Merge branch 'master' of github.com:python-hydro/pyro2

Author: harpolea

.gitignore

@@ -18,3 +18,5 @@ inputs.auto
 .cache
 
 .pytest_cache/
+
+__pycache__/

docs/source/compressible_basics.rst

@@ -181,7 +181,7 @@ escape the domain. It is run as:
 
 .. code-block:: none
 
-   ./pyro.py compressible er inputs.rt
+   ./pyro.py compressible rt inputs.rt
 
 .. raw:: html
 

docs/source/multigrid_basics.rst

@@ -32,11 +32,13 @@ Examples
 
 multigrid test
 ^^^^^^^^^^^^^^
-A basic multigrid test is run as:
+
+A basic multigrid test is run as (using a path relative to the root of the
+``pyro2`` repository):
 
 .. code-block:: none
 
-   ./mg_test_simple.py
+   ./examples/multigrid/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
@@ -77,17 +79,21 @@ The movie below shows the smoothing at each level to realize this solution:
         <iframe src="https://www.youtube.com/embed/h9MUgwJvr-g?rel=0" frameborder="0" allowfullscreen style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;"></iframe>
     </div><br>
 
+You can run this example locally by running the ``mg_vis.py`` script:
+
+.. code-block:: none
+
+   ./examples/multigrid/mg_vis.py
 
 projection
 ^^^^^^^^^^
 
-Another example (``examples/multigrid/project_periodic.py``) uses
-multigrid to extract the divergence free part of a velocity field.
-This is run as:
+Another example uses multigrid to extract the divergence free part of a velocity
+field.  This is run as:
 
 .. code-block:: none
 
-   ./project-periodic.py
+   ./examples/multigrid/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`:
 

docs/source/running.rst

@@ -63,6 +63,7 @@ Kelvin-Helmholtz problem ``kh``, we would do the following:
 
 .. code-block:: python
 
+    from pyro import Pyro
     pyro = Pyro("compressible")
     pyro.initialize_problem(problem_name="kh",
                             inputs_file="inputs.kh")

examples/multigrid/mg_test_simple.py

@@ -84,6 +84,8 @@ def test_poisson_dirichlet(N, store_bench=False, comp_bench=False,
         plt.xlabel("x")
         plt.ylabel("y")
 
+        print("Saving figure to mg_test.png")
+
         plt.savefig("mg_test.png")
 
     # store the output for later comparison
@@ -114,4 +116,4 @@ def test_poisson_dirichlet(N, store_bench=False, comp_bench=False,
 
 
 if __name__ == "__main__":
-    test_poisson_dirichlet(256, comp_bench=True)
+    test_poisson_dirichlet(256, comp_bench=True, make_plot=True)

paper/paper.md

@@ -41,20 +41,6 @@ implementation and exploration of hydrodynamics methods.  It is
 built in a object-oriented fashion, allowing for the reuse of
 the core components and fast prototyping of new methods.
 
-In the time since the first pyro paper [@pyroI], the code has
-undergone considerable development, gained a large number of solvers,
-adopted unit testing through pytest and documentation through sphinx,
-and a number of new contributors.  pyro's functionality can now
-be accessed directly through a `Pyro()` class, in addition to the
-original commandline script interface.  This new interface in particular
-allows for easy use within Jupyter notebooks.  We also now use HDF5
-for output instead of python's `pickle()` function.  Previously, we used Fortran
-to speed up some performance-critical portions of the code.  These routines
-could be called by the main python code by first compiling them using `f2py`.
-In the new version, we have replaced these Fortran routines by python functions
-that are compiled at runtime by `numba`.  Consequently, pyro is now written
-entirely in python.
-
 The original goal of pyro was to learn hydrodynamics methods through
 example, and it still serves this goal.  At Stony Brook, pyro is used
 with new undergraduate researchers in our group to introduce them to
@@ -70,6 +56,20 @@ on the Maestro code [@maestro] and the pyro implementation will be
 used to prototype new low Mach number algorithms before porting them
 to science codes.
 
+In the time since the first pyro paper [@pyroI], the code has
+undergone considerable development, gained a large number of solvers,
+adopted unit testing through pytest and documentation through sphinx,
+and a number of new contributors.  pyro's functionality can now
+be accessed directly through a `Pyro()` class, in addition to the
+original commandline script interface.  This new interface in particular
+allows for easy use within Jupyter notebooks.  We also now use HDF5
+for output instead of python's `pickle()` function.  Previously, we used Fortran
+to speed up some performance-critical portions of the code.  These routines
+could be called by the main python code by first compiling them using `f2py`.
+In the new version, we have replaced these Fortran routines by python functions
+that are compiled at runtime by `numba`.  Consequently, pyro is now written
+entirely in python.
+
 The current pyro solvers are:
 
 -   linear advection (including a second-order unsplit CTU scheme, a