updates pre-5.9.0

_sources/changes_to_master.rst.txt

@@ -25,58 +25,122 @@ Changes that are not backward compatible
 General changes
 ---------------
 
+- `'binary32`' added as an `output_format` option in both amrclaw and
+  geoclaw. (So far classic only supports `'ascii'` output.) The old
+  `'binary'` option now defaults to `'binary64'`, which dumps the raw 
+  binary of the full float64 (kind=8) Fortran variables.  The new
+  `'binary32'` option trucates to float32 (kind=4) before dumping, and
+  results in binary output files that are only half as large.  Since
+  float32 values have about 8 significant figures, this is generally
+  sufficient for most plotting and post-processing needs.  These files
+  are also much smaller than the files created with the `'ascii'`
+  option, which is generally recommended only for debugging if you need to 
+  examine the output files directly.
+
+- Adding support for `'binary32'` required changes in the pyclaw, clawutil 
+  and visclaw repositories as well.
+
+- A new `fgout` capability was added to geoclaw (see below and :ref:`fgout`),
+  which also required additional changes to other repositories.
+
+
 
 Changes to classic
 ------------------
 
+- Comments in some sample `setrun.py` files were changed to make it clear
+  that only `output_format = 'ascii'` is supported so far in classic.
 
 See `classic diffs
 <https://github.com/clawpack/classic/compare/v5.8.2...master>`_
 
 Changes to clawutil
 -------------------
 
+- Support for `'binary32'` and `fgout` grids added.
 
 See `clawutil diffs
 <https://github.com/clawpack/clawutil/compare/v5.8.2...master>`_
 
 Changes to visclaw
 ------------------
 
+- Support for `'binary32'` and `fgout` grids added.
+
+- `pcolor` plots are now rasterized by default, which greatly reduces the
+  file size in some cases.  When e.g. `savefig('filename.svg')` is used
+  the labels are still vector graphics but the flow field is rasterized.
+  Passing the option `pcolor_kwargs = {"rasterized":False}` in setplot
+  turns this off. See `<https://github.com/clawpack/visclaw/pull/286>`.
+
+- The `JSAnimation` subdirectory was removed, since we now use
+  `anim.to_jshtml` instead.
 
 See `visclaw diffs
 <https://github.com/clawpack/visclaw/compare/v5.8.2...master>`_
 
 Changes to riemann
 ------------------
 
+- None.
 
 See `riemann diffs
 <https://github.com/clawpack/riemann/compare/v5.8.2...master>`_
 
 Changes to amrclaw
 ------------------
 
+- Support for `output_format='binary32'` added for both output frames and
+  gauges.
 
 See `amrclaw diffs
 <https://github.com/clawpack/amrclaw/compare/v5.8.2...master>`_
 
 Changes to geoclaw
 ------------------
 
+- Support for `output_format='binary32'` added for both output frames and
+  gauges.
+
+- New `fgout` grid capabilities added, as described at :ref:`fgout`.
+  This allows specifying one or more fixed resolution rectangular grids on
+  which the AMR solution will be interpolated (in both space and time)
+  at each time in a specified set of times.  This does not affect the
+  time steps used in the computation and allows frequent output on a
+  fixed portion of the domain for making animations or doing
+  post-processing, such as particle tracking based on the velocity field.
 
-See `geoclaw diffs <https://github.com/clawpack/geoclaw/compare/v5.6.1...master>`_
+- The new `fgout` capability (together with :ref:`fgmax`)
+  replaces the very old `fixedgrid` capability,
+  which has now been further deprecated.
+
+- `$CLAW/geoclaw/examples/tsunami/chile2010_fgmax` has been replaced by
+  `$CLAW/geoclaw/examples/tsunami/chile2010_fgmax-fgout`.  This example
+  now also shows how to plot results on fgout grids either by 
+  using a special `setplot` function or by reading them directly.
+  It also shows how to make an animation from the fgout results.
+
+See `geoclaw diffs <https://github.com/clawpack/geoclaw/compare/v5.8.2...master>`_
 
 
 Changes to PyClaw
 ------------------
 
+- Support for reading fgout frames added, by passing the parameter
+  `file_prefix` more consistently (which can be e.g. `fgout` rather than
+  `fort`, as used for output frames).
 
-For changes in PyClaw, see the `PyClaw changelog
-<https://github.com/clawpack/pyclaw/blob/master/CHANGES.md>`_.
+- Support for reading binary output files with format `'binary32'` or
+  `'binary64'`.  Added for both output frames and gauges.  The old `'binary'`
+  format is equivalent to `'binary64'`.
 
-See `pyclaw diffs
-<https://github.com/clawpack/pyclaw/compare/v5.8.2...master>`_
+- Support reading `file_format` from the `fort.t` files, now one of `ascii`,
+  `binary32`, or `binary64`.  See General Changes above for more details.
+
+See `pyclaw diffs <https://github.com/clawpack/pyclaw/compare/v5.8.2...master>`_
+
+For older changes in PyClaw, see also the `PyClaw changelog
+<https://github.com/clawpack/pyclaw/blob/master/CHANGES.md>`_.
 
 ===========================
 Other Clawpack Repositories

_sources/sealevel.rst.txt

@@ -1,10 +1,10 @@
 .. _sealevel:
 
 ==========================
-Setting sealevel
+Setting sea_level
 ==========================
 
-GeoClaw has a parameter *sealevel* (see :ref:`setrun_geoclaw`) that can be
+GeoClaw has a parameter *sea_level* (see :ref:`setrun_geoclaw`) that can be
 used to specify the initialization of the fluid depth relative to the
 specified topography (see :ref:`topo`).  
 
@@ -13,8 +13,8 @@ elevation, see :ref:`set_eta_init`.
 
 Unless a different set of initial
 conditions is specified (see :ref:`setrun_qinit`), the default is to
-initialize with zero velocity and depth *h* chosen so that *h+B = sealevel*
-at any point where *B < sealevel*, where *B* is the topography or bathymetry
+initialize with zero velocity and depth *h* chosen so that *h+B = sea_level*
+at any point where *B < sea_level*, where *B* is the topography or bathymetry
 in the grid cell (as determined by interpolation from the specified
 *topo* files as described in :ref:`topo`).
 
@@ -25,9 +25,9 @@ modeling (e.g. from
 `NOAA NGDC inundataion relief
 <http://www.ngdc.noaa.gov/mgg/coastal/coastal.html>`_)
 is often relative to Mean High Water (MHW), in
-which case setting *sealevel = 0.* corresponds to assuming the water level
+which case setting *sea_level = 0.* corresponds to assuming the water level
 is initially at MHW.  To adjust to use a different tide level, the value of
-*sealevel* must be set appropriately.  The relation between MHW and other
+*sea_level* must be set appropriately.  The relation between MHW and other
 tide levels such as Mean Sea Level (MSL) can often be found from the NGDC
 webpages for a nearby tide gauge. 
 For example, if you go to a station page such as 
@@ -58,7 +58,7 @@ to be at rest before the tsunami arrives.
 
 If GeoClaw is used for hazard assessment based on potential tsunami
 scenarios, then thought should be given to the appropriate value of
-*sealevel* to assume.  The NCEI coastal bathymetry data is often referenced to MHW
+*sea_level* to assume.  The NCEI coastal bathymetry data is often referenced to MHW
 because this is often the level assumed for tsunami hazard assessment, but
 higher tide levels such as Mean Higher High Water (MHHW) or the Astronomical
 High Tide (AHT) are sometimes used for worst-case scenarios.  

changes_to_master.html

@@ -88,35 +88,105 @@ <h2>Changes that are not backward compatible<a class="headerlink" href="#changes
 </div>
 <div class="section" id="general-changes">
 <h2>General changes<a class="headerlink" href="#general-changes" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li><p><cite>‘binary32</cite>’ added as an <cite>output_format</cite> option in both amrclaw and
+geoclaw. (So far classic only supports <cite>‘ascii’</cite> output.) The old
+<cite>‘binary’</cite> option now defaults to <cite>‘binary64’</cite>, which dumps the raw
+binary of the full float64 (kind=8) Fortran variables.  The new
+<cite>‘binary32’</cite> option trucates to float32 (kind=4) before dumping, and
+results in binary output files that are only half as large.  Since
+float32 values have about 8 significant figures, this is generally
+sufficient for most plotting and post-processing needs.  These files
+are also much smaller than the files created with the <cite>‘ascii’</cite>
+option, which is generally recommended only for debugging if you need to
+examine the output files directly.</p></li>
+<li><p>Adding support for <cite>‘binary32’</cite> required changes in the pyclaw, clawutil
+and visclaw repositories as well.</p></li>
+<li><p>A new <cite>fgout</cite> capability was added to geoclaw (see below and <a class="reference internal" href="fgout.html#fgout"><span class="std std-ref">Fixed grid output</span></a>),
+which also required additional changes to other repositories.</p></li>
+</ul>
 </div>
 <div class="section" id="changes-to-classic">
 <h2>Changes to classic<a class="headerlink" href="#changes-to-classic" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li><p>Comments in some sample <cite>setrun.py</cite> files were changed to make it clear
+that only <cite>output_format = ‘ascii’</cite> is supported so far in classic.</p></li>
+</ul>
 <p>See <a class="reference external" href="https://github.com/clawpack/classic/compare/v5.8.2...master">classic diffs</a></p>
 </div>
 <div class="section" id="changes-to-clawutil">
 <h2>Changes to clawutil<a class="headerlink" href="#changes-to-clawutil" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li><p>Support for <cite>‘binary32’</cite> and <cite>fgout</cite> grids added.</p></li>
+</ul>
 <p>See <a class="reference external" href="https://github.com/clawpack/clawutil/compare/v5.8.2...master">clawutil diffs</a></p>
 </div>
 <div class="section" id="changes-to-visclaw">
 <h2>Changes to visclaw<a class="headerlink" href="#changes-to-visclaw" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li><p>Support for <cite>‘binary32’</cite> and <cite>fgout</cite> grids added.</p></li>
+<li><p><cite>pcolor</cite> plots are now rasterized by default, which greatly reduces the
+file size in some cases.  When e.g. <cite>savefig(‘filename.svg’)</cite> is used
+the labels are still vector graphics but the flow field is rasterized.
+Passing the option <cite>pcolor_kwargs = {“rasterized”:False}</cite> in setplot
+turns this off. See <cite>&lt;https://github.com/clawpack/visclaw/pull/286&gt;</cite>.</p></li>
+<li><p>The <cite>JSAnimation</cite> subdirectory was removed, since we now use
+<cite>anim.to_jshtml</cite> instead.</p></li>
+</ul>
 <p>See <a class="reference external" href="https://github.com/clawpack/visclaw/compare/v5.8.2...master">visclaw diffs</a></p>
 </div>
 <div class="section" id="changes-to-riemann">
 <h2>Changes to riemann<a class="headerlink" href="#changes-to-riemann" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li><p>None.</p></li>
+</ul>
 <p>See <a class="reference external" href="https://github.com/clawpack/riemann/compare/v5.8.2...master">riemann diffs</a></p>
 </div>
 <div class="section" id="changes-to-amrclaw">
 <h2>Changes to amrclaw<a class="headerlink" href="#changes-to-amrclaw" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li><p>Support for <cite>output_format=’binary32’</cite> added for both output frames and
+gauges.</p></li>
+</ul>
 <p>See <a class="reference external" href="https://github.com/clawpack/amrclaw/compare/v5.8.2...master">amrclaw diffs</a></p>
 </div>
 <div class="section" id="changes-to-geoclaw">
 <h2>Changes to geoclaw<a class="headerlink" href="#changes-to-geoclaw" title="Permalink to this headline">¶</a></h2>
-<p>See <a class="reference external" href="https://github.com/clawpack/geoclaw/compare/v5.6.1...master">geoclaw diffs</a></p>
+<ul class="simple">
+<li><p>Support for <cite>output_format=’binary32’</cite> added for both output frames and
+gauges.</p></li>
+<li><p>New <cite>fgout</cite> grid capabilities added, as described at <a class="reference internal" href="fgout.html#fgout"><span class="std std-ref">Fixed grid output</span></a>.
+This allows specifying one or more fixed resolution rectangular grids on
+which the AMR solution will be interpolated (in both space and time)
+at each time in a specified set of times.  This does not affect the
+time steps used in the computation and allows frequent output on a
+fixed portion of the domain for making animations or doing
+post-processing, such as particle tracking based on the velocity field.</p></li>
+<li><p>The new <cite>fgout</cite> capability (together with <a class="reference internal" href="fgmax.html#fgmax"><span class="std std-ref">Fixed grid monitoring</span></a>)
+replaces the very old <cite>fixedgrid</cite> capability,
+which has now been further deprecated.</p></li>
+<li><p><cite>$CLAW/geoclaw/examples/tsunami/chile2010_fgmax</cite> has been replaced by
+<cite>$CLAW/geoclaw/examples/tsunami/chile2010_fgmax-fgout</cite>.  This example
+now also shows how to plot results on fgout grids either by
+using a special <cite>setplot</cite> function or by reading them directly.
+It also shows how to make an animation from the fgout results.</p></li>
+</ul>
+<p>See <a class="reference external" href="https://github.com/clawpack/geoclaw/compare/v5.8.2...master">geoclaw diffs</a></p>
 </div>
 <div class="section" id="changes-to-pyclaw">
 <h2>Changes to PyClaw<a class="headerlink" href="#changes-to-pyclaw" title="Permalink to this headline">¶</a></h2>
-<p>For changes in PyClaw, see the <a class="reference external" href="https://github.com/clawpack/pyclaw/blob/master/CHANGES.md">PyClaw changelog</a>.</p>
+<ul class="simple">
+<li><p>Support for reading fgout frames added, by passing the parameter
+<cite>file_prefix</cite> more consistently (which can be e.g. <cite>fgout</cite> rather than
+<cite>fort</cite>, as used for output frames).</p></li>
+<li><p>Support for reading binary output files with format <cite>‘binary32’</cite> or
+<cite>‘binary64’</cite>.  Added for both output frames and gauges.  The old <cite>‘binary’</cite>
+format is equivalent to <cite>‘binary64’</cite>.</p></li>
+<li><p>Support reading <cite>file_format</cite> from the <cite>fort.t</cite> files, now one of <cite>ascii</cite>,
+<cite>binary32</cite>, or <cite>binary64</cite>.  See General Changes above for more details.</p></li>
+</ul>
 <p>See <a class="reference external" href="https://github.com/clawpack/pyclaw/compare/v5.8.2...master">pyclaw diffs</a></p>
+<p>For older changes in PyClaw, see also the <a class="reference external" href="https://github.com/clawpack/pyclaw/blob/master/CHANGES.md">PyClaw changelog</a>.</p>
 </div>
 </div>
 <div class="section" id="other-clawpack-repositories">

contents.html

@@ -229,7 +229,7 @@ <h3><a class="toc-backref" href="#id8">GeoClaw: geophysical flows</a><a class="h
 <li class="toctree-l2"><a class="reference internal" href="quick_tsunami.html">Quick start guide for tsunami modeling</a></li>
 <li class="toctree-l2"><a class="reference internal" href="quick_surge.html">Quick start guide for storm surge modeling</a></li>
 <li class="toctree-l2"><a class="reference internal" href="okada.html">Earthquake sources: Fault slip and the Okada model</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sealevel.html">Setting sealevel</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sealevel.html">Setting sea_level</a></li>
 <li class="toctree-l2"><a class="reference internal" href="set_eta_init.html">Set Eta Init – spatially varying initial surface elevation</a></li>
 <li class="toctree-l2"><a class="reference internal" href="lagrangian_gauges.html">Lagrangian gauges for particle tracking</a></li>
 <li class="toctree-l2"><a class="reference internal" href="manning.html">Manning friction term</a></li>

dev/.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: 9d073fdfe96d8d5e5fed5f9dda834925
+config: 2d711e5d7fb4afea3ff9b26f79460a34
 tags: 645f666f9bcd5a90fca523b33c5a78b7

dev/_sources/changes_to_master.rst.txt

@@ -66,29 +66,41 @@ Changes to visclaw
 ------------------
 
 - Support for `'binary32'` and `fgout` grids added.
+
+- `pcolor` plots are now rasterized by default, which greatly reduces the
+  file size in some cases.  When e.g. `savefig('filename.svg')` is used
+  the labels are still vector graphics but the flow field is rasterized.
+  Passing the option `pcolor_kwargs = {"rasterized":False}` in setplot
+  turns this off. See `<https://github.com/clawpack/visclaw/pull/286>`.
+
+- The `JSAnimation` subdirectory was removed, since we now use
+  `anim.to_jshtml` instead.
 
 See `visclaw diffs
 <https://github.com/clawpack/visclaw/compare/v5.8.2...master>`_
 
 Changes to riemann
 ------------------
 
+- None.
 
 See `riemann diffs
 <https://github.com/clawpack/riemann/compare/v5.8.2...master>`_
 
 Changes to amrclaw
 ------------------
 
-- Support for `output_format='binary32'` added.
+- Support for `output_format='binary32'` added for both output frames and
+  gauges.
 
 See `amrclaw diffs
 <https://github.com/clawpack/amrclaw/compare/v5.8.2...master>`_
 
 Changes to geoclaw
 ------------------
 
-- Support for `output_format='binary32'` added.
+- Support for `output_format='binary32'` added for both output frames and
+  gauges.
 
 - New `fgout` grid capabilities added, as described at :ref:`fgout`.
   This allows specifying one or more fixed resolution rectangular grids on
@@ -102,18 +114,33 @@ Changes to geoclaw
   replaces the very old `fixedgrid` capability,
   which has now been further deprecated.
 
+- `$CLAW/geoclaw/examples/tsunami/chile2010_fgmax` has been replaced by
+  `$CLAW/geoclaw/examples/tsunami/chile2010_fgmax-fgout`.  This example
+  now also shows how to plot results on fgout grids either by 
+  using a special `setplot` function or by reading them directly.
+  It also shows how to make an animation from the fgout results.
+
 See `geoclaw diffs <https://github.com/clawpack/geoclaw/compare/v5.8.2...master>`_
 
 
 Changes to PyClaw
 ------------------
 
+- Support for reading fgout frames added, by passing the parameter
+  `file_prefix` more consistently (which can be e.g. `fgout` rather than
+  `fort`, as used for output frames).
 
-For changes in PyClaw, see the `PyClaw changelog
-<https://github.com/clawpack/pyclaw/blob/master/CHANGES.md>`_.
+- Support for reading binary output files with format `'binary32'` or
+  `'binary64'`.  Added for both output frames and gauges.  The old `'binary'`
+  format is equivalent to `'binary64'`.
 
-See `pyclaw diffs
-<https://github.com/clawpack/pyclaw/compare/v5.8.2...master>`_
+- Support reading `file_format` from the `fort.t` files, now one of `ascii`,
+  `binary32`, or `binary64`.  See General Changes above for more details.
+
+See `pyclaw diffs <https://github.com/clawpack/pyclaw/compare/v5.8.2...master>`_
+
+For older changes in PyClaw, see also the `PyClaw changelog
+<https://github.com/clawpack/pyclaw/blob/master/CHANGES.md>`_.
 
 ===========================
 Other Clawpack Repositories

dev/_sources/releases.rst.txt

@@ -13,7 +13,9 @@ Other notes:
 * Please see :ref:`citing` for the suggested way to cite the version of
   Clawpack that you are using in publications.
 
-* For changes in PyClaw, see the `PyClaw changelog <https://github.com/clawpack/pyclaw/blob/master/CHANGES.md>`_.
+* For older changes in PyClaw, see the `PyClaw changelog <https://github.com/clawpack/pyclaw/blob/master/CHANGES.md>`_.
+  Starting with v5.9.0, changes will be recorded in the release notes along
+  with those for other repositories.
 
 * See :ref:`changes_to_master` for changes to the master branch on Github
   that are not in the most recent release.