Merge branch 'polar-coords' of https://github.com/ssagynbayeva/pyro2 into polar-coords

Author: ssagynbayeva

README.md

@@ -90,7 +90,7 @@ https://python-hydro.github.io/pyro2
  - Finally, you can run a quick test of the advection solver:
 
    ```
-   ./pyro-sim.py advection smooth inputs.smooth
+   pyro-sim.py advection smooth inputs.smooth
    ```
 
    you should see a graphing window pop up with a smooth pulse
@@ -178,18 +178,18 @@ that we describe here. Note: some problems write a report at the end
 of the simulation specifying the analysis routines that can be used
 with their data.
 
-  - `compare.py`: this takes two simulation output files as input and
-    compares zone-by-zone for exact agreement. This is used as part of
-    the regression testing.
+  - `pyro/util/compare.py`: this takes two simulation output files as
+    input and compares zone-by-zone for exact agreement. This is used as
+    part of the regression testing.
 
       usage: `./compare.py file1 file2`
 
-  - `plot.py`: this takes the an output file as input and plots the
+  - `pyro/plot.py`: this takes the an output file as input and plots the
     data using the solver's dovis method.
 
       usage: `./plot.py file`
 
-  - `analysis/`
+  - `pyro/analysis/`
 
       * `dam_compare.py`: this takes an output file from the
         shallow water dam break problem and plots a slice through the domain
@@ -251,15 +251,15 @@ with their data.
 
 ## Regression and unit testing
 
-  The `test.py` script will run several of the problems (as well as some
-  stand-alone multigrid tests) and compare the solution to stored
+  The `pyro/test.py` script will run several of the problems (as well as
+  some stand-alone multigrid tests) and compare the solution to stored
   benchmarks (in each solver's `tests/` subdirectory).  The return value
   of the script is the number of tests that failed.
 
   Unit tests are controlled by pytest and can be run simply via
 
   ```
-  pytest .
+  pytest pyro
   ```
 
 ## Acknowledgements

docs/source/advection_basics.rst

@@ -120,7 +120,7 @@ disagreement is our numerical error. This is run as:
 
 .. prompt:: bash
 
-   ./pyro_sim.py advection smooth inputs.smooth
+   pyro_sim.py advection smooth inputs.smooth
 
 
 .. raw:: html

docs/source/compressible_basics.rst

@@ -102,8 +102,8 @@ Because it is one-dimensional, we run it in narrow domains in the x- or y-direct
 
 .. prompt:: bash
 
-   ./pyro_sim.py compressible sod inputs.sod.x
-   ./pyro_sim.py compressible sod inputs.sod.y
+   pyro_sim.py compressible sod inputs.sod.x
+   pyro_sim.py compressible sod inputs.sod.y
 
 A simple script, ``sod_compare.py`` in ``analysis/`` will read a pyro output
 file and plot the solution over the exact Sod solution. Below we see
@@ -128,7 +128,7 @@ is run as:
 
 .. prompt:: bash
 
-   ./pyro_sim.py compressible sedov inputs.sedov
+   pyro_sim.py compressible sedov inputs.sedov
 
 The video below shows the output from a 128 x 128 grid with the energy
 put in a radius of 0.0125 surrounding the center of the domain. A
@@ -165,7 +165,7 @@ online by Pawel Artymowicz). It is run as:
 
 .. prompt:: bash
 
-   ./pyro_sim.py compressible quad inputs.quad
+   pyro_sim.py compressible quad inputs.quad
 
 .. image:: quad.png
    :align: center
@@ -181,7 +181,7 @@ escape the domain. It is run as:
 
 .. prompt:: bash
 
-   ./pyro_sim.py compressible rt inputs.rt
+   pyro_sim.py compressible rt inputs.rt
 
 .. raw:: html
 
@@ -199,7 +199,7 @@ watches it buoyantly rise and roll up. This is run as:
 
 .. prompt:: bash
 
-   ./pyro_sim.py compressible bubble inputs.bubble
+   pyro_sim.py compressible bubble inputs.bubble
 
 
 .. image:: bubble.png

docs/source/compressible_compare.rst

@@ -12,10 +12,10 @@ The image below shows the KH problem initialized with McNally's test. It ran on
 
 .. prompt:: bash
 
-  ./pyro_sim.py compressible kh inputs.kh kh.vbulk=0
-  ./pyro_sim.py compressible_rk kh inputs.kh kh.vbulk=0
-  ./pyro_sim.py compressible_fv4 kh inputs.kh kh.vbulk=0
-  ./pyro_sim.py compressible_sdc kh inputs.kh kh.vbulk=0
+   pyro_sim.py compressible kh inputs.kh kh.vbulk=0
+   pyro_sim.py compressible_rk kh inputs.kh kh.vbulk=0
+   pyro_sim.py compressible_fv4 kh inputs.kh kh.vbulk=0
+   pyro_sim.py compressible_sdc kh inputs.kh kh.vbulk=0
 
 .. image:: ./solver_comparisons/kh.png
    :align: center
@@ -30,10 +30,10 @@ The Sedov problem ran on a 128 x 128 grid, with gamma = 1.4, and until t = 0.1,
 
 .. prompt:: bash
 
-   ./pyro_sim.py compressible sedov inputs.sedov
-   ./pyro_sim.py compressible_rk sedov inputs.sedov
-   ./pyro_sim.py compressible_fv4 sedov inputs.sedov
-   ./pyro_sim.py compressible_sdc sedov inputs.sedov
+   pyro_sim.py compressible sedov inputs.sedov
+   pyro_sim.py compressible_rk sedov inputs.sedov
+   pyro_sim.py compressible_fv4 sedov inputs.sedov
+   pyro_sim.py compressible_sdc sedov inputs.sedov
 
 .. image:: ./solver_comparisons/sedov.png
    :align: center
@@ -53,10 +53,10 @@ The quad problem ran on a 256 x 256 grid until t = 0.8, which can be run as:
 
 .. prompt:: bash
 
-   ./pyro_sim.py compressible quad inputs.quad
-   ./pyro_sim.py compressible_rk quad inputs.quad
-   ./pyro_sim.py compressible_fv4 quad inputs.quad
-   ./pyro_sim.py compressible_sdc quad inputs.quad
+   pyro_sim.py compressible quad inputs.quad
+   pyro_sim.py compressible_rk quad inputs.quad
+   pyro_sim.py compressible_fv4 quad inputs.quad
+   pyro_sim.py compressible_sdc quad inputs.quad
 
 .. image:: ./solver_comparisons/quad.png
    :align: center
@@ -77,10 +77,10 @@ The bubble problem ran on a 128 x 256 grid until t = 3.0, which can be run as:
 
 .. prompt:: bash
 
-   ./pyro_sim.py compressible bubble inputs.bubble
-   ./pyro_sim.py compressible_rk bubble inputs.bubble
-   ./pyro_sim.py compressible_fv4 bubble inputs.bubble
-   ./pyro_sim.py compressible_sdc bubble inputs.bubble
+   pyro_sim.py compressible bubble inputs.bubble
+   pyro_sim.py compressible_rk bubble inputs.bubble
+   pyro_sim.py compressible_fv4 bubble inputs.bubble
+   pyro_sim.py compressible_sdc bubble inputs.bubble
 
 .. image:: ./solver_comparisons/bubble.png
    :align: center
@@ -101,10 +101,10 @@ The Rayleigh-Taylor problem ran on a 64 x 192 grid until t = 3.0, which can be r
 
 .. prompt:: bash
 
-   ./pyro_sim.py compressible rt inputs.rt
-   ./pyro_sim.py compressible_rk rt inputs.rt
-   ./pyro_sim.py compressible_fv4 rt inputs.rt
-   ./pyro_sim.py compressible_sdc rt inputs.rt
+   pyro_sim.py compressible rt inputs.rt
+   pyro_sim.py compressible_rk rt inputs.rt
+   pyro_sim.py compressible_fv4 rt inputs.rt
+   pyro_sim.py compressible_sdc rt inputs.rt
 
 .. image:: ./solver_comparisons/rt.png
    :align: center

docs/source/conf.py

@@ -19,9 +19,8 @@
 #
 import os
 import sys
-
-import sphinx_rtd_theme
 from importlib.metadata import version as importlib_version
+
 sys.path.insert(0, os.path.abspath('../../'))
 
 
@@ -46,6 +45,7 @@
     'sphinx.ext.graphviz',
     'sphinx_copybutton',
     'sphinx-prompt',
+    'sphinx_rtd_theme',
     'IPython.sphinxext.ipython_console_highlighting',
     'sphinx.ext.githubpages']
 
@@ -72,7 +72,7 @@
 
 # General information about the project.
 project = 'pyro'
-copyright = '2022, pyro development team'
+copyright = '2023, pyro development team'
 author = 'pyro development team'
 
 html_logo = "logo.gif"
@@ -111,7 +111,6 @@
 # a list of builtin themes.
 #
 html_theme = 'sphinx_rtd_theme'
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

docs/source/diffusion_basics.rst

@@ -29,7 +29,7 @@ compare our solver to the analytic solution. This is run as:
 
 .. prompt:: bash
 
-   ./pyro_sim.py diffusion gaussian inputs.gaussian
+   pyro_sim.py diffusion gaussian inputs.gaussian
 
 .. image:: gauss_diffusion.png
    :align: center

docs/source/incompressible_basics.rst

@@ -34,7 +34,7 @@ number of papers, for example, Bell, Colella, & Glaz (1989) and Martin
 
 .. prompt:: bash
 
-   ./pyro_sim.py incompressible shear inputs.shear
+   pyro_sim.py incompressible shear inputs.shear
 
 
 .. image:: shear.png
@@ -57,9 +57,9 @@ shown below are run as:
 
 .. prompt:: bash
 
-   ./pyro_sim.py incompressible converge inputs.converge.32 vis.dovis=0
-   ./pyro_sim.py incompressible converge inputs.converge.64 vis.dovis=0
-   ./pyro_sim.py incompressible converge inputs.converge.128 vis.dovis=0
+   pyro_sim.py incompressible converge inputs.converge.32 vis.dovis=0
+   pyro_sim.py incompressible converge inputs.converge.64 vis.dovis=0
+   pyro_sim.py incompressible converge inputs.converge.128 vis.dovis=0
 
 The error is measured by comparing with the analytic solution using
 the routine ``incomp_converge_error.py`` in ``analysis/``.

docs/source/installation.rst

@@ -44,7 +44,7 @@ Run the advection solver to quickly test if things are setup correctly:
 
 .. prompt:: bash
 
-   ./pyro_sim.py advection smooth inputs.smooth
+   pyro_sim.py advection smooth inputs.smooth
 
 You should see a plot window pop up with a smooth pulse advecting
 diagonally through the periodic domain.

docs/source/lowmach_basics.rst

@@ -33,5 +33,5 @@ rises. This is run as:
 
 .. prompt:: bash
 
-   ./pyro_sim.py lm_atm bubble inputs.bubble
+   pyro_sim.py lm_atm bubble inputs.bubble
 

docs/source/multigrid_basics.rst

@@ -41,7 +41,7 @@ A basic multigrid test is run as (using a path relative to the root of the
 
 .. prompt:: bash
 
-   ./examples/multigrid/mg_test_simple.py
+   ./pyro/multigrid/examples/mg_test_simple.py
 
 The ``mg_test_simple.py`` script solves a Poisson equation with a
 known analytic solution. This particular example comes from the text
@@ -86,7 +86,7 @@ You can run this example locally by running the ``mg_vis.py`` script:
 
 .. prompt:: bash
 
-   ./examples/multigrid/mg_vis.py
+   ./pyro/multigrid/examples/mg_vis.py
 
 projection
 ^^^^^^^^^^
@@ -96,7 +96,7 @@ field.  This is run as:
 
 .. prompt:: bash
 
-   ./examples/multigrid/project_periodic.py
+   ./pyro/multigrid/examples/project_periodic.py
 
 Given a vector field, :math:`U`, we can decompose it into a divergence free part, :math:`U_d`, and the gradient of a scalar, :math:`\phi`: