41,71,80],Going:74,One:[103,126],The:[41,48,49,88,92],Use:87,Using:[10,22,50,54,77,80,84,106,123],about:[4,64],access:62,acoust:[81,88],adapt:[5,12,22,30],add:[60,82],added:82,addit:[41,108,110],advect:81,after:102,afterfram:49,algorithm:[5,13,56,126],alias:41,all:[3,34,43],amazon:10,ami:10,amr:[3,5,19,54,93,108,110],amrclaw:[6,7,15,22,95,96,97,98,99,100,101,108,109,123],anoth:60,applic:[8,9,13,22,23,34,46,51,78],arrai:[55,87],arriv:110,artifact:41,ascii:[55,76],attribut:[0,1,2,3,24,41,60],author:4,auto:[26,37,44,120],aux:[55,66],auxiliari:80,avail:33,axes:39,b4step:[11,123],background:60,basic:[41,65,79],bathymetri:[92,122],befor:123,between:60,bibliographi:[13,22],binari:55,book:33,boundari:[5,12,80,123,126],bug:25,build:72,built:[42,71],buoi:122,burger:81,capac:126,cautionari:38,cell:[5,30],cfl:70,chang:[14,15,19,60,84,95,96,97,98,99,100,101],chardiff:94,check:[25,82,94],checkpoint:102,chile:41,choic:27,choos:5,cite:[4,75],clamshel:12,classic:[15,22,29,43,84,95,96,97,98,99,100,101,107,111],claw:57,clawcode2html:8,clawpack:[9,10,13,14,16,17,18,19,20,21,34,43,46,56,57,63,67,84,85,111,125],clawplotax:0,clawplotdata:1,clawplotfigur:2,clawplotitem:[3,60],clawutil:[15,96,97,98,99,100,101],clone:25,cloud:[43,68],code:[8,22,25,36,57,82,94,116,123],color:60,colorbar:41,colormap:60,command:[49,62,71],comment:82,commun:[21,25,57],comparison:94,compil:[32,43,46,50,87,113,121],compon:[20,60],comput:[56,102],condit:[5,12,80,88,123,126],content:[22,25,43,60,66,77,84,90,94],continu:94,contourf:60,contribut:[23,25],contributor:64,control:[66,69,88],convent:82,convers:17,convert:[8,16,17],coordin:39,copi:51,correctli:78,coverag:25,creat:[10,27,41,49,51,66],creation:66,criteria:93,current_data:[24,62],curv:60,custom:84,dart:122,data:[55,106,110,118,120,121,122,123],debug:[60,108],defin:12,depend:[70,85],depth:39,deriv:[66,77],describ:13,desir:106,dev:57,develop:[22,25,43,57],diff:94,differ:[41,56,60],dimens:[73,126],dimension:103,directli:10,directori:[46,51,60],displac:118,docstr:[26,37,44,82,120],doctest:94,document:[8,26,37,42,44,75,82,113,120],domain:[73,88],done:123,download:118,dtopo:[92,119],dtopotool:26,each:123,earth:41,earthquak:[53,92,122],ec2:10,elev:39,environ:[32,43],equat:[81,88],error:[25,87],euler:81,event:[21,41],exampl:[9,22,23,29,33,35,36,41,49,51,52,58,71,78],exe:121,exist:51,extra:42,extrapol:93,f2py:121,faq:60,faster:41,fault:53,fflag:32,fgmax:27,figur:[41,60],file:[10,27,41,42,49,60,62,94,102,110,118,123],find:[10,60],finer:5,fix:[25,27,28,54,110],flag2refin:93,flag:[5,30,46,93,108],flow:[22,66],fly:59,fork:25,format:[27,55],formul:126,fort:[55,60],fortran:[19,22,31,32,82,87,94,116,121,123],found:49,friction:47,from:[10,16,17,19,25,26,33,37,44,62,67,71,79,92,120],full:22,fund:[4,64],further:74,fvmhp:33,galleri:[34,49,72],gaug:[35,41,77,92,122],gdal:41,gener:[19,26,37,44,110,120],geo:110,geoclaw:[11,12,15,19,22,36,37,38,39,41,54,57,61,91,93,95,96,97,98,99,100,101,105,110,114,115],geometri:73,geophys:22,get:[22,49,92],gfortran:[32,85],ghost:5,git:[25,40],github:25,godunov:126,googl:41,grid:[5,12,27,28,54,73,110],guid:[25,42,92],guidelin:25,hack:57,hazard:38,hdf5:76,help:49,high:126,hint:[38,60,90],how:[60,62],hpc3:57,html:[8,62],imag:41,imagediff:94,includ:9,independ:70,indic:75,initi:[5,80,88,123],input:[19,27,76,107,108],instal:[25,43,50,56,78,85,87,90,116,121],instanc:10,instruct:[25,43,82],integr:94,intel:32,interact:[62,71],interfac:56,interpol:27,iplotclaw:62,ipython:[52,71,112],issu:25,item:60,kaust:57,keep:40,kml:41,kmltool:44,kmz:41,latest:[25,43],latex:62,latitud:39,launch:10,layout:82,level:25,lflag:32,librari:41,licens:[4,45,64],limit:70,line:[62,71,94],link:18,list:71,load:41,local:[72,113],locat:35,log:[10,77],longitud:39,machin:125,make:[60,78,112,121],makefil:[31,46,80,102],man:47,mapc2p:48,master:15,math:68,matlab:49,matplotlib:85,maxfram:49,maximum:110,mesh:[5,22],method:[0,1,2,3,126],model:[38,53,92,122],modifi:[25,102],modul:[26,37,44,75,89,90,109,111,120],monitor:[27,110],more:31,most:25,motion:92,move:26,multipl:41,name:82,need:41,netcdf:[50,55,76],next:85,nose:85,note:14,notebook:[52,90,112],numpi:85,object:[73,106],obtain:85,okada:53,onli:43,openmp:54,option:[41,59,62,78,80],order:[82,87],other:[13,20,21,43,60,92],outdir:60,output:[27,28,46,49,50,54,55,66,76,77,94,102,107,108,110,121],overlai:41,overview:[22,36,106],own:[10,80],packag:[19,43,76,81],paper:13,parallel:[43,56,73,78,79,86],paramet:[19,35,60,62,88,92,107,108,110],pass:78,patch:73,path:49,pcolor:60,petclaw:[73,86],petsc:78,photo:57,piec:82,pip:121,pixel:94,plot:[3,10,19,22,27,35,36,39,41,46,49,50,58,59,60,61,62,71,78,79,94,106,112,121,124],plot_typ:3,plotax:41,plotclaw:49,plotdata:41,plotfigur:41,plotitem:41,port:67,post:59,ppflag:32,pre:32,prerequisit:43,previou:[21,63],print:108,printfram:62,problem:[7,67,80,88,123],procedur:27,process:[27,59],processor:32,produc:62,propag:126,provid:60,publish:41,pull:25,pyclaw:[15,19,22,29,43,64,65,66,67,68,69,70,71,72,73,75,76,77,79,82,83,84,85,86,88,89,94,95,96,97,98,99,100,101,116],pyflak:25,pylint:25,python:[17,62,85,90,119],q0002:55,qinit:[91,110,118],quantiti:[66,77],quick:92,raw:55,readm:8,recent:[14,25],refer:[13,75,90],refin:[5,12,22,30,93,110],region:[30,93,110],regress:[82,94],releas:[14,95,96,97,98,99,100,101],remot:25,remov:41,report:25,repositori:[9,20],request:25,requir:[41,90,123],resolut:[41,126],resourc:22,restart:[66,102],result:[10,36,41,50,79,112],richardson:93,riemann:[15,75,80,81,95,96,97,98,99,100,101,103,123],routin:[11,19,61,91,105,114,115],rst:8,run:[29,36,43,66,68,71,78,79,94,107,108,121],sage:[68,90],sampl:[109,111],save:112,script:80,seafloor:92,sealevel:104,search:49,serial:[43,73,86,94],servic:10,session:21,set:[36,43,49,60,62,80,92,104,121],setaux:[105,123],setplot:[49,60,62,106],setrun:[19,35,92,107,108,109,110,111],shallow:81,share:112,sharpclaw:84,shoot:[25,49],should:56,signatur:84,simul:66,simultan:94,sinc:15,size:60,slip:53,softwar:[4,13],solut:[60,66,83],solv:88,solver:[56,66,75,80,81,84,88,103,123],some:[60,82,122],someth:60,sourc:[53,80,92,122,123,126],space:126,spatial:123,special:[3,108],specif:[27,88,94,123],specifi:[60,62,92,93,106,107,108,110,123],sphere:12,sphinx:[42,113],sprint:[21,57],src1d:[114,123],src:[115,123],start:[22,92],state:86,statist:117,step:[85,123],stop:10,surfac:39,t0002:55,tabl:[22,75],term:[47,80,123,126],test:[25,43,78,82,85,94,116],than:60,thi:[4,42],tide:122,tile:41,time:[107,108,110,117,123],tip:[25,31,39,41,78,82],titl:60,tool:[17,22,27,35,39,94,119],top:25,topo:[92,119],topographi:[26,36,92,110,118,120,122],topotool:120,track:40,transfer:10,travi:94,troubl:[25,49,121],troubleshoot:[87,121],tsunami:[38,41,92,122],tutori:[88,90],tvd:70,understand:66,univers:57,upcom:21,updat:[25,42],use:56,used:121,user:[12,56,123],using:[38,49,123],utah:57,util:[37,44,89],valu:[27,66],vari:123,variabl:[32,43,46,80],version:[25,31,40,43,63],view:10,virtual:125,visclaw:[15,22,59,95,96,97,98,99,100,101],visit:124,visual:[22,41],wakari:68,water:[39,81],wave:[103,126],web:10,webpag:[10,42,112],what:[60,62],when:82,which:56,without:43,work:[4,71,119,120,123],workflow:25,workshop:[21,57],write:[80,82,94],you:82,your:[10,25,41,43,78,80,85,112,116]}}) 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                                                                                                                                                                                                              (an ocean at rest remains at rest).

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                                                                                                                                                                                                              see Using src1d for source terms with AMRClaw.

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                                                                                                                                                                                                              (an ocean at rest remains at rest).

                                                                                                                                                                                                              $CLAW/geoclaw/src/2d/shallow/src2.f90:

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                                                                                                                                                                                                              diff --git a/v5.3.x/topotools_module.html b/v5.3.x/topotools_module.html index 88bd6d040a..69635f6636 100644 --- a/v5.3.x/topotools_module.html +++ b/v5.3.x/topotools_module.html @@ -300,7 +300,7 @@

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                                                                                                                                                                                                              -plot(axes=None, contour_levels=None, contour_kwargs={}, limits=None, cmap=None, add_colorbar=True, plot_box=False, fig_kwargs={}, data_break=0.0, cb_kwargs={})
                                                                                                                                                                                                              +plot(axes=None, contour_levels=None, contour_kwargs={}, limits=None, cmap=None, add_colorbar=True, plot_box=False, long_lat=True, fig_kwargs={}, data_break=0.0, cb_kwargs={})

                                                                                                                                                                                                              Plot the topography.

                                                                                                                                                                                                              Input
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                                                                                                                                                                                                            • fig_kwargs (dict) - keyword arguments to be passed to figure.

                                                                                                                                                                                                            • plot_box (bool or color specifier) - If evaluates to True, plot a box around limits of this topo.

                                                                                                                                                                                                              • +

                                                                                                                                                                                                            • long_lat (bool) - If this is a longitude-latitude plot then set the +aspect of the plot to compensate for stretching. If not then the +aspect is set to “equal”.

                                                                                                                                                                                                            • data_break (float) - when default cmap is used, the value to use to break between water and land colormaps. Defaults to 0., but for some topo files may need to use e.g. 0.01 diff --git a/v5.4.x/.buildinfo b/v5.4.x/.buildinfo index 3c172b7790..2b3c68ebeb 100644 --- a/v5.4.x/.buildinfo +++ b/v5.4.x/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. 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                                                                                                                                                                                                                Matlab tools from Clawpack 4.3 can still be used, see Plotting using Matlab.

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                                                                                                                                                                                                                as needed. Remember to change to Makefile to point to the proper version.

                                                                                                                                                                                                                $CLAW/classic/src/1d/b4step1.f90:

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                                                                                                                                                                                                                $CLAW/classic/src/2d/b4step2.f90:

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                                                                                                                                                                                                                $CLAW/classic/src/3d/b4step3.f90:

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                                                                                                                                                                                                                Navigation

                                                                                                                                                                                                                with latitude when coordinate_system == 2).

                                                                                                                                                                                                                $CLAW/geoclaw/src/2d/shallow/b4step2.f90:

                                                                                                                                                                                                                -

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                                                                                                                                                                                                                Include file ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/geoclaw/src/2d/shallow/b4step2.f90’ not found or reading it failed

                                                                                                                                                                                                                diff --git a/v5.4.x/contents.html b/v5.4.x/contents.html index 1d317ae37b..3c5a9d39e0 100644 --- a/v5.4.x/contents.html +++ b/v5.4.x/contents.html @@ -261,7 +261,7 @@

                                                                                                                                                                                                                PyClawRiemann

                                                                                                                                                                                                                All Clawpack packages make use of the same collection of Riemann solvers.

                                                                                                                                                                                                                -

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                                                                                                                                                                                                                +

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                                                                                                                                                                                                                toctree contains reference to nonexisting document ‘riemann/Shallow_water_Riemann_solvers’

                                                                                                                                                                                                                diff --git a/v5.4.x/genindex.html b/v5.4.x/genindex.html index 354c719f5d..db8f346053 100644 --- a/v5.4.x/genindex.html +++ b/v5.4.x/genindex.html @@ -970,15 +970,17 @@

                                                                                                                                                                                                                T

                                                                                                                                                                                                              • tfluct_solver (pyclaw.sharpclaw.solver.SharpClawSolver attribute)
                                                                                                                                                                                                                • -
                                                                                                                                                                                                              - +
                                                                                                                                                                                                              • time_integrator (pyclaw.sharpclaw.solver.SharpClawSolver attribute)
                                                                                                                                                                                                              • topo1writer() (in module clawpack.geoclaw.topotools)
                                                                                                                                                                                                              • topo2kml() (in module clawpack.geoclaw.kmltools) +
                                                                                                                                                                                                                • +
                                                                                                                                                                                                              • topo2kmz() (in module clawpack.geoclaw.kmltools)
                                                                                                                                                                                                              • topo2writer() (in module clawpack.geoclaw.topotools)
                                                                                                                                                                                                                • diff --git a/v5.4.x/geoclaw.html b/v5.4.x/geoclaw.html index 1e7e9bd6ca..dc2663ce09 100644 --- a/v5.4.x/geoclaw.html +++ b/v5.4.x/geoclaw.html @@ -110,15 +110,15 @@

                                                                                                                                                                                                                Navigation

                                                                                                                                                                                                                Some sample calculations can be viewed in the gallery_geoclaw. More will eventually appear in the Clawpack Applications repository.

                                                                                                                                                                                                                -

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                                                                                                                                                                                                                +

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                                                                                                                                                                                                                diff --git a/v5.4.x/geoclaw_util_module.html b/v5.4.x/geoclaw_util_module.html index da69fc1b0d..b63b76b3fc 100644 --- a/v5.4.x/geoclaw_util_module.html +++ b/v5.4.x/geoclaw_util_module.html @@ -112,7 +112,7 @@

                                                                                                                                                                                                                Navigation

                                                                                                                                                                                                                Note: If using this to initialize a radially-symmetric 2d velocity on the sphere based on a radial velocity U(r), symmetric about (x0, y0), set:

                                                                                                                                                                                                                -

                                                                                                                                                                                                                System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/util.py:docstring of clawpack.geoclaw.util.bearing, line 9)

                                                                                                                                                                                                                +

                                                                                                                                                                                                                System Message: ERROR/3 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/util.py:docstring of clawpack.geoclaw.util.bearing, line 9)

                                                                                                                                                                                                                Unexpected indentation.

                                                                                                                                                                                                                diff --git a/v5.4.x/kmltools_module.html b/v5.4.x/kmltools_module.html index ddd9114acf..79f62f2f01 100644 --- a/v5.4.x/kmltools_module.html +++ b/v5.4.x/kmltools_module.html @@ -114,6 +114,7 @@

                                                                                                                                                                                                                Navigation

                                                                                                                                                                                                              • pcolorcells_for_kml - version of pcolormesh with appropriate dpi and size

                                                                                                                                                                                                              • png2kml - create kml file wrapping a png figure to be viewed on GE

                                                                                                                                                                                                              • kml_build_colorbar - create a colorbar to display on GE

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • topo2kmz - create kmz file showing onshore and offshore topography

                                                                                                                                                                                                              • kml_header - used internally

                                                                                                                                                                                                              • kml_footer - used internally

                                                                                                                                                                                                              • kml_region - used internally

                                                                                                                                                                                                                • @@ -223,7 +224,7 @@

                                                                                                                                                                                                                Navigation

                                                                                                                                                                                                                -clawpack.geoclaw.kmltools.kml_build_colorbar(cb_filename, cmap, cmin=None, cmax=None, norm=None, label=None, title=None, extend='neither')
                                                                                                                                                                                                                +clawpack.geoclaw.kmltools.kml_build_colorbar(cb_filename, cmap, cmin=None, cmax=None, norm=None, label=None, title=None, extend='neither', close_figs=True)

                                                                                                                                                                                                                Make a png file with a colorbar corresponding to cmap, norm. cmin, cmax are used only if nrm is not provided.

                                                                                                                                                                                                                @@ -335,7 +336,7 @@

                                                                                                                                                                                                                Navigation

                                                                                                                                                                                                                Internally the value dpi (dots per inch) for the png file is determined so that it is at least 16 and so that:

                                                                                                                                                                                                                -

                                                                                                                                                                                                                System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

                                                                                                                                                                                                                +

                                                                                                                                                                                                                System Message: ERROR/3 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

                                                                                                                                                                                                                Unexpected indentation.

                                                                                                                                                                                                                @@ -343,7 +344,7 @@

                                                                                                                                                                                                                Navigation

                                                                                                                                                                                                                dpi * y_inches = dcp * y_cells

                                                                                                                                                                                                              • -

                                                                                                                                                                                                              System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 38)

                                                                                                                                                                                                              +

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                                                                                                                                                                                                              Block quote ends without a blank line; unexpected unindent.

                                                                                                                                                                                                              where x_cells, y_cells are the number of cells in each direction.

                                                                                                                                                                                                              @@ -353,14 +354,14 @@

                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              annotate the figure befor saving it as a png file, which should then be done with:

                                                                                                                                                                                                              -

                                                                                                                                                                                                              System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

                                                                                                                                                                                                              +

                                                                                                                                                                                                              System Message: ERROR/3 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

                                                                                                                                                                                                              Unexpected indentation.

                                                                                                                                                                                                              plt.savefig(png_filename, transparent=True, dpi=kml_dpi)

                                                                                                                                                                                                              -

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                                                                                                                                                                                                              +

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                                                                                                                                                                                                              Block quote ends without a blank line; unexpected unindent.

                                                                                                                                                                                                              The png_extent is needed in construcing a kml file to display the @@ -471,6 +472,39 @@

                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              Color is green by default.

                                                                                                                                                                                                              +
                                                                                                                                                                                                              +
                                                                                                                                                                                                              +clawpack.geoclaw.kmltools.topo2kmz(topo, zlim=(-20, 20), mask_outside_zlim=True, sea_level=0.0, name='topo', force_dry=None, close_figs=True)
                                                                                                                                                                                                              +

                                                                                                                                                                                                              Create kmz file showing onshore and offshore topography as separate layers. +Currently not very flexible but is useful in quickly creating kmz files +to open on Google Earth showing the onshore topography and offshore +bathymetry as two separate layers. Constant colors on rectangular grid +cells should be properly rendered to ease exploration of DEMs. +A colorbar png file is also created and included in the kmz file.

                                                                                                                                                                                                              +
                                                                                                                                                                                                              +
                                                                                                                                                                                                              Input
                                                                                                                                                                                                              +
                                                                                                                                                                                                                +

                                                                                                                                                                                                              • topo should be a topotools.Topography object,

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • zlim is the elevation z limits for choosing the color map

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • mask_outside_zlim if True, suppress plotting outsize zlim

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • sea_level is the break between water and land colors

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • name is used in the kml menu and file name

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • force_dry is currently not used

                                                                                                                                                                                                                • +

                                                                                                                                                                                                              • close_figs to close the pyplot figures after making png files

                                                                                                                                                                                                                • +
                                                                                                                                                                                                              +
                                                                                                                                                                                                              +
                                                                                                                                                                                                              Future
                                                                                                                                                                                                              +

                                                                                                                                                                                                              +
                                                                                                                                                                                                              +
                                                                                                                                                                                                              +

                                                                                                                                                                                                              System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.topo2kmz, line 18)

                                                                                                                                                                                                              +

                                                                                                                                                                                                              Field list ends without a blank line; unexpected unindent.

                                                                                                                                                                                                              +
                                                                                                                                                                                                              +

                                                                                                                                                                                                              If force_dry is an array of the same shape as topo.Z then another png +and kml file are created for land that is below sea_level but where +force_dry = True.

                                                                                                                                                                                                              +
                                                                                                                                                                                                              + diff --git a/v5.4.x/objects.inv b/v5.4.x/objects.inv index 82098bafda706c9fe01ac464ab7e4b7689243c09..c7cdede7ec458d9d4bd5b5da87640c1d9d87776d 100644 GIT binary patch delta 8045 zcmV-zAClnVPUcRKet)=<=DnUm5#@_>B8F*&k42Xmz zt|^k{k5uZb^ALNn6S4bp=Se0L{{TUXl28{ei(uxL2@pRCAd$Gs$>AX{+qX}&nODbO zlAJWnd^x`}(ihuym*2dYM>CoFjr`)t$I)JMVd1AGS&8CsP=Wd*1(%RK>2hqBKn1Av@qd}&ntIxb$}4kLTRl!XnY~$)J5nLQvG2_ zMN{5&1%(XUEh^v*>6#|40#^xWFj?EBG;}fKwAh6IUU^w;o<-eV7aFnrMp6>=Q`O{K z@O;-<1Al$NmQ>G!+-AGy1IC`RZow)IE}^Shn0P;r_7eLTzR1z2c#f`Dc4a|z1*q`V z`H-a{JDoJ!XDLk|a#GNM)>RL7(a6LQ-|Z_cnzDYVfh7rMy8i9%@z>y3!Dc1>C64P2 zf8WB!^{A}(TGu3zcGvZgyeY+LhLiK_P`~Z+{(l0YOq{$tC>a*3^63^H9EH4i<3K6h z+@`xG01y^N7@gL)0rXjKb|g?4fql54O&Bcr5wE%|PkD=4kva@!vI>J!@j?H3AROYG ziWJwQFiiB>y(h`MW@d#o^s&Ib+=MK`s8>vJ9?8`(HuP{v#+_QkPXw zz?9}K35rOcT3WP0AvY9eD!3MPi^GgunQER*1`-4X&x#oPt-zQqt*f{zz^ViD9j1zD zP<%GHG~2SKIAFP(F4v-?%^Vc4H$eyi7*22D53K{^Ryj#%T$Fs!-jlowT$iPYXMo0) zgQsKIPOaIMWxHji5frz-Lv$_TQ&6<9E$WZ!(Zpsb+hj$9!7&^z!b~Z2Q#THKkq-BGzQ7yy)m-3sggpu6TarAf9U`SoDDp%x_}FojN& zvjia)uiYd2X-;)G?GK!$xd3djK7g|B%Jq}#1SkS`)RPniNddf*UIkWv_uro7`_B<@ z@|x@>QNw(QJWZustD^}MXi)<%seLQ~NVlX&^NF;XIO}jifecrkup}qY7W5D!`CvJ? z=Po3}MFgUZ|IMk>lwUr4{j#k+Dxvch9vDvDFQFooFBqJcU_@=?oVI^vjxIvr)2 zK{_38)c%|fGiGj1N10%M37!FV(vF&r)z+kF&@iGge#Pc$z*BbE1f&N7Q^>RGc+--W zE*|l(Z}P?7jxjCny{7JIKGHp1$hn3I$AzqHKVMC(eYWld4BEz^e7woa6`%HBq6i0B zCGom0ck$(gfk5A{*X6s^}6-U0IDU{m{6rf%)ES%jVK%*iKX%?SnxR$TknEIxE`A7Mq+CmqlBbd5-g8_0!W0 z8g!E&7WeTw%V}JY-OxC50c1s-!%LS!C0m+&!!55Y6{F4dkmas|{Kfa7vMT|rP=M@% zR5e{^PXR$yg$sdy#`@5ttd5}o3$%C2t__9-$+19PgROvB-+4WBb!--X|}rxqmqkO=OcU&`k$SDWL%ImjZ?GI zU#0-V(MunH7lI@)ukZmNLa1?l?G$iVv=gx6|G%K0N&YX2(r=pyXb;d@6k26Hq%Ym*K z(*?klT>?i5RM|OLPWLpwxbX>$5-in`eSxVsg}eNJdM-b-Tz)_C=@3+*Q?O1)OI)blGhd?LPH+f6zV7RDV!pt}BQKW|_k{354q>fmOJb1{ z04^aZiQBTSvwT|?&khXzYk{Y5NDvY0JZ?Jl>7z6-T-|Ox+GPbaf`EYPO9Y0jSkD^{lvR{~c)a6Um0c0CH1`CWAO+xWIn4?Te^XbKg*UuP z2E*aMxU=dbCYfO>p5dN8Srl|)V8LeM5M^j+5vw(SC@egK%DAH#9vXL2U)5<`)_CByNP||H z^m|~qxT%xSWsrVP+n{Qmb!=lQC^OL8xS)rix?Xq|WGX!Li{7YK*Wy|Z93g?Hp9PtW z7`h*B*Ljx&&p1boM|YVn2ghLpPqA-m0v2y*_^wJ>_)2JYsqZB8wfF~Gl<`@Ik0f$` znRjR}EFQ%V|8UP~PBJgDhC96sWNs?V;Cl5r7z3*~XF&9h@t+TYzFcTIFu$wjS}=?p z82A0PE<$Rr#ps`CKZ$XcC+yMh2s^>4?RdRc>M?**>M@W{>hWrq)MEgT)IP>&V?W7# zzB}vjLT}dNh0d(UYkXOc*SNAC{hq9U7nRWkzN|;DODa}=S#4LzW!Ye{J}Uw}*ya3Z zxyJe-zKeQ)X*Sxk3bGdfKv46;DzHGKm*kX2EIR&gbOe^M%4#P!tiEWV++Ah zvTSbrFY|x={r@^L{_*$!oS6p$nM`aMk>|jmd(D)GR%NJv$&`oMIPBu^OGwLE&{7rlUog0e+Lx8?{qbPr1d^apvQcFcWbEo>7!!S zA`U8FlK@t)**02A#cfiCCeACa6;GUt#CZ)Fg5Ij};wYtjNH;t&QXD6cMcl3Fz>-1W z3Owk%=O1Xv8uW_fG^hJr*4Aayyu5X=vsJFYZv@m0<>vA#cZWLfXpan$X82k&Ykdv| ze`Se82smV$@K;hcH-F~8vc#DfBIQR)_;>lWKm5(y!Bo%!qMtg34#v;1N+Nvs>%bUG zq`hE_T>$6*WExVwAA(iiDT$kEOKUoaBwh~zfs|ddg%OsI({pGQEf`{)3*kGMOALau zmw$slSXUu?URz_fq8OVfDWOW`udwfq{*6}PwBy)t%|5A=D)JvJP4^tIsj*r^B7Na$RIgsi3{RL5&tT< z-;0D30w^galQ9o5 z0yd?SWDoKJzjKpV5Jdu2pR=D3-2nmxbd!D(WGSRweWy>N^l?q(%#GX-e zX!(irTIpo^Tv>13`cJ6I#p>}GW{R8`L5*b*Xv6e0g@$hBp zPIYA}$NY#tXXbX46fAE2;gZF6lXu(7q(tF1tump#Offq#K*fTNNQ@NAgZv>t(Pqcp zOab4PKlu~%W@f6D93;q#P)1qsYDQ=Fa|*>2WNuxT1fj!E#wJxe})-D{ZU)_q@s z4-7$k#Pu%e?$-)iW)5H?J1z1)T@ZQPcz!%1Y`9@M3xplf0#MLD2cbX(EC`eRA;}SsZel zQusL8nE&=k;iq&z4HgMM^54vm$?>3HD;FlY1tz8xe-gVWBj1c^NP;Gpa!S_r)Fu}; zXq=04lTq*3D1n?Ek1wE6lur}OnIgrcgctcyPS*a!{6Sxun<+&j~tKhNya^JiO?tF3z`PM)wq=TAW6 zMVs=SFe6BR27HT`QMrcINI6M*SyF6bLgpfQmU(yU#Q*};4jQ0ZNiZ%-n0><=M`;67 zG3I4O0ejpV2pFId<#fM%b%Jo05A7Q`ulT2te~F_uq7PJQ;Df!9iP9XMBnE>yG_>6c zce0l+$FnNPBA7&Ot4X9Uf1X74^N-WWewswaz3R9>+ewCFS-d>)h4U<-g*_yTB>qMJ z${#E`1!htLnxw_};d&=RpsGY?+y0YGci4=5Sd-D*w)e2A6Kp=o@}kY~17Ty_MH{%xpldGW9H#RmVua5H*Sq8GO-9+*ogv15e?ke`E0f zleTy7?qy>$IHpX_I61rZFe_rO%cAK+3v^LdM1s!rUz~CG7F$*2@S@#M2qv2@e>d|K ztgeKe^e`ZXyk@4rl;22dd6cjOv1p6)*Y6!(Ai?kFYkryEvl9Awkb}v>f3w35CNE#Cf5D@K0%VQ5s{Am)DJ+Auw-;-kMq#tbn5`5|blzkf z5$E{K=AvqyDTATYH(-i}$X_|+wPu2Pv&JdQU$*6&WYbX-hKQibH<#X_

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                                                                                                                                                                                                              From the command lineList of built-in examples

                                                                                                                                                                                                              You can see results from many of the examples in the galleries.

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                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              PyClaw Documentation

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,99,100,101,102,104,105,107,108,111,113,115,120,121,122,124,125,126,127,128,129,131,132,134,135],claw_1dnoncon:137,claw_git_diff:[27,46,49],claw_git_statu:[27,46,49],claw_lib:59,claw_outdir:[54,68],claw_packag:91,claw_pkg:[118,119,120,121,122],claw_topo_download:131,claw_vers:51,clawdata2pyclaw:76,clawdata:[104,108,112,118,119,120,121,122],clawdev2013:48,clawgraph:58,clawpack:[1,4,5,6,10,14,25,27,29,31,32,33,34,35,37,38,39,40,41,42,43,44,46,47,51,52,53,55,58,60,62,66,67,68,69,70,71,73,74,75,77,78,79,80,81,82,83,84,85,86,87,88,89,90,93,94,95,97,98,100,102,103,104,105,106,107,108,109,110,112,113,116,118,119,120,123,124,127,129,130,131,132,134,135,137],clawpack_src:[51,98],clawplotax:[1,2,3,26,68,117],clawplotdata:[2,3,26,40,47,68,70,78,117],clawplotfigur:[0,1,47,68,117],clawplotitem:[0,1,6,21,26,67,69,109,117],clawrundata:[40,52,112,118,119,120,122],clawsolut:1,clawsolv:[91,113],clawsolver1d:[75,78,81,91,95,113],clawsolver2d:[81,91],clawutil:[10,18,19,22,27,36,37,46,49,54,98,102,116,118,119,120,122,131,132],clawvi:49,clean:[21,49,96,108],cleaner:[27,110],cleanup:111,clear:[1,2,5,58,70],clearfigur:1,clearfram:[1,70],cleargaug:40,clearli:[40,44,47],clf:2,clf_each_fram:2,click:[4,11,12,27,47,102,111],clint:15,clobber:109,clockwis:[31,43,61,131],clone:[11,17,22,23,38,48,49,50,51,71,72,86,92,100,116,132],close:[12,47,48,58,101,119],closer:[61,120],cloud:12,cluster:[5,15,50,101,119,120],clustering_cutoff:[101,119,120],cmap:[47,52,68,131],cmap_slip:29,cmax:[47,52],cmax_dz:29,cmax_slip:29,cmin:[47,52],cmin_slip:29,cname:48,coars:[3,31,47,101,110,118,129,134],coarsen:[101,119,131],coarser:[3,14,110,118,119,134],coarsest:[5,47,63,104,112,118],coast:131,coastal:[44,114,121],coastlin:[31,47,121,133],code:[4,5,6,7,14,18,19,20,21,22,23,26,28,31,33,34,36,37,38,40,41,44,46,48,50,51,53,54,55,56,59,60,62,63,64,66,68,70,73,75,76,81,83,85,86,88,91,92,95,98,100,103,104,105,108,109,110,111,112,113,116,118,120,121,122,123,127,128,129,132],coeffici:[56,88,89,91,93,94,95,113,121],colella:[5,15],collabor:[47,123],collect:[11,24,25,27,29,31,61,67,75,91,123],collela:111,color:[3,29,47,52,58,67,117,131],colorbar:[3,52,131],colorbar_labels:29,colorbar_shrink:29,colorbar_ticks:29,colormap:[3,29,42,47,58,67,69,109,131],column:[9,29,31,40,44,85,89,108,131],column_list:29,column_map:29,com:[11,12,22,23,25,27,28,48,49,50,51,72,86,88,92,107,109,110,111],combin:[19,48,52,109,133],combinatori:102,come:[3,27,48,68,70,80,86,91,108,129,134],comfort:[51,88],comm_world:96,command:[0,1,2,3,10,12,27,28,36,46,47,49,50,51,54,60,67,68,71,75,76,78,86,87,91,95,96,97,98,102,113,116,117,118,119,129,131,132],commenc:112,comment:[10,23,45,49,111,112],commit:[29,46,48,49,102],common:[3,22,27,33,34,36,37,54,55,64,67,75,89,91,93,94,110,132,134],common_sourc:55,commonli:[3,58,68,70],commun:[24,47,73,93,96],comot:4,compact:129,compar:[21,34,40,44,47,49,68,85,101,102,114,119,121,127,133,137],compare_gaug:108,compat:[27,29,43,47,52,67,86,94,97,105,106,110,111,131],compil:[12,24,33,34,36,42,51,55,62,64,70,71,76,83,88,92,96,104,113,116],compile_librari:96,complet:[19,21,27,43,54,70,75,76,86,96,97,102],complex:[11,81],compliant:37,complic:[14,68,76,117],compon:[3,14,19,21,24,31,34,40,50,51,58,63,67,88,90,92,93,101,108,118,119,120,129,134],compos:[29,75],comprehens:102,compress:[29,131],compris:[21,83,131],comput:[3,4,5,12,14,15,26,28,29,31,40,43,47,51,52,54,59,67,68,70,76,78,81,83,85,86,91,95,97,98,101,104,105,109,110,113,118,120,121,122,129,134,137],computation:[76,91],compute_f:[78,85],compute_gauge_valu:85,compute_p:[75,78],concern:[21,41],conclus:[4,47],conda:[47,71],condit:[6,19,24,53,55,64,73,74,75,76,78,85,91,99,104,105,108,114,118,120,121,122],conf:[48,49],confer:23,config:86,config_fc:132,configur:[68,75,86,131],confirm:44,conflict:[5,27,51,54,58,94],conform:[21,27,90,129],confus:[3,51,113],conjunct:101,conlict:54,connect:[31,48,52],consequenti:[53,73],conserv:[4,5,15,85,91,93,134,137],consid:[5,44,50,51,76,116,123,131],consider:[44,75],consist:[5,31,43,47,49,52,86,110,113,121,129,134],consol:[12,85],consolid:108,constant:[29,31,44,52,56,86,89,113,121,131,134],constant_storm_modul:108,constrain:101,constraint:[40,119,137],construc:52,construct:[21,29,75,81,96,129],construct_function_handl:96,constructor:93,consult:94,contact:[80,83,92],contain:[1,3,6,11,12,19,22,24,25,29,31,33,34,35,36,38,40,41,43,45,46,47,48,49,52,54,55,58,59,63,64,68,70,71,75,76,78,79,80,81,83,84,86,88,89,90,91,93,95,96,98,102,104,105,113,117,118,121,123,129,131,134],containing_rect:29,containt:112,contamin:118,contan:47,content:[47,76,134,135],context:[26,47,134],contigu:[63,93],contingu:21,continu:[12,21,27,29,45,50,73,113,118,137],contour:[3,29,40,47,58,97,117,131],contour_color:3,contour_kwarg:[3,131],contour_level:[3,131],contour_max:3,contour_min:3,contour_nlevel:3,contour_show:3,contourf:[47,67],contract:[53,73],contribut:[4,23,24,73,76,83,88,91,102],contributor:[4,23,53,83],control:[5,6,22,24,37,40,58,70,74,79,81,83,84,85,86,88,101,110,121],conveni:[1,26,33,34,40,47,70,78,80,83,85,87,95,134,137],convens:129,convent:[3,21,29,42,89,129],converg:67,convers:[18,24,76,101,129,133],convert43to46:18,convert46to50:19,convert:[3,21,24,29,38,43,47,52,54,61,76,88,96,118,119,129,133],convert_fort_double_to_float:96,convert_readm:10,convert_to_standard_unit:29,converttopotyp:129,convex:31,coodin:29,coord:[43,47],coordin:[22,29,31,43,63,67,75,81,85,86,95,101,121,131],coordinate_specif:29,coordinate_system:[13,115,121],coorind:131,copi:[5,13,14,33,34,40,47,48,49,51,58,75,78,88,93,99,100,101,105,109,115,123,125,126,129,134],copyq1:55,copyright:[53,73],core:[4,64,102],corioli:[44,121,125,126],coriolis_forc:[44,121],corner:[3,29,31,63,81,118,120,122,129,131],correct:[19,27,37,49,55,56,58,68,75,81,86,90,96,104,105,109,118,120,122],correctli:[27,31,76,82,108,121],correspond:[3,5,22,26,29,40,43,44,48,52,58,68,75,79,81,85,88,90,93,101,102,113,114,118,119,120,122,129,133,134],cos:[43,45,75,88],cosin:75,cost:[12,91],could:[12,26,31,33,34,40,51,62,68,70,75,81,85,93,94,97,98,108,119,120,121,122,129,131,134],council:4,count:75,count_from_zero:75,counter:[96,131],counterclockwis:61,coupl:[110,137],courant:[4,5,101,111,118,119,120,122],cours:[12,25,31,40,42,61,86,87,95,121,129],cover:[5,26,27,29,31,47,52,101,105,110,120,121,129],coverag:[83,102],covert:10,cparam:[75,93],cpu:[12,109,128],crash:[109,118],creat:[0,1,2,3,5,6,18,23,24,27,29,33,34,36,38,40,41,42,46,48,50,51,52,54,63,67,68,70,76,77,80,81,83,84,87,90,93,94,95,96,102,104,108,109,110,117,118,119,120,123,124,131,133,134,135],create_dtopo_xi:29,create_dtopographi:29,create_topo_func:131,creation:[68,83,104],criteria:[5,6,21,24,93],criterion:[31,101,120],critic:[47,85,113],crop:131,cross:27,crucial:[47,129],csdm:23,cse:23,csh:86,csv:29,csvfault:29,ctrl:[28,68],cube:58,current:[3,12,19,21,26,27,28,29,31,37,40,41,44,48,49,50,52,58,59,63,68,70,81,85,86,91,93,96,98,101,102,109,111,112,114,117,118,120,121,122,129,131,133],current_data:[0,3,24,40,67,68],curv:[3,40,67],custom:[0,12,14,19,21,24,55,58,64,67,76,82,88],custom_bc:88,customari:85,cut:119,cutoff:[5,120],cvs:47,cxx:86,cyber:15,cygwin:78,cython:86,dai:[5,12,47],dalcin:73,dam:[47,80],damag:[5,53,73],damian:50,damiansra:88,darker:47,darryl:15,dart:41,dash:[3,86],daspect:58,dat:29,data:[0,1,3,24,26,29,31,33,34,36,38,40,41,42,43,48,52,53,54,58,67,68,69,70,73,75,78,81,85,87,89,90,91,93,96,99,100,101,104,106,107,109,110,113,114,120,122,128,130,135],data_break:131,data_typ:96,databas:[12,29,96,129],datadir:109,dataset:[131,133],date:[27,36,43,47,48,49,50,54,68,132],date_tim:43,datetim:43,datum:[43,44,89,114,121,133],dave:29,davi:4,david:[4,15,73,83,91],dawson:15,daylight:52,dcp:52,deal:[29,44,67,85,86,93,131],dealt:31,debian:97,debug:[6,37,50,54,63,67,85,93,98,102,116,118,120],debugg:68,decid:[75,91],decim:[43,52],decis:47,declar:[19,21,93,134],decompos:[63,113,137],decomposit:118,decor:96,decoupl:48,decreas:40,deduc:129,deep:121,deep_depth:121,deeper:121,deepli:95,def:[0,1,3,40,47,68,75,81,85,88,91,120,122],default_tfluct:91,defenc:4,defin:[0,1,3,5,21,26,29,31,37,47,52,54,58,61,68,70,75,78,81,87,88,90,91,93,95,96,101,104,113,120,122,131,132,134,137],definit:[29,58,75,101,107],deform:[15,29,61,133],deg2dm:52,degre:[29,43,47,52,61],delet:[19,27],delimit:29,delin:121,delta:[79,81,88,91,113,131,134,137],delta_h:89,delta_hu:89,delta_i:131,delta_limit:131,delta_x:131,dem:131,demo:86,demonstr:[11,80,86],denot:[5,21,40,113,131],densiti:[78,85,89,93,95,119,120,134],depart:4,depdend:79,depend:[3,12,14,27,28,29,31,33,34,36,37,42,44,47,50,54,56,58,68,74,89,90,91,96,98,101,121,131,132,134,137],deprec:[6,29,32,108,121,131],depth:[4,14,15,21,29,31,40,41,44,56,61,67,69,114,121,129],deriv:[53,61,73,78,82,83,93,102],describ:[3,4,5,6,12,14,18,25,27,29,30,31,33,34,40,42,43,44,47,48,49,50,52,54,55,58,61,63,64,67,68,69,81,90,96,101,102,110,113,114,117,118,119,121,129,130,131,133,134,137],descript:[3,4,8,21,52,58,67,96,101,113,121,129,137],design:[4,26,27,47,73,75,95,114,133],desir:[0,1,2,3,5,6,14,21,24,25,29,31,38,40,49,51,52,66,67,68,70,75,76,78,85,90,91,99,110,116,118,120,122,129,131,132],desktop:86,destin:47,detail:[4,6,9,14,21,25,27,29,31,33,34,37,41,42,44,47,48,51,53,54,58,68,73,78,79,80,81,84,85,86,87,88,89,91,100,102,105,110,113,117,118,121,123,132,134,137],detect:[47,54,84,92,96,132],deterimin:131,determin:[3,5,29,31,40,44,46,47,48,52,68,79,81,89,93,101,105,109,110,112,114,117,118,119,121,131,134],determine_topo_typ:131,dev:[23,27,86],develop:[4,5,6,12,17,21,22,44,48,51,53,58,67,71,72,73,76,83,88,91,92,102,113,114,120,129],dict:[29,78,84,89,90,93,131],dictionari:[0,1,2,3,29,40,68,75,78,84,89,90,93,95,131],dicuss:29,didn:[80,107],died:104,diff:[17,46,49,104,105,106,107,108,109,110,111],differ:[1,3,5,6,11,14,21,27,29,30,31,33,34,40,42,44,46,51,52,54,56,58,61,62,67,70,75,76,78,80,81,89,91,96,97,98,101,102,108,109,110,111,113,114,116,118,119,120,121,129,131,132,133,134,137],differenti:[15,29],difficult:40,difficulti:[92,94],diffus:88,digit:[52,68,110,111,131],dim:[88,89,91],dimens:[5,6,14,19,21,40,43,52,58,75,76,78,86,88,89,90,93,95,10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7,88,98,108,135],vogl:4,volcano:4,volum:[4,15,31,38,52,58,83,119,128,129,134],vrt:47,w_1:89,w_2:89,w_3:89,wai:[5,12,14,25,27,33,34,40,47,51,52,53,54,68,70,71,73,75,78,80,81,86,88,90,92,95,97,98,100,104,110,111,113,117,118,124,129,134,136,137],wait:12,wall:[14,37,88,95,109,118,120,122,128],wang:29,want:[0,3,9,12,18,19,23,27,28,31,33,34,35,36,37,40,43,46,47,48,49,50,51,52,54,55,56,62,68,70,75,76,77,78,85,86,98,100,102,109,113,116,117,120,121,124,129,131,132],wari:89,warm:79,warn:[27,84,85,91,118,132],warp:47,warranti:[53,73],washington:[4,23,48,53,131],water:[14,15,40,41,42,43,44,64,67,76,83,105,106,110,113,114,121,129,131,133,134],water_level:43,wave:[4,5,14,15,24,31,44,47,79,81,83,88,89,91,101,108,110,111,114,118,119,120,121,122,134],wave_toler:121,wavelength:44,web:[22,24,27,33,34,47,48,49,123,131],webpag:[21,33,34,38,42,47,49,54,114],webserv:12,websit:[14,47,48,123,131],week:28,weight:47,welcom:[23,51,73],well:[4,5,27,41,47,51,52,61,62,63,64,67,70,71,90,91,111,118,119,125,126,129,134,137],wendroff:[81,91,118,120,122,137],weno:[64,83,91],weno_ord:91,went:[50,51],were:[4,5,19,40,50,55,58,59,76,101,104,110],west:129,western:131,wet:[31,41],what:[5,8,12,21,27,29,30,44,46,47,48,49,50,51,52,54,55,58,59,63,67,75,78,82,90,93,95,97,98,100,101,102,109,114,117,118,120,121,122,123,129,131,133,134],whatev:[59,75,90,113],when:[13,14,19,27,29,31,36,37,40,45,46,47,48,49,50,51,56,58,61,62,63,64,67,68,70,75,82,86,87,91,94,98,102,104,105,107,109,110,111,113,114,115,116,117,118,119,120,121,122,123,129,131,132,133,134,135,137],whenc:85,whenev:[27,109,134],where:[1,3,5,12,14,21,26,29,31,33,34,36,40,41,44,47,48,50,51,52,54,56,58,59,63,64,70,78,81,82,84,86,89,98,101,104,105,108,109,110,112,114,116,117,118,120,121,122,128,129,131,134,137],wherea:[40,47,67,86],wherev:132,whether:[3,5,12,14,21,43,53,54,58,73,81,84,85,89,90,91,101,102,110,113,118,119,121,131],which:[0,1,3,4,5,6,10,12,14,19,21,24,27,29,31,33,34,35,40,42,44,47,48,49,51,52,54,56,58,61,62,63,68,70,71,75,76,78,79,80,81,84,85,86,87,88,89,90,91,92,94,95,96,97,101,102,104,105,108,110,112,113,114,118,119,120,121,129,131,133,134,136,137],whichclaw:132,white:52,whith:76,who:[9,18,21,23,31,37,44,50,51],whole:[27,47,85,86],whose:[3,68,76,88,89,118,119,131],wide:[51,97,98],wider:68,width:[29,47,52,61,63,81,88,93,101,120,122],wiki:92,wind:131,window:[12,29,58,70,97,116],wisdom:52,wise:[27,91],wish:[4,12,13,21,28,33,34,44,47,51,58,66,67,83,88,91,92,94,110,115,123,125,126,132],within:[5,14,27,51,64,68,87,96,98,101,113,117,123,131],without:[14,21,36,40,44,48,52,53,54,55,58,68,70,71,73,79,84,85,96,98,99,102,103,104,105,106,107,108,109,116,120,122,132,134],wkt:47,won:[12,76,131],woodward:111,word:85,work:[3,7,12,14,18,19,21,23,24,25,27,31,33,34,36,41,44,47,48,50,51,52,58,60,61,62,68,71,72,73,74,75,77,78,79,83,84,85,86,89,91,92,97,98,100,101,102,106,107,108,109,110,111,113,117,118,119,121,123,129,132,136],workflow:123,workspac:[58,93],world:[44,56,83,86],worst:114,worth:93,worthwhil:88,would:[2,3,12,14,26,27,31,37,47,49,54,55,63,68,73,75,78,81,85,96,98,102,110,114,117,118,129,134],wouldn:55,wpalg:15,wrap:[52,73,76,81,91,96],wrapper:131,write:[27,29,40,46,56,63,64,67,75,78,81,82,85,86,90,110,120,122,129,131],write_:84,write_aux:[84,90],write_aux_alwai:[75,78,85],write_aux_init:[75,78],write_aux_int:85,write_input_data:31,write_p:90,written:[5,10,24,29,36,40,52,53,63,64,68,73,82,84,88,97,110,113,118,119,120,121,122,131,134],wrong:[50,51,55,58,85,98,101],www:[4,12,15,29,39,41,48,53,59,73,76,81,83,86,111,131],x_cell:52,x_edg:52,x_i:[113,134,137],x_inch:52,x_mask:131,xarr:81,xarrai:131,xarray_d:131,xclaw:[33,34,78],xclawcmd:78,xclawerr:78,xclawout:78,xcode:71,xdir:78,xiaom:29,xleft:[119,120],xlf:92,xlimit:[0,40,47],xllcorner:129,xlow:63,xlower:[0,3,14,21,26,76,120,122,129,131,134],xlowerg:76,xmax:0,xmin:0,xpoint:121,xrang:88,xtick:45,xupper:[0,21,120,122,131],xxdiff:102,xxxx:58,xylim:29,xzvf:50,y_cell:52,y_edg:52,y_inch:52,year:[4,15,21,47,52,83,103],yellow:[52,68],yellow_red_blu:68,yes:58,yet:[1,12,19,44,48,52,67,91,110,111,113,118,120,136],yianni:[4,15,73],yield:3,yleft:[119,120],ylimit:[0,40,47,117],yllcorner:129,ylow:63,ylower:[3,21,26,76,120,129,131],ylowerg:76,ymax:0,ymin:0,yml:102,yong:15,you:[0,3,4,12,13,14,17,18,19,21,22,23,24,25,26,27,28,31,33,34,35,36,37,38,40,43,46,47,48,49,50,51,52,54,55,58,59,60,61,62,63,64,66,67,68,70,71,73,75,76,77,78,80,83,84,85,86,87,88,89,91,92,93,94,95,97,98,100,102,104,109,110,111,112,113,114,115,116,117,120,121,122,123,124,125,126,127,129,132,133,134,136],your:[5,13,14,18,19,23,24,25,31,33,35,37,40,48,49,50,51,59,62,67,68,70,73,74,75,76,77,80,82,83,85,94,95,97,98,99,101,102,104,113,115,116,125,126,129,132,134],yourself:[37,40],ypoint:121,yupper:[21,120,131],z_format:131,zenodo:[4,16,72],zero:[3,14,29,37,52,58,75,88,89,93,95,114],zip:[11,47,49],zipinfo:47,zlower:21,zone:[44,47,52,119,120],zoom:47,zsh:86,zupper:21,zvar:131},titles:["ClawPlotAxes","ClawPlotData","ClawPlotFigure","ClawPlotItem","About this software","Adaptive mesh refinement (AMR) algorithms","AMRClaw","AMRClaw for 1d problems","Doxygen documentation of AMRClaw","AMRClaw Flowcharts","Application documentation","Clawpack Applications repository","Amazon Web Services EC2 Clawpack AMI","b4step default routines","Boundary conditions","Bibliography","Recent changes \u2014 release notes","Changes to master since v5.4.1","Converting from Clawpack 4.3 to 4.6","Converting from Clawpack 4.6 to 5.0","Clawpack 4.x links","Changes in Clawpack 5.0","Clawpack components","Clawpack Community","Full Table of Contents","Contributing examples and applications","current_data","Developers\u2019 Guide","Docker for Clawpack","dtopotools module for moving topography","Fortran 77 vs. Fortran 90 files","Fixed grid monitoring","Fixed grid output","Running an example","Testing your Fortran installation and running an example","Testing a PyClaw installation and running an example","Fortran version","Fortran Compilers","Examples from the book FVMHP","<no title>","Gauges","GeoClaw","Getting started with GeoClaw","geoclaw.util module of utility functions","Cautionary Hints on using GeoClaw","GeoClaw plotting tools","Keeping track of repository versions with Git","Visualizing GeoClaw results in Google Earth","Guide for updating this documentation","Guide for doing a Clawpack release","Installation options","Installation instructions (pip)","kmltools module of utility functions","License","Clawpack Makefiles","Library routines in Makefiles","Manning friction term","The mapc2p function","Plotting using Matlab","Using NetCDF output","Creating a new application directory","Earthquake sources: Fault slip and the Okada model","Using OpenMP","Output data formats","Which Clawpack solver should I use?","Clawpack Community Photos","Plotting examples","Plotting with Visclaw","Plotting hints and FAQ","Plotting routines for GeoClaw","Plotting options in Python","Installation Prerequisites","Previous versions of Clawpack","About PyClaw","PyClaw Basics","Understanding Pyclaw Classes","Porting a problem from Clawpack 4.6.x to PyClaw","Running PyClaw in the cloud","Pyclaw Controller Class","Pyclaw Limiters","Working with PyClaw\u2019s built-in examples","PyClaw Geometry","Going Further","Pyclaw","Pyclaw Input/Output Package","PyClaw output","Running in parallel","Plotting PyClaw results","Setting up your own problem","Riemann Solver Package","PyClaw Solutions","Using PyClaw\u2019s solvers: Classic and SharpClaw","Installing PyClaw","PyClaw State","Troubleshooting","PyClaw tutorial: Solve the acoustics equations","Pyclaw Utility Module","Python Hints","Python path","qinit default routines","Quick start guide for tsunami modeling","AMR refinement criteria","Regression testing","Release 5.0.0","Release 5.1.0","Release 5.2.0","Release 5.2.1","Release 5.2.2","Release 5.3.0","Release 5.3.1","Release 5.4.0","Release 5.4.1","Checkpointing and restarting","Riemann solvers","Setting sealevel","setaux default routines","Set environment variables","Using setplot.py to specify the desired plots","Specifying classic run-time parameters in setrun.py","Specifying AMRClaw run-time parameters in setrun.py","Sample setrun.py module for AMRClaw","Specifying GeoClaw parameters in setrun.py","Sample setrun.py module for classic Clawpack","Saving and sharing results","Compiling the Sphinx documentation locally","src1d default routines","src default routines","Testing your installation","Timing Statistics","Topography data","Python tools for working with topo and dtopo","topotools module for working with topography data","Troubleshooting","Some sources of tsunami data","User files required for the Fortran code","Plotting with VisIt","Clawpack Virtual Machine","Wave-propagation 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,conveni:[1,26,33,34,40,47,70,78,80,83,85,87,95,134,137],convens:129,convent:[3,21,29,42,89,129],converg:67,convers:[18,24,76,101,129,133],convert43to46:18,convert46to50:19,convert:[3,21,24,29,38,43,47,52,54,61,76,88,96,118,119,129,133],convert_fort_double_to_float:96,convert_readm:10,convert_to_standard_unit:29,converttopotyp:129,convex:31,coodin:29,coord:[43,47],coordin:[22,29,31,43,63,67,75,81,85,86,95,101,121,131],coordinate_specif:29,coordinate_system:[13,115,121],coorind:131,copi:[5,13,14,33,34,40,47,48,49,51,58,75,78,88,93,99,100,101,105,109,115,123,125,126,129,134],copyq1:55,copyright:[53,73],core:[4,64,102],corioli:[44,121,125,126],coriolis_forc:[44,121],corner:[3,29,31,63,81,118,120,122,129,131],correct:[19,27,37,49,55,56,58,68,75,81,86,90,96,104,105,109,118,120,122],correctli:[27,31,76,82,108,121],correspond:[3,5,22,26,29,40,43,44,48,52,58,68,75,79,81,85,88,90,93,101,102,113,114,118,119,120,122,129,133,134],cos:[43,45,75,88],cosin:75,cost:[12,91],could:[12,26,31,33,34,40,51,62,68,70,75,81,85,93,94,97,98,108,119,120,121,122,129,131,134],council:4,count:75,count_from_zero:75,counter:[96,131],counterclockwis:61,coupl:[110,137],courant:[4,5,101,111,118,119,120,122],cours:[12,25,31,40,42,61,86,87,95,121,129],cover:[5,26,27,29,31,47,52,101,105,110,120,121,129],coverag:[83,102],covert:10,cparam:[75,93],cpu:[12,109,128],crash:[109,118],creat:[0,1,2,3,5,6,18,23,24,27,29,33,34,36,38,40,41,42,46,48,50,51,52,54,63,67,68,70,76,77,80,81,83,84,87,90,93,94,95,96,102,104,108,109,110,117,118,119,120,123,124,131,133,134,135],create_dtopo_xi:29,create_dtopographi:29,create_topo_func:131,creation:[68,83,104],criteria:[5,6,21,24,93],criterion:[31,101,120],critic:[47,85,113],crop:131,cross:27,crucial:[47,129],csdm:23,cse:23,csh:86,csv:29,csvfault:29,ctrl:[28,68],cube:58,current:[3,12,19,21,26,27,28,29,31,37,40,41,44,48,49,50,52,58,59,63,68,70,81,85,86,91,93,96,98,101,102,109,111,112,114,117,118,120,121,122,129,131,133],current_data:[0,3,24,40,67,68],curv:[3,40,67],custom:[0,12,14,19,21,24,55,58,64,67,76,82,88],custom_bc:88,customari:85,cut:119,cutoff:[5,120],cvs:47,cxx:86,cyber:15,cygwin:78,cython:86,dai:[5,12,47],dalcin:73,dam:[47,80],damag:[5,53,73],damian:50,damiansra:88,darker:47,darryl:15,dart:41,dash:[3,86],daspect:58,dat:29,data:[0,1,3,24,26,29,31,33,34,36,38,40,41,42,43,48,52,53,54,58,67,68,69,70,73,75,78,81,85,87,89,90,91,93,96,99,100,101,104,106,107,109,110,113,114,120,122,128,130,135],data_break:131,data_typ:96,databas:[12,29,96,129],datadir:109,dataset:[131,133],date:[27,36,43,47,48,49,50,54,68,132],date_tim:43,datetim:43,datum:[43,44,89,114,121,133],dave:29,davi:4,david:[4,15,73,83,91],dawson:15,daylight:52,dcp:52,deal:[29,44,67,85,86,93,131],dealt:31,debian:97,debug:[6,37,50,54,63,67,85,93,98,102,116,118,120],debugg:68,decid:[75,91],decim:[43,52],decis:47,declar:[19,21,93,134],decompos:[63,113,137],decomposit:118,decor:96,decoupl:48,decreas:40,deduc:129,deep:121,deep_depth:121,deeper:121,deepli:95,def:[0,1,3,40,47,68,75,81,85,88,91,120,122],default_tfluct:91,defenc:4,defin:[0,1,3,5,21,26,29,31,37,47,52,54,58,61,68,70,75,78,81,87,88,90,91,93,95,96,101,104,113,120,122,131,132,134,137],definit:[29,58,75,101,107],deform:[15,29,61,133],deg2dm:52,degre:[29,43,47,52,61],delet:[19,27],delimit:29,delin:121,delta:[79,81,88,91,113,131,134,137],delta_h:89,delta_hu:89,delta_i:131,delta_limit:131,delta_x:131,dem:[52,131],demo:86,demonstr:[11,80,86],denot:[5,21,40,113,131],densiti:[78,85,89,93,95,119,120,134],depart:4,depdend:79,depend:[3,12,14,27,28,29,31,33,34,36,37,42,44,47,50,54,56,58,68,74,89,90,91,96,98,101,121,131,132,134,137],deprec:[6,29,32,108,121,131],depth:[4,14,15,21,29,31,40,41,44,56,61,67,69,114,121,129],deriv:[53,61,73,78,82,83,93,102],describ:[3,4,5,6,12,14,18,25,27,29,30,31,33,34,40,42,43,44,47,48,49,50,52,54,55,58,61,63,64,67,68,69,81,90,96,101,102,110,113,114,117,118,119,121,129,130,131,133,134,137],descript:[3,4,8,21,52,58,67,96,101,113,121,129,137],design:[4,26,27,47,73,75,95,114,133],desir:[0,1,2,3,5,6,14,21,24,25,29,31,38,40,49,51,52,66,67,68,70,75,76,78,85,90,91,99,110,116,118,120,122,129,131,132],desktop:86,destin:47,detail:[4,6,9,14,21,25,27,29,31,33,34,37,41,42,44,47,48,51,53,54,58,68,73,78,79,80,81,84,85,86,87,88,89,91,100,102,105,110,113,117,118,121,123,132,134,137],detect:[47,54,84,92,96,132],deterimin:131,determin:[3,5,29,31,40,44,46,47,48,52,68,79,81,89,93,101,105,109,110,112,114,117,118,119,121,131,134],determine_topo_typ:131,dev:[23,27,86],develop:[4,5,6,12,17,21,22,44,48,51,53,58,67,71,72,73,76,83,88,91,92,102,113,114,120,129],dict:[29,78,84,89,90,93,131],dictionari:[0,1,2,3,29,40,68,75,78,84,89,90,93,95,131],dicuss:29,didn:[80,107],died:104,diff:[17,46,49,104,105,106,107,108,109,110,111],differ:[1,3,5,6,11,14,21,27,29,30,31,33,34,40,42,44,46,51,52,54,56,58,61,62,67,70,75,76,78,80,81,89,91,96,97,98,101,102,108,109,110,111,113,114,116,118,119,120,121,129,131,132,133,134,137],differenti:[15,29],difficult:40,difficulti:[92,94],diffus:88,digit:[52,68,110,111,131],dim:[88,89,91],dimens:[5,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,47,49],zipinfo:47,zlim:52,zlower:21,zone:[44,47,52,119,120],zoom:47,zsh:86,zupper:21,zvar:131},titles:["ClawPlotAxes","ClawPlotData","ClawPlotFigure","ClawPlotItem","About this software","Adaptive mesh refinement (AMR) algorithms","AMRClaw","AMRClaw for 1d problems","Doxygen documentation of AMRClaw","AMRClaw Flowcharts","Application documentation","Clawpack Applications repository","Amazon Web Services EC2 Clawpack AMI","b4step default routines","Boundary conditions","Bibliography","Recent changes \u2014 release notes","Changes to master since v5.4.1","Converting from Clawpack 4.3 to 4.6","Converting from Clawpack 4.6 to 5.0","Clawpack 4.x links","Changes in Clawpack 5.0","Clawpack components","Clawpack Community","Full Table of Contents","Contributing examples and applications","current_data","Developers\u2019 Guide","Docker for Clawpack","dtopotools module for moving topography","Fortran 77 vs. Fortran 90 files","Fixed grid monitoring","Fixed grid output","Running an example","Testing your Fortran installation and running an example","Testing a PyClaw installation and running an example","Fortran version","Fortran Compilers","Examples from the book FVMHP","<no title>","Gauges","GeoClaw","Getting started with GeoClaw","geoclaw.util module of utility functions","Cautionary Hints on using GeoClaw","GeoClaw plotting tools","Keeping track of repository versions with Git","Visualizing GeoClaw results in Google Earth","Guide for updating this documentation","Guide for doing a Clawpack release","Installation options","Installation instructions (pip)","kmltools module of utility functions","License","Clawpack Makefiles","Library routines in Makefiles","Manning friction term","The mapc2p function","Plotting using Matlab","Using NetCDF output","Creating a new application directory","Earthquake sources: Fault slip and the Okada model","Using OpenMP","Output data formats","Which Clawpack solver should I use?","Clawpack Community Photos","Plotting examples","Plotting with Visclaw","Plotting hints and FAQ","Plotting routines for GeoClaw","Plotting options in Python","Installation Prerequisites","Previous versions of Clawpack","About PyClaw","PyClaw Basics","Understanding Pyclaw Classes","Porting a problem from Clawpack 4.6.x to PyClaw","Running PyClaw in the cloud","Pyclaw Controller Class","Pyclaw Limiters","Working with PyClaw\u2019s built-in examples","PyClaw Geometry","Going Further","Pyclaw","Pyclaw Input/Output Package","PyClaw output","Running in parallel","Plotting PyClaw results","Setting up your own problem","Riemann Solver Package","PyClaw Solutions","Using PyClaw\u2019s solvers: Classic and SharpClaw","Installing PyClaw","PyClaw State","Troubleshooting","PyClaw tutorial: Solve the acoustics equations","Pyclaw Utility Module","Python Hints","Python path","qinit default routines","Quick start guide for tsunami modeling","AMR refinement criteria","Regression testing","Release 5.0.0","Release 5.1.0","Release 5.2.0","Release 5.2.1","Release 5.2.2","Release 5.3.0","Release 5.3.1","Release 5.4.0","Release 5.4.1","Checkpointing and restarting","Riemann solvers","Setting sealevel","setaux default routines","Set environment variables","Using setplot.py to specify the desired plots","Specifying classic run-time parameters in setrun.py","Specifying AMRClaw run-time parameters in setrun.py","Sample setrun.py module for AMRClaw","Specifying GeoClaw parameters in setrun.py","Sample setrun.py module for classic Clawpack","Saving and sharing results","Compiling the Sphinx documentation locally","src1d default routines","src default routines","Testing your installation","Timing Statistics","Topography data","Python tools for working with topo and dtopo","topotools module for working with topography data","Troubleshooting","Some sources of tsunami data","User files required for the Fortran code","Plotting with VisIt","Clawpack Virtual Machine","Wave-propagation algorithms"],titleterms:{"1d_fill_between":3,"1d_from_2d_data":3,"1d_plot":3,"2d_contour":3,"2d_pcolor":3,"catch":27,"class":[75,78],"default":[13,99,115,125,126],"final":49,"function":[43,52,57,70,85,91,137],"import":98,"new":[42,60,80,102],"switch":58,"true":68,Adding:[27,47,80,88,113],For:5,Going:82,One:[113,137],The:[47,57,58,95],Use:94,Using:[12,24,55,59,62,85,88,91,113,117,134],about:[4,73],access:70,acoust:[89,95],adapt:[5,14,24],add:68,addit:[47,119,121],advect:89,after:112,afterfram:58,algorithm:[5,15,64,137],alias:47,all:[3,51],amazon:12,ami:12,amr:[3,5,21,62,101,119,121],amrclaw:[6,7,8,9,17,24,103,104,105,106,107,108,109,110,111,119,120,134],anoth:68,app:49,applic:[10,11,15,24,25,54,60,86],approach:7,arrai:[63,94],arriv:121,artifact:47,ascii:[63,84],attribut:[0,1,2,3,26,47,68],author:4,auto:[29,43,52,131],aux:[63,75],auxiliari:88,avail:38,axes:45,b4step:[13,134],background:68,base:54,basic:[47,74,87],bathymetri:133,befor:134,between:68,bibliographi:[15,24],binari:63,book:38,boundari:[5,14,88,134,137],branch:27,bug:27,built:[48,80],buoi:133,burger:89,candid:49,capac:137,cautionari:44,cell:5,cfl:79,chang:[16,17,21,68,91,103,104,105,106,107,108,109,110,111],chardiff:102,check:[27,102],checkpoint:112,chile:47,choic:31,choos:5,cite:[4,83],clamshel:14,classic:[17,24,33,34,91,103,104,105,106,107,108,109,110,111,118,122,127],claw:[65,116],clawcode2html:10,clawpack:[11,12,15,16,17,18,19,20,21,22,23,24,28,48,49,50,54,64,65,72,76,91,92,111,122,136],clawplotax:0,clawplotdata:1,clawplotfigur:2,clawplotitem:[3,68],clawutil:[17,104,105,106,107,108,109,110,111],clinic:23,clone:27,cloud:77,code:[10,24,27,42,65,102,134],color:68,colorbar:47,colormap:68,command:[35,58,70,80],commit:27,commun:[23,27,65],comparison:102,compil:[37,50,54,59,94,124,132],compon:[22,68],comput:[64,112],conda:50,condit:[5,14,88,95,134,137],contain:28,content:[24,27,68,75,85,91,97,102],continu:102,contourf:68,contribut:[25,27],contributor:73,control:[75,78,95],convers:19,convert:[10,18,19],coordin:[45,47],copi:60,correctli:86,coverag:27,creat:[12,28,31,47,49,58,60,75],creation:75,criteria:101,current_data:[26,70],curv:68,custom:[91,113],dart:133,data:[47,63,117,121,129,131,132,133,134],debug:[68,119],defin:14,depend:[79,92],deprec:7,depth:45,deriv:[75,85],describ:15,desir:117,detail:5,dev:65,develop:[23,24,27,50,65],diff:102,differ:[47,55,64,68],dimens:[81,137],dimension:113,directli:12,directori:[54,60,68],displac:129,docker:28,dockerfil:49,docstr:[29,43,52,131],doctest:102,document:[8,10,29,43,48,49,52,83,111,124,131],doe:50,doing:49,domain:[81,95],done:134,download:129,doxygen:8,dtopo:130,dtopotool:29,duplic:54,each:[27,134],earth:47,earthquak:[61,133],easi:98,ec2:12,elev:45,environ:[37,116],equat:[89,95],error:[27,94],euler:89,event:[23,47],exampl:[11,24,25,33,34,35,38,40,42,47,58,60,66,80,86],exe:132,exist:60,extra:48,extrapol:101,f2py:132,faq:68,faster:47,fault:61,fflag:37,fgmax:31,figur:[47,68],file:[12,30,31,47,48,49,55,58,68,70,102,112,121,129,134],find:[12,68],finer:5,fix:[27,31,32,62,121],flag2refin:101,flag:[5,54,101,119],flow:[24,75],flowchart:9,fly:67,fork:27,format:[31,63],formul:137,fort:[63,68],fortran:[21,24,30,34,36,37,50,71,94,102,132,134],found:58,frame:85,friction:56,from:[12,18,19,21,24,27,29,35,38,43,50,52,70,76,80,87,131],full:24,fund:[4,73],further:82,fvmhp:38,galleri:[48,58],gaug:[40,47,85,133],gdal:47,gener:[21,29,43,48,52,121,131],geo:121,geoclaw:[13,14,17,21,24,41,42,43,44,45,47,62,65,69,99,101,103,104,105,106,107,108,109,110,111,115,121,125,126],geometri:81,geophys:24,get:[24,42,58],gfortran:[37,92],ghost:5,git:[27,46,71],github:[27,49],global:110,godunov:137,googl:47,grid:[5,14,31,32,62,81,121],guid:[27,48,49,100],guidelin:27,hack:65,hazard:44,hdf5:84,help:58,high:137,hint:[44,68,97],how:[68,70,85],hpc3:65,html:[10,70],imag:[28,47],imagediff:102,includ:11,independ:79,indic:83,initi:[5,88,95,134],input:[21,31,84,118,119],instal:[27,34,35,50,51,59,64,71,86,92,94,97,98,127,132],instanc:12,instruct:[27,51],integr:102,intel:37,interact:[70,80],interfac:64,interpol:31,interpret:35,iplotclaw:70,ipython:[35,80,123],issu:27,item:68,jupyt:[28,35],kaust:65,keep:46,kml:47,kmltool:52,kmz:47,latest:[27,50],latex:70,latitud:[45,47],launch:12,level:27,lflag:37,librari:[47,55],licens:[4,53,73],limit:79,line:[35,70,80,102],link:20,list:80,load:47,local:124,locat:40,log:[12,85],longitud:[45,47],machin:136,make:[68,86,123,132],makefil:[36,54,55,88,112],man:56,map:47,mapc2p:57,master:[17,27],math:77,matlab:58,matplotlib:92,maxfram:58,maximum:121,mesh:[5,24],method:[0,1,2,3,137],migrat:24,model:[44,61,100,133],modifi:[27,55,112],modul:[29,43,52,83,96,97,120,122,131],monitor:[31,121],more:[5,28,34,36],most:27,move:29,multipl:47,name:[54,55],need:47,netcdf:[59,63,84],never:27,next:[50,51,92],nose:92,note:[16,51],notebook:[28,35,97,123],numpi:92,object:[81,117],obtain:92,okada:61,old:[7,48],older:24,onli:[50,51],openmp:62,oper:71,option:[47,50,70,86,88],order:94,other:[15,17,22,23,50,68,111],out:27,outdir:68,output:[31,32,54,58,59,62,63,75,84,85,102,112,118,119,121,132],overlai:47,overview:[24,117],own:[12,28,88],packag:[21,50,51,84,89],page:48,paper:15,parallel:[50,64,81,86,87,93],paramet:[21,40,68,70,95,118,119,121],pass:86,patch:81,path:[58,98],pcolor:68,petclaw:[81,93],petsc:86,photo:65,pip:[50,51,71,132],pixel:102,plot:[3,12,21,24,31,40,42,45,47,54,58,59,66,67,68,69,70,80,86,87,102,117,123,132,135],plot_typ:3,plotax:47,plotclaw:58,plotdata:47,plotfigur:47,plotitem:47,pointwis:113,port:76,post:67,ppflag:37,pre:37,prepar:49,prerequisit:71,previou:[23,72],print:119,printfram:70,problem:[7,76,88,95,134],procedur:31,process:[31,67],processor:37,produc:70,propag:137,provid:68,pth:98,publish:47,pull:27,pyclaw:[17,21,24,33,35,50,51,73,74,75,76,77,78,79,80,81,83,84,85,87,90,91,92,93,95,96,102,103,104,105,106,107,108,109,110,111,127],pyflak:27,pylint:27,python:[19,70,71,92,97,98,130],pythonpath:[98,116],q0002:63,qinit:[99,121,129],quantiti:[75,85],quick:[51,100],raw:63,readm:10,recent:[16,23,27],refer:[15,83,97],refin:[5,14,24,101,121],region:[101,121],regress:102,releas:[16,49,103,104,105,106,107,108,109,110,111],remot:27,remov:47,replac:55,report:27,repositori:[11,17,22,27,46,49,111,113],request:27,requir:[47,50,97,134],resolut:[47,137],resourc:[24,28],restart:[28,75,112],result:[12,42,47,59,87,123],richardson:101,riemann:[17,24,83,88,89,103,104,105,106,107,108,109,110,111,113,134],routin:[13,21,55,69,99,115,125,126],rst:10,run:[28,33,34,35,42,50,75,77,80,86,87,102,118,119,132],sage:77,same:55,sampl:[120,122],save:[85,123],script:88,sealevel:114,search:58,serial:[81,93,102],servic:12,session:23,set:[42,58,68,70,88,114,116,132],setaux:[115,134],setplot:[58,68,70,117],setrun:[21,40,118,119,120,121,122],shallow:89,share:123,sharpclaw:91,shoot:[27,58],should:64,signatur:91,simul:75,simultan:102,sinc:17,size:68,slip:61,softwar:[4,15],solut:[68,75,90],solv:95,solver:[64,75,83,88,89,91,95,113,134],some:[68,133],someth:68,sourc:[54,61,88,133,134,137],space:137,spatial:134,special:[3,119],specif:[31,95,102,134],specifi:[68,70,101,117,118,119,121,134],sphere:14,sphinx:[48,124],sprint:[23,65],src1d:[125,134],src:[126,134],start:[24,42,100],state:93,statist:128,step:[50,51,92,134],stop:12,surfac:45,sys:98,system:71,t0002:63,tabl:[24,83],tar:49,tarfil:50,term:[56,88,134,137],test:[27,34,35,86,92,102,127],than:68,thi:[4,48],tide:133,tile:47,time:[118,119,121,128,134],tip:[27,36,45,47,86],titl:68,tool:[19,24,31,40,45,102,130],top:27,topo:130,topographi:[29,42,47,121,129,131,133],topotool:131,track:46,transfer:12,travi:102,troubl:[27,58,132],troubleshoot:[51,94,132],tsunami:[44,47,100,133],tutori:[23,95,97],tvd:79,understand:75,univers:65,upcom:23,updat:[27,48,49],use:64,used:132,user:[14,23,64,134],using:[44,50,51,58,134],utah:65,util:[43,52,96],valu:[31,75],vari:134,variabl:[37,54,88,116],version:[24,36,46,48,50,72,98],view:12,virtual:136,visclaw:[17,24,67,103,104,105,106,107,108,109,110,111],visit:135,visual:[24,47],washington:65,water:[45,89],wave:[113,137],web:12,webpag:[12,48,123],what:[68,70,85],when:85,where:85,which:[64,98],whichclaw:98,without:50,work:[4,80,130,131,134],workflow:27,workshop:[23,65],write:[88,102],written:85,your:[12,27,28,34,47,86,88,92,123,127],zenodo:49}}) 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                                                                                                                                                                                                              as needed. Remember to change to Makefile to point to the proper version.

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                                                                                                                                                                                                              (an ocean at rest remains at rest).

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                                                                                                                                                                                                              see Using src1d for source terms with AMRClaw.

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                                                                                                                                                                                                              (an ocean at rest remains at rest).

                                                                                                                                                                                                              $CLAW/geoclaw/src/2d/shallow/src2.f90:

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                                                                                                                                                                                                              Include file ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/geoclaw/src/2d/shallow/src2.f90’ not found or reading it failed

                                                                                                                                                                                                              diff --git a/v5.4.x/topotools_module.html b/v5.4.x/topotools_module.html index d1969fb211..2227673344 100644 --- a/v5.4.x/topotools_module.html +++ b/v5.4.x/topotools_module.html @@ -309,7 +309,7 @@

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                                                                                                                                                                                                              -plot(axes=None, contour_levels=None, contour_kwargs={}, limits=None, cmap=None, add_colorbar=True, plot_box=False, fig_kwargs={}, data_break=0.0, cb_kwargs={})
                                                                                                                                                                                                              +plot(axes=None, contour_levels=None, contour_kwargs={}, limits=None, cmap=None, add_colorbar=True, plot_box=False, long_lat=True, fig_kwargs={}, data_break=0.0, cb_kwargs={})

                                                                                                                                                                                                              Plot the topography.

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                                                                                                                                                                                                            • fig_kwargs (dict) - keyword arguments to be passed to figure.

                                                                                                                                                                                                            • plot_box (bool or color specifier) - If evaluates to True, plot a box around limits of this topo.

                                                                                                                                                                                                              • +

                                                                                                                                                                                                            • long_lat (bool) - If this is a longitude-latitude plot then set the +aspect of the plot to compensate for stretching. If not then the +aspect is set to “equal”.

                                                                                                                                                                                                            • data_break (float) - when default cmap is used, the value to use to break between water and land colormaps. Defaults to 0., but for some topo files may need to use e.g. 0.01 diff --git a/v5.5.x/.buildinfo b/v5.5.x/.buildinfo index 54286f815d..b6874900f1 100644 --- a/v5.5.x/.buildinfo +++ b/v5.5.x/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. 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                                                                                                                                                                                                              Matlab tools from Clawpack 4.3 can still be used, see Plotting using Matlab.

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                                                                                                                                                                                                              as needed. Remember to change to Makefile to point to the proper version.

                                                                                                                                                                                                              $CLAW/classic/src/1d/b4step1.f90:

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                                                                                                                                                                                                              $CLAW/classic/src/2d/b4step2.f90:

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                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                              with latitude when coordinate_system == 2).

                                                                                                                                                                                                              $CLAW/geoclaw/src/2d/shallow/b4step2.f90:

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                                                                                                                                                                                                              diff --git a/v5.5.x/contents.html b/v5.5.x/contents.html index 2a25fcb400..4ae0682edc 100644 --- a/v5.5.x/contents.html +++ b/v5.5.x/contents.html @@ -278,7 +278,7 @@

                                                                                                                                                                                                              PyClawRiemann

                                                                                                                                                                                                              All Clawpack packages make use of the same collection of Riemann solvers.

                                                                                                                                                                                                              -

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                                                                                                                                                                                                              toctree contains reference to nonexisting document ‘riemann/Shallow_water_Riemann_solvers’

                                                                                                                                                                                                              diff --git a/v5.5.x/genindex.html b/v5.5.x/genindex.html index 27a9f721d3..d2a381e7f5 100644 --- a/v5.5.x/genindex.html +++ b/v5.5.x/genindex.html @@ -1018,15 +1018,17 @@

                                                                                                                                                                                                              T

                                                                                                                                                                                                            • tfluct_solver (clawpack.pyclaw.sharpclaw.solver.SharpClawSolver attribute)
                                                                                                                                                                                                              • -
                                                                                                                                                                                                            - + @@ -143,7 +145,7 @@

                                                                                                                                                                                                            Version 5.8.x

                                                                                                                                                                                                            Table of Contents

                                                                                                                                                                                                            @@ -73,9 +81,29 @@

                                                                                                                                                                                                            Navigation

                                                                                                                                                                                                            -

                                                                                                                                                                                                            The Clawpack Gallery is available only for the latest release of Clawpack.

                                                                                                                                                                                                            -

                                                                                                                                                                                                            Please see -http://www.clawpack.org/gallery/index.html.

                                                                                                                                                                                                            +
                                                                                                                                                                                                            @@ -90,6 +118,8 @@

                                                                                                                                                                                                            Version 5.8.x

                                                                                                                                                                                                            Related Topics

                                                                                                                                                                                                            diff --git a/v5.8.x/genindex.html b/v5.8.x/genindex.html index 4e90ec1c0e..111a877c1f 100644 --- a/v5.8.x/genindex.html +++ b/v5.8.x/genindex.html @@ -1032,15 +1032,17 @@

                                                                                                                                                                                                            T

                                                                                                                                                                                                          • tfluct_solver (clawpack.pyclaw.sharpclaw.solver.SharpClawSolver attribute)
                                                                                                                                                                                                            • -
                                                                                                                                                                                                          - + @@ -124,7 +124,7 @@

                                                                                                                                                                                                          Version 5.8.x

                                                                                                                                                                                                          Related Topics

                                                                                                                                                                                                          • Documentation overview
                                                                                                                                                                                                              -
                                                                                                                                                                                                            • Pyclaw
                                                                                                                                                                                                                +
                                                                                                                                                                                                              • PyClaw
                                                                                                                                                                                                                • Developers’ Guide @@ -360,7 +360,7 @@

                                                                                                                                                                                                                  Table of Contents

                                                                                                                                                                                                                  Related Topics

                                                                                                                                                                                                                  • Documentation overview
                                                                                                                                                                                                                      -
                                                                                                                                                                                                                    • Pyclaw
                                                                                                                                                                                                                        +
                                                                                                                                                                                                                      • PyClaw
                                                                                                                                                                                                                        • Developers’ Guide @@ -182,7 +182,7 @@

                                                                                                                                                                                                                          Final releaseChanges to master since v5.8.0 which generate diffs between the latest version and +Changes to master since v5.8.1 which generate diffs between the latest version and the current master branch of each repository.

                                                                                                                                                                                                                          @@ -235,6 +235,12 @@

                                                                                                                                                                                                                          Zenodo +

                                                                                                                                                                                                                          Open Science Framework (OSF)

                                                                                                                                                                                                                          +

                                                                                                                                                                                                                          Go to https://osf.io/kmw6h/files/ and upload the latest tarfile to the set +of versions that can be accessed with the single DOI +10.17605/osf.io/kmw6h.

                                                                                                                                                                                                                          +

                                                                                                                                                                                                                          Updating the documentation

                                                                                                                                                                                                                          See Guide for updating this documentation for general instructions on building the documentation @@ -263,10 +269,11 @@

                                                                                                                                                                                                                          ZenodoTable of Contents

                                                                                                                                                                                                                        • Final release
                                                                                                                                                                                                                        • Pypi
                                                                                                                                                                                                                        • Zenodo
                                                                                                                                                                                                                          • +
                                                                                                                                                                                                                        • Open Science Framework (OSF)
                                                                                                                                                                                                                        • Updating the documentation
                                                                                                                                                                                                                        • Updating the apps repository
                                                                                                                                                                                                                        • Updating the Dockerfile
                                                                                                                                                                                                                          • @@ -337,7 +345,7 @@

                                                                                                                                                                                                                          Table of Contents

                                                                                                                                                                                                                          Related Topics

                                                                                                                                                                                                                          @@ -203,14 +149,10 @@

                                                                                                                                                                                                                          Version 5.8.x

                                                                                                                                                                                                                          Table of Contents

                                                                                                                                                                                                                          Related Topics

                                                                                                                                                                                                                          • Documentation overview
                                                                                                                                                                                                                              diff --git a/v5.8.x/installing_fortcodes.html b/v5.8.x/installing_fortcodes.html new file mode 100644 index 0000000000..f02ab23f6d --- /dev/null +++ b/v5.8.x/installing_fortcodes.html @@ -0,0 +1,247 @@ + + + + + + + Options for installing Clawpack Fortran codes — Clawpack 5.8.x documentation + + + + + + + + + + + + + + + + + + +
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              + +
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              + + + +
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              + +
                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              Options for installing Clawpack Fortran codes

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              This page describes ways to download and “install” Clawpack in a way that +the Fortran versions of the PDE solvers (Classic, AMRClaw, and GeoClaw) +can be used, along with Python codes that support these solvers, including +the visualization tools in VisClaw.

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              If you plan to use the PDE solvers directly from PyClaw, please +see Installing Clawpack for other options. If you are not sure, see +Which Clawpack solver should I use?

                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              tar file

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              You can download the most recent (or certain previous versions) of Clawpack +as a tar file. After untarring this, you can set environment variables +to point to this version.

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              Download a tar file from one of these sources:

                                                                                                                                                                                                                              + +

                                                                                                                                                                                                                              After downloading a tar file you can do, e.g.

                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              tar -xzf clawpack-v5.8.1.tar.gz
+cd clawpack-v5.8.1
+export CLAW=/full/path/to/clawpack-v5.8.1  # in bash
+
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              The last command sets an environment variable when using the bash shell. +The syntax may be different in other shells. Replace /full/path/to +with the appropriate full path.

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              You must also add $CLAW to your PYTHONPATH environment variable, +see Python path.

                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              git clone

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              You can clone the git repositories from https://github.com/clawpack. +This is particularly useful if you +want the latest development version or a branch that is not in a release yet, +and/or if you plan to contribute to the code yourself via a pull request. +See Developers’ Guide for more details, but the basic commands are:

                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              git clone git://github.com/clawpack/clawpack.git
+cd clawpack
+git checkout v5.8.1     # or an older version; `git tag -l` to list options
+git submodule init      # for repositories pyclaw, clawutil, visclaw, etc.
+git submodule update    # clones all the submodule repositories
+export CLAW=/full/path/to/clawpack    # in bash
+
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              The last command sets an environment variable when using the bash shell. +The syntax may be different in other shells. Replace /full/path/to +with the appropriate full path.

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              You must also add $CLAW to your PYTHONPATH environment variable, +see Python path.

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              Components: +See Clawpack components for a list of what is generally included +under the top level clawpack directory when using any of these approaches. +(And what is not included, e.g. the Clawpack Applications repository.)

                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              Next steps:

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              Once Clawpack is installed, you can get started:

                                                                                                                                                                                                                              + +
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              + + +
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              + +
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              + © Copyright CC-BY 2020, The Clawpack Development Team. + Created using Sphinx. +
                                                                                                                                                                                                                              + + + + \ No newline at end of file diff --git a/v5.8.x/installing_pip.html b/v5.8.x/installing_pip.html index 99dd42b70a..e1389957b7 100644 --- a/v5.8.x/installing_pip.html +++ b/v5.8.x/installing_pip.html @@ -20,7 +20,7 @@ - +
                                                                                                                                                                                                                              @@ -67,7 +67,7 @@

                                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                                              modules |
                                                                                                                                                                                                                            • - next |
                                                                                                                                                                                                                            • Navigation

                                                                                                                                                                                                                              pip install instructions

                                                                                                                                                                                                                              -

                                                                                                                                                                                                                              For other installation options, see Installing Clawpack.

                                                                                                                                                                                                                              -

                                                                                                                                                                                                                              See also:

                                                                                                                                                                                                                              - -

                                                                                                                                                                                                                              Register: Please register -if you have not already done so. This is very useful in helping -us track the extent of usage, and important to the Funding agencies -who support this work.

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              Note: If you only plan to use the Fortran versions of the solvers +(rather than PyClaw), and you run into problems with pip, +then you might want to try Options for installing Clawpack Fortran codes.

                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              Quick Installation of PyClaw with pip

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              Please see Which Clawpack solver should I use? before installing, particularly +if you are not sure whether you will +be using the Fortran versions of the PDE solvers +(Classic, AMRClaw, and GeoClaw) or the PyClaw version of the PDE solvers. +See Installing Clawpack for other installation options.

                                                                                                                                                                                                                              Prerequisites: Before installing, check that you have the Installation Prerequisites.

                                                                                                                                                                                                                              -

                                                                                                                                                                                                                              Installing Clawpack requires downloading some version and then setting -paths so that Python import statements (and possibly Fortran Makefiles) find -the desired version. pip can be used to reset Python paths as well as to -download a new version of Clawpack and set the path appropriately. See -Python path for more information.

                                                                                                                                                                                                                              -
                                                                                                                                                                                                                              -

                                                                                                                                                                                                                              Quick Installation of all packages

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              If you only want to use PyClaw (and associated Python +tools, e.g. VisClaw for visualization), then the simplest way to install +Clawpack is via:

                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              pip install --user clawpack
+
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              or, more specifically,

                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              pip install --user clawpack==v5.8.1
+
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              or you can choose a previous version from the PyPi history.

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              However, note that this does not download the Fortran codes in a way that they +can be used for Classic, AMRClaw, and GeoClaw.

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              If you think you might want to use the Fortran packages as well +(Classic, AMRClaw, GeoClaw) and/or want easier access to the Python source +code, it is recommended that you follow the pip instructions below.

                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +
                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              Quick Installation of all packages with pip

                                                                                                                                                                                                                              The recommended way to install the latest release of Clawpack, for -using PyClaw and/or the Fortran packages, is to give the following pip -install command +using both PyClaw and the Fortran packages, is to use pip, e.g. with the +following command (you might want to first read the notes below to see if you want to change anything in this command):

                                                                                                                                                                                                                              pip install --src=$HOME/clawpack_src --user -e \
-    git+https://github.com/clawpack/clawpack.git@v5.8.0#egg=clawpack-v5.8.0
+    git+https://github.com/clawpack/clawpack.git@v5.8.1#egg=clawpack-v5.8.1 \
+    --use-deprecated=legacy-resolver
                                                                                                                                                                                                                              -

                                                                                                                                                                                                                              This will download Clawpack (via a git clone) into the directory -$HOME/clawpack_src/clawpack-v5.8.0. The top +

                                                                                                                                                                                                                              Notes:

                                                                                                                                                                                                                              +
                                                                                                                                                                                                                                +

                                                                                                                                                                                                                              • With older versions of pip, the flag +–use-deprecated=legacy-resolver +may not be recognized and is not needed.

                                                                                                                                                                                                                                • +

                                                                                                                                                                                                                              • Using pip to install will also check some python +Installation Prerequisites and may update these on your system, and will use f2py to +convert Fortran Riemann solvers to Python versions. See +installing_options if you want more control.

                                                                                                                                                                                                                                • +

                                                                                                                                                                                                                              • This will download Clawpack (via a git clone) into the directory +$HOME/clawpack_src/clawpack-v5.8.1. The top installation directory can be changed by modifying the --src target (or omit this part to put it in your current working directory). If you have already downloaded Clawpack via a different mechanism then -see Using pip to install a different version rather than using the above command.

                                                                                                                                                                                                                                -

                                                                                                                                                                                                                                See Clawpack components for a list of what’s included in this top -level directory.

                                                                                                                                                                                                                                -

                                                                                                                                                                                                                                Note: Using pip to install will also check some python -Installation Prerequisites and may update these on your system, and will use f2py to -convert Fortran Riemann solvers to Python versions. See -Other Installation Options if you want more control.

                                                                                                                                                                                                                                -

                                                                                                                                                                                                                                The --user flag is necessary if you are installing on a shared computer +see Using pip to install a different version rather than using the above command.

                                                                                                                                                                                                                                • +

                                                                                                                                                                                                                              • See Clawpack components for a list of what’s included in this top +level directory.

                                                                                                                                                                                                                                • +

                                                                                                                                                                                                                              • The --user flag is necessary if you are installing on a shared computer where you do not have root access. If you do have root access and want it to be available to all users, you can omit this flag. See notes below for -more information.

                                                                                                                                                                                                                                -

                                                                                                                                                                                                                                The -e flag makes it an “editable” install, leaving the source code in +more information.

                                                                                                                                                                                                                                • +

                                                                                                                                                                                                                              • The -e flag makes it an “editable” install, leaving the source code in place and allowing you to modify it if desired. (Otherwise, by default, pip would move the python code to some -site-packages directory and delete everything else.)

                                                                                                                                                                                                                                -

                                                                                                                                                                                                                                In order to use the Fortran codes within Clawpack (classic, +site-packages directory and delete everything else.)

                                                                                                                                                                                                                                • +

                                                                                                                                                                                                                              • In order to use the Fortran codes within Clawpack (classic, amrclaw, or geoclaw), you should then set the environment -variable CLAW to point to the clawpack-v5.8.0 directory within +variable CLAW to point to the clawpack-v5.8.1 directory within the installation directory $HOME/clawpack_src, and FC to point to the desired Fortran compiler, e.g. in the bash shell:

                                                                                                                                                                                                                                -
                                                                                                                                                                                                                                export CLAW=$HOME/clawpack_src/clawpack-v5.8.0
+
                                                                                                                                                                                                                                export CLAW=$HOME/clawpack_src/clawpack-v5.8.1
 export FC=gfortran
 
                                                                                                                                                                                                                                
 
                                                                                                                                                                                                                                
-
                                                                                                                                                                                                                                Notes:
                                                                                                                                                                                                                                
-
                                                                                                                                                                                                                                You may want to set CLAW even if you are only using PyClaw, since $CLAW is
+
                                                                                                                                                                                                                                • +

                                                                                                                                                                                                                              • You may want to set CLAW even if you are only using PyClaw, since $CLAW is sometimes used in this documentation to indicate the top level of the -Clawpack source directory structure.

                                                                                                                                                                                                                                +Clawpack source directory structure.

                                                                                                                                                                                                                                • +

                                                                                                                                                                                                                              Installing with pip also compiles Riemann solvers written in Fortran for use in PyClaw. If you get a Fortran error message when installing, see Setting the Fortran compiler to be used by f2py (pip).

                                                                                                                                                                                                                              See Set environment variables for more information, and Python path if you are having problems with importing Python modules.

                                                                                                                                                                                                                              -
                                                                                                                                                                                                                              -
                                                                                                                                                                                                                              -

                                                                                                                                                                                                                              Quick Installation of only PyClaw

                                                                                                                                                                                                                              -

                                                                                                                                                                                                                              If you only want to use PyClaw (and associated Python -tools, e.g. VisClaw for visualization), they you could do:

                                                                                                                                                                                                                              -
                                                                                                                                                                                                                              pip install --user clawpack
-
                                                                                                                                                                                                                              -
                                                                                                                                                                                                                              -

                                                                                                                                                                                                                              or, more specifically,

                                                                                                                                                                                                                              -
                                                                                                                                                                                                                              pip install --user clawpack==v5.8.0
-
                                                                                                                                                                                                                              -
                                                                                                                                                                                                                              -

                                                                                                                                                                                                                              However, if you think you might want to use the Fortran packages as well -(Classic, AMRClaw, GeoClaw) and/or want easier access to the Python source -code, it is recommended that you follow the instructions above for -Quick Installation of all packages (or see other Additional options for installing Clawpack).

                                                                                                                                                                                                                              Next steps:

                                                                                                                                                                                                                              Once Clawpack is installed, you can go to one of the following pages to get @@ -172,6 +174,7 @@

                                                                                                                                                                                                                              Next steps:

                                                                                                                                                                                                                            • Testing a PyClaw installation and running an example

                                                                                                                                                                                                                            • Testing your Fortran installation and running an example

                                                                                                                                                                                                                              • +

                                                                                                                                                                                                                            • Troubleshooting Installation

                                                                                                                                                                                                                            @@ -257,8 +260,8 @@

                                                                                                                                                                                                                            Version 5.8.x

                                                                                                                                                                                                                            Table of Contents

                                                                                                                                                                                                                            • pip install instructions
                                                                                                                                                                                                                                -
                                                                                                                                                                                                                              • Quick Installation of all packages
                                                                                                                                                                                                                                • -
                                                                                                                                                                                                                              • Quick Installation of only PyClaw
                                                                                                                                                                                                                                  +
                                                                                                                                                                                                                                • Quick Installation of PyClaw with pip
                                                                                                                                                                                                                                  • +
                                                                                                                                                                                                                                • Quick Installation of all packages with pip
                                                                                                                                                                                                                                  • Next steps:
                                                                                                                                                                                                                                  • Using pip to install a different version
                                                                                                                                                                                                                                  • Experimenting with code in the examples directories
                                                                                                                                                                                                                                    • @@ -272,7 +275,7 @@

                                                                                                                                                                                                                                    Related Topics

                                                                                                                                                                                                                                    diff --git a/v5.8.x/kmltools_module.html b/v5.8.x/kmltools_module.html index c69bf21886..7b73994e85 100644 --- a/v5.8.x/kmltools_module.html +++ b/v5.8.x/kmltools_module.html @@ -114,6 +114,7 @@

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                                                                                                                                                                                                                                  • pcolorcells_for_kml - version of pcolormesh with appropriate dpi and size

                                                                                                                                                                                                                                  • png2kml - create kml file wrapping a png figure to be viewed on GE

                                                                                                                                                                                                                                  • kml_build_colorbar - create a colorbar to display on GE

                                                                                                                                                                                                                                    • +

                                                                                                                                                                                                                                  • topo2kmz - create kmz file showing onshore and offshore topography

                                                                                                                                                                                                                                  • kml_header - used internally

                                                                                                                                                                                                                                  • kml_footer - used internally

                                                                                                                                                                                                                                  • kml_region - used internally

                                                                                                                                                                                                                                    • @@ -223,7 +224,7 @@

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                                                                                                                                                                                                                                    -clawpack.geoclaw.kmltools.kml_build_colorbar(cb_filename, cmap, cmin=None, cmax=None, norm=None, label=None, title=None, extend='neither')
                                                                                                                                                                                                                                    +clawpack.geoclaw.kmltools.kml_build_colorbar(cb_filename, cmap, cmin=None, cmax=None, norm=None, label=None, title=None, extend='neither', close_figs=True)

                                                                                                                                                                                                                                    Make a png file with a colorbar corresponding to cmap, norm. cmin, cmax are used only if nrm is not provided.

                                                                                                                                                                                                                                    @@ -335,7 +336,7 @@

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                                                                                                                                                                                                                                    Internally the value dpi (dots per inch) for the png file is determined so that it is at least 16 and so that:

                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                    System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

                                                                                                                                                                                                                                    +

                                                                                                                                                                                                                                    System Message: ERROR/3 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

                                                                                                                                                                                                                                    Unexpected indentation.

                                                                                                                                                                                                                                    @@ -343,7 +344,7 @@

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                                                                                                                                                                                                                                    dpi * y_inches = dcp * y_cells

                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                    System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 38)

                                                                                                                                                                                                                                    +

                                                                                                                                                                                                                                    System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 38)

                                                                                                                                                                                                                                    Block quote ends without a blank line; unexpected unindent.

                                                                                                                                                                                                                                    where x_cells, y_cells are the number of cells in each direction.

                                                                                                                                                                                                                                    @@ -353,14 +354,14 @@

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                                                                                                                                                                                                                                    annotate the figure befor saving it as a png file, which should then be done with:

                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                    System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

                                                                                                                                                                                                                                    +

                                                                                                                                                                                                                                    System Message: ERROR/3 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

                                                                                                                                                                                                                                    Unexpected indentation.

                                                                                                                                                                                                                                    plt.savefig(png_filename, transparent=True, dpi=kml_dpi)

                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                    System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

                                                                                                                                                                                                                                    +

                                                                                                                                                                                                                                    System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

                                                                                                                                                                                                                                    Block quote ends without a blank line; unexpected unindent.

                                                                                                                                                                                                                                    The png_extent is needed in construcing a kml file to display the @@ -471,6 +472,39 @@

                                                                                                                                                                                                                                    Navigation

                                                                                                                                                                                                                                    Color is green by default.

                                                                                                                                                                                                                                    +
                                                                                                                                                                                                                                    +
                                                                                                                                                                                                                                    +clawpack.geoclaw.kmltools.topo2kmz(topo, zlim=(-20, 20), mask_outside_zlim=True, sea_level=0.0, name='topo', force_dry=None, close_figs=True)
                                                                                                                                                                                                                                    +

                                                                                                                                                                                                                                    Create kmz file showing onshore and offshore topography as separate layers. +Currently not very flexible but is useful in quickly creating kmz files +to open on Google Earth showing the onshore topography and offshore +bathymetry as two separate layers. Constant colors on rectangular grid +cells should be properly rendered to ease exploration of DEMs. +A colorbar png file is also created and included in the kmz file.

                                                                                                                                                                                                                                    +
                                                                                                                                                                                                                                    +
                                                                                                                                                                                                                                    Input
                                                                                                                                                                                                                                    +
                                                                                                                                                                                                                                      +

                                                                                                                                                                                                                                    • topo should be a topotools.Topography object,

                                                                                                                                                                                                                                      • +

                                                                                                                                                                                                                                    • zlim is the elevation z limits for choosing the color map

                                                                                                                                                                                                                                      • +

                                                                                                                                                                                                                                    • mask_outside_zlim if True, suppress plotting outsize zlim

                                                                                                                                                                                                                                      • +

                                                                                                                                                                                                                                    • sea_level is the break between water and land colors

                                                                                                                                                                                                                                      • +

                                                                                                                                                                                                                                    • name is used in the kml menu and file name

                                                                                                                                                                                                                                      • +

                                                                                                                                                                                                                                    • force_dry is currently not used

                                                                                                                                                                                                                                      • +

                                                                                                                                                                                                                                    • close_figs to close the pyplot figures after making png files

                                                                                                                                                                                                                                      • +
                                                                                                                                                                                                                                    +
                                                                                                                                                                                                                                    +
                                                                                                                                                                                                                                    Future
                                                                                                                                                                                                                                    +

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                                                                                                                                                                                                                                    +
                                                                                                                                                                                                                                    +

                                                                                                                                                                                                                                    System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.topo2kmz, line 18)

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                                                                                                                                                                                                                                    Field list ends without a blank line; unexpected unindent.

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                                                                                                                                                                                                                                    If force_dry is an array of the same shape as topo.Z then another png +and kml file are created for land that is below sea_level but where +force_dry = True.

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                                                                                                                                                                                                                            Clawpack includes a number of related hyperbolic PDE solvers:

                                                                                                                                                                                                                            All of them are built on common algorithmic @@ -98,25 +98,29 @@

                                                                                                                                                                                                                            Navigation

                                                                                                                                                                                                                            the main differences between them.

                                                                                                                                                                                                                            Installation and user interface

                                                                                                                                                                                                                            -

                                                                                                                                                                                                                            The AMRClaw, GeoClaw, and Classic solvers are Fortran-based +

                                                                                                                                                                                                                            The Classic, AMRClaw, and GeoClaw solvers are Fortran-based packages and rely on Makefiles and environment variables. Problems are specified partially through Python scripts at run time (setrun.py) and partially through custom Fortran code at compile time (to set initial conditions, for instance).

                                                                                                                                                                                                                            -

                                                                                                                                                                                                                            With PyClaw, problems are specified entirely at run time through +

                                                                                                                                                                                                                            With PyClaw, problems are specified entirely at run time through Python script files, or interactively (e.g., in IPython or Jupyter notebooks). Typically, the user does not need to write any Fortran code (though custom routines can be written in Fortran -when necessary for performance reasons). -PyClaw uses much of the same library of Fortran code, but that code is +when necessary for performance reasons).

                                                                                                                                                                                                                            +

                                                                                                                                                                                                                            PyClaw uses much of the same library of Fortran code, but that code is compiled during installation so that it can be imported dynamically within -Python programs.

                                                                                                                                                                                                                            +Python programs. In particular, Fortran versions of all the Riemann solvers +available in Classic or AMRClaw are also exposed in PyClaw. These are +converted using f2py, a step +that sometimes causes problems and is not required if you are only using +Fortran versions of the solvers.

                                                                                                                                                                                                                            Algorithmic differences

                                                                                                                                                                                                                            All of the Clawpack solvers include the classic algorithms described in [LeVeque-FVMHP]; if you only require those, it’s easiest to use Classic or -Pyclaw. Most of the packages contain additional algorithms:

                                                                                                                                                                                                                            +PyClaw. Most of the packages contain additional algorithms:

                                                                                                                                                                                                                            • AMRClaw includes block-structured adaptive mesh refinement that allows one diff --git a/v5.8.x/plotexamples.html b/v5.8.x/plotexamples.html index 9561897ca9..2fe96126d0 100644 --- a/v5.8.x/plotexamples.html +++ b/v5.8.x/plotexamples.html @@ -84,7 +84,7 @@

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                                                                                                                                                                                                                              Plotting examples

                                                                                                                                                                                                                              -

                                                                                                                                                                                                                              See Using setplot.py to specify the desired plots and the examples in the galleries. +

                                                                                                                                                                                                                              See Using setplot.py to specify the desired plots and the examples in the Clawpack Gallery. The code that produced each set of plots can be found in the Clawpack directory indicated.

                                                                                                                                                                                                                              If you wish to use the Matlab tools, see the Matlab Gallery.

                                                                                                                                                                                                                              diff --git a/v5.8.x/plotting_python.html b/v5.8.x/plotting_python.html index 1a503e38b9..0c4b94298f 100644 --- a/v5.8.x/plotting_python.html +++ b/v5.8.x/plotting_python.html @@ -87,7 +87,7 @@

                                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                                              Clawpack includes utilities for plotting using Python. Most of these are defined in the clawpack.visclaw module. In order to use these you will need to insure that you have the required -modules installed (see Installation of required modules).

                                                                                                                                                                                                                              +modules installed (see python-install).

                                                                                                                                                                                                                              See Python Hints for more information on Python and pointers to many tutorials.

                                                                                                                                                                                                                              Producing html plots from the command line

                                                                                                                                                                                                                              diff --git a/v5.8.x/prereqs.html b/v5.8.x/prereqs.html index f48df0b2a0..a7595f63b4 100644 --- a/v5.8.x/prereqs.html +++ b/v5.8.x/prereqs.html @@ -86,39 +86,37 @@

                                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                                              Fortran

                                                                                                                                                                                                                              -

                                                                                                                                                                                                                              PyClaw can now be installed without a Fortran compiler; see Using conda (does not require a Fortran compiler).

                                                                                                                                                                                                                              -

                                                                                                                                                                                                                              To use the other packages, you will need -gfortran or another F90 compiler

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              To use the Fortran versions of the PDE solvers (Classic, AMRClaw, and GeoClaw), +you will need +gfortran or another F90 compiler.

                                                                                                                                                                                                                              See Fortran Compilers for more about which compilers work well with Clawpack.

                                                                                                                                                                                                                              Python

                                                                                                                                                                                                                                -

                                                                                                                                                                                                                              • Python Version 2.7 or above, or (new in 5.4.0) Python 3

                                                                                                                                                                                                                                • +

                                                                                                                                                                                                                              • Python Version 3.0 or above (much of the code works in Python2, but this +is no longer officially supported; see Dropping support for Python 2.7).

                                                                                                                                                                                                                              • NumPy (for PyClaw/VisClaw)

                                                                                                                                                                                                                              • matplotlib (for PyClaw/VisClaw)

                                                                                                                                                                                                                              -

                                                                                                                                                                                                                              The Anaconda Python Distribution -is an easy way to get all of these. -See Python Hints for more information on -installing the required modules and to get started using Python if -you are not familiar with it.

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              There are many ways to install the Python scientific stack, e.g. via +apt-get or brew. On MacOS, you might check out +ScipySuperpack for Homebrew.

                                                                                                                                                                                                                              pip

                                                                                                                                                                                                                              If you are installing via pip install then you need pip. -You may already have it; in particular the Anaconda Python distribution -contains pip. If you need to install it, see -https://pip.pypa.io/en/stable/installing/

                                                                                                                                                                                                                              -

                                                                                                                                                                                                                              The version of pip install suggested for Quick Installation of all packages requires +If you need to install it, see +https://pip.pypa.io/en/stable/installation/

                                                                                                                                                                                                                              +

                                                                                                                                                                                                                              The version of pip install suggested for Quick Installation of all packages with pip requires a recent version of pip, so you may need to upgrade if you run into problems.

                                                                                                                                                                                                                              Git

                                                                                                                                                                                                                              If you are installing via pip using the command in -Quick Installation of all packages, or via git clone, then you need Git. +Quick Installation of all packages with pip, or via git clone, then you need Git. You may already have it; in particular the Xcode tools on Mac OSX contains Git. If you need to install it, see the Git book.

                                                                                                                                                                                                                              diff --git a/v5.8.x/pyclaw/about.html b/v5.8.x/pyclaw/about.html index 5672220d01..48a15c8cd6 100644 --- a/v5.8.x/pyclaw/about.html +++ b/v5.8.x/pyclaw/about.html @@ -73,7 +73,7 @@

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                                                                                                                                                                                                                            • Clawpack 5.8.x documentation »
                                                                                                                                                                                                                              • -
                                                                                                                                                                                                                            • Pyclaw »
                                                                                                                                                                                                                              • +
                                                                                                                                                                                                                            • PyClaw »
                                                                                                                                                                                                                            @@ -167,7 +167,7 @@

                                                                                                                                                                                                                            Table of Contents

                                                                                                                                                                                                                            Related Topics

                                                                                                                                                                                                                            @@ -129,7 +129,7 @@

                                                                                                                                                                                                                            Version 5.8.x

                                                                                                                                                                                                                            Related Topics

                                                                                                                                                                                                                            • Documentation overview
                                                                                                                                                                                                                                -
                                                                                                                                                                                                                              • Pyclaw @@ -339,7 +339,7 @@

                                                                                                                                                                                                                                Table of Contents

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                                                                                                                                                                                                                                • Documentation overview
                                                                                                                                                                                                                                    -
                                                                                                                                                                                                                                  • Pyclaw @@ -232,7 +232,7 @@

                                                                                                                                                                                                                                    Version 5.8.x

                                                                                                                                                                                                                                    Related Topics

                                                                                                                                                                                                                                    • Documentation overview
                                                                                                                                                                                                                                        -
                                                                                                                                                                                                                                      • Pyclaw
                                                                                                                                                                                                                                          +
                                                                                                                                                                                                                                        • PyClaw
                                                                                                                                                                                                                                          • Going Further @@ -390,7 +390,7 @@

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                                                                                                                                                                                                                                            • Documentation overview
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                                                                                                                                                                                                                                              • Pyclaw @@ -334,7 +334,7 @@

                                                                                                                                                                                                                                                Table of Contents

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                                                                                                                                                                                                                                                • Documentation overview
                                                                                                                                                                                                                                                    -
                                                                                                                                                                                                                                                  • Pyclaw @@ -134,7 +134,7 @@

                                                                                                                                                                                                                                                    From the command line

                                                                                                                                                                                                                                                    Built-in examples

                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                    You can see results from many of the examples in the galleries.

                                                                                                                                                                                                                                                    +

                                                                                                                                                                                                                                                    You can see results from many of the examples in the Clawpack Gallery.

                                                                                                                                                                                                                                                    Adding new examples

                                                                                                                                                                                                                                                    @@ -171,7 +171,7 @@

                                                                                                                                                                                                                                                    Table of Contents

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                                                                                                                                                                                                                                                    Related Topics

                                                                                                                                                                                                                                                    • Documentation overview
                                                                                                                                                                                                                                                        -
                                                                                                                                                                                                                                                      • Pyclaw @@ -136,7 +136,7 @@

                                                                                                                                                                                                                                                        Version 5.8.x

                                                                                                                                                                                                                                                        Related Topics

                                                                                                                                                                                                                                                        • Documentation overview
                                                                                                                                                                                                                                                            -
                                                                                                                                                                                                                                                          • Pyclaw
                                                                                                                                                                                                                                                              +
                                                                                                                                                                                                                                                            • PyClaw
                                                                                                                                                                                                                                                              • diff --git a/v5.8.x/pyclaw/index.html b/v5.8.x/pyclaw/index.html index 7a7ead387d..1bd58a21f9 100644 --- a/v5.8.x/pyclaw/index.html +++ b/v5.8.x/pyclaw/index.html @@ -4,7 +4,7 @@ - Pyclaw — Clawpack 5.8.x documentation + PyClaw — Clawpack 5.8.x documentation @@ -82,22 +82,34 @@

                                                                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                                                                              -

                                                                                                                                                                                                                                                              Pyclaw

                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                              PyClaw

                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                              In this section of the documentation, PyClaw refers +a Python version of the hyperbolic PDE solvers that allows solving the +problem in Python (e.g. in a Jupyter notebook) without explicitly using +any Fortran code. Versions of the solvers are written in Python. +However, they use Riemann solvers that are converted from the Fortran +versions into Python-callable versions using +f2py, +to facilitate using the same large set of solvers from either Fortran +or Python. Note that +in order for this to work the solvers must be precompiled, as is done +when using pip install, for example (see pip install instructions).

                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                              See Which Clawpack solver should I use? for more information about the different +capabilities of PyClaw relative to Classic, AMRClaw, and GeoClaw.

                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                              Note: The clawpack/pyclaw directory also contains some +Python tools that are used many places in +Clawpack, e.g. when plotting with visclaw or when compiling and +running Fortran code using a Makefile and setrun.py file +(when using Classic, AMRClaw, and GeoClaw). +These modules are mostly used “under the hood”. +Other Python tools of use in the Fortran versions +are described elsewhere; see e.g. Plotting with Visclaw or GeoClaw Description and Detailed Contents. +All of these modules are pure Python and should work fine as long +as the top level of Clawpack is on your Python path.

                                                                                                                                                                                                                                                              PyClaw installation

                                                                                                                                                                                                                                                              -

                                                                                                                                                                                                                                                              Just do this:

                                                                                                                                                                                                                                                              -
                                                                                                                                                                                                                                                              pip install clawpack
-
                                                                                                                                                                                                                                                              -
                                                                                                                                                                                                                                                              -

                                                                                                                                                                                                                                                              Installing with pip requires that you have a Fortran compiler installed.

                                                                                                                                                                                                                                                              -

                                                                                                                                                                                                                                                              Alternatively, if you use Anaconda or -Conda, you can:

                                                                                                                                                                                                                                                              -
                                                                                                                                                                                                                                                              conda install -c clawpack -c conda-forge clawpack
-
                                                                                                                                                                                                                                                              -
                                                                                                                                                                                                                                                              -

                                                                                                                                                                                                                                                              This option will also install optional dependencies including PETSc and HDF5, -which are useful for large-scale parallel runs. Installing with Conda does not -require that you have a Fortran compiler.

                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                              Using pip install is the recommended approach, see +pip install instructions.

                                                                                                                                                                                                                                                              Examples

                                                                                                                                                                                                                                                              @@ -293,7 +305,7 @@

                                                                                                                                                                                                                                                              Version 5.8.x

                                                                                                                                                                                                                                                              Table of Contents

                                                                                                                                                                                                                                                              @@ -474,7 +474,7 @@

                                                                                                                                                                                                                                                              Table of Contents

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                                                                                                                                                                                                                                                              @@ -336,7 +336,7 @@

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                                                                                                                                                                                                                                                              @@ -293,7 +293,7 @@

                                                                                                                                                                                                                                                              Table of Contents

                                                                                                                                                                                                                                                              Related Topics

                                                                                                                                                                                                                                                              • Documentation overview
                                                                                                                                                                                                                                                                  -
                                                                                                                                                                                                                                                                • Pyclaw
                                                                                                                                                                                                                                                                    +
                                                                                                                                                                                                                                                                  • PyClaw
                                                                                                                                                                                                                                                                    • Going Further @@ -150,7 +150,7 @@

                                                                                                                                                                                                                                                                      Table of Contents

                                                                                                                                                                                                                                                                      Related Topics

                                                                                                                                                                                                                                                                      • Documentation overview
                                                                                                                                                                                                                                                                          -
                                                                                                                                                                                                                                                                        • Pyclaw
                                                                                                                                                                                                                                                                            +
                                                                                                                                                                                                                                                                          • PyClaw
                                                                                                                                                                                                                                                                            • PyClaw Basics @@ -279,7 +279,7 @@

                                                                                                                                                                                                                                                                              Table of Contents

                                                                                                                                                                                                                                                                              Related Topics

                                                                                                                                                                                                                                                                              • Documentation overview
                                                                                                                                                                                                                                                                                  -
                                                                                                                                                                                                                                                                                • Pyclaw
                                                                                                                                                                                                                                                                                    +
                                                                                                                                                                                                                                                                                  • PyClaw
                                                                                                                                                                                                                                                                                    • Going Further @@ -513,7 +513,7 @@

                                                                                                                                                                                                                                                                                      Table of Contents

                                                                                                                                                                                                                                                                                      Related Topics

                                                                                                                                                                                                                                                                                      • Documentation overview
                                                                                                                                                                                                                                                                                          -
                                                                                                                                                                                                                                                                                        • Pyclaw @@ -336,7 +336,7 @@

                                                                                                                                                                                                                                                                                          Table of Contents

                                                                                                                                                                                                                                                                                          Related Topics

                                                                                                                                                                                                                                                                                          • Documentation overview
                                                                                                                                                                                                                                                                                              -
                                                                                                                                                                                                                                                                                            • Pyclaw @@ -579,7 +579,7 @@

                                                                                                                                                                                                                                                                                              Table of Contents

                                                                                                                                                                                                                                                                                              Related Topics

                                                                                                                                                                                                                                                                                              • Documentation overview
                                                                                                                                                                                                                                                                                                  -
                                                                                                                                                                                                                                                                                                • Pyclaw
                                                                                                                                                                                                                                                                                                    +
                                                                                                                                                                                                                                                                                                  • PyClaw
                                                                                                                                                                                                                                                                                                    • Going Further @@ -201,7 +201,7 @@

                                                                                                                                                                                                                                                                                                      Table of Contents

                                                                                                                                                                                                                                                                                                      Related Topics

                                                                                                                                                                                                                                                                                                      • Documentation overview
                                                                                                                                                                                                                                                                                                          -
                                                                                                                                                                                                                                                                                                        • Pyclaw
                                                                                                                                                                                                                                                                                                            +
                                                                                                                                                                                                                                                                                                          • PyClaw
                                                                                                                                                                                                                                                                                                            • PyClaw Basics @@ -451,7 +451,7 @@

                                                                                                                                                                                                                                                                                                              Table of Contents

                                                                                                                                                                                                                                                                                                              Related Topics

                                                                                                                                                                                                                                                                                                              • Documentation overview
                                                                                                                                                                                                                                                                                                                  -
                                                                                                                                                                                                                                                                                                                • Pyclaw @@ -158,7 +158,7 @@

                                                                                                                                                                                                                                                                                                                  Table of Contents

                                                                                                                                                                                                                                                                                                                  Related Topics

                                                                                                                                                                                                                                                                                                                  • Documentation overview
                                                                                                                                                                                                                                                                                                                      -
                                                                                                                                                                                                                                                                                                                    • Pyclaw @@ -225,7 +225,7 @@

                                                                                                                                                                                                                                                                                                                      Table of Contents

                                                                                                                                                                                                                                                                                                                      Related Topics

                                                                                                                                                                                                                                                                                                                      • Documentation overview
                                                                                                                                                                                                                                                                                                                          -
                                                                                                                                                                                                                                                                                                                        • Pyclaw
                                                                                                                                                                                                                                                                                                                            +
                                                                                                                                                                                                                                                                                                                          • PyClaw
                                                                                                                                                                                                                                                                                                                            • PyClaw Basics @@ -321,7 +321,7 @@

                                                                                                                                                                                                                                                                                                                              Table of Contents

                                                                                                                                                                                                                                                                                                                              Related Topics

                                                                                                                                                                                                                                                                                                                              • Documentation overview
                                                                                                                                                                                                                                                                                                                                  -
                                                                                                                                                                                                                                                                                                                                • Pyclaw
                                                                                                                                                                                                                                                                                                                                    +
                                                                                                                                                                                                                                                                                                                                  • PyClaw
                                                                                                                                                                                                                                                                                                                                    • diff --git a/v5.8.x/python.html b/v5.8.x/python.html index 8ced754ec4..90c20dfa5c 100644 --- a/v5.8.x/python.html +++ b/v5.8.x/python.html @@ -82,23 +82,9 @@

                                                                                                                                                                                                                                                                                                                                    Navigation

                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    Python Hints

                                                                                                                                                                                                                                                                                                                                    - +

                                                                                                                                                                                                                                                                                                                                    Python Hints

                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    Dropping support for Python 2.7

                                                                                                                                                                                                                                                                                                                                    +

                                                                                                                                                                                                                                                                                                                                    Dropping support for Python 2.7

                                                                                                                                                                                                                                                                                                                                    As of Clawpack v5.7.0 we are no longer supporting Python 2.7, and Python 3.x is expected, see v5.7.0 release notes. At this point we believe v5.7.0 still works with Python 2.7, but we are phasing out @@ -118,37 +104,8 @@

                                                                                                                                                                                                                                                                                                                                    Navigation

                                                                                                                                                                                                                                                                                                                                    https://docs.python.org/3/howto/pyporting.html and other online resources discussing the differences between Python 2 and 3.

                                                                                                                                                                                                                                                                                                                                    -
                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    What is Python?

                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    Python is a powerful object-oriented interpreted scripting/programming -language. Some version of Python is almost certainly on your computer -already (on unix, linux, OSX type:

                                                                                                                                                                                                                                                                                                                                    -
                                                                                                                                                                                                                                                                                                                                    $ python --version
-
                                                                                                                                                                                                                                                                                                                                    -
                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    to find out which version, or just:

                                                                                                                                                                                                                                                                                                                                    -
                                                                                                                                                                                                                                                                                                                                    $ python
-
                                                                                                                                                                                                                                                                                                                                    -
                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    to start a python shell with a prompt that looks like:

                                                                                                                                                                                                                                                                                                                                    -
                                                                                                                                                                                                                                                                                                                                    >>>
-
                                                                                                                                                                                                                                                                                                                                    -
                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    You may prefer to use IPython, which is a nicer shell -than the pure python shell, with things like command completion and history. -See the Quick IPython Tutorial.

                                                                                                                                                                                                                                                                                                                                    -
                                                                                                                                                                                                                                                                                                                                    -
                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    Installation of required modules

                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    To effectively use the pyclaw and Clawpack plotting routines that are -written in Python, you will need version 2.7 or greater -(but not 3.0 or above, which is not backwards compatible). -some modules that are not included in the standard Python distribution. -Python modules are loaded with the import statement in Python and a wide -variety of specialized modules exist for various purposes since people use -Python for many different purposes.

                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    An alternative to installing the packages discussed below, you could also use the -Clawpack Virtual Machine, which has all the required Python modules pre-installed.

                                                                                                                                                                                                                                                                                                                                    +
                                                                                                                                                                                                                                                                                                                                    +

                                                                                                                                                                                                                                                                                                                                    References and tutorials

                                                                                                                                                                                                                                                                                                                                    For use with Clawpack, you will need the Numpy module (Numerical Python) that allows working with arrays in much the same way as in Matlab. This is distributed as part of @@ -156,44 +113,24 @@

                                                                                                                                                                                                                                                                                                                                    Navigation

                                                                                                                                                                                                                                                                                                                                    See the Installing SciPy page for tips installing SciPy and NumPy on various platforms.

                                                                                                                                                                                                                                                                                                                                    For plotting you will also need the matplotlib module which provides Matlab-like -plotting commands for 1d and 2d plots (e.g. contour and pcolor plots). -This is generally the hardest thing to get going properly. See the -matplotlib Installation FAQ.

                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    Often the easiest way to get all the modules you need is to install the

                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    Anaconda Python Distribution -or the -Enthought Python Distribution, which is free for academic -users. Versions are available for Windows, Mac OS X, and Redhat linux.

                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    With some versions of Linux (e.g. debian and Ubuntu), you can easily install -what’s needed using apt-get:

                                                                                                                                                                                                                                                                                                                                    -
                                                                                                                                                                                                                                                                                                                                    $ apt-get install python-numpy
-$ apt-get install python-scipy
-$ apt-get install python-matplotlib
-
                                                                                                                                                                                                                                                                                                                                    -
                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    For OS X, you might also try the Scipy Superpack. -See also these tips on installing matplotlib on OS X.

                                                                                                                                                                                                                                                                                                                                    -
                                                                                                                                                                                                                                                                                                                                    -
                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    Notebooks

                                                                                                                                                                                                                                                                                                                                    -

                                                                                                                                                                                                                                                                                                                                    See notebooks.

                                                                                                                                                                                                                                                                                                                                    +

                                                                                                                                                                                                                                                                                                                                    Notebooks

                                                                                                                                                                                                                                                                                                                                    +

                                                                                                                                                                                                                                                                                                                                    The Clawpack Gallery of Jupyter +Notebooks +contains a number of notebooks with other examples of using Python for +Clawpack.

                                                                                                                                                                                                                                                                                                                                    @@ -212,8 +149,6 @@

                                                                                                                                                                                                                                                                                                                                    Table of Contents

                                                                                                                                                                                                                                                                                                                                    • Python Hints diff --git a/v5.8.x/python_path.html b/v5.8.x/python_path.html index a49a30aaac..296576aaa3 100644 --- a/v5.8.x/python_path.html +++ b/v5.8.x/python_path.html @@ -78,10 +78,8 @@

                                                                                                                                                                                                                                                                                                                                      Navigation

                                                                                                                                                                                                                                                                                                                                      When using PyClaw or other Python tools from Clawpack (e.g. the visualization tools in VisClaw or Python tools for working with topo and dtopo from GeoClaw), you need to be able to import various modules.

                                                                                                                                                                                                                                                                                                                                      -

                                                                                                                                                                                                                                                                                                                                      For a general discussion of importing Python modules, see the tutorial in -the Python documentation: -Python 2, -Python 3.

                                                                                                                                                                                                                                                                                                                                      +

                                                                                                                                                                                                                                                                                                                                      For a general discussion of importing Python modules, see the tutorial in the +Python3 documentation.

                                                                                                                                                                                                                                                                                                                                      Below are some hints in case you run into problems with import statements with modules not being found, or being imported from the wrong version of Clawpack (if you have more than one on your computer).

                                                                                                                                                                                                                                                                                                                                      @@ -219,13 +217,20 @@

                                                                                                                                                                                                                                                                                                                                      easy-install.pth

                                                                                                                                                                                                                                                                                                                                      PYTHONPATH

                                                                                                                                                                                                                                                                                                                                      -
                                                                                                                                                                                                                                                                                                                                      -

                                                                                                                                                                                                                                                                                                                                      Warning

                                                                                                                                                                                                                                                                                                                                      -

                                                                                                                                                                                                                                                                                                                                      Setting the environment variable PYTHONPATH is generally +

                                                                                                                                                                                                                                                                                                                                      If you install Clawpack with pip, then you do not need to include it in +environment variable PYTHONPATH.

                                                                                                                                                                                                                                                                                                                                      +

                                                                                                                                                                                                                                                                                                                                      Setting the environment variable PYTHONPATH is often considered bad practice in the Python community and can lead to problems, see for example PYTHONPATH Considered Harmful.

                                                                                                                                                                                                                                                                                                                                      -
                                                                                                                                                                                                                                                                                                                                      +

                                                                                                                                                                                                                                                                                                                                      In spite of the possible drawbacks, some Clawpack developers often +use PYTHONPATH to switch versions without difficulty, particularly +when using one of the Options for installing Clawpack Fortran codes rather than pip.

                                                                                                                                                                                                                                                                                                                                      +

                                                                                                                                                                                                                                                                                                                                      If you do wish to use it, you should set PYTHONPATH to point to the top +level of the clawpack directory for the code you wish to use. +Then use the whichclaw.py utility to check that this is where Clawpack +is imported from, and there is not an easy-install.pth file generated by +pip that points to a different location.

                                                                                                                                                                                                                                                                                                                                      If you have an environment variable PYTHONPATH set, the paths specified here may be searched before or after what is specified in the users’ site-packages/easy-install.pth, depending on how you set PYTHONPATH. @@ -240,13 +245,6 @@

                                                                                                                                                                                                                                                                                                                                      PYTHONPATHwhichclaw.py utility to report this, along with any other possibly conflicting easy-install.pth files.

                                                                                                                                                                                                                                                                                                                                      See Set environment variables for information on setting environment variables.

                                                                                                                                                                                                                                                                                                                                      -

                                                                                                                                                                                                                                                                                                                                      In spite of the possible drawbacks, some Clawpack developers often -use PYTHONPATH to switch versions without difficulty. If you do -wish to use it, you should set PYTHONPATH to point to the top -level of the clawpack directory for the code you wish to use. -Then use the whichclaw.py utility to check that this is where Clawpack -is imported from, and there is not a easy-install.pth that points to a -different location.

                                                                                                                                                                                                                                                                                                                                    diff --git a/v5.8.x/regression.html b/v5.8.x/regression.html index c70644aa22..b0a71d67c9 100644 --- a/v5.8.x/regression.html +++ b/v5.8.x/regression.html @@ -73,7 +73,7 @@

                                                                                                                                                                                                                                                                                                                                    Navigation

                                                                                                                                                                                                                                                                                                                                    previous |
                                                                                                                                                                                                                                                                                                                                  • Clawpack 5.8.x documentation »
                                                                                                                                                                                                                                                                                                                                    • -
                                                                                                                                                                                                                                                                                                                                  • Pyclaw »
                                                                                                                                                                                                                                                                                                                                    • +
                                                                                                                                                                                                                                                                                                                                  • PyClaw »
                                                                                                                                                                                                                                                                                                                                  • Developers’ Guide »
                                                                                                                                                                                                                                                                                                                                  @@ -130,7 +130,7 @@

                                                                                                                                                                                                                                                                                                                                  Fortran codesgalleries. An attempt at automating this +with those archived in the Clawpack Gallery. An attempt at automating this can be found in the $CLAW/amrclaw/examples directory, which uses the imagediff tool described below. This is still under development.

                                                                                                                                                                                                                                                                                                                                  @@ -322,7 +322,7 @@

                                                                                                                                                                                                                                                                                                                                  Table of Contents

                                                                                                                                                                                                                                                                                                                                  Related Topics

                                                                                                                                                                                                                                                                                                                                  • Documentation overview
                                                                                                                                                                                                                                                                                                                                      -
                                                                                                                                                                                                                                                                                                                                    • Pyclaw
                                                                                                                                                                                                                                                                                                                                        +
                                                                                                                                                                                                                                                                                                                                      • PyClaw
                                                                                                                                                                                                                                                                                                                                        • Developers’ Guide
                                                                                                                                                                                                                                                                                                                                          • diff --git a/v5.8.x/release_5_6_0.html b/v5.8.x/release_5_6_0.html index 061819038f..787dfd531b 100644 --- a/v5.8.x/release_5_6_0.html +++ b/v5.8.x/release_5_6_0.html @@ -78,7 +78,7 @@

                                                                                                                                                                                                                                                                                                                                          Navigation

                                                                                                                                                                                                                                                                                                                                          Clawpack 5.6.0 was released on June 2, 2019. See Installing Clawpack.

                                                                                                                                                                                                                                                                                                                                          Changes relative to Clawpack 5.5.0 (Aug 28, 2018) are shown below.

                                                                                                                                                                                                                                                                                                                                          To see more recent changes that are in the the master branch but not yet -released, see Changes to master since v5.8.0.

                                                                                                                                                                                                                                                                                                                                          +released, see Changes to master since v5.8.1.

                                                                                                                                                                                                                                                                                                                                          Changes that are not backward compatible

                                                                                                                                                                                                                                                                                                                                          diff --git a/v5.8.x/release_5_6_1.html b/v5.8.x/release_5_6_1.html index 6e27da7fb3..fbddece1e5 100644 --- a/v5.8.x/release_5_6_1.html +++ b/v5.8.x/release_5_6_1.html @@ -78,7 +78,7 @@

                                                                                                                                                                                                                                                                                                                                          Navigation

                                                                                                                                                                                                                                                                                                                                          Clawpack 5.6.1 was released on October 28, 2019. See Installing Clawpack.

                                                                                                                                                                                                                                                                                                                                          Changes relative to Clawpack 5.6.0 (June 2, 2019) are shown below.

                                                                                                                                                                                                                                                                                                                                          To see more recent changes that are in the the master branch but not yet -released, see Changes to master since v5.8.0.

                                                                                                                                                                                                                                                                                                                                          +released, see Changes to master since v5.8.1.

                                                                                                                                                                                                                                                                                                                                          Changes that are not backward compatible

                                                                                                                                                                                                                                                                                                                                          $CLAW/amrclaw/src/2d/amr_module.f90 has changed, so do a make new in diff --git a/v5.8.x/release_5_7_0.html b/v5.8.x/release_5_7_0.html index 8092c514a4..41bd35c428 100644 --- a/v5.8.x/release_5_7_0.html +++ b/v5.8.x/release_5_7_0.html @@ -80,7 +80,7 @@

                                                                                                                                                                                                                                                                                                                                          Navigation

                                                                                                                                                                                                                                                                                                                                          [DOI 10.5281/zenodo.3764278].

                                                                                                                                                                                                                                                                                                                                          Changes relative to Clawpack 5.6.1 (October 28, 2019) are shown below.

                                                                                                                                                                                                                                                                                                                                          To see more recent changes that are in the the master branch but not yet -released, see Changes to master since v5.8.0.

                                                                                                                                                                                                                                                                                                                                          +released, see Changes to master since v5.8.1.

                                                                                                                                                                                                                                                                                                                                          Python support

                                                                                                                                                                                                                                                                                                                                          As of v5.7.0 we are no longer supporting Python 2.7, and Python 3.x is diff --git a/v5.8.x/release_5_7_1.html b/v5.8.x/release_5_7_1.html index 20a54c4dcc..f7057c4d3f 100644 --- a/v5.8.x/release_5_7_1.html +++ b/v5.8.x/release_5_7_1.html @@ -80,7 +80,7 @@

                                                                                                                                                                                                                                                                                                                                          Navigation

                                                                                                                                                                                                                                                                                                                                          [DOI 10.5281/zenodo.4025432].

                                                                                                                                                                                                                                                                                                                                          Changes relative to Clawpack 5.7.0 (April 23, 2020) are shown below.

                                                                                                                                                                                                                                                                                                                                          To see more recent changes that are in the the master branch but not yet -released, see Changes to master since v5.8.0.

                                                                                                                                                                                                                                                                                                                                          +released, see Changes to master since v5.8.1.

                                                                                                                                                                                                                                                                                                                                          Changes that are not backward compatible

                                                                                                                                                                                                                                                                                                                                            diff --git a/v5.8.x/release_5_8_0.html b/v5.8.x/release_5_8_0.html index 7030136225..c8d38ef764 100644 --- a/v5.8.x/release_5_8_0.html +++ b/v5.8.x/release_5_8_0.html @@ -79,7 +79,7 @@

                                                                                                                                                                                                                                                                                                                                            Navigation

                                                                                                                                                                                                                                                                                                                                            Permanent DOI: http://doi.org/10.5281/zenodo.4503024

                                                                                                                                                                                                                                                                                                                                            Changes relative to Clawpack 5.7.1 (Sept. 11, 2020) are shown below.

                                                                                                                                                                                                                                                                                                                                            To see more recent changes that are in the the master branch but not yet -released, see Changes to master since v5.8.0.

                                                                                                                                                                                                                                                                                                                                            +released, see Changes to master since v5.8.1.

                                                                                                                                                                                                                                                                                                                                            Changes that are not backward compatible

                                                                                                                                                                                                                                                                                                                                              diff --git a/v5.8.x/release_5_8_1.html b/v5.8.x/release_5_8_1.html new file mode 100644 index 0000000000..fed5017018 --- /dev/null +++ b/v5.8.x/release_5_8_1.html @@ -0,0 +1,245 @@ + + + + + + + v5.8.1 release notes — Clawpack 5.8.x documentation + + + + + + + + + + + + + + + + +
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                                                                                                                                                                                                                                                                                                                                              v5.8.1 release notes

                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              Clawpack 5.8.1 was released on October 19, 2021. See Installing Clawpack.

                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              The installation instructions have been reorganized (once again) +in an attempt to make the different options clearer.

                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              Permanent DOI: http://doi.org/10.5281/zenodo.??

                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              Changes relative to Clawpack 5.8.0 (February 4, 2021) are shown below.

                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              To see more recent changes that are in the the master branch but not yet +released, see Changes to master since v5.8.1.

                                                                                                                                                                                                                                                                                                                                              +
                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              Changes that are not backward compatible

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                                                                                                                                                                                                                                                                                                                                              General changes

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                                                                                                                                                                                                                                                                                                                                              Changes to classic

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                                                                                                                                                                                                                                                                                                                                              No changes.

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                                                                                                                                                                                                                                                                                                                                              See classic diffs

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                                                                                                                                                                                                                                                                                                                                              Changes to clawutil

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                                                                                                                                                                                                                                                                                                                                              No changes.

                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              See clawutil diffs

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                                                                                                                                                                                                                                                                                                                                              Changes to visclaw

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                                                                                                                                                                                                                                                                                                                                              No major changes.

                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              See visclaw diffs

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                                                                                                                                                                                                                                                                                                                                              Changes to riemann

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                                                                                                                                                                                                                                                                                                                                                +

                                                                                                                                                                                                                                                                                                                                              • Fix rp1_shallow_hlle.f90 to work better near dry states.

                                                                                                                                                                                                                                                                                                                                                • +
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                                                                                                                                                                                                                                                                                                                                              See riemann diffs

                                                                                                                                                                                                                                                                                                                                              +
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                                                                                                                                                                                                                                                                                                                                              Changes to amrclaw

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                                                                                                                                                                                                                                                                                                                                              No changes.

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                                                                                                                                                                                                                                                                                                                                              See amrclaw diffs

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                                                                                                                                                                                                                                                                                                                                              Changes to geoclaw

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                                                                                                                                                                                                                                                                                                                                              • Some improvements to storm tracks

                                                                                                                                                                                                                                                                                                                                                • +

                                                                                                                                                                                                                                                                                                                                              • Reading (some) geotiff files now supported in topotools

                                                                                                                                                                                                                                                                                                                                                • +

                                                                                                                                                                                                                                                                                                                                              • Added kmltools.topo2kmz to make Google Earth overlays showing topography

                                                                                                                                                                                                                                                                                                                                                • +

                                                                                                                                                                                                                                                                                                                                              • Some other bug fixes.

                                                                                                                                                                                                                                                                                                                                                • +
                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              See geoclaw diffs

                                                                                                                                                                                                                                                                                                                                              +
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                                                                                                                                                                                                                                                                                                                                              Changes to PyClaw

                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              For changes in PyClaw, see the PyClaw changelog.

                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              See pyclaw diffs

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                                                                                                                                                                                                                                                                                                                                              Other Clawpack Repositories

                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              The repositories below are not included in the Clawpack tarfile or pip +install, but changes to these repositories may also be of interest.

                                                                                                                                                                                                                                                                                                                                              + +
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                                                                                                                                                                                                                                                                                                                                              + © Copyright CC-BY 2020, The Clawpack Development Team. + Created using Sphinx. +
                                                                                                                                                                                                                                                                                                                                              + + + + \ No newline at end of file diff --git a/v5.8.x/releases.html b/v5.8.x/releases.html index 80f7a48508..e27391b235 100644 --- a/v5.8.x/releases.html +++ b/v5.8.x/releases.html @@ -92,7 +92,7 @@

                                                                                                                                                                                                                                                                                                                                              Other notes:Citing this work for the suggested way to cite the version of Clawpack that you are using in publications.

                                                                                                                                                                                                                                                                                                                                            • For changes in PyClaw, see the PyClaw changelog.

                                                                                                                                                                                                                                                                                                                                              • -

                                                                                                                                                                                                                                                                                                                                            • See Changes to master since v5.8.0 for changes to the master branch on Github +

                                                                                                                                                                                                                                                                                                                                            • See Changes to master since v5.8.1 for changes to the master branch on Github that are not in the most recent release.

                                                                                                                                                                                                                                                                                                                                            • The “dev” branch of the documentation (selected under Versions on the menu @@ -109,6 +109,8 @@

                                                                                                                                                                                                                                                                                                                                              Releases:10.17605/osf.io/kmw6h. See Citing this work for more information on how best to cite Clawpack.

                                                                                                                                                                                                                                                                                                                                                +

                                                                                                                                                                                                                                                                                                                                              • v5.8.1 release notes – October 19, 2021 +[DOI 10.5281/zenodo.??]

                                                                                                                                                                                                                                                                                                                                              • v5.8.0 release notes – February 4, 2021 [DOI 10.5281/zenodo.4503024]

                                                                                                                                                                                                                                                                                                                                              • v5.7.1 release notes – September 11, 2020 diff --git a/v5.8.x/searchindex.js b/v5.8.x/searchindex.js index 94be04cfc2..794aa99b41 100644 --- a/v5.8.x/searchindex.js +++ b/v5.8.x/searchindex.js @@ -1 +1 @@ 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155],alloc:[20,99,117,126,138],allocat:117,allot:59,allow:[4,6,13,22,27,28,29,32,38,39,44,45,47,50,51,53,54,56,58,64,66,67,70,71,73,76,77,86,92,93,99,101,104,105,106,110,111,113,114,117,118,119,120,121,123,124,126,129,131,137,139,140,141,142,146,150,152,154],almost:105,alon:[16,51],along:[6,14,16,24,27,30,32,39,44,51,54,68,70,106,110,117,128,131,133,140,146,154],alpha:[51,55,99],alphabet:81,alreadi:[0,1,6,12,13,18,28,29,41,55,56,57,58,59,60,66,79,80,94,98,100,103,105,114,122,152],also:[3,4,5,6,7,8,9,11,12,16,17,18,20,22,23,24,25,28,29,30,32,33,35,36,37,38,39,41,42,44,47,48,51,52,53,54,55,56,57,58,59,62,63,66,67,68,70,71,72,73,76,77,79,83,85,86,89,91,93,94,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,135,137,138,139,140,141,142,144,145,146,147,148,149,150,152,153,154,155,157,158],alter:51,altern:[30,35,36,44,47,51,57,60,62,67,76,91,94,105,106,110,117,118,119],although:[30,51,63,67,95,96,98,110,122,152],alwai:[16,22,26,27,28,32,41,53,54,58,67,83,92,109,110,113,114,126,133,139,140,141,150,155],amal:[4,17,81,91],amazon:25,amazonaw:13,amdq:[97,129],ami:25,among:124,amount:[44,48,54],amplitud:[5,119],amr:[4,7,8,16,20,23,25,27,28,32,34,38,44,45,52,59,67,72,73,76,81,89,118,120,121,122,124,126,133,136,137,139,141,149,155],amr_1d:122,amr_2d:[121,122],amr_:[3,7],amr_celledges_show:3,amr_contour_color:3,amr_contour_show:3,amr_data_show:118,amr_level:72,amr_level_max:139,amr_levels_max:[32,110,138,139],amr_modul:[71,110,117,123,124],amrclaw:[4,5,6,12,15,16,19,20,22,23,24,28,36,38,39,41,44,45,46,52,55,56,57,58,60,66,67,68,71,72,73,100,106,107,110,111,128,129,131,134,135,137,140,144,145,148,149,153],amrdata:[5,22,32,110,124,126,138,139,140],amrflag:110,amrlib:117,amrnez:110,an11:54,anaconda:[51,80,91,100,105],anal:17,analog:[137,138],analysi:17,andi:4,angl:[16,30,47,70],ani:[3,4,5,6,8,13,16,18,19,20,22,27,28,29,32,35,36,37,45,48,50,51,54,55,56,58,61,62,64,66,67,69,71,72,73,77,81,87,88,89,91,92,93,94,96,98,100,104,106,109,110,111,117,121,123,128,131,132,133,136,137,138,140,146,155,158],anim:[12,16,42,51,117,124,125,142],animation_tool:[124,125],anisotrop:[6,22],anl:94,annot:[27,59],annual:24,anoth:[3,22,39,44,51,55,57,58,72,76,80,88,99,102,111,121,146,155],answer:24,anyth:[3,6,28,29,56,58,63,111,121],anywher:110,aoml:146,apach:13,apdq:[97,129],api:[47,121],app:[12,13,18,23,26,28,29,32,37,42,70,108,109,116,120,121,122,123,124,125,126,130],appar:[30,32,71],appeal:51,appear:[0,1,3,5,8,13,18,23,32,44,45,51,54,57,59,62,65,77,93,98,101,119,126,140,142,150],append:[5,20,32,38,39,44,51,60,77,86,98,110,118,119,128,129,139],appl:17,appli:[3,4,5,6,13,16,25,30,48,51,53,64,66,70,77,79,87,89,92,99,110,128,137,140,155],applic:[4,6,15,16,19,20,22,23,24,28,29,32,35,36,37,41,42,45,46,55,56,58,63,66,68,71,79,88,89,90,91,93,99,104,107,109,110,111,113,116,117,119,120,121,123,124,129,131,133,134,137,140,144,145,150,152,153,155,156],appreci:81,approach:[5,7,13,28,29,38,44,54,56,69,76,84,94,96,104,110,117,119,120,122,129,130,136,140,155,158],appropri:[4,5,6,13,16,24,28,45,48,49,51,55,56,58,59,60,64,67,68,69,71,83,86,87,88,92,94,95,96,97,98,111,123,129,132,135,137,146,155,158],approv:48,approxim:[6,16,25,33,48,51,70,129],april:[24,124,125,127],apt:[13,105],arbitrari:[32,59,99,113,131,140],arbitrarili:66,arc:132,arcgi:152,architectur:94,archiv:[12,21,36,51,55,111,142,148,152,154],arcminut:[70,150],arcsecond:[45,150],area:[15,22,45,99,108,119,133,134],arg:[89,98],argument:[0,1,2,3,27,30,45,47,50,51,53,77,83,84,88,89,92,96,98,99,101,104,111,121,129,131,136,137,138,146,152,155],argv:[139,141],aris:[61,81],arithmet:64,aron:[4,17,81,91],arora:87,arora_ro:87,around:[6,30,32,39,59,92,108,111,124,138,139,146,152,155],arrai:[0,3,6,15,20,22,27,30,32,33,38,44,45,47,49,53,59,77,83,84,86,87,89,91,92,93,96,97,98,99,101,103,104,105,113,114,115,119,121,124,126,129,130,131,134,137,138,139,140,141,146,150,152,155],arrang:152,arriv:[22,32,34,39,45,119,132,133],arrival_tol:32,articl:[4,17,91,142],artifici:[16,133],arxiv:52,asc:152,ascii:[44,53,67,83,86,93,98,119,128,137,139,141,150,156],ascii_output_format:68,ask:24,ask_us:152,aspect:[12,24,29,48,49,67],assembl:57,assert:[139,141],assess:[4,48,132],assign:[30,32,83,86,92,98],assist:[22,124],associ:[0,1,2,6,22,51,58,71,89,92,93,111],assum:[3,5,20,22,30,32,36,39,47,48,51,53,54,55,59,67,70,76,92,93,95,96,97,103,104,110,117,131,132,137,140,146,147,150,152,154,158],assumpt:[51,54],asteroid:4,astronom:132,atcf:[108,121,146,147],aterrel:4,atmospher:4,attach:[55,92,101],attempt:[5,8,11,20,33,35,36,62,92,104,111,113,146,152,153],attirbut:22,attr:[89,98],attribur:5,attribut:[5,7,22,30,38,44,66,70,76,78,79,83,86,89,92,94,96,98,99,110,113,118,122,128,136,137,138,140,146,152],attributeerror:77,aug:[17,122],aug_glob:97,augment:[66,130],august:[24,121,127],austin:4,author:[17,25,45,48,87,91,92,97,109],auto:[0,44,84],autom:[14,54,84,111],automat:[0,2,3,8,11,16,30,35,36,41,51,55,62,76,77,79,83,88,92,94,100,101,102,104,111,113,124,126,137,138,140,150],au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rown:[81,152],brows:[11,24,42,51,67,142,155],browser:[13,28,29,35,36,51,54,142],bsd:[4,61,81,121],buffer:[30,39,44,110,118,119,138,139,152],buffer_length:152,buffer_s:[30,70],bug:[4,8,12,22,24,41,51,64,71,77,81,116,117,118,119,121,126],build:[4,17,28,29,54,55,67,84,94,104,120,131],buildsystem:94,built:[28,29,64,73,82,91,94,96,98,110,111,144,145],bulk:[19,83,97,103,129,139,155],bull:[17,30],buoi:45,burger:[91,129,155],burgers_1d:97,burgers_1d_pi:97,busi:[61,81],butcher:99,button:[12,13,28,51,59,120],bzip2:124,c210:[17,91],c231:[17,91],c_center:89,c_centers_with_ghost:89,c_l:97,c_node:89,c_nodes_with_ghost:89,c_r:97,cach:[22,47,55,79,81,124,138],cache_dir:47,cada:87,cada_torrilhon_limit:87,cada_torrilhon_limiter_nonlinear:87,cake:74,cal:[129,155,158],calcul:[3,5,6,27,30,33,45,47,67,70,77,89,97,99,114,119,152],calculate_geometri:30,calculate_geometry_triangl:30,calhellev08:17,calhoun:[4,17,51],calhounhelzellevequ:16,call:[1,6,9,20,22,27,30,38,41,44,50,51,63,66,67,70,72,77,79,83,84,86,87,92,93,96,98,99,101,103,104,110,111,113,117,118,120,121,129,131,133,135,137,139,140,141,146,152,155],call_before_step_each_stag:99,call_setplot:77,callabl:104,calucl:97,cambridg:17,came:14,camera:51,can:[0,2,3,4,5,6,7,8,9,11,12,13,14,15,16,19,20,22,24,26,27,28,29,30,32,35,36,37,38,39,40,41,42,44,45,46,47,48,51,52,53,54,55,56,57,58,59,60,62,63,64,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,83,84,85,87,88,89,91,92,93,94,95,96,98,99,100,101,102,103,104,105,106,107,108,110,111,113,114,117,118,119,120,121,124,125,126,127,128,129,131,132,133,134,135,136,137,138,139,140,141,142,144,145,146,148,150,152,153,154,155,156,158],cannot:[52,58,92,126,133,146],canopi:100,capa:98,capa_index:[137,139,141],capab:152,capabili:121,capabilit:119,capabilti:121,capabl:[7,12,22,32,34,48,52,66,73,84,113,118,119,121,122,123,124,125,152,154],capac:[15,97,134,137,138,139,141],captur:[32,48,131,150],car_nam:146,care:[32,39,45,94],carefulli:[20,22,64],cartesian:[32,46,59,84,140],cartopi:146,cascad:4,cast:152,cat_nam:146,catalog:154,categor:146,categori:146,category_color:146,caus:[22,48,51,54,61,62,79,81,102,111,118,119,120,122,126,136,138,150,152],caut:87,caution:48,cautionari:[25,45,63,140],cautiou:48,caxi:67,cb_file:59,cb_filenam:59,cb_kwarg:152,cb_name:59,cb_xfrac:59,cb_yfrac:59,cbar:[97,152],cdot:[64,96,131],ceas:105,cell:[3,4,5,7,8,15,16,20,22,25,27,32,33,44,45,51,53,59,66,67,71,72,73,83,89,94,97,99,101,103,110,113,114,118,119,120,121,122,123,124,126,129,132,133,134,137,138,139,140,141,147,149,150,155,158],celledg:3,celledges_show:[3,22],cellgridintegr:113,cellgridintegrate2:113,cellsiz:[39,53,117,150],center:[4,5,27,30,32,33,39,44,51,53,59,70,83,89,96,97,103,110,121,131,133,138,139,140,146,147,150,155],centerlin:30,centers_with_ghost:89,central:[137,146,147],central_pressur:146,centroid:[30,70],certain:[14,32,45,57,66,93,110,118,131,137],certainli:[94,105],certik:[4,81],cf2py:84,cfl:[6,89,93,99,103,113,118,137,139,140,141],cfl_desir:[99,137,139,141],cfl_max:[99,137,139,141],cfl_superbe:87,cfl_superbee_theta:87,challeng:120,chanc:81,chang:[1,6,8,13,15,16,19,20,25,28,29,30,32,40,41,50,51,52,53,54,55,56,58,59,62,63,64,66,67,68,71,72,73,76,79,83,84,90,92,93,101,104,105,108,109,110,111,127,129,133,134,137,138,139,140,141,144,145,150,153,155],changelog:[18,22,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127],changes_to_mast:55,channel:24,chapter:[16,129,137,155],char_decomp:99,charact:47,characterist:99,charg:13,chava:140,cheaper:13,check:[6,14,15,16,20,32,35,36,40,41,50,51,52,54,55,56,58,62,67,77,83,84,86,91,94,98,99,101,103,104,106,107,110,114,123,131,133,134,138,139,144,145,146,152,153,154,155],check_3rd_ord_cond:99,check_diff:[104,111],check_lmm_cond:99,check_valid:86,check_valu:[104,111],checkout:[28,52,54,55],checkpoint:[25,44,118,119,121,123,126,137,139,141],checkpt_interv:[137,139],checkpt_styl:[118,128,137,139],checkpt_tim:[137,139],checksum:92,chen:[30,154],chile2010:[51,109,110,113,116,122,150],chile2010_adjoint:5,chile2010_fgmax:32,chile2010a:[29,109],chile2010b:109,chile:[45,59,70],chile_2010:51,chile_dtopo:70,chk00006:[139,141],chk00100:118,chk:118,chkaaaaa:118,chkbbbbb:118,chknnnnn:[128,137,139,141],choic:[16,45,76,99,137,139,140,141,155],choos:[0,7,70,96,137,140],chose:64,chosen:[3,29,32,38,39,51,53,66,103,110,126,132,138],chri:4,chunk:92,chunksiz:92,circl:[3,47,77],circular:17,cise:17,citat:[4,55],cite:[25,55,57,127],cjvogl:4,clamshel:114,clarifi:22,clariti:38,clash:67,classic4:141,classic:[4,6,12,15,16,19,20,22,23,24,28,41,42,46,55,56,57,58,63,69,71,72,73,81,83,86,88,89,90,91,92,96,106,107,111,128,129,134,135,138,140,145,153,155],classic_1d:63,claw1:[63,104],claw1ez:63,claw:[5,6,8,11,12,13,14,15,16,19,20,22,24,28,30,32,33,35,36,37,38,40,41,44,45,47,49,50,52,54,55,56,57,58,59,62,63,67,69,70,71,78,83,86,88,91,92,93,94,100,102,106,107,108,109,110,111,113,114,116,117,120,121,123,129,133,134,139,140,141,143,144,145,148,149,150,152,153,155,156],claw_1dnoncon:158,claw_git_diff:[28,50,55],claw_git_statu:[28,50,55,125],claw_lib:68,claw_outdir:[62,77],claw_packag:99,claw_pkg:[137,138,139,140,141],claw_topo_download:152,claw_vers:58,clawdata2pyclaw:84,clawdata:[5,38,113,117,128,137,138,139,140,141],clawdev2013:54,clawdev:54,clawgraph:67,clawicon:54,clawlogo:54,clawpack:[1,4,5,6,7,11,16,26,28,30,32,33,34,35,36,37,38,39,41,42,43,44,45,46,47,48,50,51,58,59,60,61,63,66,67,69,70,71,75,76,77,78,79,80,81,82,83,85,86,88,89,90,91,92,93,94,95,96,97,98,101,102,103,104,105,106,109,111,112,113,114,115,116,117,118,119,128,129,131,135,137,138,139,140,142,143,146,148,150,152,153,155,156,158],clawpack_gpu:52,clawpack_src:[56,58,106],clawplotax:[1,2,3,27,77,121,126,136],clawplotdata:[2,3,27,44,51,77,79,86,136],clawplotfigur:[0,1,51,77,136],clawplotitem:[0,1,7,22,27,76,78,118,121,136],clawrundata:[5,44,59,122,128,137,138,139,141],clawsolut:1,clawsolv:[99,129],clawsolver1d:[83,86,89,99,103,129],clawsolver2d:[89,99],clawutil:[5,11,14,19,20,23,28,40,41,50,55,57,62,106,111,135,137,138,139,141,152,153],clean:[22,54,55,104,117,121],cleaner:[28,119],cleanup:120,clear:[1,2,6,67,79],clearer:[123,126],clearfigur:1,clearfram:[1,79],cleargaug:44,clearli:[44,48,51,131],clf:2,clf_each_fram:2,click:[4,12,13,18,28,51,54,111,120,127],clifford:24,clint:17,clobber:[92,118],clockwis:[32,47,70,152],clone:[12,18,23,24,42,52,54,55,56,58,80,94,100,109,153],close:[13,39,51,54,66,67,92,110,124,138,146],closer:[70,139],closest:146,cloud:13,cluster:[6,17,57,110,138,139],clustering_cutoff:[110,138,139],cma:146,cmap:[39,51,59,66,77,131,152],cmap_dri:[39,66],cmap_land:66,cmap_sea:66,cmap_sea_dri:66,cmap_slip:30,cmap_topo:66,cmax:[51,59],cmax_dz:30,cmax_slip:30,cmdline:106,cmin:[51,59],cmin_slip:30,cmmi:4,cname:54,coars:[3,32,51,110,119,126,137,150,155],coarsen:[53,110,121,122,138,150,152],coarsen_method:53,coarser:[3,16,53,119,133,137,138,155],coarsest:[6,51,72,113,128,137],coast:[39,66,110,133,152],coastal:[48,124,132,133,140,150],coastlin:[32,51,66,124,131,140,154],code:[4,5,6,7,8,12,14,16,19,20,21,22,23,24,27,29,32,35,36,38,40,41,42,44,45,48,50,52,53,54,56,57,61,62,63,64,68,69,70,71,72,73,75,77,79,81,83,84,89,91,92,93,94,96,99,100,103,105,106,109,112,113,114,117,118,119,120,121,122,123,124,126,128,129,130,131,137,138,139,140,141,142,146,148,149,150],code_of_conduct:121,coeffici:[5,64,96,97,99,101,102,103,129,140],colella:[6,17],collabor:[51,142],collect:[12,25,26,28,30,32,70,76,83,99,142],collela:120,color:[3,30,39,51,59,66,67,76,131,136,146,152],colorado:24,colorbar:[3,39,59,66,121,124,131,152],colorbar_kwarg:121,colorbar_labels:30,colorbar_shrink:30,colorbar_ticks:30,colormap:[3,30,39,46,51,66,67,76,78,118,124,152],column:[10,30,32,44,48,60,93,97,117,131,152],column_list:30,column_map:30,com:[12,13,23,24,26,28,29,52,54,55,56,57,58,92,94,96,100,116,118,119,120,127,130],combin:[20,54,59,118,154],combinatori:111,come:[3,28,77,79,88,94,99,117,150,155],comfort:[58,96],comm_world:104,command:[0,1,2,3,11,13,14,28,40,50,51,52,55,56,57,58,62,69,76,77,80,83,84,86,91,94,95,99,103,104,105,106,111,129,135,136,137,138,150,152],commenc:128,comment:[5,11,24,49,55,120,128],commit:[25,30,50,54,55,111],common:[3,23,28,35,36,40,41,62,63,73,76,83,97,99,101,102,119,121,124,153,155],common_sourc:63,commonli:[3,67,77,79],commun:[25,51,81,101,104,106,110,121],comot:4,compact:[66,150],compactli:131,compar:[5,22,36,44,48,51,55,77,93,110,111,132,138,140,148,154,158],compare_gaug:117,comparison:52,compat:[28,30,47,51,59,70,76,94,102,105,114,115,119,120,152],compil:[13,25,35,36,40,46,56,58,63,71,73,79,80,84,91,92,96,100,104,113,129,130,135],compile_librari:104,complet:[20,22,28,47,62,79,83,84,94,104,105,111],complevel:92,complex:[12,38,89],compliant:41,complic:[16,77,84,131,136],compon:[3,16,20,22,25,36,44,56,58,67,72,76,96,98,100,101,110,117,126,130,137,138,139,150,155],compos:[30,83],comprehens:111,compress:[30,92,152],compris:[22,91,152],comput:[3,4,5,6,13,16,17,27,29,30,32,33,39,44,47,51,53,56,58,59,60,62,68,70,76,77,79,84,86,89,91,92,93,94,99,103,105,106,108,110,113,114,118,119,123,126,129,133,137,139,140,141,147,150,155,158],computation:[84,99],compute_f:[86,93],compute_gauge_valu:93,compute_p:[83,86],concentr:108,concept:[25,129],concern:[22,45,138],conclus:[4,51],conda:[51,56,80,91],condit:[5,7,20,25,61,63,73,81,82,83,84,86,93,99,107,113,114,117,121,132,137,139,140,141],conduct:121,conf:[54,55],confer:24,config:94,config_fc:153,configur:[77,83,94,152],confirm:48,conflict:[6,28,58,62,67,102,106],conform:[22,28,33,98,121,150],confus:[3,53,58,106,126,129],conjunct:[24,39,66,92,110],conlict:62,connect:[32,54,59,66,124,131],consequenti:[61,81],conserv:[4,5,6,17,93,99,101,122,130,155,158],consid:[6,39,48,57,58,66,84,106,135,142,152],consider:[48,83],consist:[6,25,32,47,51,55,59,94,105,119,129,131,140,150,155],consol:[13,93,140],consolid:117,constant:[30,32,48,59,64,94,97,129,130,131,133,140,152,155],constant_storm_modul:117,constrain:110,constraint:[39,44,131,138,158],construc:59,construct:[22,30,32,53,83,89,104,146,147,150],construct_function_handl:104,constructor:101,consult:102,contact:[12,88,91,100],contain:[1,3,5,12,13,20,23,25,26,30,32,33,35,36,37,40,42,44,45,47,49,50,51,52,53,54,55,57,59,60,62,63,66,67,68,72,73,77,79,80,83,84,86,87,89,92,94,96,97,98,99,101,103,104,106,110,111,113,114,121,122,127,129,131,136,137,140,142,146,150,152,153,155],containing_rect:30,contains:29,containt:128,contamin:137,contan:51,content:[4,6,23,51,55,73,84,140,150,155,156],context:[27,51,155],contigu:[72,92,101,131],continent:[7,66],contingu:22,continu:[13,22,28,30,49,54,81,105,129,137,158],contour:[3,30,44,51,53,67,105,136,152],contour_color:3,contour_kwarg:[3,152],contour_level:[3,152],contour_max:3,contour_min:3,contour_nlevel:3,contour_show:3,contourf:[51,76],contract:[4,61,81],contrast:[53,131],contribut:[4,24,25,57,81,84,91,96,99,108,111],contributor:[4,24,61,91],control:[6,7,23,25,32,41,44,54,56,58,60,67,79,82,87,89,91,92,93,94,96,110,119,124,130,140],conveni:[1,27,32,35,36,39,44,51,79,86,88,91,93,95,103,155,158],convens:150,convent:[3,22,30,46,53,70,97,150],converg:[66,76],convers:[19,25,84,92,110,131,150,154],convert43to46:19,convert46to50:20,convert:[3,22,25,30,33,42,47,51,56,58,59,62,70,84,96,104,105,121,124,137,138,146,150,154],convert_fort_double_to_float:104,convert_readm:11,convert_to_standard_unit:30,convex:[7,32],coodin:30,coord:[47,51],coordin:[4,23,30,32,47,72,76,83,89,93,94,103,110,131,140,152],coordinate_specif:[30,70],coordinate_system:[15,60,134,140],coorind:152,copi:[6,14,15,16,35,36,44,51,54,55,58,67,83,86,96,101,107,108,109,110,114,118,121,125,133,134,138,142,144,145,150,155],copyq1:63,copyright:[61,81],core:[4,12,73,111,121],corioli:[48,140,144,145],coriolis_forc:[48,140],corner:[3,30,32,53,70,72,89,131,137,139,141,150,152],correct:[20,28,41,54,55,63,64,67,77,83,89,94,98,104,113,114,118,133,137,139,140,141],correctli:[28,32,84,90,117,140],correspond:[3,6,12,23,25,27,30,44,47,48,53,54,55,59,67,70,77,83,87,89,92,93,96,98,101,110,111,129,131,132,137,138,139,140,141,146,150,154,155],correspondingli:32,cos:[39,47,49,66,83,96],cosin:83,cost:[13,99],costli:130,could:[5,12,13,27,32,35,36,39,44,53,58,60,66,70,71,77,79,83,89,93,101,102,105,106,117,126,131,133,138,139,140,141,152,155],council:4,count:83,count_from_zero:83,counter:[104,152],counterclockwis:70,coupl:[119,158],courant:[4,6,110,120,137,138,139,141],cours:[13,26,32,44,46,60,70,94,95,103,105,108,140,150],cover:[6,7,27,28,30,32,38,39,51,59,66,70,110,114,119,133,139,150],coverag:[91,111],covert:11,covid:24,cparam:[83,101],cpp:52,cpu:[13,52,118,121,123,149],crash:[118,137,138],creat:[0,1,2,3,5,6,7,19,24,25,28,30,32,33,35,36,38,40,42,44,45,46,50,52,54,57,58,59,62,70,72,76,77,79,84,85,88,89,91,92,95,98,101,102,103,104,110,111,113,117,118,119,121,122,123,126,131,136,137,138,139,142,143,146,152,154,155,156],create_dtopo_xi:[30,70],create_dtopographi:[30,70],create_topo_func:152,creation:[39,77,91,113],criteria:[6,7,22,25,32,66,101],criterion:[32,110,139],critic:[51,93,129],crop:[53,152],cross:28,crucial:[51,150],csdm:24,cse:24,csh:94,csv:[30,70,121],csvfault:[30,70],ctrl:[29,77],cube:67,cultu:66,cumul:121,current:[3,5,13,14,20,22,24,27,28,29,30,32,38,39,41,44,45,48,53,54,55,56,57,58,59,60,67,68,72,77,79,89,92,93,94,99,101,104,106,110,111,118,120,121,128,132,136,137,138,139,140,141,146,147,150,152,154],current_data:[0,3,25,44,76,77],curv:[3,44,76,131],custom:[0,13,16,20,22,25,63,67,73,76,84,90,96,133],custom_bc:96,customari:93,cut:138,cutoff:[6,139],cvf:55,cvs:51,cxx:94,cyber:17,cygwin:86,cython:94,dai:[6,13,51,140],dalcin:81,dam:[51,133],dam_break:130,damag:[6,61,81],damian:57,damiansra:96,dark:131,darker:51,darryl:17,dart:45,dash:[3,94],daspect:67,dat:[30,146],data:[0,1,3,5,25,27,30,32,35,36,38,39,40,42,44,45,46,47,53,54,59,60,61,62,66,67,76,77,78,79,81,83,86,89,92,93,95,97,98,99,101,104,107,108,109,110,113,115,116,118,119,121,122,123,124,126,129,131,132,138,139,141,146,149,151,156],data_break:[39,66,152],data_fil:33,data_limit:[39,66],data_storm:146,data_typ:104,databas:[13,30,70,104,108,121,150],datadir:118,dataset:[150,152,154],date:[5,28,40,47,51,54,55,62,77,146,153],date_tim:47,datetiem:146,datetim:[47,146],datum:[47,48,97,132,140,154],dave:30,davi:[4,17],david:[4,17,81,91,99],davis2018:[5,17],davisleveque2016:[5,17],davisleveque2018:[5,17],dawson:17,daylight:59,dcp:59,deal:[30,48,76,93,94,101,146,152],dealt:[32,39],debian:105,debug:[7,41,62,72,76,93,101,106,111,137,139],debugg:77,decid:[83,99],decim:[47,59],decimc:146,decis:51,declar:[20,22,101,126,155],decompos:[72,129,158],decomposit:137,decor:104,decoupl:54,decreas:[44,133,150],deduc:150,deep:[5,66,140],deep_depth:140,deeper:[131,140,150],deepli:103,def:[0,1,3,44,51,66,77,83,89,93,96,99,139,141,146],default_tfluct:99,defenc:4,defens:4,defin:[0,1,3,5,6,7,22,27,30,32,38,39,41,51,59,60,62,66,67,70,77,79,83,86,89,95,96,98,99,101,103,104,110,113,121,126,129,139,141,146,150,152,153,155,158],definit:[30,67,83,110,116],deform:[17,30,33,45,70,154],deg2dm:59,degener:131,degre:[30,47,51,59,70],delet:[20,28,56,58],delimit:30,delin:140,delta:[87,89,96,99,129,152,155,158],delta_h:97,delta_hu:97,delta_i:152,delta_limit:152,delta_x:152,dem:[32,45,53,121,150,152,154],demo:94,demonstr:[12,25,88,94],denot:[6,22,44,53,129,152],dens:147,densiti:[86,93,97,101,103,138,139,155],depart:[4,146],depdend:87,depend:[3,13,16,28,29,30,32,35,36,40,41,46,48,51,56,57,62,64,67,70,77,82,91,92,97,98,99,104,106,110,121,133,138,140,152,153,155,158],deprec:[7,30,34,54,117,121,140,150,152],depress:32,depth:[4,5,16,17,22,30,32,33,39,44,45,48,64,70,76,78,130,132,133,140,150],deriv:[61,70,81,86,90,91,101,111],describ:[3,4,5,6,7,13,14,16,19,26,28,30,31,32,35,36,38,39,44,46,47,48,51,52,54,55,59,60,62,63,66,67,70,72,73,76,77,78,89,92,98,104,108,110,111,119,122,123,129,131,132,136,137,138,140,146,147,150,152,154,155,158],descript:[3,4,6,9,22,23,25,30,59,67,70,73,76,92,104,108,110,129,130,140,146,150,158],design:[4,27,28,51,81,83,103,131,154],desir:[0,1,2,3,6,7,16,22,25,26,30,32,33,39,42,44,55,56,58,59,60,66,70,75,76,77,79,83,84,86,93,98,99,107,119,121,124,133,135,137,138,139,141,146,150,152,153],desktop:94,destin:51,detail:[4,5,10,16,22,23,25,26,28,29,30,32,35,36,38,41,46,48,51,54,56,57,58,61,62,66,67,70,73,77,81,86,87,88,89,92,93,94,95,96,97,99,109,110,111,114,119,121,126,129,131,136,137,140,142,146,150,153,154,155,158],detect:[51,62,92,100,104,153],deterimin:[140,152],determin:[3,5,6,30,32,39,44,45,48,50,51,54,59,70,77,87,89,92,97,101,106,110,114,118,119,128,131,132,136,137,138,140,152,155],determine_topo_typ:152,dev:[18,24,28,54,55,94,121,122,127],develop:[4,6,7,12,13,18,22,23,48,52,54,57,58,61,66,67,76,80,81,84,91,96,99,100,106,108,111,121,122,124,126,129,132,133,139],dict:[30,86,92,97,98,101,146,152],dictionari:[0,1,2,3,30,44,60,77,83,86,92,97,98,101,103,106,146,150,152],dicuss:30,did:[121,126,131,150],didn:116,died:113,diff:[18,50,55,113,114,115,116,117,118,119,120,121,122,123,124,125,126],differ:[1,3,6,7,12,15,16,22,28,30,31,35,36,39,44,46,48,50,53,56,59,62,64,66,67,70,71,76,79,83,84,86,88,89,92,97,99,104,105,106,107,110,111,117,118,119,120,121,124,126,129,132,133,134,137,138,139,140,144,145,150,152,153,154,155,158],differenti:[17,30],difficult:44,difficulti:[100,102,106],diffus:96,digit:[32,39,53,59,60,77,119,120,121,152],dike:[39,66,124],dim:[96,97,99],dimens:[5,6,7,16,20,22,25,44,47,53,59,67,83,84,86,92,94,96,97,98,101,103,110,121,124,129,137,138,139,141,152,155],dimension:[3,7,8,17,22,25,30,32,35,36,44,48,52,67,89,96,117,118,120,123,139,140,141,152,155],dimensional_split:[89,117,137,139,141],dip:[30,70],dir:[55,94,156],direct:[6,8,16,22,30,32,35,36,44,47,51,55,59,61,62,67,70,71,77,81,86,96,103,110,120,129,137,138,140,152],directli:[8,19,23,32,48,56,67,70,77,79,83,84,87,91,101,104,106,121,152,156],directori:[1,3,5,6,11,12,13,14,15,16,19,20,22,23,25,28,29,31,32,35,36,37,40,42,44,45,47,50,51,54,55,56,57,59,63,67,68,71,75,76,79,86,88,89,91,92,93,96,103,106,107,108,110,111,113,118,119,120,121,123,128,129,133,134,135,136,137,138,142,144,145,148,149,150,153,155,156],directorti:108,disabl:[49,100,140],disable_petsc:104,discard:[32,99],disclaim:[61,81],discontinu:[4,99,158],discov:64,discoveri:111,discret:99,discrib:4,discuss:[5,24,28,30,48,53,56,66,70,92,103,105,106,110,119,121,129,140,158],disk:[13,44,83,92,93,111,119],dispers:48,displac:[30,45,48,70,133,140,154],displai:[1,13,35,36,40,44,51,59,77,93,111,140],display_format:[44,60],display_landfall_tim:140,dist:55,dist_latlong2met:47,dist_meters2latlong:47,distanc:[30,47,51,70,140,150,152],distant:[108,110],distinct:[44,119],distinguish:39,distribut:[4,12,13,29,30,54,61,70,73,80,81,99,105,124],disturb:51,distutil:84,dive:105,divid:[110,137],divis:[4,51],dlgeorg:4,dms2decim:47,dnetcdf:[41,150],doc:[18,23,24,28,30,51,55,87,104,105,106,120,121,122,123,124,125,126,143],docker:[18,25,55,56,120,121,122,123,124,125,126,157],docker_disk:29,docker_imag:55,dockerfile_v5:29,dockerhub:[29,55],dockeril:29,docstr:[84,88,111],doctest:89,documen:54,document:[0,1,2,3,6,7,18,21,22,23,24,25,28,29,32,45,48,53,58,61,70,76,77,78,79,81,87,89,92,93,94,95,99,101,104,106,114,127,136,139,156,157],dodsc:[39,66],doe:[4,5,11,16,20,27,28,39,40,48,51,53,54,56,67,73,77,80,89,91,98,101,104,110,111,114,119,123,126,128,129,130,133,146,152,153,155],doesn:[28,32,58,63,101],doflag:110,doi:[4,17,52,55,57,124,125,126,127],doing:[6,11,19,25,28,33,39,44,48,50,52,54,58,63,77,79,89,91,110,111,118,119,120,121],domain:[5,6,16,17,33,38,39,48,51,54,59,70,72,82,83,84,86,94,96,98,101,108,110,138,139,141,150],don:[13,27,28,54,55,77,93,94,100,111,139,153],done:[1,6,7,8,11,13,16,19,20,28,35,36,39,44,46,51,53,54,58,59,62,66,67,70,76,77,79,83,87,88,104,110,114,118,119,123,128,129,131,136,138,140,149,152,153,154],donna:[4,17],donnabois:4,donor:[137,139,141],dontflag:110,dot:[40,44,51,57,58,59,62,153],doubl:[67,84,89,104,129,138],down:[13,30,93,118,146,150,152],download:[12,13,28,29,30,36,37,39,45,51,55,56,57,58,68,88,94,100,121,122,127,148,152,153,154],downward:70,doxygen:[6,7,25,120],dpc:59,dpi:[51,59],dpng:67,dprint:[138,139],dq_src:[96,99],dqdt:99,draft:55,drag:140,drag_law:140,draw:3,drawback:106,drawcontourlin:67,drawn:[30,51,136],driver:[20,63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106,108,110,119,134,142,144,145,153],within:[6,16,28,29,54,56,58,66,73,77,95,104,106,110,129,131,136,142,152],without:[16,22,40,44,48,57,59,61,62,63,66,67,77,79,80,81,87,92,93,104,106,111,131,139,141,146,153,155],wkt:51,wmo:146,wmo_:146,wmo_ag:146,won:[12,13,66,84,152],woodward:120,word:[93,121,146],work:[3,5,8,13,16,19,20,22,24,25,26,28,29,32,35,36,40,45,48,51,52,53,54,55,56,57,58,59,66,67,69,70,71,77,80,81,82,83,85,86,87,91,92,93,94,97,99,100,105,106,108,109,110,111,115,116,117,118,119,120,121,124,126,127,129,136,137,138,140,142,147,150,153,157],workflow:[108,142,146],workshop:[108,124],workspac:[24,67,101],world:[48,64,91,94,146],worst:132,worth:101,worthwhil:96,would:[2,3,12,13,16,24,27,28,32,38,41,51,53,55,56,58,60,62,63,66,70,72,77,81,83,86,89,93,104,111,119,131,132,133,136,137,140,146,150,155],wouldn:63,wpalg:17,wrap:[59,81,84,89,99,104,146],wrapper:152,write:[7,28,30,38,39,44,45,50,53,54,64,70,72,73,76,83,86,89,90,92,93,94,98,119,121,139,141,146,150,152],write_:92,write_arrai:92,write_atcf:146,write_aux:[92,98],write_aux_alwai:[83,86,93],write_aux_init:[83,86],write_aux_int:93,write_geoclaw:146,write_hurdat:146,write_imd:146,write_jma:146,write_p:[92,98],write_tcvit:146,written:[6,11,25,30,32,40,44,58,59,60,61,70,72,73,77,81,90,92,96,105,119,129,137,138,139,140,141,146,152,155],wrong:[58,63,67,93,106],www:[4,13,17,30,39,43,45,54,60,61,66,68,81,84,89,92,94,120,122,146,152],x1_desir:33,x1_domain:33,x1_new:33,x2_desir:33,x2_new:33,x_1:[5,131],x_2:[5,131],x_c:131,x_cell:59,x_center:131,x_edg:[59,131],x_i:[129,155,158],x_inch:59,x_mask:152,xarr:89,xarrai:152,xarray_d:152,xclaw:[35,36,86],xclawcmd:86,xclawerr:86,xclawout:86,xcode:80,xdir:86,xiaom:30,xinsheng:[4,52],xinshengqin:[4,52],xleft:[138,139],xlf:100,xlimit:[0,44,51,124],xllcenter:[53,121,150],xllcorner:[53,150],xllower:121,xlow:72,xlower:[0,3,16,22,27,39,84,121,139,141,150,152,155],xlowerg:84,xmax:0,xmin:0,xpoint:140,xrang:96,xtick:[39,49],xupper:[0,22,139,141,152],xxdiff:111,xxx:150,xxxx:67,xy_fil:32,xy_fnam:33,xylim:30,xzf:57,y_c:131,y_cell:59,y_center:131,y_edg:[59,131],y_inch:59,year:[4,17,22,51,59,91,112,122,146],yellow:[59,77,146],yellow_red_blu:77,yes:67,yet:[1,13,20,25,48,52,54,57,59,76,99,119,120,121,122,123,124,125,126,127,129,137,139,157],yianni:[4,17,81],yield:3,yleft:[138,139],ylimit:[0,44,51,124,136],yllcenter:[53,121,150],yllcorner:[53,150],yllower:121,ylow:72,ylower:[3,22,27,39,84,121,139,150,152],ylowerg:84,ymax:0,ymin:0,yml:111,yong:17,you:[0,3,4,5,12,13,14,15,16,18,19,20,22,23,24,25,26,27,28,29,32,35,36,37,38,40,41,42,44,47,50,51,52,53,54,55,56,57,58,59,62,63,66,67,68,69,70,71,72,73,75,76,77,79,80,81,83,84,85,86,88,91,92,93,94,95,96,97,99,100,101,102,103,105,106,107,108,109,111,113,118,119,120,121,124,126,127,128,129,130,131,132,133,134,135,136,138,139,140,141,142,143,144,145,146,148,150,153,154,155,157],your:[4,6,15,16,19,20,24,25,26,35,37,41,44,53,54,55,56,57,58,68,71,76,77,79,81,82,83,84,85,88,90,91,93,102,103,105,106,107,108,110,111,113,121,129,134,135,144,145,150,153,155],yourself:[41,44,57],youtub:[24,108,124],ypoint:140,yupper:[22,139,152],z_allow_wet:39,z_dry:39,z_format:[39,66,152],zdry:[39,66],zenodo:[4,57,124,125,126,127],zero:[3,16,30,32,39,41,59,67,83,96,97,101,103,126,131,132],zip:[12,51,55],zipinfo:51,zlib:92,zlower:22,zmask:66,zmax:[39,66],zmin:[39,66],znearshor:66,zone:[48,51,59,138,139],zoom:[24,51],zsh:94,zshallow:66,ztopo:66,zupper:22,zvar:152},titles:["ClawPlotAxes","ClawPlotData","ClawPlotFigure","ClawPlotItem","About this software","Guiding AMR with adjoint flagging","Adaptive mesh refinement (AMR) algorithms","AMRClaw Description and Detailed Contents","AMRClaw for 1d problems","Doxygen documentation of AMRClaw","AMRClaw Flowcharts","Application documentation","Clawpack Applications repository","Amazon Web Services EC2 Clawpack AMI","b4run function","b4step default routines","Boundary conditions","Bibliography","Changes to master since v5.8.0","Converting from Clawpack 4.3 to 4.6","Converting from Clawpack 4.6 to 5.0","Clawpack 4.x links","Changes in Clawpack 5.0","Clawpack components","Clawpack Community","Full Table of Contents","Contributing examples and applications","current_data","Developers\u2019 Guide","Docker for Clawpack","dtopotools module for moving topography","Fortran 77 vs. Fortran 90 files","Fixed grid monitoring","fgmax_tools module for working with topography data","Fixed grid output","Running an example","Testing your Fortran installation and running an example","Testing a PyClaw installation and running an example","Specifying flagregions for adaptive refinement","Force Cells to be Dry Initially","Fortran version","Fortran Compilers","Examples from the book FVMHP","<no title>","Gauges","GeoClaw Description and Detailed Contents","Getting started with GeoClaw","geoclaw.util module of utility functions","Cautionary Hints on using GeoClaw","GeoClaw plotting tools","Keeping track of repository versions with Git","Visualizing GeoClaw results in Google Earth","Using the GPU version of Clawpack","Grid registration","Guide for updating this documentation","Guide for doing a Clawpack release","Installing Clawpack","Additional options for installing Clawpack","pip install instructions","kmltools module of utility functions","Lagrangian gauges for particle tracking","License","Clawpack Makefiles","Library routines in Makefiles","Manning friction term","The mapc2p function","Marching Front algorithm","Plotting using Matlab","Using NetCDF output","Creating a new application directory","Earthquake sources: Fault slip and the Okada model","Using OpenMP","Output data formats","Which Clawpack solver should I use?","Clawpack Community Photos","Plotting examples","Plotting with Visclaw","Plotting hints and FAQ","Plotting routines for GeoClaw","Plotting options in Python","Installation Prerequisites","About PyClaw","PyClaw Basics","Understanding Pyclaw Classes","Porting a problem from Clawpack 4.6.x to PyClaw","Running PyClaw in the cloud","Pyclaw Controller Class","Pyclaw Limiters","Working with PyClaw\u2019s built-in examples","PyClaw Geometry","Going Further","Pyclaw","Pyclaw Input/Output Package","PyClaw output","Running in parallel","Plotting PyClaw results","Setting up your own problem","Riemann Solver Package","PyClaw Solutions","Using PyClaw\u2019s solvers: Classic and SharpClaw","Installing PyClaw","PyClaw State","Troubleshooting","PyClaw tutorial: Solve the acoustics equations","Pyclaw Utility Module","Python Hints","Python path","qinit 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,allocat:117,allot:59,allow:[4,6,13,22,27,28,29,32,38,39,44,45,47,50,51,53,54,58,64,66,67,70,71,73,76,77,86,91,92,93,99,101,104,105,106,110,111,113,114,117,118,119,120,121,123,124,126,130,132,138,140,141,142,143,147,151,153,155],alon:[16,51],along:[6,14,16,24,27,30,32,39,44,51,54,57,68,70,106,110,117,129,132,134,141,147,155],alpha:[51,55,99],alphabet:81,alreadi:[0,1,6,12,13,18,28,29,41,55,56,58,59,60,66,79,80,94,98,100,103,105,114,122,136,153],also:[3,4,5,6,7,8,9,11,12,16,17,18,20,22,23,24,25,28,29,30,32,33,35,36,37,38,39,41,42,43,44,47,48,51,52,53,54,55,56,57,58,59,62,63,66,67,68,70,71,72,73,76,77,79,83,85,86,89,91,93,94,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,136,138,139,140,141,142,143,145,146,147,148,149,150,151,153,154,155,156,158,159],alter:51,altern:[30,35,36,44,47,51,56,60,62,67,76,91,94,106,110,117,118,119],although:[30,51,63,67,95,96,98,110,122,153],alwai:[16,22,26,27,28,32,41,53,54,58,67,83,92,109,110,113,114,126,134,140,141,142,151,156],amal:[4,17,81,91],amazon:25,amazonaw:13,amdq:[97,130],ami:25,among:124,amount:[44,48,54],amplitud:[5,119],amr:[4,7,8,16,20,23,25,27,28,32,34,38,44,45,52,59,67,72,73,76,81,89,118,120,121,122,124,126,134,137,138,140,142,150,156],amr_1d:122,amr_2d:[121,122],amr_:[3,7],amr_celledges_show:3,amr_contour_color:3,amr_contour_show:3,amr_data_show:118,amr_level:72,amr_level_max:140,amr_levels_max:[32,110,139,140],amr_modul:[71,110,117,123,124],amrclaw:[4,5,6,12,15,16,19,20,22,23,24,28,36,38,39,41,43,44,45,46,52,55,56,57,58,60,66,67,68,71,72,73,80,91,100,106,107,110,111,129,130,132,135,136,138,141,145,146,149,150,154],amrdata:[5,22,32,110,124,126,139,140,141],amrflag:110,amrlib:117,amrnez:110,an11:54,anaconda:[51,100],anal:17,analog:[138,139],analysi:17,andi:4,angl:[16,30,47,70],ani:[3,4,5,6,8,13,16,18,19,20,22,27,28,29,32,35,36,37,45,48,50,51,54,55,57,58,61,62,64,66,67,69,71,72,73,77,81,87,88,89,91,92,93,94,96,98,100,104,106,109,110,111,117,121,123,129,132,133,134,137,138,139,141,147,156,159],anim:[12,16,42,51,117,124,125,143],animation_tool:[124,125],anisotrop:[6,22],anl:94,annot:[27,59],annual:24,anoth:[3,22,39,44,51,55,58,59,72,76,80,88,99,102,111,121,147,156],answer:24,anyth:[3,6,28,29,58,63,111,121],anywher:110,aoml:147,apach:13,apdq:[97,130],api:[47,121],app:[12,13,18,23,26,28,29,32,37,42,43,70,108,109,116,120,121,122,123,124,125,126,127,131],appar:[30,32,71],appeal:51,appear:[0,1,3,5,8,13,18,23,32,44,45,51,54,59,62,65,77,93,98,101,119,126,141,143,151],append:[5,20,32,38,39,44,51,60,77,86,98,110,118,119,129,130,140],appl:17,appli:[3,4,5,6,13,16,25,30,48,51,53,64,66,70,77,79,87,89,92,99,110,129,138,141,156],applic:[4,6,15,16,19,20,22,23,24,28,29,32,35,36,37,41,42,43,45,46,55,57,58,63,66,68,71,79,88,89,90,91,93,99,104,107,109,110,111,113,116,117,119,120,121,123,124,130,132,134,135,138,141,145,146,151,153,154,156,157],appreci:81,approach:[5,7,13,28,29,38,44,54,57,69,76,84,91,94,96,104,110,117,119,120,122,130,131,137,141,156,159],appropri:[4,5,6,13,16,24,28,45,48,49,51,55,57,59,60,64,67,68,69,71,83,86,87,88,92,94,95,96,97,98,111,123,130,133,138,147,156,159],approv:48,approxim:[6,16,25,33,48,51,70,130],april:[24,124,125,128],apt:[13,80],arbitrari:[32,59,99,113,132,141],arbitrarili:66,arc:133,arcgi:153,architectur:94,archiv:[12,21,36,51,55,111,143,149,153,155],arcminut:[70,151],arcsecond:[45,151],area:[15,22,45,99,108,119,134,135],arg:[89,98],argument:[0,1,2,3,27,30,45,47,50,51,53,77,83,84,88,89,92,96,98,99,101,104,111,121,130,132,137,138,139,147,153,156],argv:[140,142],aris:[61,81],arithmet:64,aron:[4,17,81,91],arora:87,arora_ro:87,around:[6,30,32,39,59,92,108,111,124,139,140,147,153,156],arrai:[0,3,6,15,20,22,27,30,32,33,38,44,45,47,49,53,59,77,83,84,86,87,89,91,92,93,96,97,98,99,101,103,104,105,113,114,115,119,121,124,126,130,131,132,135,138,139,140,141,142,147,151,153,156],arrang:153,arriv:[22,32,34,39,45,119,133,134],arrival_tol:32,articl:[4,17,91,143],artifici:[16,134],arxiv:52,asc:153,ascii:[44,53,67,83,86,93,98,119,129,138,140,142,151,157],ascii_output_format:68,ask:24,ask_us:153,aspect:[12,24,29,43,48,49,67,153],assert:[140,142],assess:[4,48,133],assign:[30,32,83,86,92,98],assist:[22,124],associ:[0,1,2,6,22,51,58,71,89,92,93,111],assum:[3,5,20,22,30,32,36,39,47,48,51,53,54,55,59,67,70,76,92,93,95,96,97,103,104,110,117,132,133,138,141,147,148,151,153,155,159],assumpt:[51,54],asteroid:4,astronom:133,atcf:[108,121,147,148],aterrel:4,atmospher:4,attach:[55,92,101],attempt:[5,8,11,20,33,35,36,62,92,104,111,113,127,147,153,154],attirbut:22,attr:[89,98],attribur:5,attribut:[5,7,22,30,38,44,66,70,76,78,79,83,86,89,92,94,96,98,99,110,113,118,122,129,137,138,139,141,147,153],attributeerror:77,aug:[17,122],aug_glob:97,augment:[66,131],august:[24,121,128],austin:4,author:[17,25,45,48,87,91,92,97,109],auto:[0,44,84],autom:[14,54,84,111],automat:[0,2,3,8,11,16,30,35,36,41,51,55,62,76,77,79,83,88,92,94,100,101,102,104,111,113,124,126,138,139,141,151],autonom:5,aux1:32,aux1d:156,aux:[5,6,1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,23,25,26,30,32,33,35,36,37,40,42,43,44,45,47,49,50,51,52,53,54,55,59,60,62,63,66,67,68,72,73,77,79,80,83,84,86,87,89,91,92,94,96,97,98,99,101,103,104,105,106,110,111,113,114,121,122,128,130,132,137,138,141,143,147,151,153,154,156],containing_rect:30,contains:29,containt:129,contamin:138,contan:51,content:[4,6,23,51,55,73,84,91,141,151,156,157],context:[27,51,156],contigu:[72,92,101,132],continent:[7,66],contingu:22,continu:[13,22,28,30,49,54,81,105,130,138,159],contour:[3,30,44,51,53,67,105,137,153],contour_color:3,contour_kwarg:[3,153],contour_level:[3,153],contour_max:3,contour_min:3,contour_nlevel:3,contour_show:3,contourf:[51,76],contract:[4,61,81],contrast:[53,132],contribut:[4,24,25,57,81,84,91,96,99,108,111],contributor:[4,24,61,91],control:[6,7,23,25,32,41,44,54,58,60,67,79,82,87,89,91,92,93,94,96,110,119,124,131,141],conveni:[1,27,32,35,36,39,44,51,79,86,88,91,93,95,103,156,159],convens:151,convent:[3,22,30,46,53,70,97,151],converg:[66,76],convers:[19,25,84,92,110,132,151,155],convert43to46:19,convert46to50:20,convert:[3,22,25,30,33,42,47,51,58,59,62,70,73,84,91,96,104,105,121,124,138,139,147,151,155],convert_fort_double_to_float:104,convert_readm:11,convert_to_standard_unit:30,convex:[7,32],coodin:30,coord:[47,51],coordin:[4,23,30,32,47,72,76,83,89,93,94,103,110,132,141,153],coordinate_specif:[30,70],coordinate_system:[15,60,135,141],coorind:153,copi:[6,14,15,16,35,36,44,51,54,55,58,67,83,86,96,101,107,108,109,110,114,118,121,125,134,135,139,143,145,146,151,156],copyq1:63,copyright:[61,81],core:[4,12,73,111,121],corioli:[48,141,145,146],coriolis_forc:[48,141],corner:[3,30,32,53,70,72,89,132,138,140,142,151,153],correct:[20,28,41,54,55,63,64,67,77,83,89,94,98,104,113,114,118,134,138,140,141,142],correctli:[28,32,84,90,117,141],correspond:[3,6,12,23,25,27,30,44,47,48,53,54,55,59,67,70,77,83,87,89,92,93,96,98,101,110,111,130,132,133,138,139,140,141,142,147,151,155,156],correspondingli:32,cos:[39,47,49,66,83,96],cosin:83,cost:[13,99],costli:131,could:[5,12,13,27,32,35,36,39,44,53,60,66,70,71,77,79,83,89,93,101,102,106,117,126,132,134,139,140,141,142,153,156],council:4,count:83,count_from_zero:83,counter:[104,153],counterclockwis:70,coupl:[119,159],courant:[4,6,110,120,138,139,140,142],cours:[13,26,32,44,46,60,70,94,95,103,105,108,141,151],cover:[6,7,27,28,30,32,38,39,51,59,66,70,110,114,119,134,140,151],coverag:[91,111],covert:11,covid:24,cparam:[83,101],cpp:52,cpu:[13,52,118,121,123,150],crash:[118,138,139],creat:[0,1,2,3,5,6,7,19,24,25,28,30,32,33,35,36,38,40,42,44,45,46,50,52,54,58,59,62,70,72,76,77,79,84,85,88,89,91,92,95,98,101,102,103,104,110,111,113,117,118,119,121,122,123,126,132,137,138,139,140,143,144,147,153,155,156,157],create_dtopo_xi:[30,70],create_dtopographi:[30,70],create_topo_func:153,creation:[39,77,91,113],criteria:[6,7,22,25,32,66,101],criterion:[32,110,140],critic:[51,93,130],crop:[53,153],cross:28,crucial:[51,151],csdm:24,cse:24,csh:94,csv:[30,70,121],csvfault:[30,70],ctrl:[29,77],cube:67,cultu:66,cumul:121,current:[3,5,13,14,20,22,24,27,28,29,30,32,38,39,41,44,45,48,53,54,55,57,58,59,60,67,68,72,77,79,89,92,93,94,99,101,104,106,110,111,118,120,121,129,133,137,138,139,140,141,142,147,148,151,153,155],current_data:[0,3,25,44,76,77],curv:[3,44,76,132],custom:[0,13,16,20,22,25,63,67,73,76,84,90,96,134],custom_bc:96,customari:93,cut:139,cutoff:[6,140],cvf:55,cvs:51,cxx:94,cyber:17,cygwin:86,cython:94,dai:[6,13,51,141],dalcin:81,dam:[51,134],dam_break:131,damag:[6,61,81],damiansra:96,dark:132,darker:51,darryl:17,dart:45,dash:[3,94],daspect:67,dat:[30,147],data:[0,1,3,5,25,27,30,32,35,36,38,39,40,42,44,45,46,47,53,54,59,60,61,62,66,67,76,77,78,79,81,83,86,89,92,93,95,97,98,99,101,104,107,108,109,110,113,115,116,118,119,121,122,123,124,126,130,132,133,139,140,142,147,150,152,157],data_break:[39,66,153],data_fil:33,data_limit:[39,66],data_storm:147,data_typ:104,databas:[13,30,70,104,108,121,151],datadir:118,dataset:[151,153,155],date:[5,28,40,47,51,54,55,62,77,147,154],date_tim:47,datetiem:147,datetim:[47,147],datum:[47,48,97,133,141,155],dave:30,davi:[4,17],david:[4,17,81,91,99],davis2018:[5,17],davisleveque2016:[5,17],davisleveque2018:[5,17],dawson:17,daylight:59,dcp:59,deal:[30,48,76,93,94,101,147,153],dealt:[32,39],debug:[7,41,62,72,76,93,101,106,111,138,140],debugg:77,decid:[83,99],decim:[47,59],decimc:147,decis:51,declar:[20,22,101,126,156],decompos:[72,130,159],decomposit:138,decor:104,decoupl:54,decreas:[44,134,151],deduc:151,deep:[5,66],deeper:[132,141,151],deepli:103,def:[0,1,3,44,51,66,77,83,89,93,96,99,140,142,147],default_tfluct:99,defenc:4,defens:4,defin:[0,1,3,5,6,7,22,27,30,32,38,39,41,51,59,60,62,66,67,70,77,79,83,86,89,95,96,98,99,101,103,104,110,113,121,126,130,140,142,147,151,153,154,156,159],definit:[30,67,83,110,116],deform:[17,30,33,45,70,155],deg2dm:59,degener:132,degre:[30,47,51,59,70],delet:[20,28,58],delimit:30,delin:141,delta:[87,89,96,99,130,153,156,159],delta_h:97,delta_hu:97,delta_i:153,delta_limit:153,delta_x:153,dem:[32,45,53,59,121,151,153,155],demo:94,demonstr:[12,25,88,94],denot:[6,22,44,53,130,153],dens:148,densiti:[86,93,97,101,103,139,140,156],depart:[4,147],depdend:87,depend:[3,13,16,28,29,30,32,35,36,40,41,46,48,51,62,64,67,70,77,82,92,97,98,99,104,106,110,121,134,139,141,153,154,156,159],deprec:[7,30,34,54,58,117,121,141,151,153],depress:32,depth:[4,5,16,17,22,30,32,33,39,44,45,48,64,70,76,78,131,133,134,141,151],deriv:[61,70,81,86,90,91,101,111],describ:[3,4,5,6,7,13,14,16,19,26,28,30,31,32,35,36,38,39,44,46,47,48,51,52,54,55,57,59,60,62,63,66,67,70,72,73,76,77,78,89,91,92,98,104,108,110,111,119,122,123,130,132,133,137,138,139,141,147,148,151,153,155,156,159],descript:[3,4,6,9,22,23,25,30,59,67,70,73,76,91,92,104,108,110,130,131,141,147,151,159],design:[4,27,28,51,81,83,103,132,155],desir:[0,1,2,3,6,7,16,22,25,26,30,32,33,39,42,44,55,58,59,60,66,70,75,76,77,79,83,84,86,93,98,99,107,119,121,124,134,136,138,139,140,142,147,151,153,154],desktop:94,destin:51,detail:[4,5,10,16,22,23,25,26,28,29,30,32,35,36,38,41,46,48,51,54,57,58,61,62,66,67,70,73,77,81,86,87,88,89,91,92,93,94,95,96,97,99,109,110,111,114,119,121,126,130,132,137,138,141,143,147,151,154,155,156,159],detect:[51,62,92,100,104,154],deterimin:[141,153],determin:[3,5,6,30,32,39,44,45,48,50,51,54,59,70,77,87,89,92,97,101,106,110,114,118,119,129,132,133,137,138,139,141,153,156],determine_topo_typ:153,dev:[18,24,28,54,55,94,121,122,127,128],develop:[4,6,7,12,13,18,22,23,48,52,54,57,58,61,66,67,76,80,81,84,91,96,99,100,106,108,111,121,122,124,126,130,133,134,140],dict:[30,86,92,97,98,101,147,153],dictionari:[0,1,2,3,30,44,60,77,83,86,92,97,98,101,103,106,147,151,153],dicuss:30,did:[121,126,132,151],didn:116,died:113,diff:[18,50,55,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127],differ:[1,3,6,7,12,15,16,22,28,30,31,35,36,39,44,46,48,50,53,57,59,62,64,66,67,70,71,76,79,83,84,86,88,89,91,92,97,99,104,105,106,107,110,111,117,118,119,120,121,124,126,127,130,133,134,135,136,138,139,140,141,145,146,151,153,154,155,156,159],differenti:[17,30],difficult:44,difficulti:[100,102,106],diffus:96,digit:[32,39,53,59,60,77,119,120,121,153],dike:[39,66,124],dim:[96,97,99],dimens:[5,6,7,16,20,22,25,44,47,53,59,67,83,84,86,92,94,96,97,98,101,103,110,121,124,130,138,139,140,142,153,156],dimension:[3,7,8,17,22,25,30,32,35,36,44,48,52,67,89,96,117,118,120,123,140,141,142,153,156],dimensional_split:[89,117,138,140,142],dip:[30,70],dir:[55,94,157],direct:[6,8,16,22,30,32,35,36,44,47,51,55,59,61,62,67,70,71,77,81,86,96,103,110,120,130,138,139,141,153],directli:[8,19,23,32,48,57,67,70,77,79,83,84,87,91,101,104,106,121,153,157],directori:[1,3,5,6,11,12,13,14,15,16,19,20,22,23,25,28,29,31,32,35,36,37,40,42,43,44,45,47,50,51,54,55,57,59,63,67,68,71,75,76,79,86,88,89,91,92,93,96,103,106,107,108,110,111,113,118,119,120,121,123,129,130,134,135,136,137,138,139,143,145,146,149,150,151,154,156,157],directorti:108,disabl:[49,100,141],disable_petsc:104,discard:[32,99],disclaim:[61,81],discontinu:[4,99,159],discov:64,discoveri:111,discret:99,discrib:4,discuss:[5,24,28,30,48,53,66,70,92,103,105,106,110,119,121,130,141,159],disk:[13,44,83,92,93,111,119],dispers:48,displac:[30,45,48,70,134,141,155],displai:[1,13,35,36,40,44,51,59,77,93,111,141],display_format:[44,60],display_landfall_tim:141,dist:55,dist_latlong2met:47,dist_meters2latlong:47,distanc:[30,47,51,70,141,151,153],distant:[108,110],distinct:[44,119],distinguish:39,distribut:[4,12,13,29,30,54,61,70,73,81,99,105,124],disturb:51,distutil:84,divid:[110,138],divis:[4,51],dlgeorg:4,dms2decim:47,dnetcdf:[41,151],doc:[18,23,24,28,30,51,55,87,104,105,106,120,121,122,123,124,125,126,127,144],docker:[18,25,55,56,120,121,122,123,124,125,126,127,158],docker_disk:29,docker_imag:55,dockerfile_v5:29,dockerhub:[29,55],dockeril:29,docstr:[84,88,111],doctest:89,documen:54,document:[0,1,2,3,6,7,18,21,22,23,24,25,28,29,32,45,48,53,58,61,70,76,77,78,79,81,87,89,92,93,94,95,99,101,104,106,114,127,128,137,140,157,158],dodsc:[39,66],doe:[4,5,11,16,20,27,28,39,40,48,51,53,54,58,67,73,77,80,89,98,101,104,110,111,114,119,123,126,129,130,131,134,147,153,154,156],doesn:[28,32,58,63,101],doflag:110,doi:[4,17,52,55,57,124,125,126,127,128],doing:[6,11,19,25,28,33,39,44,48,50,52,54,58,63,77,79,89,91,110,111,118,119,120,121],domain:[5,6,16,17,33,38,39,48,51,54,59,70,72,82,83,84,86,94,96,98,101,108,110,139,140,142,151],don:[13,27,28,54,55,77,93,94,100,111,140,154],done:[1,6,7,8,11,13,16,19,20,28,35,36,39,44,46,51,53,54,56,59,62,66,67,70,76,77,79,83,87,88,91,104,110,114,118,119,123,129,130,132,137,139,141,150,153,154,155],donna:[4,17],donnabois:4,donor:[138,140,142],dontflag:110,dot:[40,44,51,58,59,62,154],doubl:[67,84,89,104,130,139],down:[13,30,93,118,147,151,153],download:[12,13,28,29,30,36,37,39,45,51,55,57,58,68,88,94,100,121,122,128,149,153,154,155],downward:70,doxygen:[6,7,25,120],dpc:59,dpi:[51,59],dpng:67,dprint:[139,140],dq_src:[96,99],dqdt:99,draft:55,drag:141,drag_law:141,draw:3,drawback:106,drawcontourlin:67,drawn:[30,51,137],driver:[20,63],drop:[13,54,80,124,126,134,138],dry:[16,17,25,32,45,97,124,127,131,134],dry_point:39,dry_points_sum:39,dry_toler:97,ds824:147,dst:59,dt_check:32,dt_initi:[113,138,140,141,142],dt_max:[138,140,142],dt_max_dtopo:[113,141],dt_variabl:[138,140,142],dtdtopo:116,dtdx1d:115,dtdx:87,dtdy1d:115,dtfe:99,dtopo2kml:59,dtopo:[25,30,33,45,48,53,59,70,106,113,115,116,124,126,134,141,151,153,155],dtopo_data:[113,141],dtopo_file_nam:59,dtopo_modul:113,dtopo_path:33,dtopo_typ:[30,33,59,70],dtopofil:[59,70,141],dtopographi:[30,70],dtopotool:[45,70,115,116,118,121,122,151,152],dtopotools_exampl:[30,70,109],dtopotyp:[141,151],due:[17,24,30,39,47,70,111,120,121,126,134,154],dummi:[84,99,156],dump:[72,138],dumpgaug:117,duplic:[77,116,129],durat:[30,126,133],dure:[5,22,32,39,44,59,70,73,113,133,134,140,141,142,151],dxc:84,dyc:84,dylib:51,dynam:[6,20,30,48,70,73,139],dynamic_slip:[30,122],dz_at_t:30,dz_interv:30,dz_max:30,e10:32,e15:44,e26:44,e68:[4,17],e_format_bst:147,e_l:97,e_r:97,each:[1,2,3,5,6,7,12,16,18,22,30,32,34,44,47,51,53,54,55,59,60,63,66,67,70,71,72,75,76,77,79,83,84,87,89,92,93,94,96,97,98,99,101,103,110,111,113,114,118,119,121,122,124,129,130,131,132,134,137,138,139,140,141,142,147,150,151,153,155,159],each_fram:44,each_gaug:44,ear:4,earli:[6,20,134],earlier:[5,20,22,30,32,38,53,70,83,96,113,120,151,153],earth:[25,39,45,52,59,66,70,117,119,127,132,141],earth_radiu:141,earthquak:[25,30,45,48,109,134,141,148,151],eas:59,easi:[4,6,11,29,38,58,67,84,93,94,95,132,143,156],easier:[58,76,119,121,132,156],easiest:[19,28,41,73,77,79,110,156],easili:[3,13,28,32,51,54,67,77,84,89,100,104,111,124,143,147],east:[13,151],easy_instal:94,ec2:25,echo:106,ecosystem:[4,17],edebug:[139,140],edg:[3,6,15,16,27,30,32,33,38,59,70,89,97,130,132,135,139,140,142,156],edgecolor:132,edit:[51,54,55,58,79],editabl:28,editor:72,edu:[30,51,68,92,123],effect:[44,51,64,67,89,93,110,111,133,141,153],effici:[48,52,81,91,92,93,101,110,132,139],effort:92,efix:[97,131],egg:[29,58],eigenvalu:5,eigenvector:[5,130,159],either:[12,16,20,30,32,39,45,46,51,60,62,66,67,70,77,79,83,89,91,92,93,99,104,106,110,111,117,118,119,121,130,132,134,139,141,147,151,153,156,159],elast:[13,70],element:[0,3,22,59,97,99,101,138,139,140,141],elementwis:93,elev:[22,25,32,39,45,46,48,51,53,59,76,107,110,124,132,133,141,151,153,155],elif:[140,142],elimin:[8,22,66,84,106,121,141],ell:130,els:[27,28,58,66,101,121,132,134,142],elsewher:[5,24,39,91,132],emerg:4,emmanuel:141,emmett:[17,81,91],empir:[48,64],empti:[12,44,98,101,104,106,138,147,153],empyclaw:96,enabl:[89,93,100,104,119],encapsul:48,encount:[40,51,77,100,102],encourag:67,end:[13,29,30,32,44,47,51,55,59,86,93,97,103,105,108,110,118,119,121,129,131,132,140,142,147,150],end_dat:47,enddo:156,endian:92,endors:[61,81],energi:[93,97],enforc:132,eng:147,engin:[17,51],enhanc:[64,81,121],enlarg:119,enough:[5,54,66,139,148,150,151],ensembl:147,ensur:[35,36,37,67,108],enter:[67,92,94,100],enthought:[100,102],entir:[5,6,38,48,51,59,66,70,71,73,83,93,98,108,110,114,132,153],entireti:86,entri:[51,60,83,93,104,147],entropi:[97,131],enumer:[89,99],environ:[14,25,28,35,36,37,40,50,51,54,57,58,67,69,71,73,95,102,104,106,119,153,154],envis:16,epd:102,eprint:[139,140],epsg:51,epsilon:87,eqn:159,eqnarrai:103,equal:[16,30,32,51,70,94,96,110,129,132,138,140,142,151,153],equat:[4,5,16,17,25,35,36,45,48,60,64,77,82,83,84,86,91,92,93,96,99,100,101,114,117,119,121,122,130,138,140,141,142,151,156,159],equiv:159,equival:[6,44,52,53,59,60,123,151],err:140,errest:110,erron:[30,70],error:[5,16,20,35,36,40,51,58,67,71,77,86,91,92,93,104,110,111,122,126,139,140,147,154],escap:[110,140],escienc:13,especi:[28,51,84,96],esri:[53,151],essenti:[5,53,67,99,141,151],est:140,establis:121,establish:4,estim:[5,64,110,139,141],estimat:[5,140],eta:[25,30,32,39,44,45,110,117,124,133],eta_init:134,eta_tild:32,etc:[0,2,16,19,20,24,27,28,32,33,48,51,54,57,59,63,72,76,84,130,137,138,141,147,156],etopo1:[121,132,133,151,153,155],etopo_sample_2min:153,etopotool:[121,151],euler:[60,91,99,115,117,120,122,130,156],euler_1d_pi:97,euler_2d:[35,37,91,96],euler_exact_1d:97,euler_hll_1d:97,euler_hllc_1d:97,euler_roe_1d:97,evalu:[17,27,30,64,83,89,99,153,156],even:[39,48,51,58,61,70,81,104,110,124,139,140,151,154,156],evenli:[51,93],event:[33,45,48,59,61,70,81,133,134,138],event_tim:59,eventu:[13,45,124],ever:[137,141],everi:[6,12,28,32,44,60,62,63,83,86,88,92,93,101,110,111,119,120,130,134,136,138,140,142,147,151,153,156],everyth:[32,55,58,71,94,103,104,111,121],everywher:[38,39,47,64,101,134],evolv:[22,83,86,99],evolve_to_tim:[83,99],exact:97,exactli:[28,50,52,101,132,138],exam:77,examin:[16,35,36,44,66,106],exampl:[0,1,2,3,4,5,6,7,8,9,13,14,16,20,22,24,27,28,29,30,38,40,41,43,45,47,53,54,55,56,57,59,60,62,63,64,68,70,71,72,76,77,79,81,82,83,84,86,89,90,92,93,96,97,98,99,100,103,104,105,106,108,109,110,111,113,115,116,117,118,119,120,121,122,123,124,125,129,130,131,133,134,136,137,138,139,140,141,142,143,147,149,150,151,153,154,155,156],exce:[32,51,110,139],exceed:[110,121],except:[22,27,30,39,92,97,104,124,138,141,147,151],ex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this software","Guiding AMR with adjoint flagging","Adaptive mesh refinement (AMR) algorithms","AMRClaw Description and Detailed Contents","AMRClaw for 1d problems","Doxygen documentation of AMRClaw","AMRClaw Flowcharts","Application documentation","Clawpack Applications repository","Amazon Web Services EC2 Clawpack AMI","b4run function","b4step default routines","Boundary conditions","Bibliography","Changes to master since v5.8.1","Converting from Clawpack 4.3 to 4.6","Converting from Clawpack 4.6 to 5.0","Clawpack 4.x links","Changes in Clawpack 5.0","Clawpack components","Clawpack Community","Full Table of Contents","Contributing examples and applications","current_data","Developers\u2019 Guide","Docker for Clawpack","dtopotools module for moving topography","Fortran 77 vs. Fortran 90 files","Fixed grid monitoring","fgmax_tools module for working with topography data","Fixed grid output","Running an example","Testing your Fortran installation and running an example","Testing a PyClaw installation and running an example","Specifying flagregions for adaptive refinement","Force Cells to be Dry Initially","Fortran version","Fortran Compilers","Examples from the book FVMHP","Clawpack Gallery","Gauges","GeoClaw Description and Detailed Contents","Getting started with GeoClaw","geoclaw.util module of utility functions","Cautionary Hints on using GeoClaw","GeoClaw plotting tools","Keeping track of repository versions with Git","Visualizing GeoClaw results in Google Earth","Using the GPU version of Clawpack","Grid registration","Guide for updating this documentation","Guide for doing a Clawpack release","Installing Clawpack","Options for installing Clawpack Fortran codes","pip install instructions","kmltools module of utility functions","Lagrangian gauges for particle tracking","License","Clawpack Makefiles","Library routines in Makefiles","Manning friction term","The mapc2p function","Marching Front algorithm","Plotting using Matlab","Using NetCDF output","Creating a new application directory","Earthquake sources: Fault slip and the Okada model","Using OpenMP","Output data formats","Which Clawpack solver should I use?","Clawpack Community Photos","Plotting examples","Plotting with Visclaw","Plotting hints and FAQ","Plotting routines for GeoClaw","Plotting options in Python","Installation Prerequisites","About PyClaw","PyClaw Basics","Understanding Pyclaw Classes","Porting a problem from Clawpack 4.6.x to PyClaw","Running PyClaw in the cloud","Pyclaw Controller Class","Pyclaw Limiters","Working with PyClaw\u2019s built-in examples","PyClaw Geometry","Going Further","PyClaw","Pyclaw Input/Output Package","PyClaw output","Running in parallel","Plotting PyClaw results","Setting up your own problem","Riemann Solver Package","PyClaw Solutions","Using PyClaw\u2019s solvers: Classic and SharpClaw","Installing PyClaw","PyClaw State","Troubleshooting","PyClaw tutorial: Solve the acoustics equations","Pyclaw Utility Module","Python Hints","Python path","qinit default routines","Quick start guide for storm surge modeling","Quick start guide for tsunami modeling","AMR refinement criteria","Regression testing","v5.0.0 release notes","v5.1.0 release notes","v5.2.0 release notes","v5.2.1 release notes","v5.2.2 release notes","v5.3.0 release notes","v5.3.1 release notes","v5.4.0 release notes","v5.4.1 release notes","v5.5.0 release notes","v5.6.0 release notes","v5.6.1 release notes","v5.7.0 release notes","v5.7.1 release notes","v5.8.0 release notes","v5.8.1 release notes","Releases of Clawpack and release notes","Checkpointing and restarting","Riemann solvers","Shallow water Riemann solvers in Clawpack","Ruled Rectangles","Setting sealevel","Set Eta Init \u2013 spatially varying initial surface elevation","setaux default routines","Set environment variables","Using setplot.py to specify the desired plots","Specifying classic run-time parameters in setrun.py","Specifying AMRClaw run-time parameters in setrun.py","Sample setrun.py module for AMRClaw","Specifying GeoClaw parameters in setrun.py","Sample setrun.py module for classic Clawpack","Saving and sharing results","Compiling the Sphinx documentation locally","src1d default routines","src default routines","Storm Specification Class and Tools","Sources for Storm Surge Data","Testing your installation","Timing Statistics","Topography data","Python tools for working with topo and dtopo","topotools module for working with topography data","Troubleshooting","Some sources of tsunami data","User files required for the Fortran code","Plotting with VisIt","Clawpack Virtual Machine","Wave-propagation algorithms"],titleterms:{"1d_fill_between":3,"1d_from_2d_data":3,"1d_plot":3,"2d_contour":3,"2d_pcolor":3,"case":134,"catch":28,"class":[83,86,147],"default":[15,107,134,135,145,146],"final":55,"function":[14,47,59,65,66,79,93,99,159],"import":106,"new":[46,54,69,88,111],"switch":67,"true":77,Adding:[28,51,88,96,130],For:6,Going:90,One:[130,131,159],The:[51,65,66,67,103],Use:102,Using:[5,13,25,29,38,52,58,63,68,71,93,96,99,130,137,156],about:[4,81],abov:29,access:79,acoust:[97,103],adapt:[6,16,25,38],add:77,addit:[51,139,141],adjoint:5,adjust:134,advect:97,after:129,afterfram:67,algorithm:[6,17,66,73,159],alias:51,all:[3,58,66],along:66,amazon:13,ami:13,amr:[3,5,6,22,66,71,110,132,139,141],amrclaw:[7,8,9,10,18,25,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,139,140,156],anoth:77,app:55,applic:[11,12,17,25,26,62,69,94],approach:8,arcsecond:[39,66],area:66,argument:66,arrai:[39,66,72,102],arriv:141,artifact:51,ascii:[72,92],attribut:[0,1,2,3,27,32,51,77,132],author:4,auto:[30,33,47,59,153],aux:[72,83],auxiliari:96,avail:[24,42],axes:49,b4run:14,b4step:[15,156],background:77,backward:[18,121,122,123,124,125,126,127],base:62,basic:[51,82,95],bathymetri:155,befor:156,behavior:134,below:66,better:29,between:[29,77],bibliographi:17,binari:72,binder:29,book:42,boundari:[6,16,96,156,159],bounding_box:132,branch:[28,54],buffer:66,bug:28,built:[54,88],buoi:155,burger:97,candid:55,capac:159,cautionari:48,cell:[6,39,132],cfl:87,chang:[18,22,77,99,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127],chardiff:111,check:[28,111],checkpoint:129,chile:51,choic:32,choos:[6,66],cite:[4,91],clamshel:16,classic:[18,25,35,36,99,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,138,142,149],claw:[74,136],clawcode2html:11,clawpack:[12,13,17,18,19,20,21,22,23,24,25,29,43,52,54,55,56,57,62,73,74,84,87,99,100,120,121,122,123,124,125,126,127,128,131,142,158],clawplotax:0,clawplotdata:1,clawplotfigur:2,clawplotitem:[3,77],clawutil:[18,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127],clinic:24,clone:[28,57],cloud:85,code:[11,25,28,39,46,57,58,74,111,154,156],color:77,colorbar:51,colormap:77,command:[29,37,67,79,88,154],commit:28,commun:[24,28,74],comparison:111,compat:[18,121,122,123,124,125,126,127],compil:[41,62,68,102,144,154],compon:[23,77],comput:[73,129],condit:[6,16,96,103,156,159],configur:54,contain:29,content:[7,25,28,39,45,66,77,83,93,99,111,132],continent:132,continu:111,contourf:77,contribut:[26,28,131],contributor:81,control:[83,86,103],convers:20,convert:[11,19,20],convex:132,coordin:[49,51],copi:69,correctli:94,cover:132,coverag:28,creat:[13,29,39,51,55,66,67,69,83],creation:83,criteria:110,current_data:[27,79],curv:77,custom:[99,130],dart:155,data:[33,51,72,137,141,148,151,153,154,155,156],debug:[77,139],defin:[16,132],deform:134,dem:[39,66],demonstr:131,depend:[87,100],deprec:8,depth:49,deriv:[83,93],describ:17,descript:[7,45],desir:137,detail:[6,7,45],determin:66,dev:74,develop:[24,25,28,74],diff:111,differ:[32,51,58,63,73,77],dimens:[89,131,159],dimension:130,directli:13,directori:[58,62,69,77],displac:151,doc:54,docker:29,dockerfil:[29,55],docstr:[30,33,47,59,153],doctest:111,document:[9,11,30,33,47,54,55,59,91,120,121,144,153],doing:55,domain:[89,103],done:156,download:151,doxygen:9,drop:105,dry:[39,66],dtopo:152,dtopotool:30,duplic:62,each:[28,156],earth:51,earthquak:[70,155],easi:106,ec2:13,elev:[49,66,134],environ:[41,136],equat:[97,103,131],error:[28,102],eta:134,euler:97,event:[24,51],exampl:[12,25,26,32,35,36,37,39,42,44,46,51,58,66,67,69,75,88,91,94,132],exe:154,exist:69,experi:58,extra:54,extrapol:110,f2py:154,faq:77,faster:51,fault:70,featur:91,fflag:41,fgmax:[32,66],fgmax_tool:33,figur:[51,77],file:[13,29,31,32,39,51,53,54,55,57,63,67,77,79,111,129,132,141,151,156],fileio:92,find:[13,66,77],finer:6,fix:[28,32,34,71,141],flag2refin:110,flag:[5,6,62,66,110,132,139],flagregion:38,flow:[25,83],flowchart:10,fly:76,forc:39,force_dry_init:39,fork:28,format:[32,72,151],formul:159,fort:[72,77],fortran:[22,25,31,36,39,40,41,57,80,102,111,154,156],found:67,frame:93,framework:55,friction:64,from:[13,19,20,22,25,28,30,33,37,39,42,47,54,59,66,79,84,88,95,132,153],front:66,full:25,fund:[4,81],further:90,fvmhp:42,galleri:[43,54,67],gaug:[44,51,60,93,155],gdal:51,gener:[18,22,30,33,47,54,59,121,122,123,124,125,126,127,141,153],geo:141,geoclaw:[5,15,16,18,22,25,29,39,45,46,47,48,49,51,71,74,78,107,110,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,132,135,141,145,146],geometri:89,geophys:25,get:[25,29,46,67],gfortran:[41,100],ghost:6,git:[28,50,54,57,80],github:[28,55],given:66,global:119,godunov:159,googl:51,gpu:52,grid:[6,16,32,34,53,71,89,141],guid:[5,28,54,55,108,109],guidelin:28,hack:74,hazard:48,hdf5:92,help:67,high:159,hint:[48,77,105],hll:131,host:29,how:[77,79,93],hpc3:74,html:[11,79],imag:[29,51],imagediff:111,implement:110,includ:[12,54],independ:87,indic:[66,91],init:134,initi:[6,39,66,96,103,134,156],input:[22,32,92,138,139],instal:[28,36,37,56,57,58,68,73,80,91,94,100,102,106,149,154],instanc:13,instanti:132,instruct:[28,58],integr:111,intel:41,interact:[79,88],interfac:73,intern:39,interpol:32,interpret:37,iplotclaw:79,ipython:[37,88],issu:28,item:77,jupyt:[12,29,37,143],kaust:74,keep:50,kinemat:70,kml:51,kmltool:59,kmz:51,lagrangian:60,latest:28,latex:79,latitud:[49,51],launch:13,layer:131,level:[28,134],lflag:41,librari:[51,63],licens:[4,61,81],limit:87,line:[37,79,88,111,154],link:21,load:51,local:144,locat:44,log:[13,93],longitud:[49,51],machin:[29,158],make:[77,94,143,154],make_kml:132,makefil:[40,62,63,96,129],man:64,map:51,mapc2p:65,march:66,mask:66,mask_outsid:132,master:[18,28],math:85,matlab:67,matplotlib:100,maxfram:67,maximum:141,mesh:[6,25],method:[0,1,2,3,132,159],mhw:66,migrat:25,miss:131,model:[48,70,108,109,155],modif:39,modifi:[28,63,129],modul:[30,33,47,59,91,104,140,142,153],monitor:[32,141],more:[6,36,40],most:28,move:[29,30],multipl:51,name:[62,63],need:51,netcdf:[53,68,72,92,151],never:28,next:[56,57,58,100],nose:100,note:[112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128],notebook:[12,29,37,105,143],number:55,numpi:100,object:[89,137],obtain:100,okada:70,old:8,older:25,onli:66,open:55,openmp:71,oper:80,option:[51,57,79,94,96],order:102,osf:55,other:[17,18,23,24,29,32,54,77,120,121,122,123,124,125,126,127,128,132,134],out:[28,66],outdir:77,output:[32,34,62,66,67,68,71,72,83,92,93,111,129,138,139,141,154],overlai:51,overview:[25,137],own:[13,29,96],packag:[22,58,92,97],page:54,paper:17,parallel:[73,89,94,95,101],paramet:[22,44,77,79,103,138,139,141],particl:60,pass:94,patch:89,path:[67,106],pcolor:77,petclaw:[89,101],petsc:94,photo:74,pip:[58,80,154],pixel:111,plot:[3,13,22,25,32,44,46,49,51,60,62,67,68,75,76,77,78,79,88,94,95,111,137,143,154,157],plot_typ:3,plotax:51,plotclaw:67,plotdata:51,plotfigur:51,plotitem:51,point:[32,66],pointwis:130,polygon:132,port:84,post:76,potenti:131,ppflag:41,pre:41,prepar:55,prerequisit:80,previou:[24,54],previous_pts_chosen:66,print:139,printfram:79,problem:[8,84,96,103,156],procedur:32,process:[32,76],processor:41,produc:79,propag:159,provid:77,pth:106,publish:51,pull:28,pyclaw:[18,22,25,35,37,58,81,82,83,84,85,86,87,88,89,91,92,93,95,98,99,100,101,103,104,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,149],pyflak:28,pylint:28,pypi:55,python:[20,79,80,100,105,106,124,152],pythonpath:[106,136],q0002:72,qinit:[107,141,151],quantiti:[83,93],quick:[58,108,109],raw:72,read:[39,132],readm:11,recent:[24,28],rectangl:[38,132],rectangular:70,refer:[17,25,52,91,105],refin:[6,16,25,38,110,141],region:[66,110,132,141],registr:53,regress:111,relat:132,releas:[54,55,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128],remot:28,remov:51,replac:63,report:28,repositori:[12,18,23,28,50,54,55,120,121,122,123,124,125,126,127,130],request:28,requir:[51,156],resolut:[51,159],resourc:25,restart:[29,83,129],result:[13,46,51,68,95,143],richardson:110,riemann:[18,25,91,96,97,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,130,131,156],roe:131,routin:[15,22,63,78,107,135,145,146],rst:11,rule:[38,132],run:[29,35,36,37,46,83,85,88,94,95,111,138,139,154],ruptur:70,sage:85,same:63,sampl:[39,66,140,142],save:[93,143],scienc:55,script:96,sea:134,sealevel:133,search:67,seismic:134,select:132,serial:[89,101,111],servic:13,session:24,set:[46,67,77,79,96,133,134,136,154],setaux:[135,156],setplot:[67,77,79,137],setrun:[22,44,138,139,140,141,142],shallow:[97,131],share:143,sharpclaw:99,shelf:132,shoot:[28,67],shore:66,should:73,signatur:99,simpl:[32,132],simul:83,simultan:111,sinc:18,size:77,slip:70,slu:132,softwar:[4,17],solut:[77,83,98],solv:103,solver:[73,83,91,96,97,99,103,130,131,156],some:[29,77,155],someth:77,sourc:[62,70,96,148,155,156,159],space:159,spatial:[134,156],special:[3,139],specif:[32,103,111,141,147,156],specifi:[38,60,77,79,110,137,138,139,141,156],sphere:16,sphinx:[54,144],sprint:[24,74],src1d:[145,156],src:[146,156],start:[25,29,46,108,109],state:101,statist:150,step:[56,57,58,100,156],stop:[13,29],storm:[108,141,147,148],stream:24,style:[32,54],subfault:70,submodul:12,support:[105,124],surfac:[49,134],surg:[108,148],sys:106,system:80,t0002:72,tabl:[25,91],tag:54,tar:[55,57],term:[64,96,156,159],test:[28,36,37,94,100,111,149],than:77,thi:[4,54],tide:155,tile:51,time:[138,139,141,150,156],tip:[28,40,49,51,94],titl:77,tool:[20,25,44,49,60,111,147,152],top:28,topo:152,topofil:66,topographi:[30,33,39,46,51,66,141,151,153,155],topotool:153,track:[50,60],transfer:13,travi:111,triangular:70,troubl:[28,67,154],troubleshoot:[58,102,154],tsunami:[48,51,109,155],tutori:[24,103,105],tvd:87,two:131,understand:83,univers:74,upcom:24,updat:[28,54,55],usag:39,use:[73,134],used:154,useful:[29,131],user:[16,24,29,73,156],using:[48,67,156],utah:74,util:[47,59,104],valu:[32,83],vari:[134,156],variabl:[41,62,96,136],version:[25,29,40,50,52,54,55,58,106],view:13,virtual:158,visclaw:[18,25,60,76,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127],visit:157,visual:[25,51],washington:74,water:[49,97,131],wave:[130,159],web:13,webpag:[13,54,143],what:[77,79,93,131],when:93,where:93,which:[73,106],whichclaw:106,work:[4,33,88,152,153,156],workflow:28,workshop:[24,74],write:[66,96,111,132],written:93,your:[13,28,29,36,51,94,96,100,143,149],zenodo:55,zone:66}}) \ No newline at end of file diff --git a/v5.8.x/setenv.html b/v5.8.x/setenv.html index 658e976b1e..00397bd535 100644 --- a/v5.8.x/setenv.html +++ b/v5.8.x/setenv.html @@ -21,7 +21,7 @@ - +

                                                                                                                                                                                                                                                                                                                                                @@ -70,7 +70,7 @@

                                                                                                                                                                                                                                                                                                                                                Navigation

                                                                                                                                                                                                                                                                                                                                                next |
                                                                                                                                                                                                                                                                                                                                              • - previous |
                                                                                                                                                                                                                                                                                                                                              • Clawpack 5.8.x documentation »
                                                                                                                                                                                                                                                                                                                                              @@ -83,6 +83,8 @@

                                                                                                                                                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                                                                                                                                                              Set environment variables

                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              The export commands below work in the bash shell. The syntax may +be different in other shells.

                                                                                                                                                                                                                                                                                                                                              CLAW

                                                                                                                                                                                                                                                                                                                                              To use the Fortran versions of Clawpack you will need to set the @@ -117,9 +119,15 @@

                                                                                                                                                                                                                                                                                                                                              FC

                                                                                                                                                                                                                                                                                                                                              PYTHONPATH

                                                                                                                                                                                                                                                                                                                                              -

                                                                                                                                                                                                                                                                                                                                              We do not recommend setting this environment variable. See -Python path for more information. Instead we recommend using pip -install to set the Python path appropriately, see pip install instructions.

                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              If you used pip to install Clawpack then you should not set this +environment variable. But if you installed without pip, e.g. following +Options for installing Clawpack Fortran codes, then you need to set PYTHONPATH to include +the directory $CLAW. If PYTHONPATH is already set, then you may want to +insert $CLAW into the list of directories searched by Python via:

                                                                                                                                                                                                                                                                                                                                              +
                                                                                                                                                                                                                                                                                                                                              export PYTHONPATH=$CLAW:$PYTHONPATH
+
                                                                                                                                                                                                                                                                                                                                              +
                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              See Python path for more information.

                                                                                                                                                                                                                                                                                                                                              @@ -146,7 +154,7 @@

                                                                                                                                                                                                                                                                                                                                              Table of Contents

                                                                                                                                                                                                                                                                                                                                              Related Topics

                                                                                                                                                                                                                                                                                                                                              diff --git a/v5.8.x/setrun_geoclaw.html b/v5.8.x/setrun_geoclaw.html index 55b87f65e1..42eb9b7732 100644 --- a/v5.8.x/setrun_geoclaw.html +++ b/v5.8.x/setrun_geoclaw.html @@ -142,23 +142,6 @@

                                                                                                                                                                                                                                                                                                                                              Additional AMR parameters -
                                                                                                                                                                                                                                                                                                                                              -rundata.refinement_data.max_level_deep : int
                                                                                                                                                                                                                                                                                                                                              -

                                                                                                                                                                                                                                                                                                                                              For simulations over the ocean, it is often useful to specify -a maximum refinement level allowed in deep parts of the ocean. This is -useful if a high level of refinement is specified on some rectangular -region but only the parts of this region near the shore actually need to -be refined.

                                                                                                                                                                                                                                                                                                                                              -
                                                                                                                                                                                                                                                                                                                                              - -
                                                                                                                                                                                                                                                                                                                                              -
                                                                                                                                                                                                                                                                                                                                              -rundata.refinement_data.deep_depth : float
                                                                                                                                                                                                                                                                                                                                              -

                                                                                                                                                                                                                                                                                                                                              The deepness that triggers the refinement limitation imposed by -max_level_deep above.

                                                                                                                                                                                                                                                                                                                                              -
                                                                                                                                                                                                                                                                                                                                              -

                                                                                                                                                                                                                                                                                                                                              • General geo parameters

                                                                                                                                                                                                                                                                                                                                              diff --git a/v5.8.x/sharing.html b/v5.8.x/sharing.html index 24c304c582..a9a6eced82 100644 --- a/v5.8.x/sharing.html +++ b/v5.8.x/sharing.html @@ -87,7 +87,7 @@

                                                                                                                                                                                                                                                                                                                                              Navigation

                                                                                                                                                                                                                                                                                                                                              results that you have obtained with this software. These make it relatively easy to generate a set of webpages such as those seen when browsing the examples collected in -galleries.

                                                                                                                                                                                                                                                                                                                                              +Clawpack Gallery.

                                                                                                                                                                                                                                                                                                                                              These webpages can easily be posted on your own website to be viewed by others if you wish, for example to share on-going work with collaborators or to supplement a journal article.

                                                                                                                                                                                                                                                                                                                                              @@ -106,11 +106,13 @@

                                                                                                                                                                                                                                                                                                                                              Sharing your results

                                                                                                                                                                                                                                                                                                                                              -
                                                                                                                                                                                                                                                                                                                                              -

                                                                                                                                                                                                                                                                                                                                              IPython notebooks

                                                                                                                                                                                                                                                                                                                                              -

                                                                                                                                                                                                                                                                                                                                              You should also consider creating an IPython notebook to explain your +

                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              Jupyter notebooks

                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              You should also consider creating an Jupyter notebook to explain your problem, illustrate your workflow, and present plots and animations all in -one. See notebooks for some examples.

                                                                                                                                                                                                                                                                                                                                              +one. See the +Gallery of Notebooks +for some examples.

                                                                                                                                                                                                                                                                                                                                              @@ -130,7 +132,7 @@

                                                                                                                                                                                                                                                                                                                                              Table of Contents

                                                                                                                                                                                                                                                                                                                                            • Saving and sharing results
                                                                                                                                                                                                                                                                                                                                            diff --git a/v5.8.x/storm_module.html b/v5.8.x/storm_module.html index c8125be069..1b8f3e0799 100644 --- a/v5.8.x/storm_module.html +++ b/v5.8.x/storm_module.html @@ -586,7 +586,7 @@

                                                                                                                                                                                                                                                                                                                                            Navigation

                                                                                                                                                                                                                                                                                                                                            -

                                                                                                                                                                                                                                                                                                                                            System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/surge/storm.py:docstring of clawpack.geoclaw.surge.storm.fill_rad_w_other_source, line 15)

                                                                                                                                                                                                                                                                                                                                            +

                                                                                                                                                                                                                                                                                                                                            System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/surge/storm.py:docstring of clawpack.geoclaw.surge.storm.fill_rad_w_other_source, line 15)

                                                                                                                                                                                                                                                                                                                                            Field list ends without a blank line; unexpected unindent.

                                                                                                                                                                                                                                                                                                                                              @@ -617,7 +617,7 @@

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                                                                                                                                                                                                                                                                                                                                              -

                                                                                                                                                                                                                                                                                                                                              System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/geoclaw/surge/storm.py:docstring of clawpack.geoclaw.surge.storm.fill_rad_w_other_source, line 26)

                                                                                                                                                                                                                                                                                                                                              +

                                                                                                                                                                                                                                                                                                                                              System Message: WARNING/2 (/Users/rjl/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/surge/storm.py:docstring of clawpack.geoclaw.surge.storm.fill_rad_w_other_source, line 26)

                                                                                                                                                                                                                                                                                                                                              Field list ends without a blank line; unexpected unindent.

                                                                                                                                                                                                                                                                                                                                                diff --git a/v5.8.x/testing.html b/v5.8.x/testing.html index feb323703d..94eb5cd72d 100644 --- a/v5.8.x/testing.html +++ b/v5.8.x/testing.html @@ -85,7 +85,7 @@

                                                                                                                                                                                                                                                                                                                                                Navigation

                                                                                                                                                                                                                                                                                                                                                Testing your installation

                                                                                                                                                                                                                                                                                                                                                PyClaw

                                                                                                                                                                                                                                                                                                                                                -

                                                                                                                                                                                                                                                                                                                                                If you downloaded Clawpack manually, you can test your Pyclaw +

                                                                                                                                                                                                                                                                                                                                                If you downloaded Clawpack manually, you can test your PyClaw installation as follows (starting from your clawpack directory):

                                                                                                                                                                                                                                                                                                                                                cd pyclaw
 nosetests
@@ -118,7 +118,7 @@ 
                                                                                                                                                                                                                                                                                                                                                Classicgalleries.  See also Regression testing.
                                                                                                                                                                                                                                                                                                                                                
+archived in the Clawpack Gallery.  See also Regression testing.
                                                                                                                                                                                                                                                                                                                                                diff --git a/v5.8.x/topo.html b/v5.8.x/topo.html index 50849233ec..1f700c2ad6 100644 --- a/v5.8.x/topo.html +++ b/v5.8.x/topo.html @@ -147,8 +147,10 @@

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                                                                                                                                                                                                                                                                                                                                                These files are larger than necessary since they store the x,y values at each point even though the points are required to be equally spaced. Many data sets come this way, but note that you can convert a file of -this type to one of the more compact types below using:

                                                                                                                                                                                                                                                                                                                                                -
                                                                                                                                                                                                                                                                                                                                                [insert python code]
+this type to one of the more compact types below using e.g.:
                                                                                                                                                                                                                                                                                                                                                
+
                                                                                                                                                                                                                                                                                                                                                from clawpack.geoclaw import topotools
+topo = topotools.Topography(input_path, topo_type=1)
+topo.write(output_path, topo_type=3)
                                                                                                                                                                                                                                                                                                                                          diff --git a/v5.8.x/topotools_module.html b/v5.8.x/topotools_module.html index 2df7e7e219..eaddf28db8 100644 --- a/v5.8.x/topotools_module.html +++ b/v5.8.x/topotools_module.html @@ -314,7 +314,7 @@

                                                                                                                                                                                                                                                                                                                                          Navigation

                                                                                                                                                                                                                                                                                                                                          -plot(axes=None, contour_levels=None, contour_kwargs={}, limits=None, cmap=None, add_colorbar=True, plot_box=False, fig_kwargs={}, data_break=0.0, cb_kwargs={})
                                                                                                                                                                                                                                                                                                                                          +plot(axes=None, contour_levels=None, contour_kwargs={}, limits=None, cmap=None, add_colorbar=True, plot_box=False, long_lat=True, fig_kwargs={}, data_break=0.0, cb_kwargs={})

                                                                                                                                                                                                                                                                                                                                          Plot the topography.

                                                                                                                                                                                                                                                                                                                                          Input
                                                                                                                                                                                                                                                                                                                                          @@ -334,6 +334,9 @@

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                                                                                                                                                                                                                                                                                                                                        • fig_kwargs (dict) - keyword arguments to be passed to figure.

                                                                                                                                                                                                                                                                                                                                        • plot_box (bool or color specifier) - If evaluates to True, plot a box around limits of this topo.

                                                                                                                                                                                                                                                                                                                                          • +

                                                                                                                                                                                                                                                                                                                                        • long_lat (bool) - If this is a longitude-latitude plot then set the +aspect of the plot to compensate for stretching. If not then the +aspect is set to “equal”.

                                                                                                                                                                                                                                                                                                                                        • data_break (float) - when default cmap is used, the value to use to break between water and land colormaps. Defaults to 0., but for some topo files may need to use e.g. 0.01 diff --git a/v5.8.x/user_routines.html b/v5.8.x/user_routines.html index 6bdb3755fb..7d4a31d70c 100644 --- a/v5.8.x/user_routines.html +++ b/v5.8.x/user_routines.html @@ -101,7 +101,7 @@

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                                                                                                                                                                                                                                                                                                                                        • $CLAW/amrclaw/examples

                                                                                                                                                                                                                                                                                                                                        • $CLAW/geoclaw/examples

                                                                                                                                                                                                                                                                                                                                        -

                                                                                                                                                                                                                                                                                                                                        You can also browse from the galleries to the README file for an +

                                                                                                                                                                                                                                                                                                                                        You can also browse from the Clawpack Gallery to the README file for an example and then to the source code for the application-specific codes.

                                                                                                                                                                                                                                                                                                                                        Specifying the initial conditions