Merge branch 'main' into zingale-patch-1

README.md

@@ -105,10 +105,10 @@ on the grid are described in a jupyter notebook:
 https://github.com/python-hydro/pyro2/blob/main/pyro/mesh/mesh-examples.ipynb
 
 
-Many of the methods here rely on multigrid.  The multigrid solver is
+Many of the methods here rely on multigrid.  The basic multigrid solver is
 demonstrated in the juputer notebook:
 
-https://github.com/python-hydro/pyro2/blob/main/pyro/multigrid/multigrid-examples.ipynb
+https://github.com/python-hydro/pyro2/blob/main/pyro/multigrid/multigrid-constant-coefficients.ipynb
 
 
 ## Solvers
@@ -251,7 +251,7 @@ with their data.
   There is a set of notes that describe the background and details of the
   algorithms that pyro implements:
 
-  http://bender.astro.sunysb.edu/hydro_by_example/CompHydroTutorial.pdf
+  http://open-astrophysics-bookshelf.github.io/numerical_exercises/
 
   The source for these notes is also available on github:
 

docs/source/multigrid_basics.rst

@@ -4,7 +4,7 @@ Multigrid Class Overview
 pyro solves elliptic problems (like Laplace's equation or Poisson's
 equation) through multigrid. This accelerates the convergence of
 simple relaxation by moving the solution down and up through a series
-of grids. Chapter 9 of the `pdf notes <http://bender.astro.sunysb.edu/hydro_by_example/CompHydroTutorial.pdf>`_ gives an introduction to solving elliptic equations, including multigrid.
+of grids. Chapter 9 of the `pdf notes <http://open-astrophysics-bookshelf.github.io/numerical_exercises/CompHydroTutorial.pdf>`_ gives an introduction to solving elliptic equations, including multigrid.
 
 There are three solvers:
 

docs/source/notes.rst

@@ -6,7 +6,7 @@ Notes on the numerical methods
 Detailed discussions and derivations of the numerical methods used in
 pyro are given in the set of notes `Introduction to Computational
 Astrophysical Hydrodynamics
-<http://bender.astro.sunysb.edu/hydro_by_example/CompHydroTutorial.pdf>`_,
+<http://open-astrophysics-bookshelf.github.io/numerical_exercises/CompHydroTutorial.pdf>`_,
 part of the `Open Astrophysics Bookshelf
 <https://github.com/Open-Astrophysics-Bookshelf>`_.
 

pyro/analysis/plotvar.py

@@ -1,4 +1,9 @@
 #!/usr/bin/env python3
+"""
+plot a single variable from an output file
+
+Usage: ./plotvar.py filename variable
+"""
 
 import argparse
 
@@ -8,46 +13,59 @@
 import pyro.util.io_pyro as io
 from pyro.mesh import patch
 
-# plot a single variable from an output file
-#
-# Usage: ./plotvar.py filename variable
-
 
 def makeplot(plotfile, variable, outfile,
-             width=6.5, height=5.25,
+             width=6.5, height=5.25, dpi=100, notitle=False,
              log=False, compact=False, quiet=False):
 
     sim = io.read(plotfile)
+    sim.cc_data.fill_BC_all()
 
     if isinstance(sim, patch.CellCenterData2d):
         myd = sim
     else:
         myd = sim.cc_data
     myg = myd.grid
 
-    plt.figure(num=1, figsize=(width, height), dpi=100, facecolor='w')
+    fig = plt.figure(num=1, figsize=(width, height), dpi=100, facecolor='w')
+    ax = fig.add_subplot(111)
+
+    if variable == "vort":
+        vx = myd.get_var("x-velocity")
+        vy = myd.get_var("y-velocity")
+
+        var = myg.scratch_array()
 
-    var = myd.get_var(variable)
+        var[myg.ilo:myg.ihi+1, myg.jlo:myg.jhi+1] = \
+             0.5*(vy[myg.ilo+1:myg.ihi+2, myg.jlo:myg.jhi+1] -
+                  vy[myg.ilo-1:myg.ihi, myg.jlo:myg.jhi+1])/myg.dx - \
+             0.5*(vx[myg.ilo:myg.ihi+1, myg.jlo+1:myg.jhi+2] -
+                  vx[myg.ilo:myg.ihi+1, myg.jlo-1:myg.jhi])/myg.dy
+
+    else:
+        var = myd.get_var(variable)
 
     if log:
         var = np.log10(var)
 
-    img = plt.imshow(np.transpose(var.v()),
-               interpolation="nearest", origin="lower",
-               extent=[myg.xmin, myg.xmax, myg.ymin, myg.ymax])
+    img = ax.imshow(np.transpose(var.v()),
+                    interpolation="nearest", origin="lower",
+                    extent=[myg.xmin, myg.xmax, myg.ymin, myg.ymax])
 
     if not compact:
-        plt.colorbar(img)
-
-        plt.xlabel("x")
-        plt.ylabel("y")
+        fig.colorbar(img)
+        if not notitle:
+            fig.suptitle(f"{variable}")
+        ax.set_xlabel("x")
+        ax.set_ylabel("y")
 
     if compact:
-        plt.axis("off")
-        plt.subplots_adjust(bottom=0.0, top=1.0, left=0.0, right=1.0)
-        plt.savefig(outfile)
+        ax.axis("off")
+        fig.subplots_adjust(bottom=0.0, top=1.0, left=0.0, right=1.0)
+        fig.savefig(outfile, bbox_inches="tight")
     else:
-        plt.savefig(outfile, bbox_inches="tight")
+        fig.tight_layout()
+        fig.savefig(outfile, bbox_inches="tight", dpi=dpi)
 
     if not quiet:
         plt.show()
@@ -61,6 +79,8 @@ def get_args():
                         metavar="plot.png", help="output file name")
     parser.add_argument("--log", action="store_true",
                         help="plot log of variable")
+    parser.add_argument("--notitle", action="store_true",
+                        help="suppress the title at the top of the figure")
     parser.add_argument("--compact", action="store_true",
                         help="remove axes and border")
     parser.add_argument("--quiet", action="store_true",
@@ -69,6 +89,8 @@ def get_args():
                         metavar="width", help="plot width (inches)")
     parser.add_argument("-H", type=float, default=5.25,
                         metavar="height", help="plot height (inches)")
+    parser.add_argument("--dpi", type=int, default=100,
+                        metavar="dpi", help="dots per inch")
     parser.add_argument("plotfile", type=str, nargs=1,
                         help="the plotfile you wish to plot")
     parser.add_argument("variable", type=str, nargs=1,
@@ -82,5 +104,5 @@ def get_args():
     args = get_args()
 
     makeplot(args.plotfile[0], args.variable[0], args.o,
-             width=args.W, height=args.H,
+             width=args.W, height=args.H, dpi=args.dpi, notitle=args.notitle,
              log=args.log, compact=args.compact, quiet=args.quiet)