[cig-commits] r21840 - in short/3D/PyLith/trunk: applications modulesrc/meshio pylith pylith/apps pylith/meshio
brad at geodynamics.org
brad at geodynamics.org
Fri Apr 12 10:43:55 PDT 2013
Author: brad
Date: 2013-04-12 10:43:55 -0700 (Fri, 12 Apr 2013)
New Revision: 21840
Removed:
short/3D/PyLith/trunk/applications/pylith_prepmesh.in
short/3D/PyLith/trunk/modulesrc/meshio/MeshIOSieve.i
short/3D/PyLith/trunk/pylith/apps/PrepMeshApp.py
short/3D/PyLith/trunk/pylith/meshio/MeshIOSieve.py
Modified:
short/3D/PyLith/trunk/applications/Makefile.am
short/3D/PyLith/trunk/modulesrc/meshio/Makefile.am
short/3D/PyLith/trunk/pylith/Makefile.am
Log:
Removed MeshIOSieve stuff, since this was never fully implemented or tested.
Modified: short/3D/PyLith/trunk/applications/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/applications/Makefile.am 2013-04-12 17:40:44 UTC (rev 21839)
+++ short/3D/PyLith/trunk/applications/Makefile.am 2013-04-12 17:43:55 UTC (rev 21840)
@@ -22,8 +22,7 @@
noinstINTERPRETER = $(PYTHON)
bin_SCRIPTS = \
- pylith \
- pylith_prepmesh
+ pylith
do_build = sed -e s%[@]INTERPRETER[@]%$(noinstINTERPRETER)%g -e s%[@]PYTHONPATH[@]%$(noinstPYTHONPATH)%g
do_install = sed -e s%[@]INTERPRETER[@]%$(INTERPRETER)%g -e s%[@]PYTHONPATH[@]%$(PYTHONPATH)%g
@@ -32,10 +31,6 @@
$(do_build) < $(srcdir)/pylith.in > $@ || (rm -f $@ && exit 1)
chmod +x $@
-pylith_prepmesh: $(srcdir)/pylith_prepmesh.in Makefile
- $(do_build) < $(srcdir)/pylith_prepmesh.in > $@ || (rm -f $@ && exit 1)
- chmod +x $@
-
install-binSCRIPTS: $(bin_SCRIPTS)
@$(NORMAL_INSTALL)
test -z "$(bindir)" || $(mkdir_p) "$(DESTDIR)$(bindir)"
@@ -51,8 +46,7 @@
done
EXTRA_DIST = \
- pylith.in \
- pylith_prepmesh.in
+ pylith.in
CLEANFILES = $(bin_SCRIPTS)
Deleted: short/3D/PyLith/trunk/applications/pylith_prepmesh.in
===================================================================
--- short/3D/PyLith/trunk/applications/pylith_prepmesh.in 2013-04-12 17:40:44 UTC (rev 21839)
+++ short/3D/PyLith/trunk/applications/pylith_prepmesh.in 2013-04-12 17:43:55 UTC (rev 21840)
@@ -1,42 +0,0 @@
-#!@INTERPRETER@
-# -*- Python -*-
-#
-# ----------------------------------------------------------------------
-#
-# Brad T. Aagaard, U.S. Geological Survey
-# Charles A. Williams, GNS Science
-# Matthew G. Knepley, University of Chicago
-#
-# This code was developed as part of the Computational Infrastructure
-# for Geodynamics (http://geodynamics.org).
-#
-# Copyright (c) 2010-2012 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ----------------------------------------------------------------------
-#
-
-## @file applications/pylith_prepmesh
-## @brief Python PyLith application driver
-
-__requires__ = "PyLith"
-
-if __name__ == "__main__":
-
- # re-create the PYTHONPATH at 'configure' time
- import os.path, sys, site
- path = '@PYTHONPATH@'.split(':')
- path.reverse()
- for directory in path:
- if directory:
- directory = os.path.abspath(directory)
- sys.path.insert(1, directory)
- site.addsitedir(directory)
-
- from pylith.apps.PrepMeshApp import PrepMeshApp
- from pyre.applications import start
- start(applicationClass=PrepMeshApp)
-
-
-# End of file
Modified: short/3D/PyLith/trunk/modulesrc/meshio/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/modulesrc/meshio/Makefile.am 2013-04-12 17:40:44 UTC (rev 21839)
+++ short/3D/PyLith/trunk/modulesrc/meshio/Makefile.am 2013-04-12 17:43:55 UTC (rev 21840)
@@ -29,7 +29,6 @@
MeshIOAscii.i \
MeshIOLagrit.i \
MeshIOCubit.i \
- MeshIOSieve.i \
VertexFilter.i \
VertexFilterVecNorm.i \
CellFilter.i \
Deleted: short/3D/PyLith/trunk/modulesrc/meshio/MeshIOSieve.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/meshio/MeshIOSieve.i 2013-04-12 17:40:44 UTC (rev 21839)
+++ short/3D/PyLith/trunk/modulesrc/meshio/MeshIOSieve.i 2013-04-12 17:43:55 UTC (rev 21840)
@@ -1,70 +0,0 @@
-// -*- C++ -*-
-//
-// ======================================================================
-//
-// Brad T. Aagaard, U.S. Geological Survey
-// Charles A. Williams, GNS Science
-// Matthew G. Knepley, University of Chicago
-//
-// This code was developed as part of the Computational Infrastructure
-// for Geodynamics (http://geodynamics.org).
-//
-// Copyright (c) 2010-2012 University of California, Davis
-//
-// See COPYING for license information.
-//
-// ======================================================================
-//
-
-/**
- * @file modulesrc/meshio/MeshIOSieve.i
- *
- * @brief Python interface to C++ MeshIOSieve object.
- */
-
-namespace pylith {
- namespace meshio {
-
- class MeshIOSieve : public MeshIO
- { // MeshIOSieve
-
- // PUBLIC METHODS /////////////////////////////////////////////////
- public :
-
- /// Constructor
- MeshIOSieve(void);
-
- /// Destructor
- ~MeshIOSieve(void);
-
- /// Deallocate PETSc and local data structures.
- void deallocate(void);
-
- /** Set filename for Sieve mesh file.
- *
- * @param filename Name of file
- */
- void filename(const char* name);
-
- /** Get filename of Sieve mesh file.
- *
- * @returns Name of file
- */
- const char* filename(void) const;
-
- // PROTECTED METHODS //////////////////////////////////////////////
- protected :
-
- /// Write mesh
- void _write(void) const;
-
- /// Read mesh
- void _read(void);
-
- }; // MeshIOSieve
-
- } // meshio
-} // pylith
-
-
-// End of file
Modified: short/3D/PyLith/trunk/pylith/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/pylith/Makefile.am 2013-04-12 17:40:44 UTC (rev 21839)
+++ short/3D/PyLith/trunk/pylith/Makefile.am 2013-04-12 17:43:55 UTC (rev 21840)
@@ -22,7 +22,6 @@
apps/PyLithApp.py \
apps/PetscApplication.py \
apps/EqInfoApp.py \
- apps/PrepMeshApp.py \
bc/__init__.py \
bc/AbsorbingDampers.py \
bc/BoundaryCondition.py \
@@ -104,7 +103,6 @@
meshio/MeshIOObj.py \
meshio/MeshIOAscii.py \
meshio/MeshIOLagrit.py \
- meshio/MeshIOSieve.py \
meshio/OutputDirichlet.py \
meshio/OutputManager.py \
meshio/OutputManagerMesh.py \
Deleted: short/3D/PyLith/trunk/pylith/apps/PrepMeshApp.py
===================================================================
--- short/3D/PyLith/trunk/pylith/apps/PrepMeshApp.py 2013-04-12 17:40:44 UTC (rev 21839)
+++ short/3D/PyLith/trunk/pylith/apps/PrepMeshApp.py 2013-04-12 17:43:55 UTC (rev 21840)
@@ -1,158 +0,0 @@
-#!/usr/bin/env python
-#
-# ----------------------------------------------------------------------
-#
-# Brad T. Aagaard, U.S. Geological Survey
-# Charles A. Williams, GNS Science
-# Matthew G. Knepley, University of Chicago
-#
-# This code was developed as part of the Computational Infrastructure
-# for Geodynamics (http://geodynamics.org).
-#
-# Copyright (c) 2010-2012 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ----------------------------------------------------------------------
-#
-
-## @file pylith/apps/PrepMeshApp.py
-##
-## @brief Python pre-processing application to adjust topology of a
-## mesh and partition it before running PyLith. This alleviates the
-## need to redo these steps for every simulation when reusing the same
-## faults.
-##
-## WARNING: This preprocessing application MUST be rerun if you change
-## which faults are used in a problem.
-
-from PetscApplication import PetscApplication
-
-def faultFactory(name):
- """
- Factory for fault items.
- """
- from pyre.inventory import facility
- from pylith.faults.FaultCohesiveKin import FaultCohesiveKin
- return facility(name, family="fault", factory=FaultCohesiveKin)
-
-
-# PrepMeshApp class
-class PrepMeshApp(PetscApplication):
- """
- Python PrepMeshApp application.
- """
-
- # INVENTORY //////////////////////////////////////////////////////////
-
- ## \b Properties
- ## @li None
- ##
- ## \b Facilities
- ## @li \b mesher Generates or imports the computational mesh.
- ## @li \b writer Writer for processed mesh.
- ## @li \b interfaces Interior surfaces with constraints or
- ## constitutive models.
-
- import pyre.inventory
- from pylith.utils.EmptyBin import EmptyBin
-
- from pylith.topology.MeshImporter import MeshImporter
- mesher = pyre.inventory.facility("mesh_generator", family="mesh_generator",
- factory=MeshImporter)
- mesher.meta['tip'] = "Generates or imports the computational mesh."
-
- from pylith.meshio.MeshIOSieve import MeshIOSieve
- writer = pyre.inventory.facility("writer", family="mesh_io",
- factory=MeshIOSieve)
- writer.meta['tip'] = "Writer for processed mesh."
-
- interfaces = pyre.inventory.facilityArray("interfaces",
- itemFactory=faultFactory,
- factory=EmptyBin)
- interfaces.meta['tip'] = "Interior surfaces with constraints or " \
- "constitutive models."
-
- from pylith.perf.MemoryLogger import MemoryLogger
- perfLogger = pyre.inventory.facility("perf_logger", family="perf_logger",
- factory=MemoryLogger)
- perfLogger.meta['tip'] = "Performance and memory logging."
-
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, name="prepmeshapp"):
- """
- Constructor.
- """
- PetscApplication.__init__(self, name)
- self._loggingPrefix = "PrepMeshApp "
- return
-
-
- def main(self, *args, **kwds):
- """
- Run the application.
- """
- from pylith.utils.profiling import resourceUsageString
-
- self._debug.log(resourceUsageString())
-
- self._setupLogging()
-
- # Create mesh (adjust to account for interfaces (faults) if necessary)
- self._eventLogger.stagePush("Meshing")
- interfaces = None
- if "interfaces" in dir(self.problem):
- interfaces = self.problem.interfaces.components()
- mesh = self.mesher.create(self.problem.normalizer, interfaces)
- del interfaces
- del self.mesher
- self._debug.log(resourceUsageString())
- self._eventLogger.stagePop()
-
- self._eventLogger.stagePush("Output")
- writer.write(mesh)
- self._eventLogger.stagePop()
-
-
- # Cleanup
- self.perfLogger.logMesh('Mesh', mesh)
- self.compilePerformanceLog()
- if self.perfLogger.verbose:
- self.perfLogger.show()
-
- del mesh
- del self.problem
- return
-
-
- # PRIVATE METHODS ////////////////////////////////////////////////////
-
- def _configure(self):
- """
- Setup members using inventory.
- """
- PetscApplication._configure(self)
- self.mesher = self.inventory.mesher
- self.problem = self.inventory.problem
- self.perfLogger = self.inventory.perfLogger
-
- import journal
- self._debug = journal.debug(self.name)
- return
-
- def _setupLogging(self):
- """
- Setup event logging.
- """
- from pylith.utils.EventLogger import EventLogger
- logger = EventLogger()
- logger.className("PyLith")
- logger.initialize()
-
- self._eventLogger = logger
- return
-
-
-# End of file
Deleted: short/3D/PyLith/trunk/pylith/meshio/MeshIOSieve.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/MeshIOSieve.py 2013-04-12 17:40:44 UTC (rev 21839)
+++ short/3D/PyLith/trunk/pylith/meshio/MeshIOSieve.py 2013-04-12 17:43:55 UTC (rev 21840)
@@ -1,104 +0,0 @@
-#!/usr/bin/env python
-#
-# ----------------------------------------------------------------------
-#
-# Brad T. Aagaard, U.S. Geological Survey
-# Charles A. Williams, GNS Science
-# Matthew G. Knepley, University of Chicago
-#
-# This code was developed as part of the Computational Infrastructure
-# for Geodynamics (http://geodynamics.org).
-#
-# Copyright (c) 2010-2012 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ----------------------------------------------------------------------
-#
-
-## @file pyre/meshio/MeshIOSieve.py
-##
-## @brief Python object for reading/writing a partitioned
-## finite-element mesh associated with the PETSc Sieve representation.
-##
-## Factory: mesh_io
-
-from MeshIOObj import MeshIOObj
-from meshio import MeshIOSieve as ModuleMeshIOSieve
-
-# MeshIOSieve class
-class MeshIOSieve(MeshIOObj, ModuleMeshIOSieve):
- """
- Python object for reading/writing finite-element mesh from simple
- ASCII file.
-
- Factory: mesh_io
- """
-
- # INVENTORY //////////////////////////////////////////////////////////
-
- class Inventory(MeshIOObj.Inventory):
- """
- Python object for managing MeshIOSieve facilities and properties.
- """
-
- ## @class Inventory
- ## Python object for managing MeshIOSieve facilities and properties.
- ##
- ## \b Properties
- ## @li \b filename Name of mesh file
- ##
- ## \b Facilities
- ## @li coordsys Coordinate system associated with mesh.
-
- import pyre.inventory
-
- filename = pyre.inventory.str("filename", default="")
- filename.meta['tip'] = "Name of mesh file"
-
- from spatialdata.geocoords.CSCart import CSCart
- coordsys = pyre.inventory.facility("coordsys", family="coordsys",
- factory=CSCart)
- coordsys.meta['tip'] = "Coordinate system associated with mesh."
-
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, name="meshiosieve"):
- """
- Constructor.
- """
- MeshIOObj.__init__(self, name)
- return
-
-
- # PRIVATE METHODS ////////////////////////////////////////////////////
-
- def _configure(self):
- """
- Set members based using inventory.
- """
- MeshIOObj._configure(self)
- self.coordsys = self.inventory.coordsys
- self.filename(self.inventory.filename)
- return
-
-
- def _createModuleObj(self):
- """
- Create C++ MeshIOSieve object.
- """
- ModuleMeshIOSieve.__init__(self)
- return
-
-
-# FACTORIES ////////////////////////////////////////////////////////////
-
-def mesh_io():
- """
- Factory associated with MeshIOSieve.
- """
- return MeshIOSieve()
-
-
-# End of file
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