Merge 414250e into 9426db9

examples/acoustics_1d_homogeneous/acoustics_1d.py

@@ -7,8 +7,8 @@
 
 Solve the (linear) acoustics equations:
 
-.. math:: 
-    p_t + K u_x & = 0 \\ 
+.. math::
+    p_t + K u_x & = 0 \\
     u_t + p_x / \rho & = 0.
 
 Here p is the pressure, u is the velocity, K is the bulk modulus,
@@ -18,16 +18,19 @@
 The final solution is identical to the initial data because both waves have
 crossed the domain exactly once.
 """
+
 from numpy import sqrt, exp, cos
 from clawpack import riemann
-    
-def setup(use_petsc=False, kernel_language='Fortran', solver_type='classic',
-              outdir='./_output', ptwise=False, weno_order=5, 
-              time_integrator='SSP104', 
+
+def setup(use_petsc=False, use_boxlib=False, kernel_language='Fortran', solver_type='classic',
+              outdir='./_output', ptwise=False, weno_order=5,
+              time_integrator='SSP104',
               disable_output=False):
 
     if use_petsc:
         import clawpack.petclaw as pyclaw
+    elif use_boxlib:
+        import clawpack.boxclaw as pyclaw
     else:
         from clawpack import pyclaw
 
@@ -37,7 +40,7 @@ def setup(use_petsc=False, kernel_language='Fortran', solver_type='classic',
         else:
             riemann_solver = riemann.acoustics_1D
 
-    elif kernel_language=='Python': 
+    elif kernel_language=='Python':
         riemann_solver = riemann.acoustics_1D_py.acoustics_1D
 
     if solver_type=='classic':
@@ -66,7 +69,7 @@ def setup(use_petsc=False, kernel_language='Fortran', solver_type='classic',
     state.problem_data['bulk']=bulk
     state.problem_data['zz']=sqrt(rho*bulk) # Impedance
     state.problem_data['cc']=sqrt(bulk/rho) # Sound speed
- 
+
     xc=domain.grid.x.centers
     beta=100; gamma=0; x0=0.75
     state.q[0,:] = exp(-beta * (xc-x0)**2) * cos(gamma * (xc - x0))
@@ -89,11 +92,11 @@ def setup(use_petsc=False, kernel_language='Fortran', solver_type='classic',
 
 
 def setplot(plotdata):
-    """ 
+    """
     Specify what is to be plotted at each frame.
     Input:  plotdata, an instance of visclaw.data.ClawPlotData.
     Output: a modified version of plotdata.
-    """ 
+    """
     plotdata.clearfigures()  # clear any old figures,axes,items data
 
     # Figure for pressure
@@ -111,7 +114,7 @@ def setplot(plotdata):
     plotitem.plotstyle = '-o'
     plotitem.color = 'b'
     plotitem.kwargs = {'linewidth':2,'markersize':5}
-    
+
     # Set up for axes in this figure:
     plotaxes = plotfigure.new_plotaxes()
     plotaxes.axescmd = 'subplot(212)'
@@ -125,7 +128,7 @@ def setplot(plotdata):
     plotitem.plotstyle = '-'
     plotitem.color = 'b'
     plotitem.kwargs = {'linewidth':3,'markersize':5}
-    
+
     return plotdata
 
 

examples/acoustics_1d_homogeneous/test_acoustics.py

@@ -53,6 +53,14 @@ def acoustics_verify(claw):
         yield test
 
 
-if __name__=="__main__":
-    import nose
-    nose.main()
+if __name__=='__main__':
+    for test in test_1d_acoustics():
+        test()
+
+    # monkey patch util.build_variant_arg_dicts and rerun tests
+    import clawpack.pyclaw.util
+    import clawpack.boxclaw.util
+    clawpack.pyclaw.util.build_variant_arg_dicts = clawpack.boxclaw.util.boxlib_build_variant_arg_dicts
+
+    for test in test_1d_acoustics():
+        test()

examples/acoustics_3d_variable/acoustics_3d_interface.py

@@ -18,10 +18,10 @@
 This example shows how to solve a problem with variable coefficients.
 The left and right halves of the domain consist of different materials.
 """
- 
+
 import numpy as np
 
-def setup(use_petsc=False,outdir='./_output',solver_type='classic',
+def setup(use_petsc=False,use_boxlib=False,outdir='./_output',solver_type='classic',
           mx=30,my=30,mz=30,disable_output=False,problem='heterogeneous',**kwargs):
     """
     Example python script for solving the 3d acoustics equations.
@@ -30,6 +30,8 @@ def setup(use_petsc=False,outdir='./_output',solver_type='classic',
 
     if use_petsc:
         import clawpack.petclaw as pyclaw
+    elif use_boxlib:
+        import clawpack.boxclaw as pyclaw
     else:
         from clawpack import pyclaw
 

examples/advection_1d/advection_1d.py

@@ -19,11 +19,13 @@
 import numpy as np
 from clawpack import riemann
 
-def setup(nx=100, kernel_language='Python', use_petsc=False, solver_type='classic', weno_order=5, 
+def setup(nx=100, kernel_language='Python', use_petsc=False, use_boxlib=False, solver_type='classic', weno_order=5,
           time_integrator='SSP104', outdir='./_output'):
 
     if use_petsc:
         import clawpack.petclaw as pyclaw
+    elif use_boxlib:
+        import clawpack.boxclaw as pyclaw
     else:
         from clawpack import pyclaw
 

examples/advection_1d/test_advection.py

@@ -37,7 +37,7 @@ def advection_verify(claw):
                                  solver_type='sharpclaw',time_integrator='SSPMS32', outdir=None)
 
     weno_tests = gen_variants(advection_1d.setup, verify_expected(7.489618e-06),
-                                 kernel_languages=('Fortran',), solver_type='sharpclaw', 
+                                 kernel_languages=('Fortran',), solver_type='sharpclaw',
                                  time_integrator='SSP104', weno_order=17,
                                  outdir=None)
 
@@ -46,6 +46,14 @@ def advection_verify(claw):
         yield test
 
 
-if __name__=="__main__":
-    import nose
-    nose.main()
+if __name__=='__main__':
+    for test in test_1d_advection():
+        test()
+
+    # monkey patch util.build_variant_arg_dicts and rerun tests
+    import clawpack.pyclaw.util
+    import clawpack.boxclaw.util
+    clawpack.pyclaw.util.build_variant_arg_dicts = clawpack.boxclaw.util.boxlib_build_variant_arg_dicts
+
+    for test in test_1d_advection():
+        test()

examples/advection_2d/advection_2d.py

@@ -24,12 +24,14 @@ def qinit(state):
     """
     X, Y = state.grid.p_centers
     state.q[0,:,:] = 0.9*(0.1<X)*(X<0.6)*(0.1<Y)*(Y<0.6) + 0.1
-
 
-def setup(use_petsc=False,outdir='./_output',solver_type='classic'):
+
+def setup(use_petsc=False,use_boxlib=False,outdir='./_output',solver_type='classic'):
 
     if use_petsc:
         import clawpack.petclaw as pyclaw
+    elif use_boxlib:
+        import clawpack.boxclaw as pyclaw
     else:
         from clawpack import pyclaw
 

src/boxclaw/README.rst

@@ -0,0 +1,17 @@
+
+BoxLib backend for PyClaw
+=========================
+
+This backend uses the C++ version of the CCSE BoxLib_ library.  To
+install BoxLib, `download BoxLib`_ and
+
+.. code-block:: sh
+
+   git clone https://ccse.lbl.gov/pub/Downloads/BoxLib.git
+   cd BoxLib/Src/Python
+   python setup.py install --user
+
+
+.. _BoxLib: https://ccse.lbl.gov/BoxLib/index.html
+.. _`download BoxLib`: https://ccse.lbl.gov/Downloads/downloadBoxLib.html
+

src/boxclaw/__init__.py

@@ -0,0 +1,37 @@
+"""Main boxclaw package"""
+
+import os
+import logging, logging.config
+
+# Default logging configuration file
+_DEFAULT_LOG_CONFIG_PATH = os.path.join(os.path.dirname(__file__),'log.config')
+del os
+
+# Setup loggers
+logging.config.fileConfig(_DEFAULT_LOG_CONFIG_PATH)
+
+__all__ = []
+
+# Module imports
+__all__.extend(['Controller','Dimension','Patch','Domain','Solution','State','CFL','riemann'])
+from .controller import Controller
+from clawpack.boxclaw.geometry import Patch, Domain
+from clawpack.pyclaw.geometry import Dimension
+from .solution import Solution
+from .state import State
+from .cfl import CFL
+
+__all__.extend(['ClawSolver1D','ClawSolver2D','ClawSolver3D','SharpClawSolver1D','SharpClawSolver2D','SharpClawSolver3D'])
+from .classic.solver import ClawSolver1D,ClawSolver2D,ClawSolver3D
+from .sharpclaw.solver import SharpClawSolver1D,SharpClawSolver2D,SharpClawSolver3D
+
+__all__.append('BC')
+from clawpack.pyclaw.solver import BC
+
+# Sub-packages
+import limiters
+from limiters import *
+__all__.extend(limiters.__all__)
+
+import plot
+__all__.append('plot')

src/boxclaw/cfl.py

@@ -0,0 +1,32 @@
+
+class CFL(object):
+    """Parallel CFL object, responsible for computing the
+    Courant-Friedrichs-Lewy condition across all processes.
+    """
+
+    def __init__(self, global_max):
+        self._local_max = global_max
+        self._global_max = global_max
+
+    def get_global_max(self):
+        r"""
+        Compute the maximum CFL number over all processes for the current step.
+
+        This is used to determine whether the CFL condition was
+        violated and adjust the timestep.
+        """
+        import boxlib
+        self._reduce_vec.array = self._local_max
+        self._global_max = boxlib.bl[0].ReduceRealMax(self._local_max)
+        return self._global_max
+
+    def get_cached_max(self):
+        return self._global_max
+
+    def set_local_max(self,new_local_max):
+        self._local_max = new_local_max
+
+    def update_global_max(self,new_local_max):
+        import boxlib
+        self._global_max = boxlib.bl[0].ReduceRealMax(new_local_max)
+

src/boxclaw/classic/setup.py

@@ -0,0 +1,10 @@
+#!/usr/bin/env python
+
+def configuration(parent_package='',top_path=None):
+    from numpy.distutils.misc_util import Configuration
+    config = Configuration('classic', parent_package, top_path)
+    return config
+
+if __name__ == '__main__':
+    from numpy.distutils.core import setup
+    setup(**configuration(top_path='').todict())

src/boxclaw/classic/solver.py

@@ -0,0 +1,31 @@
+r"""
+Module containing the PetClaw solvers
+
+This file currently only exists so that these solvers have a different
+__module__ property, used by pyclaw.solver.Solver.__init__ to
+determine the containing claw_package to use.
+"""
+
+from __future__ import absolute_import
+from clawpack import pyclaw
+
+class ClawSolver1D(pyclaw.ClawSolver1D):
+    r"""
+    Parallel solver for 1D problems using classic Clawpack algorithms.
+    """
+
+    __doc__ += pyclaw.util.add_parent_doc(pyclaw.ClawSolver1D)
+
+class ClawSolver2D(pyclaw.ClawSolver2D):
+    r"""
+    Parallel solver for 2D problems using classic Clawpack algorithms.
+    """
+
+    __doc__ += pyclaw.util.add_parent_doc(pyclaw.ClawSolver2D)
+
+class ClawSolver3D(pyclaw.ClawSolver3D):
+    r"""
+    Parallel solver for 3D problems using classic Clawpack algorithms.
+    """
+
+    __doc__ += pyclaw.util.add_parent_doc(pyclaw.ClawSolver3D)

src/boxclaw/controller.py

@@ -0,0 +1,25 @@
+"""
+Module for BoxClaw controller class.
+"""
+
+from clawpack import pyclaw
+
+class Controller(pyclaw.controller.Controller):
+    """Parallel Controller Class"""
+
+    __doc__ += pyclaw.util.add_parent_doc(pyclaw.controller.Controller)
+
+    def __init__(self):
+        super(Controller,self).__init__()
+        self.output_format = 'multifab'
+
+    def is_proc_0(self):
+        import boxlib
+        return boxlib.rank() == 0
+
+    def log_info(self, str):
+        import logging
+        if self.is_proc_0():
+            logging.info(str)
+        else:
+            pass