Merge branch 'master' into euler_3d_examples

* master:
  Clean up some of the code and add more doc-strings
  Add normal CLI to quadrants example
  Update CHANGES.md for 5.2.0.
  Fix HashDist to 0.3 tag
  Correct solution.read docstring

Conflicts:
	src/pyclaw/solution.py

.travis_build_petsc4py.sh

@@ -2,6 +2,10 @@
 
 # Get <#>
 git clone https://github.com/hashdist/hashdist
+( 
+    cd hashdist
+    git checkout v0.3
+)
 export PATH=`pwd`/hashdist/bin:$PATH
 
 # a reasonable profile for building petsc4py on Travis

CHANGES.md

@@ -1,4 +1,4 @@
-# Changes since 5.1.0
+# 5.2.0 release
 
 - **Linear multistep methods for timestepping in SharpClaw**: 
   Previously, only Runge-Kutta time stepping was included in SharpClaw.
@@ -9,12 +9,16 @@
   The user must provide a routine that computes the eigenvectors.  See 
   `clawpack/pyclaw/examples/euler_1d/`.
 - **Logging control**: it is now easy to modify the logging levels interactively,
-  without modifying the logger files.
+  without modifying the logger files.  All logging configuration is
+  set by default with `pyclaw/log.config`; the file `petclaw/log.config` is
+  no longer used.
 - It is no longer necessary to compile dummy transverse Riemann solvers when using
   an algorithm with no transverse wave propagation.
 - Add functions to compute cell centers of ghost cells.
 - Tests run in parallel on Travis.
-- Writing of HDF5 and netcdf files now works in serial and parallel.
+- All tests now run in under two minutes on most systems.
+- PyWENO-generated code updated to match latest PyWENO release.
+- Writing and reading of HDF5 and netcdf files now works in serial and parallel.
 - Improvements to examples.
 - Miscellaneous bug fixes.
 

examples/euler_2d/quadrants.py

@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 # encoding: utf-8
 """
-2D Euler Riemann problem
-================================
+Euler 2D Quadrants example
+==========================
 
-Solve the Euler equations of compressible fluid dynamics:
+Simple example solving the Euler equations of compressible fluid dynamics:
 
 .. math::
     \rho_t + (\rho u)_x + (\rho v)_y & = 0 \\
@@ -15,37 +15,124 @@
 Here :math:`\rho` is the density, (u,v) is the velocity, and E is the total energy.
 The initial condition is one of the 2D Riemann problems from the paper of
 Liska and Wendroff.
+
 """
 
-from clawpack import pyclaw
-from clawpack import riemann
-
-solver = pyclaw.ClawSolver2D(riemann.euler_4wave_2D)
-solver.all_bcs = pyclaw.BC.extrap
-
-domain = pyclaw.Domain([0.,0.],[1.,1.],[100,100])
-solution = pyclaw.Solution(solver.num_eqn,domain)
-gamma = 1.4
-solution.problem_data['gamma']  = gamma
-solver.dimensional_split = False
-solver.transverse_waves = 2
-
-# Set initial data
-xx,yy = domain.grid.p_centers
-l = xx<0.8; r = xx>=0.8; b = yy<0.8; t = yy>=0.8
-solution.q[0,...] = 1.5*r*t + 0.532258064516129*l*t + 0.137992831541219*l*b + 0.532258064516129*r*b
-u = 0.*r*t + 1.206045378311055*l*t + 1.206045378311055*l*b + 0.*r*b
-v = 0.*r*t + 0.*l*t + 1.206045378311055*l*b + 1.206045378311055*r*b
-p = 1.5*r*t + 0.3*l*t + 0.029032258064516*l*b + 0.3*r*b
-solution.q[1,...] = solution.q[0,...] * u
-solution.q[2,...] = solution.q[0,...] * v
-solution.q[3,...] = 0.5*solution.q[0,...]*(u**2+v**2) + p/(gamma-1.)
-
-claw = pyclaw.Controller()
-claw.tfinal = 0.8
-claw.solution = solution
-claw.solver = solver
-
-status = claw.run()
-
-#pyclaw.plot.interactive_plot()
+def setplot(plotdata):
+    r"""Plotting settings
+
+    Should plot two figures both of density.
+
+    """
+
+    from clawpack.visclaw import colormaps
+
+    plotdata.clearfigures()  # clear any old figures,axes,items data
+
+    # Figure for density - pcolor
+    plotfigure = plotdata.new_plotfigure(name='Density', figno=0)
+
+    # Set up for axes in this figure:
+    plotaxes = plotfigure.new_plotaxes()
+    plotaxes.xlimits = 'auto'
+    plotaxes.ylimits = 'auto'
+    plotaxes.scaled = True
+    plotaxes.title = 'Density'
+
+    # Set up for item on these axes:
+    plotitem = plotaxes.new_plotitem(plot_type='2d_pcolor')
+    plotitem.plot_var = 0
+    plotitem.pcolor_cmap = colormaps.yellow_red_blue
+    plotitem.pcolor_cmin = 0.
+    plotitem.pcolor_cmax = 2.
+    plotitem.add_colorbar = True
+
+    # Figure for density - Schlieren
+    plotfigure = plotdata.new_plotfigure(name='Schlieren', figno=1)
+
+    # Set up for axes in this figure:
+    plotaxes = plotfigure.new_plotaxes()
+    plotaxes.xlimits = 'auto'
+    plotaxes.ylimits = 'auto'
+    plotaxes.title = 'Density'
+    plotaxes.scaled = True      # so aspect ratio is 1
+
+    # Set up for item on these axes:
+    plotitem = plotaxes.new_plotitem(plot_type='2d_schlieren')
+    plotitem.schlieren_cmin = 0.0
+    plotitem.schlieren_cmax = 1.0
+    plotitem.plot_var = 0
+    plotitem.add_colorbar = False
+
+    return plotdata
+
+
+def setup(use_petsc=False):
+    r"""Setup for Euler 2D quadrants example
+
+    Simple example solving the Euler equations of compressible fluid dynamics:
+
+    .. math::
+        \rho_t + (\rho u)_x + (\rho v)_y & = 0 \\
+        (\rho u)_t + (\rho u^2 + p)_x + (\rho uv)_y & = 0 \\
+        (\rho v)_t + (\rho uv)_x + (\rho v^2 + p)_y & = 0 \\
+        E_t + (u (E + p) )_x + (v (E + p))_y & = 0.
+
+    Here :math:`\rho` is the density, (u,v) is the velocity, and E is the total energy.
+    The initial condition is one of the 2D Riemann problems from the paper of
+    Liska and Wendroff.
+
+    Currently the only setup option is the *use_petsc* argument.
+
+    """
+
+    if use_petsc:
+        import clawpack.petclaw as pyclaw
+    else:
+        from clawpack import pyclaw
+    from clawpack import riemann
+
+    solver = pyclaw.ClawSolver2D(riemann.euler_4wave_2D)
+    solver.all_bcs = pyclaw.BC.extrap
+
+    domain = pyclaw.Domain([0.,0.],[1.,1.],[100,100])
+    solution = pyclaw.Solution(solver.num_eqn,domain)
+    gamma = 1.4
+    solution.problem_data['gamma']  = gamma
+    solver.dimensional_split = False
+    solver.transverse_waves = 2
+
+    # Set initial data
+    xx, yy = domain.grid.p_centers
+    l = xx < 0.8
+    r = xx >= 0.8
+    b = yy < 0.8
+    t = yy >= 0.8
+    solution.q[0,...] = 1.5 * r * t + 0.532258064516129 * l * t                \
+                                    + 0.137992831541219 * l * b                \
+                                    + 0.532258064516129 * r * b
+    u = 0.0 * r * t + 1.206045378311055 * l * t                                \
+                    + 1.206045378311055 * l * b                                \
+                    + 0.0 * r * b
+    v = 0.0 * r * t + 0.0 * l * t                                              \
+                    + 1.206045378311055 * l * b                                \
+                    + 1.206045378311055 * r * b
+    p = 1.5 * r * t + 0.3 * l * t + 0.029032258064516 * l * b + 0.3 * r * b
+    solution.q[1,...] = solution.q[0, ...] * u
+    solution.q[2,...] = solution.q[0, ...] * v
+    solution.q[3,...] = 0.5 * solution.q[0,...]*(u**2 + v**2) + p / (gamma - 1.0)
+
+    claw = pyclaw.Controller()
+    claw.tfinal = 0.8
+    claw.solution = solution
+    claw.solver = solver
+
+    claw.output_format = 'ascii'    
+    claw.outdir = "./_output"
+    claw.setplot = setplot
+
+    return claw
+
+if __name__ == "__main__":
+    from clawpack.pyclaw.util import run_app_from_main
+    output = run_app_from_main(setup, setplot)

src/pyclaw/solution.py

@@ -305,8 +305,8 @@ def write(self,frame,path='./',file_format='ascii',file_prefix=None,
             logging.getLogger('pyclaw.io').info(msg)
 
 
-    def read(self,frame,path='./_output',file_format='ascii',file_prefix=None,
-                read_aux=True,options={}, **kargs):
+    def read(self, frame, path='./_output', file_format='ascii', 
+                          file_prefix=None, read_aux=True, options={}, **kargs):
         r"""
         Reads in a Solution object from a file
         
@@ -325,7 +325,7 @@ def read(self,frame,path='./_output',file_format='ascii',file_prefix=None,
         :Input:
          - *frame* - (int) Frame number to be read in
          - *path* - (string) Base path to the files to be read. 
-           ``default = './'``
+           ``default = './_output'``
          - *file_format* - (string) Format of the file, should match on of the 
            modules inside of the io package.  ``default = 'ascii'``
          - *file_prefix* - (string) Name prefix in front of all the files, 
@@ -337,20 +337,20 @@ def read(self,frame,path='./_output',file_format='ascii',file_prefix=None,
          - (bool) - True if read was successful, False otherwise
         """
 
-        if file_format=='petsc':
+        if file_format == 'petsc':
             from clawpack.petclaw import io
             read_func = io.petsc.read
         elif file_format == 'binary':
             from clawpack.pyclaw import io 
             read_func = io.binary.read
-        elif file_format=='ascii': 
+        elif file_format == 'ascii': 
             from clawpack.pyclaw import io
             read_func = io.ascii.read
         elif file_format in ('hdf','hdf5'): 
             from clawpack.pyclaw import io
             read_func = io.hdf5.read
         else:
-            raise Exception('Unrecognized file format: '+file_format)
+            raise ValueError("File format %s not supported." % file_format)
 
         path = os.path.expandvars(os.path.expanduser(path))
         if file_prefix is None: