From 6bbc5ec1ea7e271e34261dd5610a2499d069bf1a Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Sun, 24 Oct 2021 17:24:28 -0700 Subject: [PATCH] add zenodo doi for v5.8.1, doc@450677c15 --- _sources/howto_doc.rst.txt | 3 ++- _sources/release_5_8_1.rst.txt | 2 +- _sources/releases.rst.txt | 2 +- dev/.buildinfo | 2 +- dev/.doctrees/ClawPlotAxes.doctree | Bin 21072 -> 21072 bytes dev/.doctrees/ClawPlotData.doctree | Bin 36961 -> 36961 bytes dev/.doctrees/ClawPlotFigure.doctree | Bin 14589 -> 14589 bytes dev/.doctrees/ClawPlotItem.doctree | Bin 60183 -> 60183 bytes dev/.doctrees/about.doctree | Bin 47427 -> 47427 bytes dev/.doctrees/adjoint.doctree | Bin 36838 -> 36838 bytes dev/.doctrees/amr_algorithm.doctree | Bin 40243 -> 40243 bytes dev/.doctrees/amrclaw.doctree | Bin 11644 -> 11644 bytes dev/.doctrees/amrclaw1d.doctree | Bin 8466 -> 8466 bytes dev/.doctrees/amrclaw_doxygen.doctree | Bin 5937 -> 5937 bytes dev/.doctrees/amrclaw_flowcharts.doctree | Bin 6077 -> 6077 bytes 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v5.8.x/.doctrees/topotools_module.doctree | Bin 157152 -> 157218 bytes v5.8.x/.doctrees/trouble.doctree | Bin 29048 -> 29048 bytes v5.8.x/.doctrees/tsunamidata.doctree | Bin 23667 -> 23667 bytes v5.8.x/.doctrees/user_routines.doctree | Bin 58472 -> 58472 bytes v5.8.x/.doctrees/visit_plotting.doctree | Bin 8455 -> 8455 bytes v5.8.x/.doctrees/vm.doctree | Bin 5045 -> 5045 bytes v5.8.x/.doctrees/wp_algorithms.doctree | Bin 30513 -> 30513 bytes v5.8.x/_sources/howto_doc.rst.txt | 3 ++- v5.8.x/_sources/release_5_8_1.rst.txt | 2 +- v5.8.x/_sources/releases.rst.txt | 2 +- v5.8.x/geoclaw_util_module.html | 2 +- v5.8.x/howto_doc.html | 3 ++- v5.8.x/kmltools_module.html | 10 ++++---- v5.8.x/release_5_8_1.html | 2 +- v5.8.x/releases.html | 2 +- v5.8.x/storm_module.html | 4 ++-- 1426 files changed, 324 insertions(+), 318 deletions(-) diff --git a/_sources/howto_doc.rst.txt b/_sources/howto_doc.rst.txt index 3ddea4e654..ccb9d76877 100644 --- a/_sources/howto_doc.rst.txt +++ b/_sources/howto_doc.rst.txt @@ -192,7 +192,8 @@ For detailed instructions, see `CLAW/doc/gallery/README.md Then do the following:: - cd $CLAW/doc/gallery make html + cd $CLAW/doc/gallery + make html Note that we don't track past versions in the gallery. diff --git a/_sources/release_5_8_1.rst.txt b/_sources/release_5_8_1.rst.txt index 4ba8cde17c..611f804c2d 100644 --- a/_sources/release_5_8_1.rst.txt +++ b/_sources/release_5_8_1.rst.txt @@ -11,7 +11,7 @@ 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.?? +Permanent DOI: http://doi.org/10.5281/zenodo.5595424 Changes relative to Clawpack 5.8.0 (February 4, 2021) are shown below. diff --git a/_sources/releases.rst.txt b/_sources/releases.rst.txt index 22ff38421d..7c77a844b3 100644 --- a/_sources/releases.rst.txt +++ b/_sources/releases.rst.txt @@ -36,7 +36,7 @@ can also be referenced with the single DOI See :ref:`citing` for more information on how best to cite Clawpack. * :ref:`release_5_8_1` -- October 19, 2021 - `[DOI 10.5281/zenodo.??] `_ + `[DOI 10.5281/zenodo.5595424] `_ * :ref:`release_5_8_0` -- February 4, 2021 `[DOI 10.5281/zenodo.4503024] `_ * :ref:`release_5_7_1` -- September 11, 2020 diff --git a/dev/.buildinfo b/dev/.buildinfo index 79856588f6..bcc9ba4fae 100644 --- a/dev/.buildinfo +++ b/dev/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. 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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.?? +Permanent DOI: http://doi.org/10.5281/zenodo.5595424 Changes relative to Clawpack 5.8.0 (February 4, 2021) are shown below. diff --git a/dev/_sources/releases.rst.txt b/dev/_sources/releases.rst.txt index 22ff38421d..7c77a844b3 100644 --- a/dev/_sources/releases.rst.txt +++ b/dev/_sources/releases.rst.txt @@ -36,7 +36,7 @@ can also be referenced with the single DOI See :ref:`citing` for more information on how best to cite Clawpack. * :ref:`release_5_8_1` -- October 19, 2021 - `[DOI 10.5281/zenodo.??] `_ + `[DOI 10.5281/zenodo.5595424] `_ * :ref:`release_5_8_0` -- February 4, 2021 `[DOI 10.5281/zenodo.4503024] `_ * :ref:`release_5_7_1` -- September 11, 2020 diff --git a/dev/geoclaw_util_module.html b/dev/geoclaw_util_module.html index 658d92cf46..a40edf63d6 100644 --- a/dev/geoclaw_util_module.html +++ b/dev/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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/util.py:docstring of clawpack.geoclaw.util.bearing, line 9)

+

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

Unexpected indentation.

diff --git a/dev/howto_doc.html b/dev/howto_doc.html index fe89727f2c..c0fe10c0f1 100644 --- a/dev/howto_doc.html +++ b/dev/howto_doc.html @@ -240,7 +240,8 @@

Updating the gallery

For detailed instructions, see CLAW/doc/gallery/README.md.

Then do the following:

-
cd $CLAW/doc/gallery    make html
+
cd $CLAW/doc/gallery
+make html
 

Note that we don’t track past versions in the gallery.

diff --git a/dev/kmltools_module.html b/dev/kmltools_module.html index e14a64fb6c..f75decde34 100644 --- a/dev/kmltools_module.html +++ b/dev/kmltools_module.html @@ -336,7 +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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

+

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

Unexpected indentation.

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

Navigation

dpi * y_inches = dcp * y_cells

-

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)

+

System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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.

@@ -354,14 +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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

+

System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

+

System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 @@ -497,7 +497,7 @@

Navigation

-

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)

+

System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 diff --git a/dev/release_5_8_1.html b/dev/release_5_8_1.html index 3576f60c75..df48c0fd07 100644 --- a/dev/release_5_8_1.html +++ b/dev/release_5_8_1.html @@ -78,7 +78,7 @@

Navigation

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.??

+

Permanent DOI: http://doi.org/10.5281/zenodo.5595424

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.

diff --git a/dev/releases.html b/dev/releases.html index d5d140b2ea..1add7cf4e1 100644 --- a/dev/releases.html +++ b/dev/releases.html @@ -110,7 +110,7 @@

Releases:Citing this work for more information on how best to cite Clawpack.

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

  • +[DOI 10.5281/zenodo.5595424]

  • 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/storm_module.html b/dev/storm_module.html index 7169651601..e94d2c3fa4 100644 --- a/dev/storm_module.html +++ b/dev/storm_module.html @@ -586,7 +586,7 @@

    Navigation

    -

    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)

    +

    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)

    Field list ends without a blank line; unexpected unindent.

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

      Navigation

      -

      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)

      +

      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)

      Field list ends without a blank line; unexpected unindent.

        diff --git a/geoclaw_util_module.html b/geoclaw_util_module.html index 9520baf955..a55505d2f8 100644 --- a/geoclaw_util_module.html +++ b/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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/util.py:docstring of clawpack.geoclaw.util.bearing, line 9)

        +

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

        Unexpected indentation.

        diff --git a/howto_doc.html b/howto_doc.html index 2248b2419a..e211b1a9e2 100644 --- a/howto_doc.html +++ b/howto_doc.html @@ -240,7 +240,8 @@

        Updating the gallery

        For detailed instructions, see CLAW/doc/gallery/README.md.

        Then do the following:

        -
        cd $CLAW/doc/gallery    make html
        +
        cd $CLAW/doc/gallery
        +make html
         

        Note that we don’t track past versions in the gallery.

        diff --git a/kmltools_module.html b/kmltools_module.html index 9c2e46489a..18ac1d54db 100644 --- a/kmltools_module.html +++ b/kmltools_module.html @@ -336,7 +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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

        +

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

        Unexpected indentation.

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

        Navigation

        dpi * y_inches = dcp * y_cells

        -

        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)

        +

        System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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.

        @@ -354,14 +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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

        +

        System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

        +

        System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 @@ -497,7 +497,7 @@

        Navigation

        -

        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)

        +

        System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 diff --git a/release_5_8_1.html b/release_5_8_1.html index 86ae504ffd..55bd206558 100644 --- a/release_5_8_1.html +++ b/release_5_8_1.html @@ -78,7 +78,7 @@

        Navigation

        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.??

        +

        Permanent DOI: http://doi.org/10.5281/zenodo.5595424

        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.

        diff --git a/releases.html b/releases.html index cf9b5ab793..ff25da6543 100644 --- a/releases.html +++ b/releases.html @@ -110,7 +110,7 @@

        Releases:Citing this work for more information on how best to cite Clawpack.

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

        • +[DOI 10.5281/zenodo.5595424]

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

        • v5.7.1 release notes – September 11, 2020 diff --git a/storm_module.html b/storm_module.html index 75fa6c81c4..609a2938c7 100644 --- a/storm_module.html +++ b/storm_module.html @@ -586,7 +586,7 @@

          Navigation

          -

          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)

          +

          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)

          Field list ends without a blank line; unexpected unindent.

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            -

            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)

            +

            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)

            Field list ends without a blank line; unexpected unindent.

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              +

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              Navigation

              with latitude when coordinate_system == 2).

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              Navigation

              Galleries of all Clawpack applications

              See also IPython notebook examples.

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              diff --git a/v5.1.x/git_resources.html b/v5.1.x/git_resources.html index e936febc5a..d7261ac8bd 100644 --- a/v5.1.x/git_resources.html +++ b/v5.1.x/git_resources.html @@ -139,9 +139,9 @@

              Manual pages online`git status`_

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            Problems with “include” directive path: -InputError: [Errno 2] No such file or directory: ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/6c7c4a351d3bdc60fa855e7f5fa7fcf9fa1676ae/git_links.inc’.

            +InputError: [Errno 2] No such file or directory: ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/6c7c4a351d3bdc60fa855e7f5fa7fcf9fa1676ae/git_links.inc’.

            .. include:: git_links.inc
             
            diff --git a/v5.1.x/pyclaw/examples.html b/v5.1.x/pyclaw/examples.html index f6d86b1156..8f1587d2b5 100644 --- a/v5.1.x/pyclaw/examples.html +++ b/v5.1.x/pyclaw/examples.html @@ -136,47 +136,47 @@

            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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            diff --git a/v5.1.x/pyclaw/index.html b/v5.1.x/pyclaw/index.html index 9aa9fd53e9..437723eb0c 100644 --- a/v5.1.x/pyclaw/index.html +++ b/v5.1.x/pyclaw/index.html @@ -116,7 +116,7 @@

            PyClaw is:

            PyClaw Documentation

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            References and tutorialsMatplotlib gallery

          • `LeVeque’s class notes

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            Navigation

            the initial conditions as desired.

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

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            qinit data file parameters.

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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 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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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            Navigation

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

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

            -

            System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/5fcd911597685d99d94bee49a3dcea97a4bab85a/b4step_defaults.rst, line 18)

            +

            System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/5fcd911597685d99d94bee49a3dcea97a4bab85a/b4step_defaults.rst, line 18)

            Include file ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/classic/src/1d/b4step1.f90’ not found or reading it failed

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

            -

            System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/5fcd911597685d99d94bee49a3dcea97a4bab85a/b4step_defaults.rst, line 24)

            +

            System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/5fcd911597685d99d94bee49a3dcea97a4bab85a/b4step_defaults.rst, line 24)

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

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

            -

            System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/5fcd911597685d99d94bee49a3dcea97a4bab85a/b4step_defaults.rst, line 30)

            +

            System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/5fcd911597685d99d94bee49a3dcea97a4bab85a/b4step_defaults.rst, line 30)

            Include file ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/classic/src/3d/b4step3.f90’ not found or reading it failed

            @@ -104,7 +104,7 @@

            Navigation

            with latitude when coordinate_system == 2).

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

            -

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

            +

            System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/5fcd911597685d99d94bee49a3dcea97a4bab85a/b4step_defaults.rst, line 48)

            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 43f722bb5a..cc5d811930 100644 --- a/v5.2.x/galleries.html +++ b/v5.2.x/galleries.html @@ -85,19 +85,19 @@

            Navigation

            Galleries of all Clawpack applications

            See also IPython notebook examples.

            -

            System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/5fcd911597685d99d94bee49a3dcea97a4bab85a/galleries.rst, line 10)

            +

            System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/5fcd911597685d99d94bee49a3dcea97a4bab85a/galleries.rst, line 10)

            toctree contains reference to nonexisting document ‘gallery/gallery_classic_amrclaw’

            -

            System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/5fcd911597685d99d94bee49a3dcea97a4bab85a/galleries.rst, line 10)

            +

            System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/5fcd911597685d99d94bee49a3dcea97a4bab85a/galleries.rst, line 10)

            toctree contains reference to nonexisting document ‘pyclaw/gallery/gallery_all’

            -

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            +

            System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/5fcd911597685d99d94bee49a3dcea97a4bab85a/galleries.rst, line 10)

            toctree contains reference to nonexisting document ‘gallery/gallery_geoclaw’

            -

            System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/5fcd911597685d99d94bee49a3dcea97a4bab85a/galleries.rst, line 10)

            +

            System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/5fcd911597685d99d94bee49a3dcea97a4bab85a/galleries.rst, line 10)

            toctree contains reference to nonexisting document ‘gallery/gallery_fvmbook’

            diff --git a/v5.2.x/geoclaw_util_module.html b/v5.2.x/geoclaw_util_module.html index e10a709613..8a09e2a167 100644 --- a/v5.2.x/geoclaw_util_module.html +++ b/v5.2.x/geoclaw_util_module.html @@ -105,7 +105,7 @@

            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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/util.py:docstring of clawpack.geoclaw.util.bearing, line 9)

            +

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

            Unexpected indentation.

            diff --git a/v5.2.x/git_resources.html b/v5.2.x/git_resources.html index 955e372eed..10da382bb4 100644 --- a/v5.2.x/git_resources.html +++ b/v5.2.x/git_resources.html @@ -139,9 +139,9 @@

            Manual pages online`git status`_

          -

          System Message: SEVERE/4 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/5fcd911597685d99d94bee49a3dcea97a4bab85a/git_resources.rst, line 62)

          +

          System Message: SEVERE/4 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/5fcd911597685d99d94bee49a3dcea97a4bab85a/git_resources.rst, line 62)

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

          +InputError: [Errno 2] No such file or directory: ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/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 783784f9dc..2b267adf96 100644 --- a/v5.2.x/kmltools_module.html +++ b/v5.2.x/kmltools_module.html @@ -329,7 +329,7 @@

          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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

          +

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

          Unexpected indentation.

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

          Navigation

          dpi * y_inches = dcp * y_cells

          -

          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)

          +

          System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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.

          @@ -347,14 +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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

          +

          System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

          +

          System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 @@ -490,7 +490,7 @@

          Navigation

          -

          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)

          +

          System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 diff --git a/v5.2.x/pyclaw/examples.html b/v5.2.x/pyclaw/examples.html index dd5c13ffa7..e4d519ad4d 100644 --- a/v5.2.x/pyclaw/examples.html +++ b/v5.2.x/pyclaw/examples.html @@ -136,47 +136,47 @@

          From the command lineList of built-in examples

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

          -

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/5fcd911597685d99d94bee49a3dcea97a4bab85a/pyclaw/examples.rst, line 62)

          +

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          toctree glob pattern ‘gallery/*adv*’ didn’t match any documents

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          +

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          toctree glob pattern ‘gallery/*acoust*’ didn’t match any documents

          -

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          +

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          toctree glob pattern ‘gallery/*burg*’ didn’t match any documents

          -

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          +

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          toctree glob pattern ‘gallery/*shallow*’ didn’t match any documents

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          PyClaw is:

          PyClaw Documentation

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          References and tutorialsMatplotlib gallery

        • `LeVeque’s class notes

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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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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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          (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).

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          Navigation

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

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

          -

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/24e2c68df118c5a00b116198860c806cae4b064d/b4step_defaults.rst, line 18)

          +

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          Include file ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/classic/src/1d/b4step1.f90’ not found or reading it failed

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

          -

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          +

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

          -

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/24e2c68df118c5a00b116198860c806cae4b064d/b4step_defaults.rst, line 30)

          +

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          @@ -104,7 +104,7 @@

          Navigation

          with latitude when coordinate_system == 2).

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

          -

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          +

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          diff --git a/v5.3.x/galleries.html b/v5.3.x/galleries.html index b40cdca6a1..d24e250a20 100644 --- a/v5.3.x/galleries.html +++ b/v5.3.x/galleries.html @@ -85,19 +85,19 @@

          Navigation

          Galleries of all Clawpack applications

          See also IPython notebook examples.

          -

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          toctree contains reference to nonexisting document ‘gallery/gallery_fvmbook’

          diff --git a/v5.3.x/geoclaw_util_module.html b/v5.3.x/geoclaw_util_module.html index 27829d965a..d7df70b485 100644 --- a/v5.3.x/geoclaw_util_module.html +++ b/v5.3.x/geoclaw_util_module.html @@ -102,7 +102,7 @@

          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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/util.py:docstring of clawpack.geoclaw.util.bearing, line 9)

          +

          System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 74db7d39b8..2579028048 100644 --- a/v5.3.x/kmltools_module.html +++ b/v5.3.x/kmltools_module.html @@ -326,7 +326,7 @@

          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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

          +

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          Unexpected indentation.

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

          Navigation

          dpi * y_inches = dcp * y_cells

          -

          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)

          +

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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.

          @@ -344,14 +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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

          +

          System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

          +

          System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 @@ -487,7 +487,7 @@

          Navigation

          -

          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)

          +

          System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 diff --git a/v5.3.x/pyclaw/examples.html b/v5.3.x/pyclaw/examples.html index c701bef081..a2b391fc67 100644 --- a/v5.3.x/pyclaw/examples.html +++ b/v5.3.x/pyclaw/examples.html @@ -136,47 +136,47 @@

          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 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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          (an ocean at rest remains at rest).

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          Navigation

          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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          with latitude when coordinate_system == 2).

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

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          diff --git a/v5.4.x/contents.html b/v5.4.x/contents.html index 3c5a9d39e0..6f985c2c28 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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          Navigation

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

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

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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:

          -

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          diff --git a/v5.4.x/kmltools_module.html b/v5.4.x/kmltools_module.html index 79f62f2f01..08d30b4778 100644 --- a/v5.4.x/kmltools_module.html +++ b/v5.4.x/kmltools_module.html @@ -336,7 +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:

          -

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          dpi * y_inches = dcp * y_cells

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

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

          -

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

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          The png_extent is needed in construcing a kml file to display the @@ -497,7 +497,7 @@

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          -

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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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          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/56744eeda50bfc1d8fec79d45060637228943b2f/src_defaults.rst, line 36)

          +

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/56744eeda50bfc1d8fec79d45060637228943b2f/src_defaults.rst, line 36)

          Include file ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/classic/src/3d/src3.f90’ not found or reading it failed

          @@ -106,7 +106,7 @@

          Navigation

          (an ocean at rest remains at rest).

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

          -

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/56744eeda50bfc1d8fec79d45060637228943b2f/src_defaults.rst, line 53)

          +

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/56744eeda50bfc1d8fec79d45060637228943b2f/src_defaults.rst, line 53)

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

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          Navigation

          Matlab tools from Clawpack 4.3 can still be used, see
          Plotting using Matlab.

          -

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/fb4627276cba3e955dae8c68ce115eeba7df6b18/amrclaw.rst, line 36)

          +

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/fb4627276cba3e955dae8c68ce115eeba7df6b18/amrclaw.rst, line 36)

          toctree contains reference to nonexisting document ‘amrclaw/amrclaw_advection_2d_square’

          diff --git a/v5.5.x/b4step_defaults.html b/v5.5.x/b4step_defaults.html index 9eec625bb6..85fa141a61 100644 --- a/v5.5.x/b4step_defaults.html +++ b/v5.5.x/b4step_defaults.html @@ -82,17 +82,17 @@

          Navigation

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

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

          -

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/fb4627276cba3e955dae8c68ce115eeba7df6b18/b4step_defaults.rst, line 19)

          +

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          Include file ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/classic/src/1d/b4step1.f90’ not found or reading it failed

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

          -

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          +

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/fb4627276cba3e955dae8c68ce115eeba7df6b18/b4step_defaults.rst, line 25)

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

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

          -

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          +

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          Include file ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/classic/src/3d/b4step3.f90’ not found or reading it failed

          @@ -104,7 +104,7 @@

          Navigation

          with latitude when coordinate_system == 2).

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

          -

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/fb4627276cba3e955dae8c68ce115eeba7df6b18/b4step_defaults.rst, line 49)

          +

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/fb4627276cba3e955dae8c68ce115eeba7df6b18/b4step_defaults.rst, line 49)

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

          diff --git a/v5.5.x/contents.html b/v5.5.x/contents.html index 4ae0682edc..04d09ed561 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.

          -

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/fb4627276cba3e955dae8c68ce115eeba7df6b18/contents.rst, line 123)

          +

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          toctree contains reference to nonexisting document ‘riemann/Shallow_water_Riemann_solvers’

          diff --git a/v5.5.x/geoclaw.html b/v5.5.x/geoclaw.html index 702da45a76..c10628cedb 100644 --- a/v5.5.x/geoclaw.html +++ b/v5.5.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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          toctree contains reference to nonexisting document ‘geoclaw/topotools_examples’

          -

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          +

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          toctree contains reference to nonexisting document ‘geoclaw/dtopotools_examples’

          -

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          +

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          toctree contains reference to nonexisting document ‘geoclaw/Okada’

          diff --git a/v5.5.x/geoclaw_util_module.html b/v5.5.x/geoclaw_util_module.html index a5c3e5f4d9..587976d3fa 100644 --- a/v5.5.x/geoclaw_util_module.html +++ b/v5.5.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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/util.py:docstring of clawpack.geoclaw.util.bearing, line 9)

          +

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

          Unexpected indentation.

          diff --git a/v5.5.x/kmltools_module.html b/v5.5.x/kmltools_module.html index aebcc7d3b5..652a3fbf9f 100644 --- a/v5.5.x/kmltools_module.html +++ b/v5.5.x/kmltools_module.html @@ -336,7 +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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

          +

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

          Unexpected indentation.

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

          Navigation

          dpi * y_inches = dcp * y_cells

          -

          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)

          +

          System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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.

          @@ -354,14 +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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

          +

          System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

          +

          System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 @@ -497,7 +497,7 @@

          Navigation

          -

          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)

          +

          System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 diff --git a/v5.5.x/pyclaw/index.html b/v5.5.x/pyclaw/index.html index a327714848..d67ff2b55c 100644 --- a/v5.5.x/pyclaw/index.html +++ b/v5.5.x/pyclaw/index.html @@ -138,7 +138,7 @@

          Features

          PyClaw Documentation

          -

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              Navigation

              Matlab tools from Clawpack 4.3 can still be used, see Plotting using Matlab.

              -

              System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/f252c5a15de9002dc8d27779e60acdf65e22a383/amrclaw.rst, line 36)

              +

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              Navigation

              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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              +

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

              -

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              +

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              @@ -104,7 +104,7 @@

              Navigation

              with latitude when coordinate_system == 2).

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

              -

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              +

              System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/f252c5a15de9002dc8d27779e60acdf65e22a383/b4step_defaults.rst, line 49)

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              diff --git a/v5.6.x/contents.html b/v5.6.x/contents.html index c9a685065b..8ba6efbbf6 100644 --- a/v5.6.x/contents.html +++ b/v5.6.x/contents.html @@ -279,7 +279,7 @@

              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/v5.6.x/geoclaw.html b/v5.6.x/geoclaw.html index 67c4a48318..b92d30511c 100644 --- a/v5.6.x/geoclaw.html +++ b/v5.6.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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              toctree contains reference to nonexisting document ‘geoclaw/dtopotools_examples’

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              +

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              diff --git a/v5.6.x/geoclaw_util_module.html b/v5.6.x/geoclaw_util_module.html index d811e1630c..aa4c42b5a8 100644 --- a/v5.6.x/geoclaw_util_module.html +++ b/v5.6.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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/util.py:docstring of clawpack.geoclaw.util.bearing, line 9)

              +

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

              Unexpected indentation.

              diff --git a/v5.6.x/howto_release.html b/v5.6.x/howto_release.html index ec2a75f150..74924d42c5 100644 --- a/v5.6.x/howto_release.html +++ b/v5.6.x/howto_release.html @@ -256,7 +256,7 @@

              Updating the documentation -

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              +

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              Bullet list ends without a blank line; unexpected unindent.

              diff --git a/v5.6.x/kmltools_module.html b/v5.6.x/kmltools_module.html index 7c6641849d..bc5529b618 100644 --- a/v5.6.x/kmltools_module.html +++ b/v5.6.x/kmltools_module.html @@ -336,7 +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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

              +

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

              Unexpected indentation.

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

              Navigation

              dpi * y_inches = dcp * y_cells

              -

              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)

              +

              System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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.

              @@ -354,14 +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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

              +

              System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

              +

              System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 @@ -497,7 +497,7 @@

              Navigation

              -

              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)

              +

              System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 diff --git a/v5.6.x/pyclaw/index.html b/v5.6.x/pyclaw/index.html index 8e67a1ed31..e997044c78 100644 --- a/v5.6.x/pyclaw/index.html +++ b/v5.6.x/pyclaw/index.html @@ -138,7 +138,7 @@

              Features

              PyClaw Documentation

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b/v5.7.x/geoclaw_util_module.html index 27438cbacc..fa4b36781a 100644 --- a/v5.7.x/geoclaw_util_module.html +++ b/v5.7.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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/util.py:docstring of clawpack.geoclaw.util.bearing, line 9)

                  +

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

                  Unexpected indentation.

                  diff --git a/v5.7.x/kmltools_module.html b/v5.7.x/kmltools_module.html index 3e284f39c4..b9fe478e57 100644 --- a/v5.7.x/kmltools_module.html +++ b/v5.7.x/kmltools_module.html @@ -336,7 +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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

                  +

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

                  Unexpected indentation.

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

                  Navigation

                  dpi * y_inches = dcp * y_cells

              -

              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)

              +

              System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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.

              @@ -354,14 +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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

              +

              System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

              +

              System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 @@ -497,7 +497,7 @@

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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)

              +

              System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 diff --git a/v5.7.x/storm_module.html b/v5.7.x/storm_module.html index aba3f35658..70cedc5f4b 100644 --- a/v5.7.x/storm_module.html +++ b/v5.7.x/storm_module.html @@ -586,7 +586,7 @@

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              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)

              +

              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)

              Field list ends without a blank line; unexpected unindent.

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                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)

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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)

                Field list ends without a blank line; unexpected unindent.

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cd $CLAW/doc/gallery make html + cd $CLAW/doc/gallery + make html Note that we don't track past versions in the gallery. diff --git a/v5.8.x/_sources/release_5_8_1.rst.txt b/v5.8.x/_sources/release_5_8_1.rst.txt index 4ba8cde17c..611f804c2d 100644 --- a/v5.8.x/_sources/release_5_8_1.rst.txt +++ b/v5.8.x/_sources/release_5_8_1.rst.txt @@ -11,7 +11,7 @@ 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.?? +Permanent DOI: http://doi.org/10.5281/zenodo.5595424 Changes relative to Clawpack 5.8.0 (February 4, 2021) are shown below. diff --git a/v5.8.x/_sources/releases.rst.txt b/v5.8.x/_sources/releases.rst.txt index 22ff38421d..7c77a844b3 100644 --- a/v5.8.x/_sources/releases.rst.txt +++ b/v5.8.x/_sources/releases.rst.txt @@ -36,7 +36,7 @@ can also be referenced with the single DOI See :ref:`citing` for more information on how best to cite Clawpack. * :ref:`release_5_8_1` -- October 19, 2021 - `[DOI 10.5281/zenodo.??] `_ + `[DOI 10.5281/zenodo.5595424] `_ * :ref:`release_5_8_0` -- February 4, 2021 `[DOI 10.5281/zenodo.4503024] `_ * :ref:`release_5_7_1` -- September 11, 2020 diff --git a/v5.8.x/geoclaw_util_module.html b/v5.8.x/geoclaw_util_module.html index 939396c88a..20df25ecf3 100644 --- a/v5.8.x/geoclaw_util_module.html +++ b/v5.8.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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/util.py:docstring of clawpack.geoclaw.util.bearing, line 9)

                  +

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

                  Unexpected indentation.

                  diff --git a/v5.8.x/howto_doc.html b/v5.8.x/howto_doc.html index 70ce53d127..69754e3812 100644 --- a/v5.8.x/howto_doc.html +++ b/v5.8.x/howto_doc.html @@ -240,7 +240,8 @@

                  Updating the gallery

                  For detailed instructions, see CLAW/doc/gallery/README.md.

                  Then do the following:

                  -
                  cd $CLAW/doc/gallery    make html
                  +
                  cd $CLAW/doc/gallery
                  +make html
                   

                  Note that we don’t track past versions in the gallery.

                  diff --git a/v5.8.x/kmltools_module.html b/v5.8.x/kmltools_module.html index 7b73994e85..5b59b8b639 100644 --- a/v5.8.x/kmltools_module.html +++ b/v5.8.x/kmltools_module.html @@ -336,7 +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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 36)

                  +

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

                  Unexpected indentation.

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

                  Navigation

                  dpi * y_inches = dcp * y_cells

                  -

                  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)

                  +

                  System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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.

                  @@ -354,14 +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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 46)

                  +

                  System Message: ERROR/3 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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/D/clawpack-v5.8.1/geoclaw/src/python/geoclaw/kmltools.py:docstring of clawpack.geoclaw.kmltools.pcolorcells_for_kml, line 47)

                  +

                  System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 @@ -497,7 +497,7 @@

                  Navigation

                  -

                  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)

                  +

                  System Message: WARNING/2 (/Users/rjl/clawpack_src/clawpack_master/clawpack/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 diff --git a/v5.8.x/release_5_8_1.html b/v5.8.x/release_5_8_1.html index fed5017018..87d47328e2 100644 --- a/v5.8.x/release_5_8_1.html +++ b/v5.8.x/release_5_8_1.html @@ -78,7 +78,7 @@

                  Navigation

                  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.??

                  +

                  Permanent DOI: http://doi.org/10.5281/zenodo.5595424

                  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.

                  diff --git a/v5.8.x/releases.html b/v5.8.x/releases.html index e27391b235..a07c346365 100644 --- a/v5.8.x/releases.html +++ b/v5.8.x/releases.html @@ -110,7 +110,7 @@

                  Releases:Citing this work for more information on how best to cite Clawpack.

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

                  • +[DOI 10.5281/zenodo.5595424]

                  • 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/storm_module.html b/v5.8.x/storm_module.html index 1b8f3e0799..c8125be069 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/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)

                    +

                    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)

                    Field list ends without a blank line; unexpected unindent.

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

                      Navigation

                      -

                      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)

                      +

                      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)

                      Field list ends without a blank line; unexpected unindent.