diff --git a/_sources/howto_doc.rst.txt b/_sources/howto_doc.rst.txt index 3ddea4e65..ccb9d7687 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 4ba8cde17..611f804c2 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 22ff38421..7c77a844b 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 79856588f..bcc9ba4fa 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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b/dev/.doctrees/vm.doctree index a7e977b3d..f71a691b7 100644 Binary files a/dev/.doctrees/vm.doctree and b/dev/.doctrees/vm.doctree differ diff --git a/dev/.doctrees/wp_algorithms.doctree b/dev/.doctrees/wp_algorithms.doctree index 36477ed3f..93d155591 100644 Binary files a/dev/.doctrees/wp_algorithms.doctree and b/dev/.doctrees/wp_algorithms.doctree differ diff --git a/dev/_sources/howto_doc.rst.txt b/dev/_sources/howto_doc.rst.txt index 3ddea4e65..ccb9d7687 100644 --- a/dev/_sources/howto_doc.rst.txt +++ b/dev/_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/dev/_sources/release_5_8_1.rst.txt b/dev/_sources/release_5_8_1.rst.txt index 4ba8cde17..611f804c2 100644 --- a/dev/_sources/release_5_8_1.rst.txt +++ b/dev/_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/dev/_sources/releases.rst.txt b/dev/_sources/releases.rst.txt index 22ff38421..7c77a844b 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 658d92cf4..a40edf63d 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 fe89727f2..c0fe10c0f 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 e14a64fb6..f75decde3 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 3576f60c7..df48c0fd0 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 d5d140b2e..1add7cf4e 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 716965160..e94d2c3fa 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 9520baf95..a55505d2f 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 2248b2419..e211b1a9e 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 9c2e46489..18ac1d54d 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 86ae504ff..55bd20655 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 cf9b5ab79..ff25da654 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 75fa6c81c..609a2938c 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.

            @@ -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/v5.1.x/.buildinfo b/v5.1.x/.buildinfo index 884588cad..c190da06d 100644 --- a/v5.1.x/.buildinfo +++ b/v5.1.x/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 4a46dbd4a03a142ab769f9a577faf713 +config: 62904148c0c7ca11c323fca6e6324419 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/v5.1.x/.doctrees/ClawPlotAxes.doctree b/v5.1.x/.doctrees/ClawPlotAxes.doctree index 907b67f36..a3d66190e 100644 Binary files a/v5.1.x/.doctrees/ClawPlotAxes.doctree and b/v5.1.x/.doctrees/ClawPlotAxes.doctree differ diff --git a/v5.1.x/.doctrees/ClawPlotData.doctree b/v5.1.x/.doctrees/ClawPlotData.doctree index 3c8aabf5e..f64920e61 100644 Binary files a/v5.1.x/.doctrees/ClawPlotData.doctree and b/v5.1.x/.doctrees/ClawPlotData.doctree differ diff --git a/v5.1.x/.doctrees/ClawPlotFigure.doctree b/v5.1.x/.doctrees/ClawPlotFigure.doctree index 86cf4f13d..712bfa873 100644 Binary files a/v5.1.x/.doctrees/ClawPlotFigure.doctree and b/v5.1.x/.doctrees/ClawPlotFigure.doctree differ diff --git a/v5.1.x/.doctrees/ClawPlotItem.doctree b/v5.1.x/.doctrees/ClawPlotItem.doctree index 197857bb7..430912b2f 100644 Binary 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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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              +

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

              -

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              +

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              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/v5.1.x/galleries.html b/v5.1.x/galleries.html index 75d198d49..71627a911 100644 --- a/v5.1.x/galleries.html +++ b/v5.1.x/galleries.html @@ -85,19 +85,19 @@

              Navigation

              Galleries of all Clawpack applications

              See also IPython notebook examples.

              -

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              +

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              -

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              +

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              toctree contains reference to nonexisting document ‘gallery/gallery_fvmbook’

              diff --git a/v5.1.x/git_resources.html b/v5.1.x/git_resources.html index e936febc5..d7261ac8b 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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            +

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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 f6d86b115..8f1587d2b 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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            PyClaw is:

            PyClaw Documentation

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            References and tutorialsMatplotlib gallery

          • `LeVeque’s class notes

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            Navigation

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

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            with latitude when coordinate_system == 2).

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            -

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            +

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            diff --git a/v5.2.x/galleries.html b/v5.2.x/galleries.html index 43f722bb5..cc5d81193 100644 --- a/v5.2.x/galleries.html +++ b/v5.2.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/v5.2.x/geoclaw_util_module.html b/v5.2.x/geoclaw_util_module.html index e10a70961..8a09e2a16 100644 --- a/v5.2.x/geoclaw_util_module.html +++ b/v5.2.x/geoclaw_util_module.html @@ -105,7 +105,7 @@

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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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            +

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            Unexpected indentation.

            diff --git a/v5.2.x/git_resources.html b/v5.2.x/git_resources.html index 955e372ee..10da382bb 100644 --- a/v5.2.x/git_resources.html +++ b/v5.2.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/5fcd911597685d99d94bee49a3dcea97a4bab85a/git_links.inc’.

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          .. include:: git_links.inc
          diff --git a/v5.2.x/kmltools_module.html b/v5.2.x/kmltools_module.html index 783784f9d..2b267adf9 100644 --- a/v5.2.x/kmltools_module.html +++ b/v5.2.x/kmltools_module.html @@ -329,7 +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:

          -

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          +

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          Unexpected indentation.

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          dpi * y_inches = dcp * y_cells

          -

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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.

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

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

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          Unexpected indentation.

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

          -

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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 @@ -490,7 +490,7 @@

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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)

          +

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          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 dd5c13ffa..e4d519ad4 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.

          -

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          PyClaw is:

          PyClaw Documentation

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          diff --git a/v5.2.x/python.html b/v5.2.x/python.html index 36c8ad77f..c766b3b72 100644 --- a/v5.2.x/python.html +++ b/v5.2.x/python.html @@ -163,7 +163,7 @@

          References and tutorialsMatplotlib gallery

        • `LeVeque’s class notes

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          • diff --git a/v5.2.x/qinit_defaults.html b/v5.2.x/qinit_defaults.html index 7fa1a8829..bc8e2d2ea 100644 --- a/v5.2.x/qinit_defaults.html +++ b/v5.2.x/qinit_defaults.html @@ -82,17 +82,17 @@

          Navigation

          the initial conditions as desired.

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

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

          -

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          qinit data file parameters.

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

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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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          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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          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/24e2c68df118c5a00b116198860c806cae4b064d/b4step_defaults.rst, line 18)

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

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

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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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          Galleries of all Clawpack applications

          See also IPython notebook examples.

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          diff --git a/v5.3.x/geoclaw_util_module.html b/v5.3.x/geoclaw_util_module.html index 27829d965..d7df70b48 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:

          -

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          diff --git a/v5.3.x/kmltools_module.html b/v5.3.x/kmltools_module.html index 74db7d39b..257902804 100644 --- a/v5.3.x/kmltools_module.html +++ b/v5.3.x/kmltools_module.html @@ -326,7 +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:

          -

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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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          -

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          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 c701bef08..a2b391fc6 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.

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

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          qinit data file parameters.

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

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          with latitude when coordinate_system == 2).

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          (an ocean at rest remains at rest).

          $CLAW/geoclaw/src/2d/shallow/src1d.f90:

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          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/24e2c68df118c5a00b116198860c806cae4b064d/src1d_defaults.rst, line 46)

          +

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/24e2c68df118c5a00b116198860c806cae4b064d/src1d_defaults.rst, line 46)

          Include file ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/geoclaw/src/2d/shallow/src1d.f90’ not found or reading it failed

          diff --git a/v5.3.x/src_defaults.html b/v5.3.x/src_defaults.html index c3831f6f3..74d86979b 100644 --- a/v5.3.x/src_defaults.html +++ b/v5.3.x/src_defaults.html @@ -85,17 +85,17 @@

          Navigation

          see Using src1d for source terms with AMRClaw.

          $CLAW/classic/src/1d/src1.f90:

          -

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/24e2c68df118c5a00b116198860c806cae4b064d/src_defaults.rst, line 23)

          +

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/24e2c68df118c5a00b116198860c806cae4b064d/src_defaults.rst, line 23)

          Include file ‘/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/classic/src/1d/src1.f90’ not found or reading it failed

          $CLAW/classic/src/2d/src2.f90:

          -

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/24e2c68df118c5a00b116198860c806cae4b064d/src_defaults.rst, line 29)

          +

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/24e2c68df118c5a00b116198860c806cae4b064d/src_defaults.rst, line 29)

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

          $CLAW/classic/src/3d/src3.f90:

          -

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpbgykzejv/24e2c68df118c5a00b116198860c806cae4b064d/src_defaults.rst, line 35)

          +

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/24e2c68df118c5a00b116198860c806cae4b064d/src_defaults.rst, line 35)

          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/24e2c68df118c5a00b116198860c806cae4b064d/src_defaults.rst, line 52)

          +

          System Message: WARNING/2 (/var/folders/_s/dx0xgftn3_x04rdx0_w5nq7w0000gn/T/tmpnt4d249q/24e2c68df118c5a00b116198860c806cae4b064d/src_defaults.rst, line 52)

          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.

          -

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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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          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 3c5a9d39e..6f985c2c2 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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          Some sample calculations can be viewed in the gallery_geoclaw. More will eventually appear in the Clawpack Applications repository.

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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 79f62f2f0..08d30b477 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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          -

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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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          (an ocean at rest remains at rest).

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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

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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/3d/b4step3.f90:

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          with latitude when coordinate_system == 2).

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

          -

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          +

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          diff --git a/v5.5.x/contents.html b/v5.5.x/contents.html index 4ae0682ed..04d09ed56 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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          Navigation

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

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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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          +

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          diff --git a/v5.5.x/kmltools_module.html b/v5.5.x/kmltools_module.html index aebcc7d3b..652a3fbf9 100644 --- a/v5.5.x/kmltools_module.html +++ b/v5.5.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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          +

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          Unexpected indentation.

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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.

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

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

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          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)

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          Unexpected indentation.

          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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          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 a32771484..d67ff2b55 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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          the initial conditions as desired.

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

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

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          qinit data file parameters.

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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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              +

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              diff --git a/v5.6.x/contents.html b/v5.6.x/contents.html index c9a685065..8ba6efbbf 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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              Some sample calculations can be viewed in the gallery_geoclaw. More will eventually appear in the Clawpack Applications repository.

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              toctree contains reference to nonexisting document ‘geoclaw/dtopotools_examples’

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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/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.

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              Updating the documentation -

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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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              Unexpected indentation.

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              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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              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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              Unexpected indentation.

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              -

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              PyClaw Documentation

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              the initial conditions as desired.

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              qinit data file parameters.

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

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              diff --git a/v5.6.x/src_defaults.html b/v5.6.x/src_defaults.html index 541d85137..f5a520ae8 100644 --- a/v5.6.x/src_defaults.html +++ b/v5.6.x/src_defaults.html @@ -85,17 +85,17 @@

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a/v5.7.x/geoclaw_util_module.html b/v5.7.x/geoclaw_util_module.html index 27438cbac..fa4b36781 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 3e284f39c..b9fe478e5 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 @@

              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/v5.7.x/storm_module.html b/v5.7.x/storm_module.html index aba3f3565..70cedc5f4 100644 --- a/v5.7.x/storm_module.html +++ b/v5.7.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.

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100644 Binary files a/v5.8.x/.doctrees/vm.doctree and b/v5.8.x/.doctrees/vm.doctree differ diff --git a/v5.8.x/.doctrees/wp_algorithms.doctree b/v5.8.x/.doctrees/wp_algorithms.doctree index 3fc11cae1..33e0a9b3b 100644 Binary files a/v5.8.x/.doctrees/wp_algorithms.doctree and b/v5.8.x/.doctrees/wp_algorithms.doctree differ diff --git a/v5.8.x/_sources/howto_doc.rst.txt b/v5.8.x/_sources/howto_doc.rst.txt index 3ddea4e65..ccb9d7687 100644 --- a/v5.8.x/_sources/howto_doc.rst.txt +++ b/v5.8.x/_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/v5.8.x/_sources/release_5_8_1.rst.txt b/v5.8.x/_sources/release_5_8_1.rst.txt index 4ba8cde17..611f804c2 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 22ff38421..7c77a844b 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 939396c88..20df25ecf 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 70ce53d12..69754e381 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 7b73994e8..5b59b8b63 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 fed501701..87d47328e 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 e27391b23..a07c34636 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 1b8f3e079..c8125be06 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.