update docs: pyro.py -> pyro_sim.py (#118)

Author: zingale

docs/source/advection_basics.rst

@@ -120,7 +120,7 @@ disagreement is our numerical error. This is run as:
 
 .. code-block:: none
 
-   ./pyro.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
 
 .. code-block:: none
 
-   ./pyro.py compressible sod inputs.sod.x
-   ./pyro.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:
 
 .. code-block:: none
 
-   ./pyro.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:
 
 .. code-block:: none
 
-   ./pyro.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:
 
 .. code-block:: none
 
-   ./pyro.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:
 
 .. code-block:: none
 
-   ./pyro.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
 
 .. code-block:: none
 
-  ./pyro.py compressible kh inputs.kh kh.vbulk=0
-  ./pyro.py compressible_rk kh inputs.kh kh.vbulk=0
-  ./pyro.py compressible_fv4 kh inputs.kh kh.vbulk=0
-  ./pyro.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,
 
 .. code-block:: none
 
-   ./pyro.py compressible sedov inputs.sedov
-   ./pyro.py compressible_rk sedov inputs.sedov
-   ./pyro.py compressible_fv4 sedov inputs.sedov
-   ./pyro.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:
 
 .. code-block:: none
 
-   ./pyro.py compressible quad inputs.quad
-   ./pyro.py compressible_rk quad inputs.quad
-   ./pyro.py compressible_fv4 quad inputs.quad
-   ./pyro.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:
 
 .. code-block:: none
 
-   ./pyro.py compressible bubble inputs.bubble
-   ./pyro.py compressible_rk bubble inputs.bubble
-   ./pyro.py compressible_fv4 bubble inputs.bubble
-   ./pyro.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
 
 .. code-block:: none
 
-   ./pyro.py compressible rt inputs.rt
-   ./pyro.py compressible_rk rt inputs.rt
-   ./pyro.py compressible_fv4 rt inputs.rt
-   ./pyro.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/design.rst

@@ -30,7 +30,7 @@ top-level ``pyro2/`` directory.
 The overall structure is:
 
 * ``pyro2/``: This is the top-level directory.  The main driver,
-  ``pyro.py``, is here, and all pyro simulations should be run from
+  ``pyro_sim.py``, is here, and all pyro simulations should be run from
   this directory.
 
 * ``advection/``: The linear advection equation solver using the CTU
@@ -148,7 +148,7 @@ simulation.
 Main driver
 -----------
 
-All the solvers use the same driver, the main ``pyro.py`` script. The
+All the solvers use the same driver, the main ``pyro_sim.py`` script. The
 flowchart for the driver is:
 
 * parse runtime parameters

docs/source/diffusion_basics.rst

@@ -29,7 +29,7 @@ compare our solver to the analytic solution. This is run as:
 
 .. code-block:: none
 
-   ./pyro.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
 
 .. code-block:: none
 
-   ./pyro.py incompressible shear inputs.shear
+   ./pyro_sim.py incompressible shear inputs.shear
 
 
 .. image:: shear.png
@@ -57,9 +57,9 @@ shown below are run as:
 
 .. code-block:: none
 
-   ./pyro.py incompressible converge inputs.converge.32 vis.dovis=0
-   ./pyro.py incompressible converge inputs.converge.64 vis.dovis=0
-   ./pyro.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

@@ -22,7 +22,7 @@ The following steps are needed before running pyro:
 * add ``pyro/`` to your ``PYTHONPATH`` environment variable (note this
   is only needed if you wish to use pyro as a python module - this
   step is not necessary if you only run pyro via the commandline using
-  the ``pyro.py`` script).  For the bash shell, this is done as:
+  the ``pyro_sim.py`` script).  For the bash shell, this is done as:
 
     .. code-block:: none
 
@@ -42,7 +42,7 @@ Run the advection solver to quickly test if things are setup correctly:
 
 .. code-block:: none
 
-   ./pyro.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:
 
 .. code-block:: none
 
-   ./pyro.py lm_atm bubble inputs.bubble
+   ./pyro_sim.py lm_atm bubble inputs.bubble
 

docs/source/multigrid_basics.rst

@@ -25,7 +25,10 @@ There are three solvers:
 We simply use V-cycles in our implementation, and restrict ourselves
 to square grids with zoning a power of 2.
 
-The multigrid solver is not controlled through pyro.py since there is no time-dependence in pure elliptic problems. Instead, there are a few scripts in the multigrid/ subdirectory that demonstrate its use.
+The multigrid solver is not controlled through ``pyro_sim.py`` since
+there is no time-dependence in pure elliptic problems. Instead, there
+are a few scripts in the multigrid/ subdirectory that demonstrate its
+use.
 
 Examples
 --------

docs/source/running.rst

@@ -1,14 +1,14 @@
 Running
 =======
 
-Pyro can be run in two ways: either from the commandline, using the ``pyro.py``
+Pyro can be run in two ways: either from the commandline, using the ``pyro_sim.py``
 script and passing in the solver, problem and inputs as arguments, or by using
-the :func:`Pyro <pyro.Pyro>` class.
+the :func:`Pyro <pyro_sim.pyro>` class.
 
 Commandline
 ------------
 
-The ``pyro.py`` script takes 3
+The ``pyro_sim.py`` script takes 3
 arguments: the solver name, the problem setup to run with that solver
 (this is defined in the solver's ``problems/`` sub-directory), and the
 inputs file (again, usually from the solver's ``problems/``
@@ -18,7 +18,7 @@ For example, to run the Sedov problem with the compressible solver we would do:
 
 .. code-block:: none
 
-   ./pyro.py compressible sedov inputs.sedov
+   ./pyro_sim.py compressible sedov inputs.sedov
 
 This knows to look for ``inputs.sedov`` in ``compressible/problems/``
 (alternately, you can specify the full path for the inputs file).
@@ -27,15 +27,15 @@ To run the smooth Gaussian advection problem with the advection solver, we would
 
 .. code-block:: none
 
-   ./pyro.py advection smooth inputs.smooth
+   ./pyro_sim.py advection smooth inputs.smooth
 
 Any runtime parameter can also be specified on the command line, after
 the inputs file. For example, to disable runtime visualization for the
 above run, we could do:
 
 .. code-block:: none
 
-   ./pyro.py advection smooth inputs.smooth vis.dovis=0
+   ./pyro_sim.py advection smooth inputs.smooth vis.dovis=0
 
 
 .. note::
@@ -49,12 +49,12 @@ above run, we could do:
 Pyro class
 ----------
 
-Alternatively, pyro can be run using the :func:`Pyro <pyro.Pyro>` class. This provides
+Alternatively, pyro can be run using the :func:`Pyro <pyro_sim.pyro>` class. This provides
 an interface that enables simulations to be set up and run in a Jupyter notebook -- see
 ``examples/examples.ipynb`` for an example notebook. A simulation can be set up and run
 by carrying out the following steps:
 
-* create a :func:`Pyro <pyro.Pyro>` object, initializing it with a specific solver
+* create a :func:`Pyro <pyro_sim.pyro>` object, initializing it with a specific solver
 * initialize the problem, passing in runtime parameters and inputs
 * run the simulation
 
@@ -71,7 +71,7 @@ Kelvin-Helmholtz problem ``kh``, we would do the following:
 
 Instead of using an inputs file to define the problem parameters, we can define a
 dictionary of parameters and pass them into the :func:`initialize_problem
-<pyro.Pyro.initialize_problem>` function using the keyword argument ``inputs_dict``.
+<pyro_sim.pyro.initialize_problem>` function using the keyword argument ``inputs_dict``.
 If an inputs file is also passed into the function, the parameters in the dictionary
 will override any parameters in the file. For example, if we wished to turn off
 visualization for the previous example, we would do:
@@ -84,8 +84,8 @@ visualization for the previous example, we would do:
                             inputs_dict=parameters)
 
 It's possible to evolve the simulation forward timestep by timestep manually using
-the :func:`single_step <pyro.Pyro.single_step>` function (rather than allowing
-:func:`run_sim <pyro.Pyro.run_sim>` to do this for us). To evolve our example
+the :func:`single_step <pyro_sim.pyro.single_step>` function (rather than allowing
+:func:`run_sim <pyro_sim.pyro.run_sim>` to do this for us). To evolve our example
 simulation forward by a single step, we'd run
 
 .. code-block:: python