[cig-commits] r22058 - in short/3D/PyLith/trunk: libsrc/pylith libsrc/pylith/bc libsrc/pylith/faults libsrc/pylith/friction libsrc/pylith/meshio libsrc/pylith/problems libsrc/pylith/topology modulesrc/bc modulesrc/faults modulesrc/feassemble modulesrc/friction modulesrc/include modulesrc/meshio modulesrc/problems modulesrc/topology pylith pylith/bc pylith/faults pylith/feassemble pylith/meshio pylith/problems pylith/topology unittests/libtests/bc unittests/libtests/faults unittests/libtests/feassemble unittests/libtests/friction unittests/libtests/meshio unittests/libtests/topology unittests/pytests/bc unittests/pytests/faults unittests/pytests/feassemble unittests/pytests/meshio unittests/pytests/problems unittests/pytests/topology
brad at geodynamics.org
brad at geodynamics.org
Mon May 13 16:33:38 PDT 2013
Author: brad
Date: 2013-05-13 16:33:37 -0700 (Mon, 13 May 2013)
New Revision: 22058
Removed:
short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.cc
short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.hh
short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.icc
short/3D/PyLith/trunk/modulesrc/include/submeshfield.i
short/3D/PyLith/trunk/modulesrc/topology/SubMesh.i
short/3D/PyLith/trunk/pylith/meshio/CellFilterAvgSubMesh.py
short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5ExtSubMesh.py
short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5ExtSubSubMesh.py
short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5SubMesh.py
short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5SubSubMesh.py
short/3D/PyLith/trunk/pylith/meshio/DataWriterVTKSubMesh.py
short/3D/PyLith/trunk/pylith/meshio/DataWriterVTKSubSubMesh.py
short/3D/PyLith/trunk/pylith/meshio/OutputManagerSubMesh.py
short/3D/PyLith/trunk/pylith/meshio/VertexFilterVecNormSubMesh.py
short/3D/PyLith/trunk/pylith/topology/SubMesh.py
short/3D/PyLith/trunk/unittests/pytests/feassemble/TestSubMeshQuadrature.py
Modified:
short/3D/PyLith/trunk/libsrc/pylith/Makefile.am
short/3D/PyLith/trunk/libsrc/pylith/bc/AbsorbingDampers.cc
short/3D/PyLith/trunk/libsrc/pylith/bc/BCIntegratorSubMesh.cc
short/3D/PyLith/trunk/libsrc/pylith/bc/BCIntegratorSubMesh.hh
short/3D/PyLith/trunk/libsrc/pylith/bc/BCIntegratorSubMesh.icc
short/3D/PyLith/trunk/libsrc/pylith/bc/DirichletBoundary.cc
short/3D/PyLith/trunk/libsrc/pylith/bc/DirichletBoundary.hh
short/3D/PyLith/trunk/libsrc/pylith/bc/DirichletBoundary.icc
short/3D/PyLith/trunk/libsrc/pylith/bc/Neumann.cc
short/3D/PyLith/trunk/libsrc/pylith/bc/Neumann.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/CohesiveTopology.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/CohesiveTopology.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/EqKinSrc.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/EqKinSrc.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/Fault.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/Fault.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesive.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesive.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesive.icc
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveImpulses.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveImpulses.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveKin.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveKin.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveTract.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveTract.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/SlipTimeFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/SlipTimeFn.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/TopologyOps.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/TopologyOps.hh
short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.hh
short/3D/PyLith/trunk/libsrc/pylith/friction/FrictionModel.cc
short/3D/PyLith/trunk/libsrc/pylith/friction/FrictionModel.hh
short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnSubset.cc
short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnSubset.hh
short/3D/PyLith/trunk/libsrc/pylith/problems/Formulation.cc
short/3D/PyLith/trunk/libsrc/pylith/problems/Formulation.hh
short/3D/PyLith/trunk/libsrc/pylith/topology/Jacobian.cc
short/3D/PyLith/trunk/libsrc/pylith/topology/Jacobian.hh
short/3D/PyLith/trunk/libsrc/pylith/topology/Makefile.am
short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.cc
short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.hh
short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.icc
short/3D/PyLith/trunk/libsrc/pylith/topology/MeshOps.cc
short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorMesh.hh
short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorMesh.icc
short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorSubMesh.hh
short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorSubMesh.icc
short/3D/PyLith/trunk/libsrc/pylith/topology/topologyfwd.hh
short/3D/PyLith/trunk/modulesrc/bc/BCIntegratorSubMesh.i
short/3D/PyLith/trunk/modulesrc/bc/DirichletBoundary.i
short/3D/PyLith/trunk/modulesrc/bc/Neumann.i
short/3D/PyLith/trunk/modulesrc/bc/bc.i
short/3D/PyLith/trunk/modulesrc/faults/BruneSlipFn.i
short/3D/PyLith/trunk/modulesrc/faults/ConstRateSlipFn.i
short/3D/PyLith/trunk/modulesrc/faults/EqKinSrc.i
short/3D/PyLith/trunk/modulesrc/faults/Fault.i
short/3D/PyLith/trunk/modulesrc/faults/FaultCohesive.i
short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveDyn.i
short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveImpulses.i
short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveKin.i
short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveTract.i
short/3D/PyLith/trunk/modulesrc/faults/LiuCosSlipFn.i
short/3D/PyLith/trunk/modulesrc/faults/Makefile.am
short/3D/PyLith/trunk/modulesrc/faults/SlipTimeFn.i
short/3D/PyLith/trunk/modulesrc/faults/StepSlipFn.i
short/3D/PyLith/trunk/modulesrc/faults/TimeHistorySlipFn.i
short/3D/PyLith/trunk/modulesrc/faults/TractPerturbation.i
short/3D/PyLith/trunk/modulesrc/faults/faults.i
short/3D/PyLith/trunk/modulesrc/feassemble/feassemble.i
short/3D/PyLith/trunk/modulesrc/friction/FrictionModel.i
short/3D/PyLith/trunk/modulesrc/include/Makefile.am
short/3D/PyLith/trunk/modulesrc/include/integratorarray.i
short/3D/PyLith/trunk/modulesrc/meshio/OutputSolnPoints.i
short/3D/PyLith/trunk/modulesrc/meshio/OutputSolnSubset.i
short/3D/PyLith/trunk/modulesrc/meshio/meshio.i
short/3D/PyLith/trunk/modulesrc/problems/Formulation.i
short/3D/PyLith/trunk/modulesrc/topology/Jacobian.i
short/3D/PyLith/trunk/modulesrc/topology/Makefile.am
short/3D/PyLith/trunk/modulesrc/topology/Mesh.i
short/3D/PyLith/trunk/modulesrc/topology/topology.i
short/3D/PyLith/trunk/pylith/Makefile.am
short/3D/PyLith/trunk/pylith/bc/AbsorbingDampers.py
short/3D/PyLith/trunk/pylith/bc/Neumann.py
short/3D/PyLith/trunk/pylith/faults/Fault.py
short/3D/PyLith/trunk/pylith/feassemble/Quadrature.py
short/3D/PyLith/trunk/pylith/meshio/MeshIOObj.py
short/3D/PyLith/trunk/pylith/meshio/OutputDirichlet.py
short/3D/PyLith/trunk/pylith/meshio/OutputFaultDyn.py
short/3D/PyLith/trunk/pylith/meshio/OutputFaultImpulses.py
short/3D/PyLith/trunk/pylith/meshio/OutputFaultKin.py
short/3D/PyLith/trunk/pylith/meshio/OutputNeumann.py
short/3D/PyLith/trunk/pylith/meshio/OutputSolnSubset.py
short/3D/PyLith/trunk/pylith/meshio/__init__.py
short/3D/PyLith/trunk/pylith/problems/TimeStep.py
short/3D/PyLith/trunk/pylith/topology/Field.py
short/3D/PyLith/trunk/pylith/topology/Fields.py
short/3D/PyLith/trunk/pylith/topology/Mesh.py
short/3D/PyLith/trunk/pylith/topology/MeshImporter.py
short/3D/PyLith/trunk/pylith/topology/RefineUniform.py
short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.cc
short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.hh
short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampersCases.cc
short/3D/PyLith/trunk/unittests/libtests/bc/TestBoundaryMesh.cc
short/3D/PyLith/trunk/unittests/libtests/bc/TestDirichletBoundary.cc
short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumann.cc
short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumann.hh
short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumannCases.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestBruneSlipFn.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestBruneSlipFn.hh
short/3D/PyLith/trunk/unittests/libtests/faults/TestConstRateSlipFn.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestConstRateSlipFn.hh
short/3D/PyLith/trunk/unittests/libtests/faults/TestEqKinSrc.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestEqKinSrc.hh
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDyn.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDyn.hh
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDynCases.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulses.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulses.hh
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulsesCases.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.hh
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKinCases.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKinSrcsCases.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKinSrcsTet4.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultMesh.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultMesh.hh
short/3D/PyLith/trunk/unittests/libtests/faults/TestLiuCosSlipFn.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestLiuCosSlipFn.hh
short/3D/PyLith/trunk/unittests/libtests/faults/TestSlipFn.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestSlipFn.hh
short/3D/PyLith/trunk/unittests/libtests/faults/TestStepSlipFn.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestStepSlipFn.hh
short/3D/PyLith/trunk/unittests/libtests/faults/TestTimeHistorySlipFn.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestTimeHistorySlipFn.hh
short/3D/PyLith/trunk/unittests/libtests/faults/TestTractPerturbation.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestTractPerturbation.hh
short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicit.cc
short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitLgDeform.cc
short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTet4.cc
short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTri3.cc
short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicit.cc
short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicitLgDeform.cc
short/3D/PyLith/trunk/unittests/libtests/friction/TestFrictionModel.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestCellFilterAvg.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterBCMesh.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterBCMesh.hh
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterFaultMesh.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterFaultMesh.hh
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5BCMesh.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5BCMesh.hh
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5BCMeshCases.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtBCMesh.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtBCMesh.hh
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtBCMeshCases.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtFaultMesh.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtFaultMesh.hh
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtFaultMeshCases.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtSubMesh.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtSubMesh.hh
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtSubMeshCases.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5FaultMesh.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5FaultMesh.hh
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5FaultMeshCases.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5SubMesh.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5SubMesh.hh
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5SubMeshCases.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterSubMesh.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterSubMesh.hh
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKBCMesh.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKBCMesh.hh
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKBCMeshCases.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKFaultMesh.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKFaultMesh.hh
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKFaultMeshCases.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKSubMesh.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKSubMesh.hh
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKSubMeshCases.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestOutputSolnSubset.cc
short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldSubMesh.cc
short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldSubMesh.hh
short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsSubMesh.cc
short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsSubMesh.hh
short/3D/PyLith/trunk/unittests/libtests/topology/TestJacobian.cc
short/3D/PyLith/trunk/unittests/libtests/topology/TestMesh.cc
short/3D/PyLith/trunk/unittests/libtests/topology/TestSubMesh.cc
short/3D/PyLith/trunk/unittests/libtests/topology/TestSubMesh.hh
short/3D/PyLith/trunk/unittests/pytests/bc/TestAbsorbingDampers.py
short/3D/PyLith/trunk/unittests/pytests/bc/TestNeumann.py
short/3D/PyLith/trunk/unittests/pytests/faults/TestFaultCohesiveDyn.py
short/3D/PyLith/trunk/unittests/pytests/faults/TestFaultCohesiveImpulses.py
short/3D/PyLith/trunk/unittests/pytests/faults/TestFaultCohesiveKin.py
short/3D/PyLith/trunk/unittests/pytests/feassemble/Makefile.am
short/3D/PyLith/trunk/unittests/pytests/feassemble/testfeassemble.py
short/3D/PyLith/trunk/unittests/pytests/meshio/TestCellFilterAvg.py
short/3D/PyLith/trunk/unittests/pytests/meshio/TestDataWriterHDF5.py
short/3D/PyLith/trunk/unittests/pytests/meshio/TestDataWriterHDF5Ext.py
short/3D/PyLith/trunk/unittests/pytests/meshio/TestDataWriterVTK.py
short/3D/PyLith/trunk/unittests/pytests/meshio/TestOutputManagerSubMesh.py
short/3D/PyLith/trunk/unittests/pytests/meshio/TestVertexFilterVecNorm.py
short/3D/PyLith/trunk/unittests/pytests/meshio/testhdf5.py
short/3D/PyLith/trunk/unittests/pytests/meshio/testmeshio.py
short/3D/PyLith/trunk/unittests/pytests/problems/TestTimeStepAdapt.py
short/3D/PyLith/trunk/unittests/pytests/problems/TestTimeStepUniform.py
short/3D/PyLith/trunk/unittests/pytests/problems/TestTimeStepUser.py
short/3D/PyLith/trunk/unittests/pytests/topology/TestJacobian.py
short/3D/PyLith/trunk/unittests/pytests/topology/TestMesh.py
short/3D/PyLith/trunk/unittests/pytests/topology/TestSubMesh.py
Log:
Removed SubMesh. Mesh is now used for both the domain mesh and the boundary meshes.
Modified: short/3D/PyLith/trunk/libsrc/pylith/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/Makefile.am 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/Makefile.am 2013-05-13 23:33:37 UTC (rev 22058)
@@ -149,7 +149,6 @@
topology/Jacobian.cc \
topology/Mesh.cc \
topology/MeshOps.cc \
- topology/SubMesh.cc \
topology/SolutionFields.cc \
topology/Distributor.cc \
topology/ReverseCuthillMcKee.cc \
Modified: short/3D/PyLith/trunk/libsrc/pylith/bc/AbsorbingDampers.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/bc/AbsorbingDampers.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/bc/AbsorbingDampers.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -105,7 +105,7 @@
const int fiberDim = numQuadPts * spaceDim;
delete _parameters;
- _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(*_boundaryMesh);
+ _parameters = new topology::Fields<topology::Field<topology::Mesh> >(*_boundaryMesh);
assert(_parameters);
_parameters->add("damping constants", "damping_constants", topology::FieldBase::FACES_FIELD, fiberDim);
_parameters->get("damping constants").allocate();
@@ -136,7 +136,7 @@
// Container for damping constants for current cell
scalar_array dampingConstsLocal(spaceDim);
- topology::Field<topology::SubMesh>& dampingConsts = _parameters->get("damping constants");
+ topology::Field<topology::Mesh>& dampingConsts = _parameters->get("damping constants");
topology::VecVisitorMesh dampingConstsVisitor(dampingConsts);
topology::CoordsVisitor coordsVisitor(dmSubMesh);
@@ -252,7 +252,7 @@
_initCellVector();
// Get sections
- topology::Field<topology::SubMesh>& dampingConsts = _parameters->get("damping constants");
+ topology::Field<topology::Mesh>& dampingConsts = _parameters->get("damping constants");
topology::VecVisitorMesh dampingConstsVisitor(dampingConsts);
PetscScalar* dampingConstsArray = dampingConstsVisitor.localArray();
@@ -393,7 +393,7 @@
const PetscInt cEnd = cellsStratum.end();
// Get sections
- topology::Field<topology::SubMesh>& dampingConsts = _parameters->get("damping constants");
+ topology::Field<topology::Mesh>& dampingConsts = _parameters->get("damping constants");
topology::VecVisitorMesh dampingConstsVisitor(dampingConsts);
PetscScalar* dampingConstsArray = dampingConstsVisitor.localArray();
@@ -525,7 +525,7 @@
const PetscInt cEnd = cellsStratum.end();
// Get sections
- topology::Field<topology::SubMesh>& dampingConsts = _parameters->get("damping constants");
+ topology::Field<topology::Mesh>& dampingConsts = _parameters->get("damping constants");
topology::VecVisitorMesh dampingConstsVisitor(dampingConsts);
PetscScalar* dampingConstsArray = dampingConstsVisitor.localArray();
@@ -667,7 +667,7 @@
_initCellVector();
// Get sections
- topology::Field<topology::SubMesh>& dampingConsts = _parameters->get("damping constants");
+ topology::Field<topology::Mesh>& dampingConsts = _parameters->get("damping constants");
topology::VecVisitorMesh dampingConstsVisitor(dampingConsts);
PetscScalar* dampingConstsArray = dampingConstsVisitor.localArray();
Modified: short/3D/PyLith/trunk/libsrc/pylith/bc/BCIntegratorSubMesh.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/bc/BCIntegratorSubMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/bc/BCIntegratorSubMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,7 +20,7 @@
#include "BCIntegratorSubMesh.hh" // implementation of object methods
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Stratum.hh" // USES Stratum
@@ -48,7 +48,7 @@
PYLITH_METHOD_BEGIN;
BoundaryCondition::deallocate();
- feassemble::Integrator<feassemble::Quadrature<topology::SubMesh> >::deallocate();
+ feassemble::Integrator<feassemble::Quadrature<topology::Mesh> >::deallocate();
delete _boundaryMesh; _boundaryMesh = 0;
delete _parameters; _parameters = 0;
@@ -66,7 +66,7 @@
delete _boundaryMesh; _boundaryMesh = 0;
delete _parameters; _parameters = 0;
- _boundaryMesh = new topology::SubMesh(mesh, _label.c_str());
+ _boundaryMesh = new topology::Mesh(mesh, _label.c_str());
assert(_boundaryMesh);
PYLITH_METHOD_END;
Modified: short/3D/PyLith/trunk/libsrc/pylith/bc/BCIntegratorSubMesh.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/bc/BCIntegratorSubMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/bc/BCIntegratorSubMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -31,9 +31,9 @@
// Include directives ---------------------------------------------------
#include "BoundaryCondition.hh" // ISA BoundaryCondition
-#include "pylith/topology/topologyfwd.hh" // HOLDSA Fields, SubMesh
+#include "pylith/topology/topologyfwd.hh" // HOLDSA Fields, Mesh
-#include "pylith/topology/SubMesh.hh" // ISA Quadrature<SubMesh>
+#include "pylith/topology/Mesh.hh" // ISA Quadrature<Mesh>
#include "pylith/feassemble/Quadrature.hh" // ISA Integrator<Quadrature>
#include "pylith/feassemble/Integrator.hh" // ISA Integrator
@@ -41,7 +41,7 @@
/// @brief Abstract base classs for BoundaryCondition object with
/// boundary condition applied at a simple-connect surface (submesh).
class pylith::bc::BCIntegratorSubMesh : public BoundaryCondition,
- public feassemble::Integrator<feassemble::Quadrature<topology::SubMesh> >
+ public feassemble::Integrator<feassemble::Quadrature<topology::Mesh> >
{ // class BCIntegratorSubMesh
friend class TestBCIntegratorSubMesh; // unit testing
@@ -63,14 +63,14 @@
*
* @returns Parameter fields.
*/
- const topology::Fields<topology::Field<topology::SubMesh> >*
+ const topology::Fields<topology::Field<topology::Mesh> >*
parameterFields(void) const;
/** Get boundary mesh.
*
* @return Boundary mesh.
*/
- const topology::SubMesh& boundaryMesh(void) const;
+ const topology::Mesh& boundaryMesh(void) const;
/** Get mesh labels for submesh associated with applied forces.
*
@@ -87,10 +87,10 @@
// PROTECTED MEMBERS //////////////////////////////////////////////////
protected :
- topology::SubMesh* _boundaryMesh; ///< Boundary mesh.
+ topology::Mesh* _boundaryMesh; ///< Boundary mesh.
/// Parameters for boundary condition.
- topology::Fields<topology::Field<topology::SubMesh> >* _parameters;
+ topology::Fields<topology::Field<topology::Mesh> >* _parameters;
// NOT IMPLEMENTED ////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/trunk/libsrc/pylith/bc/BCIntegratorSubMesh.icc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/bc/BCIntegratorSubMesh.icc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/bc/BCIntegratorSubMesh.icc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -24,14 +24,14 @@
// Get parameter fields.
inline
-const pylith::topology::Fields<pylith::topology::Field<pylith::topology::SubMesh> >*
+const pylith::topology::Fields<pylith::topology::Field<pylith::topology::Mesh> >*
pylith::bc::BCIntegratorSubMesh::parameterFields(void) const {
return _parameters;
} // parameterFields
// Get boundary mesh.
inline
-const pylith::topology::SubMesh&
+const pylith::topology::Mesh&
pylith::bc::BCIntegratorSubMesh::boundaryMesh(void) const {
assert(_boundaryMesh);
return *_boundaryMesh;
Modified: short/3D/PyLith/trunk/libsrc/pylith/bc/DirichletBoundary.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/bc/DirichletBoundary.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/bc/DirichletBoundary.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -21,7 +21,6 @@
#include "DirichletBoundary.hh" // implementation of object methods
#include "pylith/topology/Mesh.hh" // USES Mesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/VisitorMesh.hh" // USES VecVisitorMesh
@@ -73,7 +72,7 @@
DirichletBC::initialize(mesh, upDir);
- _boundaryMesh = new topology::SubMesh(mesh, _label.c_str());
+ _boundaryMesh = new topology::Mesh(mesh, _label.c_str());
assert(_boundaryMesh);
PYLITH_METHOD_END;
@@ -81,7 +80,7 @@
// ----------------------------------------------------------------------
// Get vertex field of BC initial or rate of change of values.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::bc::DirichletBoundary::vertexField(const char* name,
const topology::SolutionFields& fields)
{ // getVertexField
@@ -98,17 +97,17 @@
const int spaceDim = cs->spaceDim();
if (!_outputFields) {
- _outputFields = new topology::Fields<topology::Field<topology::SubMesh> >(*_boundaryMesh);
+ _outputFields = new topology::Fields<topology::Field<topology::Mesh> >(*_boundaryMesh);
} // if
assert(_outputFields);
_outputFields->add("buffer (vector)", "buffer_vector", topology::FieldBase::FACES_FIELD, spaceDim);
- topology::Field<topology::SubMesh>& bufferVector = _outputFields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& bufferVector = _outputFields->get("buffer (vector)");
bufferVector.vectorFieldType(topology::FieldBase::VECTOR);
bufferVector.scale(lengthScale);
bufferVector.allocate();
_outputFields->add("buffer (scalar)", "buffer_scalar", topology::FieldBase::FACES_FIELD, 1);
- topology::Field<topology::SubMesh>& bufferScalar = _outputFields->get("buffer (scalar)");
+ topology::Field<topology::Mesh>& bufferScalar = _outputFields->get("buffer (scalar)");
bufferScalar.vectorFieldType(topology::FieldBase::SCALAR);
bufferScalar.scale(timeScale);
bufferScalar.allocate();
@@ -138,7 +137,7 @@
// ----------------------------------------------------------------------
// Get vertex vector field with BC information.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::bc::DirichletBoundary::_bufferVector(const char* name,
const char* label,
const PylithScalar scale)
@@ -157,7 +156,7 @@
} // if
assert(_outputFields->hasField("buffer (vector)"));
- topology::Field<topology::SubMesh>& buffer = _outputFields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _outputFields->get("buffer (vector)");
topology::VecVisitorMesh bufferVisitor(buffer);
PetscScalar* bufferArray = bufferVisitor.localArray();
@@ -191,7 +190,7 @@
// ----------------------------------------------------------------------
// Get vertex scalar field with BC information.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::bc::DirichletBoundary::_bufferScalar(const char* name,
const char* label,
const PylithScalar scale)
@@ -210,7 +209,7 @@
} // if
assert(_outputFields->hasField("buffer (scalar)"));
- topology::Field<topology::SubMesh>& buffer = _outputFields->get("buffer (scalar)");
+ topology::Field<topology::Mesh>& buffer = _outputFields->get("buffer (scalar)");
topology::VecVisitorMesh bufferVisitor(buffer);
PetscScalar* bufferArray = bufferVisitor.localArray();
Modified: short/3D/PyLith/trunk/libsrc/pylith/bc/DirichletBoundary.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/bc/DirichletBoundary.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/bc/DirichletBoundary.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -59,7 +59,7 @@
*
* @return Boundary mesh.
*/
- const topology::SubMesh& boundaryMesh(void) const;
+ const topology::Mesh& boundaryMesh(void) const;
/** Get vertex field with BC information.
*
@@ -68,7 +68,7 @@
*
* @returns Field over vertices.
*/
- const topology::Field<topology::SubMesh>&
+ const topology::Field<topology::Mesh>&
vertexField(const char* name,
const topology::SolutionFields& fields);
@@ -83,7 +83,7 @@
*
* @returns Field over vertices.
*/
- const topology::Field<topology::SubMesh>&
+ const topology::Field<topology::Mesh>&
_bufferVector(const char* name,
const char* label,
const PylithScalar scale);
@@ -96,7 +96,7 @@
*
* @returns Field over vertices.
*/
- const topology::Field<topology::SubMesh>&
+ const topology::Field<topology::Mesh>&
_bufferScalar(const char* name,
const char* label,
const PylithScalar scale);
@@ -104,10 +104,10 @@
// PRIVATE MEMBERS ////////////////////////////////////////////////////
private :
- topology::SubMesh* _boundaryMesh; ///< Boundary mesh.
+ topology::Mesh* _boundaryMesh; ///< Boundary mesh.
/// Fields manager (holds temporary field for output).
- topology::Fields<topology::Field<topology::SubMesh> >* _outputFields;
+ topology::Fields<topology::Field<topology::Mesh> >* _outputFields;
// NOT IMPLEMENTED ////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/trunk/libsrc/pylith/bc/DirichletBoundary.icc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/bc/DirichletBoundary.icc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/bc/DirichletBoundary.icc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -24,9 +24,9 @@
// Get boundary mesh.
inline
-const pylith::topology::SubMesh&
+const pylith::topology::Mesh&
pylith::bc::DirichletBoundary::boundaryMesh(void) const {
- assert(0 != _boundaryMesh);
+ assert(_boundaryMesh);
return *_boundaryMesh;
} // boundaryMesh
Modified: short/3D/PyLith/trunk/libsrc/pylith/bc/Neumann.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/bc/Neumann.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/bc/Neumann.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,7 +20,7 @@
#include "Neumann.hh" // implementation of object methods
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/Fields.hh" // HOLDSA Fields
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/CoordsVisitor.hh" // USES CoordsVisitor
@@ -112,7 +112,7 @@
// Get sections
_calculateValue(t);
- topology::Field<topology::SubMesh>& valueField = _parameters->get("value");
+ topology::Field<topology::Mesh>& valueField = _parameters->get("value");
topology::VecVisitorMesh valueVisitor(valueField);
PetscScalar* valueArray = valueVisitor.localArray();
@@ -181,7 +181,7 @@
// ----------------------------------------------------------------------
// Get cell field for tractions.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::bc::Neumann::cellField(const char* name,
topology::SolutionFields* const fields)
{ // cellField
@@ -234,41 +234,41 @@
const int numQuadPts = _quadrature->numQuadPts();
delete _parameters;
- _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(*_boundaryMesh);
+ _parameters = new topology::Fields<topology::Field<topology::Mesh> >(*_boundaryMesh);
// Create section to hold time dependent values
_parameters->add("value", "traction", topology::FieldBase::FACES_FIELD, numQuadPts*spaceDim);
- topology::Field<topology::SubMesh>& value = _parameters->get("value");
+ topology::Field<topology::Mesh>& value = _parameters->get("value");
value.vectorFieldType(topology::FieldBase::MULTI_VECTOR);
value.scale(pressureScale);
value.allocate();
if (_dbInitial) {
_parameters->add("initial", "initial_traction", topology::FieldBase::FACES_FIELD, numQuadPts*spaceDim);
- topology::Field<topology::SubMesh>& initial = _parameters->get("initial");
+ topology::Field<topology::Mesh>& initial = _parameters->get("initial");
initial.vectorFieldType(topology::FieldBase::MULTI_VECTOR);
initial.scale(pressureScale);
initial.allocate();
}
if (_dbRate) {
_parameters->add("rate", "traction_rate", topology::FieldBase::FACES_FIELD, numQuadPts*spaceDim);
- topology::Field<topology::SubMesh>& rate = _parameters->get("rate");
+ topology::Field<topology::Mesh>& rate = _parameters->get("rate");
rate.vectorFieldType(topology::FieldBase::MULTI_VECTOR);
rate.scale(rateScale);
rate.allocate();
_parameters->add("rate time", "traction_rate_time", topology::FieldBase::FACES_FIELD, numQuadPts);
- topology::Field<topology::SubMesh>& rateTime = _parameters->get("rate time");
+ topology::Field<topology::Mesh>& rateTime = _parameters->get("rate time");
rateTime.vectorFieldType(topology::FieldBase::MULTI_VECTOR);
rateTime.scale(timeScale);
rateTime.allocate();
} // if
if (_dbChange) {
_parameters->add("change", "change_traction", topology::FieldBase::FACES_FIELD, numQuadPts*spaceDim);
- topology::Field<topology::SubMesh>& change = _parameters->get("change");
+ topology::Field<topology::Mesh>& change = _parameters->get("change");
change.vectorFieldType(topology::FieldBase::MULTI_VECTOR);
change.scale(pressureScale);
change.allocate();
_parameters->add("change time", "change_traction_time", topology::FieldBase::FACES_FIELD, numQuadPts);
- topology::Field<topology::SubMesh>& changeTime = _parameters->get("change time");
+ topology::Field<topology::Mesh>& changeTime = _parameters->get("change time");
changeTime.vectorFieldType(topology::FieldBase::MULTI_VECTOR);
changeTime.scale(timeScale);
changeTime.allocate();
@@ -412,7 +412,7 @@
scalar_array quadPtsGlobal(numQuadPts*spaceDim);
// Get sections.
- topology::Field<topology::SubMesh>& valueField = _parameters->get(name);
+ topology::Field<topology::Mesh>& valueField = _parameters->get(name);
topology::VecVisitorMesh valueVisitor(valueField);
PetscScalar* valueArray = valueVisitor.localArray();
@@ -512,15 +512,15 @@
// Get sections
scalar_array tmpLocal(spaceDim);
- topology::Field<topology::SubMesh>* initialField = (_dbInitial) ? &_parameters->get("initial") : 0;
+ topology::Field<topology::Mesh>* initialField = (_dbInitial) ? &_parameters->get("initial") : 0;
topology::VecVisitorMesh* initialVisitor = (initialField) ? new topology::VecVisitorMesh(*initialField) : 0;
PetscScalar* initialArray = (initialVisitor) ? initialVisitor->localArray() : NULL;
- topology::Field<topology::SubMesh>* rateField = (_dbRate) ? &_parameters->get("rate") : 0;
+ topology::Field<topology::Mesh>* rateField = (_dbRate) ? &_parameters->get("rate") : 0;
topology::VecVisitorMesh* rateVisitor = (rateField) ? new topology::VecVisitorMesh(*rateField) : 0;
PetscScalar* rateArray = (rateVisitor) ? rateVisitor->localArray() : NULL;
- topology::Field<topology::SubMesh>* changeField = (_dbChange) ? &_parameters->get("change") : 0;
+ topology::Field<topology::Mesh>* changeField = (_dbChange) ? &_parameters->get("change") : 0;
topology::VecVisitorMesh* changeVisitor = (changeField) ? new topology::VecVisitorMesh(*changeField) : 0;
PetscScalar* changeArray = (changeVisitor) ? changeVisitor->localArray() : NULL;
@@ -621,27 +621,27 @@
const int numQuadPts = _quadrature->numQuadPts();
// Get sections
- topology::Field<topology::SubMesh>& valueField = _parameters->get("value");
+ topology::Field<topology::Mesh>& valueField = _parameters->get("value");
topology::VecVisitorMesh valueVisitor(valueField);
PetscScalar* valueArray = valueVisitor.localArray();
- topology::Field<topology::SubMesh>* initialField = (_dbInitial) ? &_parameters->get("initial") : 0;
+ topology::Field<topology::Mesh>* initialField = (_dbInitial) ? &_parameters->get("initial") : 0;
topology::VecVisitorMesh* initialVisitor = (initialField) ? new topology::VecVisitorMesh(*initialField) : 0;
PetscScalar* initialArray = (initialVisitor) ? initialVisitor->localArray() : NULL;
- topology::Field<topology::SubMesh>* rateField = (_dbRate) ? &_parameters->get("rate") : 0;
+ topology::Field<topology::Mesh>* rateField = (_dbRate) ? &_parameters->get("rate") : 0;
topology::VecVisitorMesh* rateVisitor = (rateField) ? new topology::VecVisitorMesh(*rateField) : 0;
PetscScalar* rateArray = (rateVisitor) ? rateVisitor->localArray() : NULL;
- topology::Field<topology::SubMesh>* rateTimeField = (_dbRate) ? &_parameters->get("rate time") : 0;
+ topology::Field<topology::Mesh>* rateTimeField = (_dbRate) ? &_parameters->get("rate time") : 0;
topology::VecVisitorMesh* rateTimeVisitor = (rateTimeField) ? new topology::VecVisitorMesh(*rateTimeField) : 0;
PetscScalar* rateTimeArray = (rateTimeVisitor) ? rateTimeVisitor->localArray() : NULL;
- topology::Field<topology::SubMesh>* changeField = (_dbChange) ? &_parameters->get("change") : 0;
+ topology::Field<topology::Mesh>* changeField = (_dbChange) ? &_parameters->get("change") : 0;
topology::VecVisitorMesh* changeVisitor = (changeField) ? new topology::VecVisitorMesh(*changeField) : 0;
PetscScalar* changeArray = (changeVisitor) ? changeVisitor->localArray() : NULL;
- topology::Field<topology::SubMesh>* changeTimeField = (_dbChange) ? &_parameters->get("change time") : 0;
+ topology::Field<topology::Mesh>* changeTimeField = (_dbChange) ? &_parameters->get("change time") : 0;
topology::VecVisitorMesh* changeTimeVisitor = (changeTimeField) ? new topology::VecVisitorMesh(*changeTimeField) : 0;
PetscScalar* changeTimeArray = (changeTimeVisitor) ? changeTimeVisitor->localArray() : NULL;
Modified: short/3D/PyLith/trunk/libsrc/pylith/bc/Neumann.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/bc/Neumann.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/bc/Neumann.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -81,7 +81,7 @@
*
* @returns Traction vector at integration points.
*/
- const topology::Field<topology::SubMesh>&
+ const topology::Field<topology::Mesh>&
cellField(const char* name,
topology::SolutionFields* const fields =0);
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,7 +20,7 @@
#include "BruneSlipFn.hh" // implementation of object methods
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/CoordsVisitor.hh" // USES CoordsVisitor
@@ -72,7 +72,7 @@
// ----------------------------------------------------------------------
// Initialize slip time function.
void
-pylith::faults::BruneSlipFn::initialize(const topology::SubMesh& faultMesh,
+pylith::faults::BruneSlipFn::initialize(const topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime)
{ // initialize
@@ -94,10 +94,10 @@
const PetscInt vStart = verticesStratum.begin();
const PetscInt vEnd = verticesStratum.end();
- delete _parameters; _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
+ delete _parameters; _parameters = new topology::Fields<topology::Field<topology::Mesh> >(faultMesh);
assert(_parameters);
_parameters->add("final slip", "final_slip");
- topology::Field<topology::SubMesh>& finalSlip = _parameters->get("final slip");
+ topology::Field<topology::Mesh>& finalSlip = _parameters->get("final slip");
finalSlip.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim);
finalSlip.allocate();
finalSlip.scale(lengthScale);
@@ -106,7 +106,7 @@
PetscScalar* finalSlipArray = finalSlipVisitor.localArray();
_parameters->add("slip time", "slip_time");
- topology::Field<topology::SubMesh>& slipTime = _parameters->get("slip time");
+ topology::Field<topology::Mesh>& slipTime = _parameters->get("slip time");
slipTime.newSection(finalSlip, 1);
slipTime.allocate();
slipTime.scale(timeScale);
@@ -115,7 +115,7 @@
PetscScalar* slipTimeArray = slipTimeVisitor.localArray();
_parameters->add("rise time", "rise_time");
- topology::Field<topology::SubMesh>& riseTime = _parameters->get("rise time");
+ topology::Field<topology::Mesh>& riseTime = _parameters->get("rise time");
riseTime.newSection(finalSlip, 1);
riseTime.allocate();
riseTime.scale(timeScale);
@@ -234,7 +234,7 @@
// ----------------------------------------------------------------------
// Get slip on fault surface at time t.
void
-pylith::faults::BruneSlipFn::slip(topology::Field<topology::SubMesh>* slip,
+pylith::faults::BruneSlipFn::slip(topology::Field<topology::Mesh>* slip,
const PylithScalar t)
{ // slip
PYLITH_METHOD_BEGIN;
@@ -249,15 +249,15 @@
const PetscInt vEnd = verticesStratum.end();
// Get sections
- const topology::Field<topology::SubMesh>& finalSlip = _parameters->get("final slip");
+ const topology::Field<topology::Mesh>& finalSlip = _parameters->get("final slip");
topology::VecVisitorMesh finalSlipVisitor(finalSlip);
const PetscScalar* finalSlipArray = finalSlipVisitor.localArray();
- const topology::Field<topology::SubMesh>& slipTime = _parameters->get("slip time");
+ const topology::Field<topology::Mesh>& slipTime = _parameters->get("slip time");
topology::VecVisitorMesh slipTimeVisitor(slipTime);
const PetscScalar* slipTimeArray = slipTimeVisitor.localArray();
- const topology::Field<topology::SubMesh>& riseTime = _parameters->get("rise time");
+ const topology::Field<topology::Mesh>& riseTime = _parameters->get("rise time");
topology::VecVisitorMesh riseTimeVisitor(riseTime);
const PetscScalar* riseTimeArray = riseTimeVisitor.localArray();
@@ -297,7 +297,7 @@
// ----------------------------------------------------------------------
// Get final slip.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::BruneSlipFn::finalSlip(void)
{ // finalSlip
PYLITH_METHOD_BEGIN;
@@ -307,7 +307,7 @@
// ----------------------------------------------------------------------
// Get time when slip begins at each point.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::BruneSlipFn::slipTime(void)
{ // slipTime
PYLITH_METHOD_BEGIN;
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -27,7 +27,7 @@
// Include directives ---------------------------------------------------
#include "SlipTimeFn.hh"
-#include "pylith/topology/topologyfwd.hh" // USES Fields<Field<SubMesh> >
+#include "pylith/topology/topologyfwd.hh" // USES Fields<Field<Mesh> >
#include "spatialdata/spatialdb/spatialdbfwd.hh" // USES SpatialDB
@@ -84,7 +84,7 @@
* @param normalizer Nondimensionalization of scales.
* @param originTime Origin time for earthquake source.
*/
- void initialize(const topology::SubMesh& faultMesh,
+ void initialize(const topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime =0.0);
@@ -95,20 +95,20 @@
*
* @returns Slip vector as left-lateral/reverse/normal.
*/
- void slip(topology::Field<topology::SubMesh>* const slipField,
+ void slip(topology::Field<topology::Mesh>* const slipField,
const PylithScalar t);
/** Get final slip.
*
* @returns Final slip.
*/
- const topology::Field<topology::SubMesh>& finalSlip(void);
+ const topology::Field<topology::Mesh>& finalSlip(void);
/** Get time when slip begins at each point.
*
* @returns Time when slip begins.
*/
- const topology::Field<topology::SubMesh>& slipTime(void);
+ const topology::Field<topology::Mesh>& slipTime(void);
// NOT IMPLEMENTED //////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/CohesiveTopology.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/CohesiveTopology.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/CohesiveTopology.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -21,7 +21,7 @@
#include "CohesiveTopology.hh" // implementation of object methods
#include "TopologyOps.hh" // USES TopologyOps
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include <cassert> // USES assert()
@@ -40,7 +40,7 @@
// ----------------------------------------------------------------------
void
-pylith::faults::CohesiveTopology::createFault(topology::SubMesh* faultMesh,
+pylith::faults::CohesiveTopology::createFault(topology::Mesh* faultMesh,
PetscDM& faultBoundary,
const topology::Mesh& mesh,
PetscDMLabel groupField,
@@ -52,7 +52,7 @@
assert(groupField);
PetscErrorCode err;
- faultMesh->coordsys(mesh);
+ faultMesh->coordsys(mesh.coordsys());
PetscDM dmMesh = mesh.dmMesh();assert(dmMesh);
PetscInt dim, depth;
@@ -156,7 +156,7 @@
// ----------------------------------------------------------------------
void
pylith::faults::CohesiveTopology::create(topology::Mesh* mesh,
- const topology::SubMesh& faultMesh,
+ const topology::Mesh& faultMesh,
DM faultBoundary,
DMLabel groupField,
const int materialId,
@@ -631,7 +631,7 @@
void
pylith::faults::CohesiveTopology::createInterpolated(topology::Mesh* mesh,
- const topology::SubMesh& faultMesh,
+ const topology::Mesh& faultMesh,
PetscDM faultBoundary,
PetscDMLabel groupField,
const int materialId,
@@ -660,7 +660,7 @@
// ----------------------------------------------------------------------
// Form a parallel fault mesh using the cohesive cell information
void
-pylith::faults::CohesiveTopology::createFaultParallel(topology::SubMesh* faultMesh,
+pylith::faults::CohesiveTopology::createFaultParallel(topology::Mesh* faultMesh,
const topology::Mesh& mesh,
const int materialId,
const char* label,
@@ -671,7 +671,7 @@
assert(faultMesh);
PetscErrorCode err;
- faultMesh->coordsys(mesh);
+ faultMesh->coordsys(mesh.coordsys());
PetscDM dmMesh = mesh.dmMesh();assert(dmMesh);
PetscDM dmFaultMesh;
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/CohesiveTopology.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/CohesiveTopology.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/CohesiveTopology.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -51,7 +51,7 @@
* of the fault.
*/
static
- void createFault(topology::SubMesh* faultMesh,
+ void createFault(topology::Mesh* faultMesh,
DM& faultBoundary,
const topology::Mesh& mesh,
DMLabel groupField,
@@ -73,7 +73,7 @@
*/
static
void create(topology::Mesh* mesh,
- const topology::SubMesh& faultMesh,
+ const topology::Mesh& faultMesh,
DM faultBoundary,
DMLabel groupField,
const int materialId,
@@ -98,7 +98,7 @@
*/
static
void createInterpolated(topology::Mesh* mesh,
- const topology::SubMesh& faultMesh,
+ const topology::Mesh& faultMesh,
DM faultBoundary,
DMLabel groupField,
const int materialId,
@@ -117,7 +117,7 @@
* Lagrange multipliers that require extra vertices, false otherwise.
*/
static
- void createFaultParallel(topology::SubMesh* faultMesh,
+ void createFaultParallel(topology::Mesh* faultMesh,
const topology::Mesh& mesh,
const int materialId,
const char* label,
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,7 +20,7 @@
#include "ConstRateSlipFn.hh" // implementation of object methods
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/CoordsVisitor.hh" // USES CoordsVisitor
@@ -69,10 +69,9 @@
// ----------------------------------------------------------------------
// Initialize slip time function.
void
-pylith::faults::ConstRateSlipFn::initialize(
- const topology::SubMesh& faultMesh,
- const spatialdata::units::Nondimensional& normalizer,
- const PylithScalar originTime)
+pylith::faults::ConstRateSlipFn::initialize(const topology::Mesh& faultMesh,
+ const spatialdata::units::Nondimensional& normalizer,
+ const PylithScalar originTime)
{ // initialize
PYLITH_METHOD_BEGIN;
@@ -92,10 +91,10 @@
const PetscInt vStart = verticesStratum.begin();
const PetscInt vEnd = verticesStratum.end();
- delete _parameters; _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
+ delete _parameters; _parameters = new topology::Fields<topology::Field<topology::Mesh> >(faultMesh);
assert(_parameters);
_parameters->add("slip rate", "slip_rate");
- topology::Field<topology::SubMesh>& slipRate = _parameters->get("slip rate");
+ topology::Field<topology::Mesh>& slipRate = _parameters->get("slip rate");
slipRate.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim);
slipRate.allocate();
slipRate.scale(velocityScale);
@@ -104,7 +103,7 @@
PetscScalar* slipRateArray = slipRateVisitor.localArray();
_parameters->add("slip time", "slip_time");
- topology::Field<topology::SubMesh>& slipTime = _parameters->get("slip time");
+ topology::Field<topology::Mesh>& slipTime = _parameters->get("slip time");
slipTime.newSection(slipRate, 1);
slipTime.allocate();
slipTime.scale(timeScale);
@@ -203,7 +202,7 @@
// ----------------------------------------------------------------------
// Get slip on fault surface at time t.
void
-pylith::faults::ConstRateSlipFn::slip(topology::Field<topology::SubMesh>* slip,
+pylith::faults::ConstRateSlipFn::slip(topology::Field<topology::Mesh>* slip,
const PylithScalar t)
{ // slip
PYLITH_METHOD_BEGIN;
@@ -218,11 +217,11 @@
const PetscInt vEnd = verticesStratum.end();
// Get sections
- const topology::Field<topology::SubMesh>& slipRate = _parameters->get("slip rate");
+ const topology::Field<topology::Mesh>& slipRate = _parameters->get("slip rate");
topology::VecVisitorMesh slipRateVisitor(slipRate);
const PetscScalar* slipRateArray = slipRateVisitor.localArray();
- const topology::Field<topology::SubMesh>& slipTime = _parameters->get("slip time");
+ const topology::Field<topology::Mesh>& slipTime = _parameters->get("slip time");
topology::VecVisitorMesh slipTimeVisitor(slipTime);
const PetscScalar* slipTimeArray = slipTimeVisitor.localArray();
@@ -254,7 +253,7 @@
// ----------------------------------------------------------------------
// Get final slip.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::ConstRateSlipFn::finalSlip(void)
{ // finalSlip
PYLITH_METHOD_BEGIN;
@@ -265,7 +264,7 @@
// ----------------------------------------------------------------------
// Get time when slip begins at each point.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::ConstRateSlipFn::slipTime(void)
{ // slipTime
PYLITH_METHOD_BEGIN;
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -27,7 +27,7 @@
// Include directives ---------------------------------------------------
#include "SlipTimeFn.hh"
-#include "pylith/topology/topologyfwd.hh" // USES Fields<Field<SubMesh> >
+#include "pylith/topology/topologyfwd.hh" // USES Fields<Field<Mesh> >
#include "spatialdata/spatialdb/spatialdbfwd.hh" // USES SpatialDB
@@ -76,7 +76,7 @@
* @param normalizer Nondimensionalization of scales.
* @param originTime Origin time for earthquake source.
*/
- void initialize(const topology::SubMesh& faultMesh,
+ void initialize(const topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime =0.0);
@@ -87,20 +87,20 @@
*
* @returns Slip vector as left-lateral/reverse/normal.
*/
- void slip(topology::Field<topology::SubMesh>* const slipField,
+ void slip(topology::Field<topology::Mesh>* const slipField,
const PylithScalar t);
/** Get final slip.
*
* @returns Final slip.
*/
- const topology::Field<topology::SubMesh>& finalSlip(void);
+ const topology::Field<topology::Mesh>& finalSlip(void);
/** Get time when slip begins at each point.
*
* @returns Time when slip begins.
*/
- const topology::Field<topology::SubMesh>& slipTime(void);
+ const topology::Field<topology::Mesh>& slipTime(void);
// NOT IMPLEMENTED //////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/EqKinSrc.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/EqKinSrc.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/EqKinSrc.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -78,7 +78,7 @@
// ----------------------------------------------------------------------
// Initialize slip time function.
void
-pylith::faults::EqKinSrc::initialize(const topology::SubMesh& faultMesh,
+pylith::faults::EqKinSrc::initialize(const topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer)
{ // initialize
PYLITH_METHOD_BEGIN;
@@ -94,7 +94,7 @@
// ----------------------------------------------------------------------
// Get slip on fault surface at time t.
void
-pylith::faults::EqKinSrc::slip(topology::Field<topology::SubMesh>* const slipField,
+pylith::faults::EqKinSrc::slip(topology::Field<topology::Mesh>* const slipField,
const PylithScalar t)
{ // slip
PYLITH_METHOD_BEGIN;
@@ -107,7 +107,7 @@
// ----------------------------------------------------------------------
// Get final slip.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::EqKinSrc::finalSlip(void) const
{ // finalSlip
PYLITH_METHOD_BEGIN;
@@ -118,7 +118,7 @@
// ----------------------------------------------------------------------
// Get time when slip begins at each point.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::EqKinSrc::slipTime(void) const
{ // slipTime
PYLITH_METHOD_BEGIN;
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/EqKinSrc.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/EqKinSrc.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/EqKinSrc.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -28,7 +28,7 @@
// Include directives ---------------------------------------------------
#include "faultsfwd.hh" // forward declarations
-#include "pylith/topology/topologyfwd.hh" // USES Field<SubMesh>
+#include "pylith/topology/topologyfwd.hh" // USES Field<Mesh>
#include "spatialdata/units/unitsfwd.hh" // USES Nondimensional
@@ -78,7 +78,7 @@
* @param faultMesh Finite-element mesh of fault.
* @param normalizer Nondimensionalization of scales.
*/
- void initialize(const topology::SubMesh& faultMesh,
+ void initialize(const topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer);
/** Get slip on fault surface at time t.
@@ -86,20 +86,20 @@
* @param slipField Slip field over fault mesh.
* @param t Time t.
*/
- void slip(topology::Field<topology::SubMesh>* const slipField,
+ void slip(topology::Field<topology::Mesh>* const slipField,
const PylithScalar t);
/** Get final slip.
*
* @returns Final slip.
*/
- const topology::Field<topology::SubMesh>& finalSlip(void) const;
+ const topology::Field<topology::Mesh>& finalSlip(void) const;
/** Get time when slip begins at each point.
*
* @returns Time when slip begins.
*/
- const topology::Field<topology::SubMesh>& slipTime(void) const;
+ const topology::Field<topology::Mesh>& slipTime(void) const;
// NOT IMPLEMENTED ////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/Fault.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/Fault.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/Fault.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,7 +20,7 @@
#include "Fault.hh" // implementation of object methods
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
// ----------------------------------------------------------------------
// Default constructor.
@@ -48,7 +48,7 @@
// ----------------------------------------------------------------------
// Get mesh associated with fault fields.
-const pylith::topology::SubMesh&
+const pylith::topology::Mesh&
pylith::faults::Fault::faultMesh(void) const
{ // faultMesh
return *_faultMesh;
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/Fault.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/Fault.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/Fault.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -26,7 +26,7 @@
// Include directives ---------------------------------------------------
#include "faultsfwd.hh" // forward declarations
-#include "pylith/topology/topologyfwd.hh" // USES Field<SubMesh>, SubMesh
+#include "pylith/topology/topologyfwd.hh" // USES Field<Mesh>, Mesh
#include "pylith/utils/arrayfwd.hh" // USES scalar_array
#include "spatialdata/spatialdb/spatialdbfwd.hh" // USES SpatialDB
@@ -146,7 +146,7 @@
*
* @returns PETSc mesh object
*/
- const topology::SubMesh& faultMesh(void) const;
+ const topology::Mesh& faultMesh(void) const;
/** Get vertex field associated with integrator.
*
@@ -155,7 +155,7 @@
* @returns Vertex field.
*/
virtual
- const topology::Field<topology::SubMesh>&
+ const topology::Field<topology::Mesh>&
vertexField(const char* name,
const topology::SolutionFields* fields =0) = 0;
@@ -166,7 +166,7 @@
* @returns Cell field.
*/
virtual
- const topology::Field<topology::SubMesh>&
+ const topology::Field<topology::Mesh>&
cellField(const char* name,
const topology::SolutionFields* fields =0) = 0;
@@ -179,7 +179,7 @@
// PROTECTED MEMBERS ////////////////////////////////////////////////////
protected :
- topology::SubMesh* _faultMesh; ///< Mesh over fault surface
+ topology::Mesh* _faultMesh; ///< Mesh over fault surface
// PRIVATE MEMBERS ////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesive.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesive.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesive.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -51,7 +51,7 @@
PYLITH_METHOD_BEGIN;
Fault::deallocate();
- feassemble::Integrator<feassemble::Quadrature<topology::SubMesh> >::deallocate();
+ feassemble::Integrator<feassemble::Quadrature<topology::Mesh> >::deallocate();
delete _fields; _fields = 0;
@@ -115,8 +115,8 @@
assert(std::string("") != label());
try {
- topology::SubMesh faultMesh;
- DM faultBoundary = NULL;
+ topology::Mesh faultMesh;
+ PetscDM faultBoundary = NULL;
// Get group of vertices associated with fault
PetscDM dmMesh = mesh->dmMesh();assert(dmMesh);
@@ -135,11 +135,9 @@
throw std::runtime_error(msg.str());
} // if
err = DMPlexGetLabel(dmMesh, charlabel, &groupField);PYLITH_CHECK_ERROR(err);
- CohesiveTopology::createFault(&faultMesh, faultBoundary, *mesh, groupField,
- flipFault);
+ CohesiveTopology::createFault(&faultMesh, faultBoundary, *mesh, groupField, flipFault);
- CohesiveTopology::create(mesh, faultMesh, faultBoundary, groupField, id(),
- *firstFaultVertex, *firstLagrangeVertex, *firstFaultCell, useLagrangeConstraints());
+ CohesiveTopology::create(mesh, faultMesh, faultBoundary, groupField, id(), *firstFaultVertex, *firstLagrangeVertex, *firstFaultCell, useLagrangeConstraints());
err = DMDestroy(&faultBoundary);PYLITH_CHECK_ERROR(err);
} else {
const int faultDim = 2;
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesive.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesive.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesive.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -28,14 +28,14 @@
// Include directives ---------------------------------------------------
#include "Fault.hh" // ISA Fault
-#include "pylith/topology/SubMesh.hh" // ISA Integrator<Quadrature<SubMesh> >
+#include "pylith/topology/Mesh.hh" // ISA Integrator<Quadrature<Mesh> >
#include "pylith/feassemble/Quadrature.hh" // ISA Integrator<Quadrature>
#include "pylith/feassemble/Integrator.hh" // ISA Integrator
// FaultCohesive --------------------------------------------------------
/// Absract base class for fault surface implemented with cohesive cells.
class pylith::faults::FaultCohesive : public Fault,
- public feassemble::Integrator<feassemble::Quadrature<topology::SubMesh> >
+ public feassemble::Integrator<feassemble::Quadrature<topology::Mesh> >
{ // class FaultCohesive
friend class TestFaultCohesive; // unit testing
@@ -102,14 +102,14 @@
*
* @returns Fields associated with fault.
*/
- const topology::Fields<topology::Field<topology::SubMesh> >*
+ const topology::Fields<topology::Field<topology::Mesh> >*
fields(void) const;
// PROTECTED MEMBERS //////////////////////////////////////////////////
protected :
/// Fields for fault information.
- topology::Fields<topology::Field<topology::SubMesh> >* _fields;
+ topology::Fields<topology::Field<topology::Mesh> >* _fields;
bool _useLagrangeConstraints; ///< True if uses Lagrange multipliers.
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesive.icc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesive.icc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesive.icc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -29,7 +29,7 @@
// Get fields associated with fault.
inline
-const pylith::topology::Fields<pylith::topology::Field<pylith::topology::SubMesh> >*
+const pylith::topology::Fields<pylith::topology::Field<pylith::topology::Mesh> >*
pylith::faults::FaultCohesive::fields(void) const {
return _fields;
} // fields
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -26,7 +26,6 @@
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
#include "pylith/feassemble/CellGeometry.hh" // USES CellGeometry
#include "pylith/topology/Mesh.hh" // USES Mesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Jacobian.hh" // USES Jacobian
@@ -146,7 +145,7 @@
// Get initial tractions using a spatial database.
if (_tractPerturbation) {
- const topology::Field<topology::SubMesh>& orientation = _fields->get("orientation");
+ const topology::Field<topology::Mesh>& orientation = _fields->get("orientation");
_tractPerturbation->initialize(*_faultMesh, orientation, *_normalizer);
} // if
@@ -162,8 +161,8 @@
// Create field for relative velocity associated with Lagrange vertex k
_fields->add("relative velocity", "relative_velocity");
- topology::Field<topology::SubMesh>& velRel = _fields->get("relative velocity");
- topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
+ topology::Field<topology::Mesh>& velRel = _fields->get("relative velocity");
+ topology::Field<topology::Mesh>& dispRel = _fields->get("relative disp");
velRel.cloneSection(dispRel);
velRel.vectorFieldType(topology::FieldBase::VECTOR);
velRel.scale(_normalizer->lengthScale() / _normalizer->timeScale());
@@ -226,18 +225,18 @@
if (_tractPerturbation) {
_tractPerturbation->calculate(t);
- const topology::Fields<topology::Field<topology::SubMesh> >* params = _tractPerturbation->parameterFields();assert(params);
- const topology::Field<topology::SubMesh>& tractions = params->get("value");
+ const topology::Fields<topology::Field<topology::Mesh> >* params = _tractPerturbation->parameterFields();assert(params);
+ const topology::Field<topology::Mesh>& tractions = params->get("value");
tractionsVisitor = new topology::VecVisitorMesh(tractions);
tractionsArray = tractionsVisitor->localArray();
} // if
- topology::Field<topology::SubMesh>& area = _fields->get("area");
+ topology::Field<topology::Mesh>& area = _fields->get("area");
topology::VecVisitorMesh areaVisitor(area);
const PetscScalar* areaArray = areaVisitor.localArray();
- topology::Field<topology::SubMesh>& orientation = _fields->get("orientation");
+ topology::Field<topology::Mesh>& orientation = _fields->get("orientation");
topology::VecVisitorMesh orientationVisitor(orientation);
const PetscScalar* orientationArray = orientationVisitor.localArray();
@@ -388,16 +387,16 @@
const PetscScalar* dispTIncrArray = dispTIncrVisitor.localArray();
scalar_array slipVertex(spaceDim);
- topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
+ topology::Field<topology::Mesh>& dispRel = _fields->get("relative disp");
topology::VecVisitorMesh dispRelVisitor(dispRel);
const PetscScalar* dispRelArray = dispRelVisitor.localArray();
scalar_array slipRateVertex(spaceDim);
- topology::Field<topology::SubMesh>& velRel = _fields->get("relative velocity");
+ topology::Field<topology::Mesh>& velRel = _fields->get("relative velocity");
topology::VecVisitorMesh velRelVisitor(velRel);
const PetscScalar* velRelArray = velRelVisitor.localArray();
- topology::Field<topology::SubMesh>& orientation = _fields->get("orientation");
+ topology::Field<topology::Mesh>& orientation = _fields->get("orientation");
topology::VecVisitorMesh orientationVisitor(orientation);
const PetscScalar* orientationArray = orientationVisitor.localArray();
@@ -1320,7 +1319,7 @@
// ----------------------------------------------------------------------
// Get vertex field associated with integrator.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::FaultCohesiveDyn::vertexField(const char* name,
const topology::SolutionFields* fields)
{ // vertexField
@@ -1335,23 +1334,23 @@
const int cohesiveDim = _faultMesh->dimension();
const int spaceDim = _quadrature->spaceDim();
- const topology::Field<topology::SubMesh>& orientation = _fields->get("orientation");
+ const topology::Field<topology::Mesh>& orientation = _fields->get("orientation");
PylithScalar scale = 0.0;
int fiberDim = 0;
if (0 == strcasecmp("slip", name)) {
- const topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
+ const topology::Field<topology::Mesh>& dispRel = _fields->get("relative disp");
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
buffer.copy(dispRel);
buffer.label("slip");
FaultCohesiveLagrange::globalToFault(&buffer, orientation);
PYLITH_METHOD_RETURN(buffer);
} else if (0 == strcasecmp("slip_rate", name)) {
- const topology::Field<topology::SubMesh>& velRel = _fields->get("relative velocity");
+ const topology::Field<topology::Mesh>& velRel = _fields->get("relative velocity");
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
buffer.copy(velRel);
buffer.label("slip_rate");
FaultCohesiveLagrange::globalToFault(&buffer, orientation);
@@ -1361,7 +1360,7 @@
PetscSection orientationSection = _fields->get("orientation").petscSection();assert(orientationSection);
PetscVec orientationVec = _fields->get("orientation").localVector();assert(orientationVec);
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
buffer.copy(orientationSection, 0, PETSC_DETERMINE, orientationVec);
buffer.label("strike_dir");
buffer.scale(1.0);
@@ -1371,7 +1370,7 @@
PetscSection orientationSection = _fields->get("orientation").petscSection();assert(orientationSection);
PetscVec orientationVec = _fields->get("orientation").localVector();assert(orientationVec);
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
buffer.copy(orientationSection, 1, PETSC_DETERMINE, orientationVec);
buffer.label("dip_dir");
buffer.scale(1.0);
@@ -1381,7 +1380,7 @@
PetscSection orientationSection = _fields->get("orientation").petscSection();assert(orientationSection);
PetscVec orientationVec = _fields->get("orientation").localVector();assert(orientationVec);
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
buffer.copy(orientationSection, cohesiveDim, PETSC_DETERMINE, orientationVec);
buffer.label("normal_dir");
buffer.scale(1.0);
@@ -1391,7 +1390,7 @@
assert(fields);
const topology::Field<topology::Mesh>& dispT = fields->get("disp(t)");
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
_calcTractions(&buffer, dispT);
PYLITH_METHOD_RETURN(buffer);
@@ -1399,10 +1398,10 @@
PYLITH_METHOD_RETURN(_friction->getField(name));
} else if (_tractPerturbation && _tractPerturbation->hasParameter(name)) {
- const topology::Field<topology::SubMesh>& param = _tractPerturbation->vertexField(name, fields);
+ const topology::Field<topology::Mesh>& param = _tractPerturbation->vertexField(name, fields);
if (param.vectorFieldType() == topology::FieldBase::VECTOR) {
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
buffer.copy(param);
FaultCohesiveLagrange::globalToFault(&buffer, orientation);
PYLITH_METHOD_RETURN(buffer);
@@ -1422,7 +1421,7 @@
// Satisfy return values
assert(_fields);
- const topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ const topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
PYLITH_METHOD_RETURN(buffer);
} // vertexField
@@ -1430,7 +1429,7 @@
// ----------------------------------------------------------------------
// Compute tractions on fault surface using solution.
void
-pylith::faults::FaultCohesiveDyn::_calcTractions(topology::Field<topology::SubMesh>* tractions,
+pylith::faults::FaultCohesiveDyn::_calcTractions(topology::Field<topology::Mesh>* tractions,
const topology::Field<topology::Mesh>& dispT)
{ // _calcTractions
PYLITH_METHOD_BEGIN;
@@ -1452,7 +1451,7 @@
// Allocate buffer for tractions field (if necessary).
if (!tractions->petscSection()) {
- const topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
+ const topology::Field<topology::Mesh>& dispRel = _fields->get("relative disp");
tractions->cloneSection(dispRel);
} // if
const PylithScalar pressureScale = _normalizer->pressureScale();
@@ -1586,34 +1585,34 @@
// Setup fields involved in sensitivity solve.
if (!_fields->hasField("sensitivity solution")) {
_fields->add("sensitivity solution", "sensitivity_soln");
- topology::Field<topology::SubMesh>& solution = _fields->get("sensitivity solution");
- const topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
+ topology::Field<topology::Mesh>& solution = _fields->get("sensitivity solution");
+ const topology::Field<topology::Mesh>& dispRel = _fields->get("relative disp");
solution.cloneSection(dispRel);
solution.createScatter(solution.mesh());
} // if
- const topology::Field<topology::SubMesh>& solution = _fields->get("sensitivity solution");
+ const topology::Field<topology::Mesh>& solution = _fields->get("sensitivity solution");
if (!_fields->hasField("sensitivity residual")) {
_fields->add("sensitivity residual", "sensitivity_residual");
- topology::Field<topology::SubMesh>& residual = _fields->get("sensitivity residual");
+ topology::Field<topology::Mesh>& residual = _fields->get("sensitivity residual");
residual.cloneSection(solution);
residual.createScatter(solution.mesh());
} // if
if (!_fields->hasField("sensitivity relative disp")) {
_fields->add("sensitivity relative disp", "sensitivity_relative_disp");
- topology::Field<topology::SubMesh>& dispRel = _fields->get("sensitivity relative disp");
+ topology::Field<topology::Mesh>& dispRel = _fields->get("sensitivity relative disp");
dispRel.cloneSection(solution);
} // if
- topology::Field<topology::SubMesh>& dispRel = _fields->get("sensitivity relative disp");
+ topology::Field<topology::Mesh>& dispRel = _fields->get("sensitivity relative disp");
dispRel.zero();
if (!_fields->hasField("sensitivity dLagrange")) {
_fields->add("sensitivity dLagrange", "sensitivity_dlagrange");
- topology::Field<topology::SubMesh>& dLagrange = _fields->get("sensitivity dLagrange");
+ topology::Field<topology::Mesh>& dLagrange = _fields->get("sensitivity dLagrange");
dLagrange.cloneSection(solution);
} // if
- topology::Field<topology::SubMesh>& dLagrange = _fields->get("sensitivity dLagrange");
+ topology::Field<topology::Mesh>& dLagrange = _fields->get("sensitivity dLagrange");
dLagrange.zero();
// Setup Jacobian sparse matrix for sensitivity solve.
@@ -1822,7 +1821,7 @@
topology::VecVisitorMesh dLagrangeVisitor(_fields->get("sensitivity dLagrange"));
scalar_array residualCell(numBasis*spaceDim);
- topology::Field<topology::SubMesh>& residual = _fields->get("sensitivity residual");
+ topology::Field<topology::Mesh>& residual = _fields->get("sensitivity residual");
topology::VecVisitorMesh residualVisitor(residual);
residual.zero();
@@ -1890,8 +1889,8 @@
assert(_jacobian);
assert(_ksp);
- topology::Field<topology::SubMesh>& residual = _fields->get("sensitivity residual");
- topology::Field<topology::SubMesh>& solution = _fields->get("sensitivity solution");
+ topology::Field<topology::Mesh>& residual = _fields->get("sensitivity residual");
+ topology::Field<topology::Mesh>& solution = _fields->get("sensitivity solution");
// Assemble residual over processors.
residual.complete();
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -145,7 +145,7 @@
* @param fields Solution fields.
* @returns Vertex field.
*/
- const topology::Field<topology::SubMesh>&
+ const topology::Field<topology::Mesh>&
vertexField(const char* name,
const topology::SolutionFields* fields =0);
@@ -157,7 +157,7 @@
* @param tractions Field for tractions.
* @param solution Solution over domain
*/
- void _calcTractions(topology::Field<topology::SubMesh>* tractions,
+ void _calcTractions(topology::Field<topology::Mesh>* tractions,
const topology::Field<topology::Mesh>& solution);
/** Update relative displacement and velocity associated with
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveImpulses.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveImpulses.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveImpulses.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -25,7 +25,6 @@
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
#include "pylith/feassemble/CellGeometry.hh" // USES CellGeometry
#include "pylith/topology/Mesh.hh" // USES Mesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Jacobian.hh" // USES Jacobian
@@ -166,14 +165,14 @@
const int setupEvent = _logger->eventId("FaIR setup");
_logger->eventBegin(setupEvent);
- topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
+ topology::Field<topology::Mesh>& dispRel = _fields->get("relative disp");
dispRel.zero();
// Set impulse corresponding to current time.
_setRelativeDisp(dispRel, int(t+0.1));
// Transform slip from local (fault) coordinate system to relative
// displacement field in global coordinate system
- const topology::Field<topology::SubMesh>& orientation = _fields->get("orientation");
+ const topology::Field<topology::Mesh>& orientation = _fields->get("orientation");
FaultCohesiveLagrange::faultToGlobal(&dispRel, orientation);
_logger->eventEnd(setupEvent);
@@ -185,7 +184,7 @@
// ----------------------------------------------------------------------
// Get vertex field associated with integrator.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::FaultCohesiveImpulses::vertexField(const char* name,
const topology::SolutionFields* fields)
{ // vertexField
@@ -199,14 +198,14 @@
const int cohesiveDim = _faultMesh->dimension();
const int spaceDim = _quadrature->spaceDim();
- const topology::Field<topology::SubMesh>& orientation = _fields->get("orientation");
+ const topology::Field<topology::Mesh>& orientation = _fields->get("orientation");
PylithScalar scale = 0.0;
int fiberDim = 0;
if (0 == strcasecmp("slip", name)) {
- const topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
+ const topology::Field<topology::Mesh>& dispRel = _fields->get("relative disp");
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
buffer.copy(dispRel);
buffer.label("slip");
FaultCohesiveLagrange::globalToFault(&buffer, orientation);
@@ -216,7 +215,7 @@
PetscSection orientationSection = _fields->get("orientation").petscSection();assert(orientationSection);
PetscVec orientationVec = _fields->get("orientation").localVector();assert(orientationVec);
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
buffer.copy(orientationSection, 0, PETSC_DETERMINE, orientationVec);
buffer.label("strike_dir");
buffer.scale(1.0);
@@ -227,7 +226,7 @@
PetscVec orientationVec = _fields->get("orientation").localVector();assert(orientationVec);
assert(orientationSection);assert(orientationVec);
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
buffer.copy(orientationSection, 1, PETSC_DETERMINE, orientationVec);
buffer.label("dip_dir");
buffer.scale(1.0);
@@ -238,25 +237,25 @@
PetscVec orientationVec = _fields->get("orientation").localVector();assert(orientationVec);
assert(orientationSection);assert(orientationVec);
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
buffer.copy(orientationSection, cohesiveDim, PETSC_DETERMINE, orientationVec);
buffer.label("normal_dir");
buffer.scale(1.0);
PYLITH_METHOD_RETURN(buffer);
} else if (0 == strcasecmp("impulse_amplitude", name)) {
- topology::Field<topology::SubMesh>& amplitude = _fields->get("impulse amplitude");
+ topology::Field<topology::Mesh>& amplitude = _fields->get("impulse amplitude");
PYLITH_METHOD_RETURN(amplitude);
} else if (0 == strcasecmp("area", name)) {
- topology::Field<topology::SubMesh>& area = _fields->get("area");
+ topology::Field<topology::Mesh>& area = _fields->get("area");
PYLITH_METHOD_RETURN(area);
} else if (0 == strcasecmp("traction_change", name)) {
assert(fields);
const topology::Field<topology::Mesh>& dispT = fields->get("disp(t)");
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
_calcTractionsChange(&buffer, dispT);
PYLITH_METHOD_RETURN(buffer);
@@ -273,7 +272,7 @@
// Satisfy return values
assert(_fields);
- const topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ const topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
PYLITH_METHOD_RETURN(buffer);
} // vertexField
@@ -297,8 +296,8 @@
// Create section to hold amplitudes of impulses.
_fields->add("impulse amplitude", "impulse_amplitude");
- topology::Field<topology::SubMesh>& amplitude = _fields->get("impulse amplitude");
- topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
+ topology::Field<topology::Mesh>& amplitude = _fields->get("impulse amplitude");
+ topology::Field<topology::Mesh>& dispRel = _fields->get("relative disp");
const int fiberDim = 1;
amplitude.newSection(dispRel, fiberDim);
amplitude.allocate();
@@ -431,7 +430,7 @@
// ----------------------------------------------------------------------
// Set relative displacemet associated with impulse.
void
-pylith::faults::FaultCohesiveImpulses::_setRelativeDisp(const topology::Field<topology::SubMesh>& dispRel,
+pylith::faults::FaultCohesiveImpulses::_setRelativeDisp(const topology::Field<topology::Mesh>& dispRel,
const int impulse)
{ // _setRelativeDisp
PYLITH_METHOD_BEGIN;
@@ -445,7 +444,7 @@
const spatialdata::geocoords::CoordSys* cs = _faultMesh->coordsys();assert(cs);
const int spaceDim = cs->spaceDim();
- topology::Field<topology::SubMesh>& amplitude = _fields->get("impulse amplitude");
+ topology::Field<topology::Mesh>& amplitude = _fields->get("impulse amplitude");
topology::VecVisitorMesh amplitudeVisitor(amplitude);
const PetscScalar* amplitudeArray = amplitudeVisitor.localArray();
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveImpulses.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveImpulses.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveImpulses.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -116,7 +116,7 @@
* @param fields Solution fields.
* @returns Vertex field.
*/
- const topology::Field<topology::SubMesh>&
+ const topology::Field<topology::Mesh>&
vertexField(const char* name,
const topology::SolutionFields* fields =0);
@@ -137,7 +137,7 @@
* @param dispRel Relative displacement field.
* @parm impulse Index of impulse.
*/
- void _setRelativeDisp(const topology::Field<topology::SubMesh>& dispRel,
+ void _setRelativeDisp(const topology::Field<topology::Mesh>& dispRel,
const int impulse);
// PRIVATE TYPEDEFS ///////////////////////////////////////////////////
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveKin.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveKin.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveKin.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -26,7 +26,6 @@
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
#include "pylith/feassemble/CellGeometry.hh" // USES CellGeometry
#include "pylith/topology/Mesh.hh" // USES Mesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Jacobian.hh" // USES Jacobian
@@ -132,7 +131,7 @@
const int setupEvent = _logger->eventId("FaIR setup");
_logger->eventBegin(setupEvent);
- topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
+ topology::Field<topology::Mesh>& dispRel = _fields->get("relative disp");
dispRel.zero();
// Compute slip field at current time step
const srcs_type::const_iterator srcsEnd = _eqSrcs.end();
@@ -145,7 +144,7 @@
// Transform slip from local (fault) coordinate system to relative
// displacement field in global coordinate system
- const topology::Field<topology::SubMesh>& orientation = _fields->get("orientation");
+ const topology::Field<topology::Mesh>& orientation = _fields->get("orientation");
FaultCohesiveLagrange::faultToGlobal(&dispRel, orientation);
_logger->eventEnd(setupEvent);
@@ -158,7 +157,7 @@
// ----------------------------------------------------------------------
// Get vertex field associated with integrator.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::FaultCohesiveKin::vertexField(const char* name,
const topology::SolutionFields* fields)
{ // vertexField
@@ -172,7 +171,7 @@
const int cohesiveDim = _faultMesh->dimension();
const int spaceDim = _quadrature->spaceDim();
- const topology::Field<topology::SubMesh>& orientation = _fields->get("orientation");
+ const topology::Field<topology::Mesh>& orientation = _fields->get("orientation");
const int slipStrLen = strlen("final_slip");
const int timeStrLen = strlen("slip_time");
@@ -180,9 +179,9 @@
PylithScalar scale = 0.0;
int fiberDim = 0;
if (0 == strcasecmp("slip", name)) {
- const topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
+ const topology::Field<topology::Mesh>& dispRel = _fields->get("relative disp");
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
buffer.copy(dispRel);
buffer.label("slip");
FaultCohesiveLagrange::globalToFault(&buffer, orientation);
@@ -192,7 +191,7 @@
PetscSection orientationSection = _fields->get("orientation").petscSection();assert(orientationSection);
PetscVec orientationVec = _fields->get("orientation").localVector();assert(orientationVec);
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
buffer.copy(orientationSection, 0, PETSC_DETERMINE, orientationVec);
buffer.label("strike_dir");
buffer.scale(1.0);
@@ -203,7 +202,7 @@
PetscVec orientationVec = _fields->get("orientation").localVector();assert(orientationVec);
assert(orientationSection);assert(orientationVec);
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
buffer.copy(orientationSection, 1, PETSC_DETERMINE, orientationVec);
buffer.label("dip_dir");
buffer.scale(1.0);
@@ -214,7 +213,7 @@
PetscVec orientationVec = _fields->get("orientation").localVector();assert(orientationVec);
assert(orientationSection);assert(orientationVec);
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
buffer.copy(orientationSection, cohesiveDim, PETSC_DETERMINE, orientationVec);
buffer.label("normal_dir");
buffer.scale(1.0);
@@ -228,7 +227,7 @@
// Need to append name of rupture to final slip label. Because
// Field is const, we use a buffer.
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
buffer.copy(s_iter->second->finalSlip());
assert(value.length() > 0);
const std::string& label = (_eqSrcs.size() > 1) ?
@@ -245,7 +244,7 @@
// Need to append name of rupture to final slip label. Because
// Field is const, we use a buffer.
_allocateBufferScalarField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (scalar)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (scalar)");
buffer.copy(s_iter->second->slipTime());
assert(value.length() > 0);
const std::string& label = (_eqSrcs.size() > 1) ?
@@ -257,7 +256,7 @@
assert(fields);
const topology::Field<topology::Mesh>& dispT = fields->get("disp(t)");
_allocateBufferVectorField();
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
_calcTractionsChange(&buffer, dispT);
PYLITH_METHOD_RETURN(buffer);
@@ -274,7 +273,7 @@
// Satisfy return values
assert(_fields);
- const topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ const topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
PYLITH_METHOD_RETURN(buffer);
} // vertexField
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveKin.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveKin.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveKin.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -92,7 +92,7 @@
* @param fields Solution fields.
* @returns Vertex field.
*/
- const topology::Field<topology::SubMesh>&
+ const topology::Field<topology::Mesh>&
vertexField(const char* name,
const topology::SolutionFields* fields =0);
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -25,7 +25,6 @@
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
#include "pylith/feassemble/CellGeometry.hh" // USES CellGeometry
#include "pylith/topology/Mesh.hh" // USES Mesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Jacobian.hh" // USES Jacobian
@@ -91,16 +90,17 @@
const spatialdata::geocoords::CoordSys* cs = mesh.coordsys();assert(cs);
- delete _faultMesh; _faultMesh = new topology::SubMesh();assert(_faultMesh);
+ const bool isSubMesh = true;
+ delete _faultMesh; _faultMesh = new topology::Mesh(isSubMesh);assert(_faultMesh);
CohesiveTopology::createFaultParallel(_faultMesh, mesh, id(), label(), _useLagrangeConstraints);
_initializeCohesiveInfo(mesh);
delete _fields;
- _fields = new topology::Fields<topology::Field<topology::SubMesh> >(*_faultMesh);
+ _fields = new topology::Fields<topology::Field<topology::Mesh> >(*_faultMesh);
// Allocate dispRel field
_fields->add("relative disp", "relative_disp");
- topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
+ topology::Field<topology::Mesh>& dispRel = _fields->get("relative disp");
dispRel.newSection(topology::FieldBase::VERTICES_FIELD, cs->spaceDim());
dispRel.allocate();
dispRel.vectorFieldType(topology::FieldBase::VECTOR);
@@ -210,11 +210,11 @@
topology::VecVisitorMesh dispTIncrVisitor(dispTIncr);
PetscScalar* dispTIncrArray = dispTIncrVisitor.localArray();
- topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
+ topology::Field<topology::Mesh>& dispRel = _fields->get("relative disp");
topology::VecVisitorMesh dispRelVisitor(dispRel);
PetscScalar* dispRelArray = dispRelVisitor.localArray();
- topology::Field<topology::SubMesh>& area = _fields->get("area");
+ topology::Field<topology::Mesh>& area = _fields->get("area");
topology::VecVisitorMesh areaVisitor(area);
PetscScalar* areaArray = areaVisitor.localArray();
@@ -337,7 +337,7 @@
const int spaceDim = _quadrature->spaceDim();
// Get fields.
- topology::Field<topology::SubMesh>& area = _fields->get("area");
+ topology::Field<topology::Mesh>& area = _fields->get("area");
topology::VecVisitorMesh areaVisitor(area);
const PetscScalar* areaArray = areaVisitor.localArray();
@@ -600,7 +600,7 @@
} // for
// Get fields
- topology::Field<topology::SubMesh>& area = _fields->get("area");
+ topology::Field<topology::Mesh>& area = _fields->get("area");
topology::VecVisitorMesh areaVisitor(area);
const PetscScalar* areaArray = areaVisitor.localArray();
@@ -752,7 +752,7 @@
const int spaceDim = _quadrature->spaceDim();
// Get fields
- topology::Field<topology::SubMesh>& area = _fields->get("area");
+ topology::Field<topology::Mesh>& area = _fields->get("area");
topology::VecVisitorMesh areaVisitor(area);
const PetscScalar* areaArray = areaVisitor.localArray();
@@ -1141,8 +1141,8 @@
// Transform field from local (fault) coordinate system to
// global coordinate system.
void
-pylith::faults::FaultCohesiveLagrange::faultToGlobal(topology::Field<topology::SubMesh>* field,
- const topology::Field<topology::SubMesh>& faultOrientation)
+pylith::faults::FaultCohesiveLagrange::faultToGlobal(topology::Field<topology::Mesh>* field,
+ const topology::Field<topology::Mesh>& faultOrientation)
{ // faultToGlobal
PYLITH_METHOD_BEGIN;
@@ -1196,8 +1196,8 @@
// Transform field from global coordinate system to local (fault)
// coordinate system.
void
-pylith::faults::FaultCohesiveLagrange::globalToFault(topology::Field<topology::SubMesh>* field,
- const topology::Field<topology::SubMesh>& faultOrientation)
+pylith::faults::FaultCohesiveLagrange::globalToFault(topology::Field<topology::Mesh>* field,
+ const topology::Field<topology::Mesh>& faultOrientation)
{ // globalToFault
PYLITH_METHOD_BEGIN;
@@ -1291,8 +1291,8 @@
// Allocate orientation field.
scalar_array orientationVertex(orientationSize);
_fields->add("orientation", "orientation");
- topology::Field<topology::SubMesh>& orientation = _fields->get("orientation");
- const topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
+ topology::Field<topology::Mesh>& orientation = _fields->get("orientation");
+ const topology::Field<topology::Mesh>& dispRel = _fields->get("relative disp");
if (spaceDim > 1) orientation.addField("strike_dir", spaceDim);
if (spaceDim > 2) orientation.addField("dip_dir", spaceDim);
orientation.addField("normal_dir", spaceDim);
@@ -1549,8 +1549,8 @@
// Allocate area field.
_fields->add("area", "area");
- topology::Field<topology::SubMesh>& area = _fields->get("area");
- const topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
+ topology::Field<topology::Mesh>& area = _fields->get("area");
+ const topology::Field<topology::Mesh>& dispRel = _fields->get("relative disp");
area.newSection(dispRel, 1);
area.allocate();
area.vectorFieldType(topology::FieldBase::SCALAR);
@@ -1603,7 +1603,7 @@
// ----------------------------------------------------------------------
// Compute change in tractions on fault surface using solution.
void
-pylith::faults::FaultCohesiveLagrange::_calcTractionsChange(topology::Field<topology::SubMesh>* tractions,
+pylith::faults::FaultCohesiveLagrange::_calcTractionsChange(topology::Field<topology::Mesh>* tractions,
const topology::Field<topology::Mesh>& dispT)
{ // _calcTractionsChange
PYLITH_METHOD_BEGIN;
@@ -1623,13 +1623,13 @@
topology::VecVisitorMesh dispTVisitor(dispT);
const PetscScalar* dispTArray = dispTVisitor.localArray();
- topology::Field<topology::SubMesh>& orientation = _fields->get("orientation");
+ topology::Field<topology::Mesh>& orientation = _fields->get("orientation");
topology::VecVisitorMesh orientationVisitor(orientation);
const PetscScalar* orientationArray = orientationVisitor.localArray();
// Allocate buffer for tractions field (if necessary).
if (!tractions->petscSection()) {
- const topology::Field<topology::SubMesh>& dispRel = _fields->get("relative disp");
+ const topology::Field<topology::Mesh>& dispRel = _fields->get("relative disp");
tractions->cloneSection(dispRel);
} // if
tractions->zero();
@@ -1685,8 +1685,8 @@
// displacement field.
assert(_faultMesh);
_fields->add("buffer (vector)", "buffer");
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
- const topology::Field<topology::SubMesh>& dispRel =
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
+ const topology::Field<topology::Mesh>& dispRel =
_fields->get("relative disp");
buffer.cloneSection(dispRel);
buffer.zero();
@@ -1709,7 +1709,7 @@
// Create vector field; use same shape/chart as area field.
assert(_faultMesh);
_fields->add("buffer (scalar)", "buffer");
- topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (scalar)");
+ topology::Field<topology::Mesh>& buffer = _fields->get("buffer (scalar)");
buffer.newSection(topology::FieldBase::VERTICES_FIELD, 1);
buffer.allocate();
buffer.vectorFieldType(topology::FieldBase::SCALAR);
@@ -1820,7 +1820,7 @@
// ----------------------------------------------------------------------
// Get cell field associated with integrator.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::FaultCohesiveLagrange::cellField(const char* name,
const topology::SolutionFields* fields)
{ // cellField
@@ -1835,7 +1835,7 @@
const int fiberDim = 1;
_fields->add("partition", "partition", pylith::topology::FieldBase::CELLS_FIELD, fiberDim);
- topology::Field<topology::SubMesh>& partition = _fields->get("partition");
+ topology::Field<topology::Mesh>& partition = _fields->get("partition");
partition.allocate();
topology::VecVisitorMesh partitionVisitor(partition);
PetscScalar* partitionArray = partitionVisitor.localArray();
@@ -1859,7 +1859,7 @@
// Satisfy return values
assert(_fields);
- const topology::Field<topology::SubMesh>& buffer = _fields->get("buffer (vector)");
+ const topology::Field<topology::Mesh>& buffer = _fields->get("buffer (vector)");
PYLITH_METHOD_RETURN(buffer);
} // cellField
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -202,7 +202,7 @@
* @param fields Solution fields.
* @returns Cell field.
*/
- const topology::Field<topology::SubMesh>&
+ const topology::Field<topology::Mesh>&
cellField(const char* name,
const topology::SolutionFields* fields =0);
@@ -213,8 +213,8 @@
* @param faultOrientation Orientation of vertices on fault.
*/
static
- void faultToGlobal(topology::Field<topology::SubMesh>* field,
- const topology::Field<topology::SubMesh>& faultOrientation);
+ void faultToGlobal(topology::Field<topology::Mesh>* field,
+ const topology::Field<topology::Mesh>& faultOrientation);
/** Transform field from global coordinate system to local (fault)
* coordinate system.
@@ -223,8 +223,8 @@
* @param faultOrientation Orientation of vertices on fault.
*/
static
- void globalToFault(topology::Field<topology::SubMesh>* field,
- const topology::Field<topology::SubMesh>& faultOrientation);
+ void globalToFault(topology::Field<topology::Mesh>* field,
+ const topology::Field<topology::Mesh>& faultOrientation);
// PROTECTED STRUCTS //////////////////////////////////////////////////
protected :
@@ -253,7 +253,7 @@
* @param tractions Field for tractions.
* @param solution Solution over domain
*/
- void _calcTractionsChange(topology::Field<topology::SubMesh>* tractions,
+ void _calcTractionsChange(topology::Field<topology::Mesh>* tractions,
const topology::Field<topology::Mesh>& solution);
/// Allocate buffer for vector field.
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveTract.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveTract.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveTract.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -66,13 +66,13 @@
assert(upDir);
assert(_quadrature);
- delete _faultMesh; _faultMesh = new topology::SubMesh();
+ delete _faultMesh; _faultMesh = new topology::Mesh();
CohesiveTopology::createFaultParallel(_faultMesh, mesh, id(), label(), useLagrangeConstraints());
// Reset fields.
delete _fields;
_fields =
- new topology::Fields<topology::Field<topology::SubMesh> >(*_faultMesh);
+ new topology::Fields<topology::Field<topology::Mesh> >(*_faultMesh);
// Initialize quadrature geometry.
_quadrature->initializeGeometry();
@@ -156,7 +156,7 @@
// ----------------------------------------------------------------------
// Get vertex field associated with integrator.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::FaultCohesiveTract::vertexField(const char* name,
const topology::SolutionFields* fields)
{ // vertexField
@@ -165,7 +165,7 @@
// ----------------------------------------------------------------------
// Get cell field associated with integrator.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::FaultCohesiveTract::cellField(const char* name,
const topology::SolutionFields* fields)
{ // cellField
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveTract.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveTract.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveTract.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -96,7 +96,7 @@
*
* @returns Vertex field.
*/
- const topology::Field<topology::SubMesh>&
+ const topology::Field<topology::Mesh>&
vertexField(const char* name,
const topology::SolutionFields* fields =0);
@@ -107,7 +107,7 @@
*
* @returns Cell field.
*/
- const topology::Field<topology::SubMesh>&
+ const topology::Field<topology::Mesh>&
cellField(const char* name,
const topology::SolutionFields* fields =0);
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,7 +20,7 @@
#include "LiuCosSlipFn.hh" // implementation of object methods
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/CoordsVisitor.hh" // USES CoordsVisitor
@@ -72,7 +72,7 @@
// ----------------------------------------------------------------------
// Initialize slip time function.
void
-pylith::faults::LiuCosSlipFn::initialize(const topology::SubMesh& faultMesh,
+pylith::faults::LiuCosSlipFn::initialize(const topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime)
{ // initialize
@@ -94,10 +94,10 @@
const PetscInt vStart = verticesStratum.begin();
const PetscInt vEnd = verticesStratum.end();
- delete _parameters; _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
+ delete _parameters; _parameters = new topology::Fields<topology::Field<topology::Mesh> >(faultMesh);
assert(_parameters);
_parameters->add("final slip", "final_slip");
- topology::Field<topology::SubMesh>& finalSlip = _parameters->get("final slip");
+ topology::Field<topology::Mesh>& finalSlip = _parameters->get("final slip");
finalSlip.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim);
finalSlip.allocate();
finalSlip.scale(lengthScale);
@@ -106,7 +106,7 @@
PetscScalar* finalSlipArray = finalSlipVisitor.localArray();
_parameters->add("slip time", "slip_time");
- topology::Field<topology::SubMesh>& slipTime = _parameters->get("slip time");
+ topology::Field<topology::Mesh>& slipTime = _parameters->get("slip time");
slipTime.newSection(finalSlip, 1);
slipTime.allocate();
slipTime.scale(timeScale);
@@ -115,7 +115,7 @@
PetscScalar* slipTimeArray = slipTimeVisitor.localArray();
_parameters->add("rise time", "rise_time");
- topology::Field<topology::SubMesh>& riseTime = _parameters->get("rise time");
+ topology::Field<topology::Mesh>& riseTime = _parameters->get("rise time");
riseTime.newSection(finalSlip, 1);
riseTime.allocate();
riseTime.scale(timeScale);
@@ -234,7 +234,7 @@
// ----------------------------------------------------------------------
// Get slip on fault surface at time t.
void
-pylith::faults::LiuCosSlipFn::slip(topology::Field<topology::SubMesh>* slip,
+pylith::faults::LiuCosSlipFn::slip(topology::Field<topology::Mesh>* slip,
const PylithScalar t)
{ // slip
PYLITH_METHOD_BEGIN;
@@ -249,15 +249,15 @@
const PetscInt vEnd = verticesStratum.end();
// Get sections
- const topology::Field<topology::SubMesh>& finalSlip = _parameters->get("final slip");
+ const topology::Field<topology::Mesh>& finalSlip = _parameters->get("final slip");
topology::VecVisitorMesh finalSlipVisitor(finalSlip);
const PetscScalar* finalSlipArray = finalSlipVisitor.localArray();
- const topology::Field<topology::SubMesh>& slipTime = _parameters->get("slip time");
+ const topology::Field<topology::Mesh>& slipTime = _parameters->get("slip time");
topology::VecVisitorMesh slipTimeVisitor(slipTime);
const PetscScalar* slipTimeArray = slipTimeVisitor.localArray();
- const topology::Field<topology::SubMesh>& riseTime = _parameters->get("rise time");
+ const topology::Field<topology::Mesh>& riseTime = _parameters->get("rise time");
topology::VecVisitorMesh riseTimeVisitor(riseTime);
const PetscScalar* riseTimeArray = riseTimeVisitor.localArray();
@@ -297,7 +297,7 @@
// ----------------------------------------------------------------------
// Get final slip.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::LiuCosSlipFn::finalSlip(void)
{ // finalSlip
PYLITH_METHOD_BEGIN;
@@ -307,7 +307,7 @@
// ----------------------------------------------------------------------
// Get time when slip begins at each point.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::LiuCosSlipFn::slipTime(void)
{ // slipTime
PYLITH_METHOD_BEGIN;
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -27,7 +27,7 @@
// Include directives ---------------------------------------------------
#include "SlipTimeFn.hh"
-#include "pylith/topology/topologyfwd.hh" // USES Fields<Field<SubMesh> >
+#include "pylith/topology/topologyfwd.hh" // USES Fields<Field<Mesh> >
#include "spatialdata/spatialdb/spatialdbfwd.hh" // USES SpatialDB
@@ -84,7 +84,7 @@
* @param normalizer Nondimensionalization of scales.
* @param originTime Origin time for earthquake source.
*/
- void initialize(const topology::SubMesh& faultMesh,
+ void initialize(const topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime =0.0);
@@ -95,20 +95,20 @@
*
* @returns Slip vector as left-lateral/reverse/normal.
*/
- void slip(topology::Field<topology::SubMesh>* const slipField,
+ void slip(topology::Field<topology::Mesh>* const slipField,
const PylithScalar t);
/** Get final slip.
*
* @returns Final slip.
*/
- const topology::Field<topology::SubMesh>& finalSlip(void);
+ const topology::Field<topology::Mesh>& finalSlip(void);
/** Get time when slip begins at each point.
*
* @returns Time when slip begins.
*/
- const topology::Field<topology::SubMesh>& slipTime(void);
+ const topology::Field<topology::Mesh>& slipTime(void);
// NOT IMPLEMENTED //////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/SlipTimeFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/SlipTimeFn.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/SlipTimeFn.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,7 +20,7 @@
#include "SlipTimeFn.hh" // implementation of object methods
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Field.hh" // USES Field
@@ -52,7 +52,7 @@
// ----------------------------------------------------------------------
// Get parameter fields.
-const pylith::topology::Fields<pylith::topology::Field<pylith::topology::SubMesh> >*
+const pylith::topology::Fields<pylith::topology::Field<pylith::topology::Mesh> >*
pylith::faults::SlipTimeFn::parameterFields(void) const
{ // parameterFields
return _parameters;
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/SlipTimeFn.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/SlipTimeFn.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/SlipTimeFn.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -27,7 +27,7 @@
// Include directives ---------------------------------------------------
#include "faultsfwd.hh" // forward declarations
-#include "pylith/topology/topologyfwd.hh" // USES Fields<SubMesh>
+#include "pylith/topology/topologyfwd.hh" // USES Fields<Mesh>
#include "spatialdata/units/unitsfwd.hh" // USES Nondimensional
@@ -62,7 +62,7 @@
* @param originTime Origin time for earthquake source.
*/
virtual
- void initialize(const topology::SubMesh& faultMesh,
+ void initialize(const topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime =0.0) = 0;
@@ -72,7 +72,7 @@
* @param t Time t.
*/
virtual
- void slip(topology::Field<topology::SubMesh>* const slipField,
+ void slip(topology::Field<topology::Mesh>* const slipField,
const PylithScalar t) = 0;
/** Get final slip.
@@ -80,27 +80,27 @@
* @returns Final slip.
*/
virtual
- const topology::Field<topology::SubMesh>& finalSlip(void) = 0;
+ const topology::Field<topology::Mesh>& finalSlip(void) = 0;
/** Get time when slip begins at each point.
*
* @returns Time when slip begins.
*/
virtual
- const topology::Field<topology::SubMesh>& slipTime(void) = 0;
+ const topology::Field<topology::Mesh>& slipTime(void) = 0;
/** Get parameter fields.
*
* @returns Parameter fields.
*/
- const topology::Fields<topology::Field<topology::SubMesh> >*
+ const topology::Fields<topology::Field<topology::Mesh> >*
parameterFields(void) const;
// PROTECTED MEMBERS ////////////////////////////////////////////////////
protected :
/// Parameters for slip time function.
- topology::Fields<topology::Field<topology::SubMesh> >* _parameters;
+ topology::Fields<topology::Field<topology::Mesh> >* _parameters;
// NOT IMPLEMENTED ////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,7 +20,7 @@
#include "StepSlipFn.hh" // implementation of object methods
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/CoordsVisitor.hh" // USES CoordsVisitor
@@ -69,7 +69,7 @@
// ----------------------------------------------------------------------
// Initialize slip time function.
void
-pylith::faults::StepSlipFn::initialize(const topology::SubMesh& faultMesh,
+pylith::faults::StepSlipFn::initialize(const topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime)
{ // initialize
@@ -90,11 +90,11 @@
const PetscInt vStart = verticesStratum.begin();
const PetscInt vEnd = verticesStratum.end();
- delete _parameters; _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
+ delete _parameters; _parameters = new topology::Fields<topology::Field<topology::Mesh> >(faultMesh);
assert(_parameters);
_parameters->add("final slip", "final_slip");
- topology::Field<topology::SubMesh>& finalSlip = _parameters->get("final slip");
+ topology::Field<topology::Mesh>& finalSlip = _parameters->get("final slip");
finalSlip.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim);
finalSlip.allocate();
finalSlip.scale(lengthScale);
@@ -103,7 +103,7 @@
PetscScalar* finalSlipArray = finalSlipVisitor.localArray();
_parameters->add("slip time", "slip_time");
- topology::Field<topology::SubMesh>& slipTime = _parameters->get("slip time");
+ topology::Field<topology::Mesh>& slipTime = _parameters->get("slip time");
slipTime.newSection(finalSlip, 1);
slipTime.allocate();
slipTime.scale(timeScale);
@@ -202,7 +202,7 @@
// ----------------------------------------------------------------------
// Get slip on fault surface at time t.
void
-pylith::faults::StepSlipFn::slip(topology::Field<topology::SubMesh>* slip,
+pylith::faults::StepSlipFn::slip(topology::Field<topology::Mesh>* slip,
const PylithScalar t)
{ // slip
PYLITH_METHOD_BEGIN;
@@ -217,11 +217,11 @@
const PetscInt vEnd = verticesStratum.end();
// Get sections
- const topology::Field<topology::SubMesh>& finalSlip = _parameters->get("final slip");
+ const topology::Field<topology::Mesh>& finalSlip = _parameters->get("final slip");
topology::VecVisitorMesh finalSlipVisitor(finalSlip);
const PetscScalar* finalSlipArray = finalSlipVisitor.localArray();
- const topology::Field<topology::SubMesh>& slipTime = _parameters->get("slip time");
+ const topology::Field<topology::Mesh>& slipTime = _parameters->get("slip time");
topology::VecVisitorMesh slipTimeVisitor(slipTime);
const PetscScalar* slipTimeArray = slipTimeVisitor.localArray();
@@ -253,7 +253,7 @@
// ----------------------------------------------------------------------
// Get final slip.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::StepSlipFn::finalSlip(void)
{ // finalSlip
PYLITH_METHOD_BEGIN;
@@ -263,7 +263,7 @@
// ----------------------------------------------------------------------
// Get time when slip begins at each point.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::StepSlipFn::slipTime(void)
{ // slipTime
PYLITH_METHOD_BEGIN;
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -75,7 +75,7 @@
* @param normalizer Nondimensionalization of scales.
* @param originTime Origin time for earthquake source.
*/
- void initialize(const topology::SubMesh& faultMesh,
+ void initialize(const topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime =0.0);
@@ -86,20 +86,20 @@
*
* @returns Slip vector as left-lateral/reverse/normal.
*/
- void slip(topology::Field<topology::SubMesh>* const slipField,
+ void slip(topology::Field<topology::Mesh>* const slipField,
const PylithScalar t);
/** Get final slip.
*
* @returns Final slip.
*/
- const topology::Field<topology::SubMesh>& finalSlip(void);
+ const topology::Field<topology::Mesh>& finalSlip(void);
/** Get time when slip begins at each point.
*
* @returns Time when slip begins.
*/
- const topology::Field<topology::SubMesh>& slipTime(void);
+ const topology::Field<topology::Mesh>& slipTime(void);
// NOT IMPLEMENTED //////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,7 +20,7 @@
#include "TimeHistorySlipFn.hh" // implementation of object methods
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/CoordsVisitor.hh" // USES CoordsVisitor
@@ -75,7 +75,7 @@
// ----------------------------------------------------------------------
// Initialize slip time function.
void
-pylith::faults::TimeHistorySlipFn::initialize(const topology::SubMesh& faultMesh,
+pylith::faults::TimeHistorySlipFn::initialize(const topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime)
{ // initialize
@@ -96,11 +96,11 @@
const PetscInt vStart = verticesStratum.begin();
const PetscInt vEnd = verticesStratum.end();
- delete _parameters; _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
+ delete _parameters; _parameters = new topology::Fields<topology::Field<topology::Mesh> >(faultMesh);
assert(_parameters);
_parameters->add("slip amplitude", "slip_amplitude");
- topology::Field<topology::SubMesh>& slipAmplitude = _parameters->get("slip amplitude");
+ topology::Field<topology::Mesh>& slipAmplitude = _parameters->get("slip amplitude");
slipAmplitude.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim);
slipAmplitude.allocate();
slipAmplitude.scale(lengthScale);
@@ -109,7 +109,7 @@
PetscScalar* slipAmplitudeArray = slipAmplitudeVisitor.localArray();
_parameters->add("slip time", "slip_time");
- topology::Field<topology::SubMesh>& slipTime = _parameters->get("slip time");
+ topology::Field<topology::Mesh>& slipTime = _parameters->get("slip time");
slipTime.newSection(slipAmplitude, 1);
slipTime.allocate();
slipTime.scale(timeScale);
@@ -212,7 +212,7 @@
// ----------------------------------------------------------------------
// Get slip on fault surface at time t.
void
-pylith::faults::TimeHistorySlipFn::slip(topology::Field<topology::SubMesh>* slip,
+pylith::faults::TimeHistorySlipFn::slip(topology::Field<topology::Mesh>* slip,
const PylithScalar t)
{ // slip
PYLITH_METHOD_BEGIN;
@@ -228,11 +228,11 @@
const PetscInt vEnd = verticesStratum.end();
// Get sections
- const topology::Field<topology::SubMesh>& slipAmplitude = _parameters->get("slip amplitude");
+ const topology::Field<topology::Mesh>& slipAmplitude = _parameters->get("slip amplitude");
topology::VecVisitorMesh slipAmplitudeVisitor(slipAmplitude);
const PetscScalar* slipAmplitudeArray = slipAmplitudeVisitor.localArray();
- const topology::Field<topology::SubMesh>& slipTime = _parameters->get("slip time");
+ const topology::Field<topology::Mesh>& slipTime = _parameters->get("slip time");
topology::VecVisitorMesh slipTimeVisitor(slipTime);
const PetscScalar* slipTimeArray = slipTimeVisitor.localArray();
@@ -275,7 +275,7 @@
// ----------------------------------------------------------------------
// Get final slip.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::TimeHistorySlipFn::finalSlip(void)
{ // finalSlip
PYLITH_METHOD_BEGIN;
@@ -285,7 +285,7 @@
// ----------------------------------------------------------------------
// Get time when slip begins at each point.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::TimeHistorySlipFn::slipTime(void)
{ // slipTime
PYLITH_METHOD_BEGIN;
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -81,7 +81,7 @@
* @param normalizer Nondimensionalization of scales.
* @param originTime Origin time for earthquake source.
*/
- void initialize(const topology::SubMesh& faultMesh,
+ void initialize(const topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime =0.0);
@@ -92,20 +92,20 @@
*
* @returns Slip vector as left-lateral/reverse/normal.
*/
- void slip(topology::Field<topology::SubMesh>* const slipField,
+ void slip(topology::Field<topology::Mesh>* const slipField,
const PylithScalar t);
/** Get final slip.
*
* @returns Final slip.
*/
- const topology::Field<topology::SubMesh>& finalSlip(void);
+ const topology::Field<topology::Mesh>& finalSlip(void);
/** Get time when slip begins at each point.
*
* @returns Time when slip begins.
*/
- const topology::Field<topology::SubMesh>& slipTime(void);
+ const topology::Field<topology::Mesh>& slipTime(void);
// NOT IMPLEMENTED //////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/TopologyOps.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/TopologyOps.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/TopologyOps.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -24,7 +24,7 @@
// ----------------------------------------------------------------------
void
-pylith::faults::TopologyOps::classifyCellsDM(DM dmMesh,
+pylith::faults::TopologyOps::classifyCellsDM(PetscDM dmMesh,
PetscInt vertex,
const int depth,
const int faceSize,
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/TopologyOps.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/TopologyOps.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/TopologyOps.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -36,20 +36,23 @@
// PUBLIC TYPEDEFS ////////////////////////////////////////////////////
public :
- typedef std::set<PetscInt> PointSet;
+
+ typedef std::set<PetscInt> PointSet;
typedef std::vector<PetscInt> PointArray;
// PUBLIC METHODS /////////////////////////////////////////////////////
public :
+
static
- void classifyCellsDM(DM dmMesh,
- PetscInt vertex,
- const int depth,
- const int faceSize,
- PetscInt firstCohesiveCell,
- PointSet& replaceCells,
- PointSet& noReplaceCells,
- const int debug);
+ void classifyCellsDM(PetscDM dmMesh,
+ PetscInt vertex,
+ const int depth,
+ const int faceSize,
+ PetscInt firstCohesiveCell,
+ PointSet& replaceCells,
+ PointSet& noReplaceCells,
+ const int debug);
+
}; // class CohesiveTopology
#endif // pylith_faults_cohesivetopology_hh
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -22,7 +22,7 @@
#include "FaultCohesiveLagrange.hh" // USES faultToGlobal()
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/Fields.hh" // HOLDSA Fields
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/CoordsVisitor.hh" // USES CoordsVisitor
@@ -78,7 +78,7 @@
// ----------------------------------------------------------------------
// Get parameter fields.
-const pylith::topology::Fields<pylith::topology::Field<pylith::topology::SubMesh> >*
+const pylith::topology::Fields<pylith::topology::Field<pylith::topology::Mesh> >*
pylith::faults::TractPerturbation::parameterFields(void) const
{ // parameterFields
return _parameters;
@@ -87,8 +87,8 @@
// ----------------------------------------------------------------------
// Initialize traction perturbation function.
void
-pylith::faults::TractPerturbation::initialize(const topology::SubMesh& faultMesh,
- const topology::Field<topology::SubMesh>& faultOrientation,
+pylith::faults::TractPerturbation::initialize(const topology::Mesh& faultMesh,
+ const topology::Field<topology::Mesh>& faultOrientation,
const spatialdata::units::Nondimensional& normalizer)
{ // initialize
PYLITH_METHOD_BEGIN;
@@ -102,41 +102,41 @@
const int spaceDim = cs->spaceDim();
delete _parameters;
- _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
+ _parameters = new topology::Fields<topology::Field<topology::Mesh> >(faultMesh);
// Create section to hold time dependent values
_parameters->add("value", "traction", topology::FieldBase::VERTICES_FIELD, spaceDim);
- topology::Field<topology::SubMesh>& value = _parameters->get("value");
+ topology::Field<topology::Mesh>& value = _parameters->get("value");
value.vectorFieldType(topology::FieldBase::VECTOR);
value.scale(pressureScale);
value.allocate();
if (_dbInitial) {
_parameters->add("initial", "traction_initial", topology::FieldBase::VERTICES_FIELD, spaceDim);
- topology::Field<topology::SubMesh>& initial = _parameters->get("initial");
+ topology::Field<topology::Mesh>& initial = _parameters->get("initial");
initial.vectorFieldType(topology::FieldBase::VECTOR);
initial.scale(pressureScale);
initial.allocate();
}
if (_dbRate) {
_parameters->add("rate", "traction_rate", topology::FieldBase::VERTICES_FIELD, spaceDim);
- topology::Field<topology::SubMesh>& rate = _parameters->get("rate");
+ topology::Field<topology::Mesh>& rate = _parameters->get("rate");
rate.vectorFieldType(topology::FieldBase::VECTOR);
rate.scale(rateScale);
rate.allocate();
_parameters->add("rate time", "rate_start_time", topology::FieldBase::VERTICES_FIELD, 1);
- topology::Field<topology::SubMesh>& rateTime = _parameters->get("rate time");
+ topology::Field<topology::Mesh>& rateTime = _parameters->get("rate time");
rateTime.vectorFieldType(topology::FieldBase::SCALAR);
rateTime.scale(timeScale);
rateTime.allocate();
} // if
if (_dbChange) {
_parameters->add("change", "traction_change", topology::FieldBase::VERTICES_FIELD, spaceDim);
- topology::Field<topology::SubMesh>& change = _parameters->get("change");
+ topology::Field<topology::Mesh>& change = _parameters->get("change");
change.vectorFieldType(topology::FieldBase::VECTOR);
change.scale(pressureScale);
change.allocate();
_parameters->add("change time", "change_start_time", topology::FieldBase::VERTICES_FIELD, 1);
- topology::Field<topology::SubMesh>& changeTime = _parameters->get("change time");
+ topology::Field<topology::Mesh>& changeTime = _parameters->get("change time");
changeTime.vectorFieldType(topology::FieldBase::SCALAR);
changeTime.scale(timeScale);
changeTime.allocate();
@@ -170,7 +170,7 @@
} // switch
_queryDB("initial", _dbInitial, spaceDim, pressureScale, normalizer);
_dbInitial->close();
- pylith::topology::Field<pylith::topology::SubMesh>& initial = _parameters->get("initial");
+ pylith::topology::Field<pylith::topology::Mesh>& initial = _parameters->get("initial");
FaultCohesiveLagrange::faultToGlobal(&initial, faultOrientation);
} // if
@@ -207,7 +207,7 @@
_dbRate->queryVals(timeNames, 1);
_queryDB("rate time", _dbRate, 1, timeScale, normalizer);
_dbRate->close();
- pylith::topology::Field<pylith::topology::SubMesh>& rate = _parameters->get("rate");
+ pylith::topology::Field<pylith::topology::Mesh>& rate = _parameters->get("rate");
FaultCohesiveLagrange::faultToGlobal(&rate, faultOrientation);
} // if
@@ -243,7 +243,7 @@
_dbChange->queryVals(timeNames, 1);
_queryDB("change time", _dbChange, 1, timeScale, normalizer);
_dbChange->close();
- pylith::topology::Field<pylith::topology::SubMesh>& change = _parameters->get("change");
+ pylith::topology::Field<pylith::topology::Mesh>& change = _parameters->get("change");
FaultCohesiveLagrange::faultToGlobal(&change, faultOrientation);
if (_dbTimeHistory)
@@ -273,27 +273,27 @@
const spatialdata::geocoords::CoordSys* cs = _parameters->mesh().coordsys();assert(cs);
const int spaceDim = cs->spaceDim();
- topology::Field<topology::SubMesh>& valueField = _parameters->get("value");
+ topology::Field<topology::Mesh>& valueField = _parameters->get("value");
topology::VecVisitorMesh valueVisitor(valueField);
PetscScalar* valueArray = valueVisitor.localArray();
- topology::Field<topology::SubMesh>* initialField = (_dbInitial) ? &_parameters->get("initial") : 0;
+ topology::Field<topology::Mesh>* initialField = (_dbInitial) ? &_parameters->get("initial") : 0;
topology::VecVisitorMesh* initialVisitor = (initialField) ? new topology::VecVisitorMesh(*initialField) : 0;
PetscScalar* initialArray = (initialVisitor) ? initialVisitor->localArray() : NULL;
- topology::Field<topology::SubMesh>* rateField = (_dbRate) ? &_parameters->get("rate") : 0;
+ topology::Field<topology::Mesh>* rateField = (_dbRate) ? &_parameters->get("rate") : 0;
topology::VecVisitorMesh* rateVisitor = (rateField) ? new topology::VecVisitorMesh(*rateField) : 0;
PetscScalar* rateArray = (rateVisitor) ? rateVisitor->localArray() : NULL;
- topology::Field<topology::SubMesh>* rateTimeField = (_dbRate) ? &_parameters->get("rate time") : 0;
+ topology::Field<topology::Mesh>* rateTimeField = (_dbRate) ? &_parameters->get("rate time") : 0;
topology::VecVisitorMesh* rateTimeVisitor = (rateTimeField) ? new topology::VecVisitorMesh(*rateTimeField) : 0;
PetscScalar* rateTimeArray = (rateTimeVisitor) ? rateTimeVisitor->localArray() : NULL;
- topology::Field<topology::SubMesh>* changeField = (_dbChange) ? &_parameters->get("change") : 0;
+ topology::Field<topology::Mesh>* changeField = (_dbChange) ? &_parameters->get("change") : 0;
topology::VecVisitorMesh* changeVisitor = (changeField) ? new topology::VecVisitorMesh(*changeField) : 0;
PetscScalar* changeArray = (changeVisitor) ? changeVisitor->localArray() : NULL;
- topology::Field<topology::SubMesh>* changeTimeField = (_dbChange) ? &_parameters->get("change time") : 0;
+ topology::Field<topology::Mesh>* changeTimeField = (_dbChange) ? &_parameters->get("change time") : 0;
topology::VecVisitorMesh* changeTimeVisitor = (changeTimeField) ? new topology::VecVisitorMesh(*changeTimeField) : 0;
PetscScalar* changeTimeArray = (changeTimeVisitor) ? changeTimeVisitor->localArray() : NULL;
@@ -390,7 +390,7 @@
// ----------------------------------------------------------------------
// Get vertex field with traction perturbation information.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::faults::TractPerturbation::vertexField(const char* name,
const topology::SolutionFields* const fields)
{ // vertexField
@@ -462,7 +462,7 @@
topology::CoordsVisitor coordsVisitor(dmMesh);
PetscScalar *coordArray = coordsVisitor.localArray();
- topology::Field<topology::SubMesh>& parametersField = _parameters->get(name);
+ topology::Field<topology::Mesh>& parametersField = _parameters->get(name);
topology::VecVisitorMesh parametersVisitor(parametersField);
PetscScalar* parametersArray = parametersVisitor.localArray();
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -64,7 +64,7 @@
*
* @returns Parameter fields.
*/
- const topology::Fields<topology::Field<topology::SubMesh> >* parameterFields(void) const;
+ const topology::Fields<topology::Field<topology::Mesh> >* parameterFields(void) const;
/** Initialize slip time function.
*
@@ -72,8 +72,8 @@
* @param faultOrientation Orientation of fault.
* @param normalizer Nondimensionalization of scales.
*/
- void initialize(const topology::SubMesh& faultMesh,
- const topology::Field<topology::SubMesh>& faultOrientation,
+ void initialize(const topology::Mesh& faultMesh,
+ const topology::Field<topology::Mesh>& faultOrientation,
const spatialdata::units::Nondimensional& normalizer);
/** Calculate spatial and temporal variation of value.
@@ -96,7 +96,7 @@
*
* @returns Traction vector field.
*/
- const topology::Field<topology::SubMesh>&
+ const topology::Field<topology::Mesh>&
vertexField(const char* name,
const topology::SolutionFields* const fields =0);
@@ -127,7 +127,7 @@
private :
/// Parameters for perturbations.
- topology::Fields<topology::Field<topology::SubMesh> >* _parameters;
+ topology::Fields<topology::Field<topology::Mesh> >* _parameters;
/// Time scale for current time.
PylithScalar _timeScale;
Modified: short/3D/PyLith/trunk/libsrc/pylith/friction/FrictionModel.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/friction/FrictionModel.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/friction/FrictionModel.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,7 +20,7 @@
#include "FrictionModel.hh" // implementation of object methods
-#include "pylith/topology/SubMesh.hh" // USES Mesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Stratum.hh" // USES Stratum
@@ -97,8 +97,8 @@
// ----------------------------------------------------------------------
// Get physical property parameters and initial state (if used) from database.
void
-pylith::friction::FrictionModel::initialize(const topology::SubMesh& faultMesh,
- feassemble::Quadrature<topology::SubMesh>* quadrature)
+pylith::friction::FrictionModel::initialize(const topology::Mesh& faultMesh,
+ feassemble::Quadrature<topology::Mesh>* quadrature)
{ // initialize
PYLITH_METHOD_BEGIN;
@@ -125,7 +125,7 @@
// Create fields to hold physical properties and state variables.
delete _fieldsPropsStateVars;
- _fieldsPropsStateVars = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
+ _fieldsPropsStateVars = new topology::Fields<topology::Field<topology::Mesh> >(faultMesh);
assert(_fieldsPropsStateVars);
_setupPropsStateVars();
@@ -169,7 +169,7 @@
for (int i=0; i < _metadata.numProperties(); ++i) {
const materials::Metadata::ParamDescription& property = _metadata.getProperty(i);
// TODO This needs to be an integer instead of a string
- topology::Field<topology::SubMesh>& propertyField = _fieldsPropsStateVars->get(property.name.c_str());
+ topology::Field<topology::Mesh>& propertyField = _fieldsPropsStateVars->get(property.name.c_str());
topology::VecVisitorMesh propertyVisitor(propertyField);
PetscScalar* propertyArray = propertyVisitor.localArray();
const PetscInt off = propertyVisitor.sectionOffset(v);
@@ -222,7 +222,7 @@
for (int i=0; i < _metadata.numStateVars(); ++i) {
const materials::Metadata::ParamDescription& stateVar = _metadata.getStateVar(i);
// TODO This needs to be an integer instead of a string
- topology::Field<topology::SubMesh>& stateVarField = _fieldsPropsStateVars->get(stateVar.name.c_str());
+ topology::Field<topology::Mesh>& stateVarField = _fieldsPropsStateVars->get(stateVar.name.c_str());
topology::VecVisitorMesh stateVarVisitor(stateVarField);
PetscScalar* stateVarArray = stateVarVisitor.localArray();
const PetscInt off = stateVarVisitor.sectionOffset(v);
@@ -247,7 +247,7 @@
// ----------------------------------------------------------------------
// Get the field with all properties and state variables.
-const pylith::topology::Fields<pylith::topology::Field<pylith::topology::SubMesh> >&
+const pylith::topology::Fields<pylith::topology::Field<pylith::topology::Mesh> >&
pylith::friction::FrictionModel::fieldsPropsStateVars(void) const
{ // fieldsPropsStateVars
PYLITH_METHOD_BEGIN;
@@ -290,7 +290,7 @@
// ----------------------------------------------------------------------
// Get physical property or state variable field.
-const pylith::topology::Field<pylith::topology::SubMesh>&
+const pylith::topology::Field<pylith::topology::Mesh>&
pylith::friction::FrictionModel::getField(const char* name)
{ // getField
PYLITH_METHOD_BEGIN;
@@ -314,7 +314,7 @@
for (int i=0; i < _metadata.numProperties(); ++i) {
const materials::Metadata::ParamDescription& property = _metadata.getProperty(i);
// TODO This needs to be an integer instead of a string
- topology::Field<topology::SubMesh>& propertyField = _fieldsPropsStateVars->get(property.name.c_str());
+ topology::Field<topology::Mesh>& propertyField = _fieldsPropsStateVars->get(property.name.c_str());
topology::VecVisitorMesh propertyVisitor(propertyField);
PetscScalar* propertyArray = propertyVisitor.localArray();
const PetscInt off = propertyVisitor.sectionOffset(point);
@@ -326,7 +326,7 @@
for (int i=0; i < _metadata.numStateVars(); ++i) {
const materials::Metadata::ParamDescription& stateVar = _metadata.getStateVar(i);
// TODO This needs to be an integer instead of a string
- topology::Field<topology::SubMesh>& stateVarField = _fieldsPropsStateVars->get(stateVar.name.c_str());
+ topology::Field<topology::Mesh>& stateVarField = _fieldsPropsStateVars->get(stateVar.name.c_str());
topology::VecVisitorMesh stateVarVisitor(stateVarField);
PetscScalar* stateVarArray = stateVarVisitor.localArray();
const PetscInt off = stateVarVisitor.sectionOffset(point);
@@ -391,7 +391,7 @@
for (int i=0; i < _metadata.numProperties(); ++i) {
const materials::Metadata::ParamDescription& property = _metadata.getProperty(i);
// TODO This needs to be an integer instead of a string
- topology::Field<topology::SubMesh>& propertyField = _fieldsPropsStateVars->get(property.name.c_str());
+ topology::Field<topology::Mesh>& propertyField = _fieldsPropsStateVars->get(property.name.c_str());
topology::VecVisitorMesh propertyVisitor(propertyField);
PetscScalar* propertyArray = propertyVisitor.localArray();
const PetscInt off = propertyVisitor.sectionOffset(vertex);
@@ -403,7 +403,7 @@
for (int i=0; i < _metadata.numStateVars(); ++i) {
const materials::Metadata::ParamDescription& stateVar = _metadata.getStateVar(i);
// TODO This needs to be an integer instead of a string
- topology::Field<topology::SubMesh>& stateVarField = _fieldsPropsStateVars->get(stateVar.name.c_str());
+ topology::Field<topology::Mesh>& stateVarField = _fieldsPropsStateVars->get(stateVar.name.c_str());
topology::VecVisitorMesh stateVarVisitor(stateVarField);
PetscScalar* stateVarArray = stateVarVisitor.localArray();
const PetscInt off = stateVarVisitor.sectionOffset(vertex);
@@ -472,7 +472,7 @@
const materials::Metadata::ParamDescription& property =
_metadata.getProperty(i);
_fieldsPropsStateVars->add(property.name.c_str(), property.name.c_str());
- topology::Field<topology::SubMesh>& propertyField = _fieldsPropsStateVars->get(property.name.c_str());
+ topology::Field<topology::Mesh>& propertyField = _fieldsPropsStateVars->get(property.name.c_str());
propertyField.newSection(topology::FieldBase::VERTICES_FIELD, property.fiberDim);
propertyField.allocate();
propertyField.vectorFieldType(property.fieldType);
@@ -485,7 +485,7 @@
const materials::Metadata::ParamDescription& stateVar =
_metadata.getStateVar(i);
_fieldsPropsStateVars->add(stateVar.name.c_str(), stateVar.name.c_str());
- topology::Field<topology::SubMesh>& stateVarField = _fieldsPropsStateVars->get(stateVar.name.c_str());
+ topology::Field<topology::Mesh>& stateVarField = _fieldsPropsStateVars->get(stateVar.name.c_str());
stateVarField.newSection(topology::FieldBase::VERTICES_FIELD, stateVar.fiberDim);
stateVarField.allocate();
stateVarField.vectorFieldType(stateVar.fieldType);
Modified: short/3D/PyLith/trunk/libsrc/pylith/friction/FrictionModel.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/friction/FrictionModel.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/friction/FrictionModel.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -118,8 +118,8 @@
* @param quadrature Quadrature for finite-element integration
*/
virtual
- void initialize(const topology::SubMesh& mesh,
- feassemble::Quadrature<topology::SubMesh>* quadrature);
+ void initialize(const topology::Mesh& mesh,
+ feassemble::Quadrature<topology::Mesh>* quadrature);
/** Check whether friction model has a field as a property or state
* variable.
@@ -143,13 +143,13 @@
* @param name Name of field to retrieve.
* @returns Field over fault interface cells.
*/
- const topology::Field<topology::SubMesh>& getField(const char* name);
+ const topology::Field<topology::Mesh>& getField(const char* name);
/** Get the field with all properties and state variables.
*
* @returns Properties field.
*/
- const topology::Fields<topology::Field<topology::SubMesh> >& fieldsPropsStateVars() const;
+ const topology::Fields<topology::Field<topology::Mesh> >& fieldsPropsStateVars() const;
/** Retrieve properties and state variables for a point.
*
@@ -323,7 +323,7 @@
/// Field containing physical properties and state variables of
/// friction model.
- topology::Fields<topology::Field<topology::SubMesh> >* _fieldsPropsStateVars;
+ topology::Fields<topology::Field<topology::Mesh> >* _fieldsPropsStateVars;
/// Buffer for properties and state variables at vertex.
scalar_array _propsStateVarsVertex;
Modified: short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnSubset.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnSubset.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnSubset.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -44,7 +44,7 @@
{ // deallocate
PYLITH_METHOD_BEGIN;
- OutputManager<topology::SubMesh, topology::Field<topology::Mesh> >::deallocate();
+ OutputManager<topology::Mesh, topology::Field<topology::Mesh> >::deallocate();
delete _submesh; _submesh = 0;
@@ -85,12 +85,12 @@
// ----------------------------------------------------------------------
// Get mesh associated with subdomain.
-const pylith::topology::SubMesh&
+const pylith::topology::Mesh&
pylith::meshio::OutputSolnSubset::subdomainMesh(const topology::Mesh& mesh)
{ // subdomainMesh
PYLITH_METHOD_BEGIN;
- delete _submesh; _submesh = new topology::SubMesh(mesh, _label.c_str());assert(_submesh);
+ delete _submesh; _submesh = new topology::Mesh(mesh, _label.c_str());assert(_submesh);
PYLITH_METHOD_RETURN(*_submesh);
} // subdomainMesh
Modified: short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnSubset.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnSubset.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnSubset.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -29,8 +29,7 @@
// Include directives ---------------------------------------------------
#include "meshiofwd.hh" // forward declarations
-#include "pylith/topology/SubMesh.hh" // ISA OutputManager<SubMesh>
-#include "pylith/topology/Mesh.hh" // ISA OutputManager<Field<Mesh>>
+#include "pylith/topology/Mesh.hh" // ISA OutputManager<Mesh>
#include "pylith/topology/Field.hh" // ISA OutputManager<Field<Mesh>>
#include "OutputManager.hh" // ISA OutputManager
@@ -41,7 +40,7 @@
* a subdomain.
*/
class pylith::meshio::OutputSolnSubset :
- public OutputManager<topology::SubMesh, topology::Field<topology::Mesh> >
+ public OutputManager<topology::Mesh, topology::Field<topology::Mesh> >
{ // OutputSolnSubset
friend class TestOutputSolnSubset; // unit testing
@@ -73,7 +72,7 @@
*
* @returns Mesh associated with subdomain.
*/
- const topology::SubMesh& subdomainMesh(const topology::Mesh& mesh);
+ const topology::Mesh& subdomainMesh(const topology::Mesh& mesh);
// NOT IMPLEMENTED //////////////////////////////////////////////////////
private :
@@ -85,7 +84,7 @@
private :
std::string _label; ///< Label of subdomain.
- topology::SubMesh* _submesh; ///< Mesh of subdomain.
+ topology::Mesh* _submesh; ///< Mesh of subdomain.
}; // OutputSolnSubset
Modified: short/3D/PyLith/trunk/libsrc/pylith/problems/Formulation.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/problems/Formulation.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/problems/Formulation.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -21,7 +21,6 @@
#include "Formulation.hh" // implementation of class methods
#include "pylith/topology/Mesh.hh" // USES Quadrature<Mesh>
-#include "pylith/topology/SubMesh.hh" // USES Quadrature<SubMesh>
#include "pylith/feassemble/Quadrature.hh" // USES Integrator<Quadrature>
#include "pylith/feassemble/Integrator.hh" // USES Integrator
#include "pylith/topology/Jacobian.hh" // USES Jacobian
@@ -156,7 +155,7 @@
// ----------------------------------------------------------------------
// Set integrators over lower-dimension meshes.
void
-pylith::problems::Formulation::submeshIntegrators(IntegratorSubMesh** integrators,
+pylith::problems::Formulation::submeshIntegrators(IntegratorMesh** integrators,
const int numIntegrators)
{ // submeshIntegrators
assert( (!integrators && 0 == numIntegrators) ||
Modified: short/3D/PyLith/trunk/libsrc/pylith/problems/Formulation.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/problems/Formulation.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/problems/Formulation.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -47,7 +47,6 @@
private :
typedef feassemble::Integrator<feassemble::Quadrature<topology::Mesh> > IntegratorMesh;
- typedef feassemble::Integrator<feassemble::Quadrature<topology::SubMesh> > IntegratorSubMesh;
// PUBLIC MEMBERS ///////////////////////////////////////////////////////
public :
@@ -122,7 +121,7 @@
* @param integrators Integrators over lower-dimension meshes.
* @param numIntegrators Number of integrators.
*/
- void submeshIntegrators(IntegratorSubMesh** integrators,
+ void submeshIntegrators(IntegratorMesh** integrators,
const int numIntegrators);
/** Set handle to preconditioner.
@@ -210,7 +209,7 @@
std::vector<IntegratorMesh*> _meshIntegrators;
///< Integrators over lower-dimensional subdomains of the mesh.
- std::vector<IntegratorSubMesh*> _submeshIntegrators;
+ std::vector<IntegratorMesh*> _submeshIntegrators;
bool _isJacobianSymmetric; ///< Is system Jacobian symmetric?
bool _splitFields; ///< True if splitting fields.
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/Jacobian.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/Jacobian.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/Jacobian.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -21,7 +21,6 @@
#include "Jacobian.hh" // implementation of class methods
#include "Mesh.hh" // USES Mesh
-#include "SubMesh.hh" // USES SubMesh
#include "Field.hh" // USES Field
#include "pylith/utils/error.h" // USES PYLITH_CHECK_ERROR
@@ -51,30 +50,6 @@
} // constructor
// ----------------------------------------------------------------------
-// Default constructor.
-pylith::topology::Jacobian::Jacobian(const Field<SubMesh>& field,
- const char* matrixType,
- const bool blockOkay) :
- _matrix(0),
- _valuesChanged(true)
-{ // constructor
- PYLITH_METHOD_BEGIN;
-
- PetscDM dmMesh = field.dmMesh();assert(dmMesh);
-
- // Set blockFlag to -1 if okay to set block size equal to fiber
- // dimension, otherwise use a block size of 1.
- const int blockFlag = (blockOkay) ? -1 : 1;
-
- const char* msg = "Could not create PETSc sparse matrix associated with subsystem Jacobian.";
- PetscErrorCode err = DMCreateMatrix(dmMesh, matrixType, &_matrix);PYLITH_CHECK_ERROR_MSG(err, msg);
-
- _type = matrixType;
-
- PYLITH_METHOD_END;
-} // constructor
-
-// ----------------------------------------------------------------------
// Destructor.
pylith::topology::Jacobian::~Jacobian(void)
{ // destructor
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/Jacobian.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/Jacobian.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/Jacobian.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -55,17 +55,6 @@
const char* matrixType ="aij",
const bool blockOkay =false);
- /** Constructor with field for submesh.
- *
- * @param field Fields associated with submesh and solution of the problem.
- * @param matrixType Type of PETSc sparse matrix.
- * @param blockOkay True if okay to use block size equal to fiberDim
- * (all or none of the DOF at each point are constrained).
- */
- Jacobian(const Field<SubMesh>& field,
- const char* matrixType ="aij",
- const bool blockOkay =true);
-
/// Destructor.
~Jacobian(void);
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/Makefile.am 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/Makefile.am 2013-05-13 23:33:37 UTC (rev 22058)
@@ -37,9 +37,6 @@
SolutionFields.hh \
Stratum.hh \
Stratum.icc \
- SubMesh.hh \
- SubMesh.icc \
- SubMesh.cc \
VisitorMesh.hh \
VisitorMesh.icc \
VisitorSubMesh.hh \
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -32,7 +32,7 @@
// ----------------------------------------------------------------------
// Default constructor
-pylith::topology::Mesh::Mesh(void) :
+pylith::topology::Mesh::Mesh(const bool isSubMesh) :
_dmMesh(NULL),
_numNormalCells(0),
_numCohesiveCells(0),
@@ -40,9 +40,8 @@
_numShadowVertices(0),
_numLagrangeVertices(0),
_coordsys(0),
- _comm(PETSC_COMM_WORLD),
_debug(false),
- _isSubMesh(false)
+ _isSubMesh(isSubMesh)
{ // constructor
} // constructor
@@ -57,14 +56,13 @@
_numShadowVertices(0),
_numLagrangeVertices(0),
_coordsys(0),
- _comm(comm),
_debug(false),
_isSubMesh(false)
{ // constructor
PYLITH_METHOD_BEGIN;
PetscErrorCode err;
- err = DMCreate(_comm, &_dmMesh);PYLITH_CHECK_ERROR(err);
+ err = DMCreate(comm, &_dmMesh);PYLITH_CHECK_ERROR(err);
err = DMSetType(_dmMesh, DMPLEX);PYLITH_CHECK_ERROR(err);
err = DMPlexSetDimension(_dmMesh, dim);PYLITH_CHECK_ERROR(err);
err = PetscObjectSetName((PetscObject) _dmMesh, "domain");PYLITH_CHECK_ERROR(err);
@@ -83,8 +81,7 @@
_numShadowVertices(0),
_numLagrangeVertices(0),
_coordsys(0),
- _comm(mesh.comm()),
- _debug(mesh.debug()),
+ _debug(mesh._debug),
_isSubMesh(true)
{ // Submesh constructor
PYLITH_METHOD_BEGIN;
@@ -159,14 +156,50 @@
{ // coordsys
PYLITH_METHOD_BEGIN;
- delete _coordsys; _coordsys = (0 != cs) ? cs->clone() : 0;
- if (0 != _coordsys)
+ delete _coordsys; _coordsys = (cs) ? cs->clone() : 0;
+ if (_coordsys)
_coordsys->initialize();
PYLITH_METHOD_END;
} // coordsys
// ----------------------------------------------------------------------
+// Get MPI communicator associated with mesh.
+MPI_Comm
+pylith::topology::Mesh::comm(void) const
+{ // comm
+ PYLITH_METHOD_BEGIN;
+
+ MPI_Comm comm;
+ if (_dmMesh) {
+ PetscObjectGetComm((PetscObject) _dmMesh, &comm);
+ } else {
+ comm = PETSC_COMM_WORLD;
+ } // if/else
+
+ PYLITH_METHOD_RETURN(comm);
+} // comm
+
+// ----------------------------------------------------------------------
+// Get MPI rank.
+int
+pylith::topology::Mesh::commRank(void) const
+{ // commRank
+ PYLITH_METHOD_BEGIN;
+
+ int rank = 0;
+ MPI_Comm comm;
+ if (_dmMesh) {
+ PetscObjectGetComm((PetscObject) _dmMesh, &comm);
+ } else {
+ comm = PETSC_COMM_WORLD;
+ } // if/else
+ MPI_Comm_rank(comm, &rank);
+
+ PYLITH_METHOD_RETURN(rank);
+} // commRank
+
+// ----------------------------------------------------------------------
// Return the names of all vertex groups.
void
pylith::topology::Mesh::groups(int* numNames,
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -44,8 +44,11 @@
// PUBLIC METHODS ///////////////////////////////////////////////////////
public :
- /// Default constructor.
- Mesh(void);
+ /** Default constructor.
+ *
+ * @param isSubMesh True if mesh is a submesh of another mesh.
+ */
+ Mesh(const bool isSubMesh =false);
/** Constructor with dimension and communicator.
*
@@ -159,25 +162,17 @@
*/
int numCells(void) const;
- /** Set MPI communicator associated with mesh.
- *
- * @param value MPI communicator.
- */
- void comm(const MPI_Comm value);
-
/** Get MPI communicator associated with mesh.
*
* @returns MPI communicator.
*/
- const MPI_Comm comm(void) const;
+ MPI_Comm comm(void) const;
/** Get MPI rank.
*
* @returns MPI rank.
*/
int commRank(void) const;
-
- /** Get
/** Print mesh to stdout.
*
@@ -210,9 +205,8 @@
PetscInt _numNormalCells, _numCohesiveCells, _numNormalVertices, _numShadowVertices, _numLagrangeVertices;
spatialdata::geocoords::CoordSys* _coordsys; ///< Coordinate system.
- MPI_Comm _comm; ///< MPI communicator for mesh.
bool _debug; ///< Debugging flag for mesh.
- bool _isSubMesh; ///< True if mesh is a submesh of another mesh.
+ const bool _isSubMesh; ///< True if mesh is a submesh of another mesh.
// NOT IMPLEMENTED //////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.icc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.icc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.icc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -172,32 +172,6 @@
}
// ----------------------------------------------------------------------
-// Set MPI communicator associated with mesh.
-inline
-void
-pylith::topology::Mesh::comm(const MPI_Comm value) {
- _comm = value;
-}
-
-// ----------------------------------------------------------------------
-// Get MPI communicator associated with mesh.
-inline
-const MPI_Comm
-pylith::topology::Mesh::comm(void) const {
- return _comm;
-}
-
-// ----------------------------------------------------------------------
-// Get MPI rank.
-inline
-int
-pylith::topology::Mesh::commRank(void) const {
- int rank = 0;
- MPI_Comm_rank(_comm, &rank);
- return rank;
-}
-
-// ----------------------------------------------------------------------
// Print mesh to stdout.
inline
void
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/MeshOps.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/MeshOps.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/MeshOps.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -50,7 +50,6 @@
err = DMSetType(dmMesh, DMPLEX);PYLITH_CHECK_ERROR(err);
err = DMPlexSetDimension(dmMesh, dim);PYLITH_CHECK_ERROR(err);
mesh->dmMesh(dmMesh, label);
- mesh->comm(comm);
PYLITH_METHOD_END;
} // createDMMesh
Deleted: short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,154 +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) 2010-2013 University of California, Davis
-//
-// See COPYING for license information.
-//
-// ======================================================================
-//
-
-#include <portinfo>
-
-#include "SubMesh.hh" // implementation of class methods
-
-#include "spatialdata/units/Nondimensional.hh" // USES Nondimensional
-#include "spatialdata/geocoords/CoordSys.hh" // USES CoordSys
-#include "pylith/utils/petscfwd.h" // USES PetscVec
-#include "pylith/utils/error.h" // USES PYLITH_CHECK_ERROR
-
-#include <stdexcept> // USES std::runtime_error
-#include <sstream> // USES std::ostringstream
-#include <cassert> // USES assert()
-
-// ----------------------------------------------------------------------
-// Default constructor
-pylith::topology::SubMesh::SubMesh(void) :
- _newMesh(NULL),
- _coordsys(0),
- _debug(false)
-{ // constructor
-} // constructor
-
-// ----------------------------------------------------------------------
-// Constructor with mesh and label for vertices marking boundary.
-pylith::topology::SubMesh::SubMesh(const Mesh& mesh,
- const char* label) :
- _newMesh(NULL),
- _coordsys(0),
- _debug(false)
-{ // constructor
- PYLITH_METHOD_BEGIN;
-
- createSubMesh(mesh, label);
-
- PYLITH_METHOD_END;
-} // constructor
-
-// ----------------------------------------------------------------------
-// Default destructor
-pylith::topology::SubMesh::~SubMesh(void)
-{ // destructor
- deallocate();
-} // destructor
-
-// ----------------------------------------------------------------------
-// Deallocate PETSc and local data structures.
-void
-pylith::topology::SubMesh::deallocate(void)
-{ // deallocate
- PYLITH_METHOD_BEGIN;
-
- delete _coordsys; _coordsys = 0;
- PetscErrorCode err = DMDestroy(&_newMesh);PYLITH_CHECK_ERROR(err);
-
- PYLITH_METHOD_END;
-} // deallocate
-
-// ----------------------------------------------------------------------
-// Create PETSc mesh.
-void
-pylith::topology::SubMesh::createSubMesh(const Mesh& mesh,
- const char* label)
-{ // createSubMesh
- PYLITH_METHOD_BEGIN;
-
- PetscDM dmMesh = mesh.dmMesh();assert(dmMesh);
- PetscBool hasLabel;
- PetscErrorCode err;
-
- err = DMPlexHasLabel(dmMesh, label, &hasLabel);PYLITH_CHECK_ERROR(err);
- if (!hasLabel) {
- std::ostringstream msg;
- msg << "Could not find group of points '" << label << "' in DM mesh.";
- throw std::runtime_error(msg.str());
- } // if
-
- /* TODO: Add creation of pointSF for submesh */
- err = DMDestroy(&_newMesh);PYLITH_CHECK_ERROR(err);
- err = DMPlexCreateSubmesh(dmMesh, label, 1, &_newMesh);PYLITH_CHECK_ERROR(err);
-
- // Set data from mesh.
- coordsys(mesh);
-
- // Set name
- std::string meshLabel = "subdomain_" + std::string(label);
- err = PetscObjectSetName((PetscObject) _newMesh, meshLabel.c_str());PYLITH_CHECK_ERROR(err);
- PetscInt maxConeSizeLocal, maxConeSize = 0;
-
- err = DMPlexGetMaxSizes(dmMesh, &maxConeSizeLocal, NULL);PYLITH_CHECK_ERROR(err);
- err = MPI_Allreduce(&maxConeSizeLocal, &maxConeSize, 1, MPI_INT, MPI_MAX,
- PetscObjectComm((PetscObject) dmMesh)); PYLITH_CHECK_ERROR(err);
-
- if (maxConeSize <= 0) {
- std::ostringstream msg;
- msg << "Error while creating submesh. Submesh '"
- << label << "' does not contain any cells.\n"
- << "Submeshes must be one dimension lower than the domain mesh.";
- throw std::runtime_error(msg.str());
- } // if
-
- PYLITH_METHOD_END;
-} // createSubMesh
-
-// ----------------------------------------------------------------------
-// Set coordinate system using mesh.
-void
-pylith::topology::SubMesh::coordsys(const Mesh& mesh)
-{ // coordsys
- PYLITH_METHOD_BEGIN;
-
- delete _coordsys; _coordsys = 0;
- const spatialdata::geocoords::CoordSys* cs = mesh.coordsys();
- if (cs) {
- _coordsys = cs->clone();assert(_coordsys);
- _coordsys->initialize();
- } // if
-
- PYLITH_METHOD_END;
-} // coordsys
-
-// ----------------------------------------------------------------------
-// Initialize the finite-element mesh.
-void
-pylith::topology::SubMesh::initialize(void)
-{ // initialize
- PYLITH_METHOD_BEGIN;
-
- assert(0);
- if (_coordsys)
- _coordsys->initialize();
-
- PYLITH_METHOD_END;
-} // initialize
-
-// End of file
Deleted: short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,184 +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) 2010-2013 University of California, Davis
-//
-// See COPYING for license information.
-//
-// ======================================================================
-//
-
-/**
- * @file libsrc/topology/SubMesh.hh
- *
- * @brief C++ PyLith finite-element mesh.
- */
-
-#if !defined(pylith_topology_submesh_hh)
-#define pylith_topology_submesh_hh
-
-// Include directives ---------------------------------------------------
-#include "topologyfwd.hh" // forward declarations
-#include "spatialdata/geocoords/geocoordsfwd.hh" // forward declarations
-
-#include "Mesh.hh" // USES Mesh
-
-// SubMesh -----------------------------------------------------------------
-/** @brief C++ PyLith finite-element mesh.
- *
- * Extends mesh over subset of domain to include coordinate
- * system associated with domain. Also has functions to simply
- * creating submeshes from groups of vertices.
- */
-class pylith::topology::SubMesh
-{ // SubMesh
- friend class TestSubMesh; // unit testing
-
-// PUBLIC METHODS ///////////////////////////////////////////////////////
-public :
-
- /// Default constructor.
- SubMesh(void);
-
- /** Constructor with mesh and label for vertices marking boundary.
- *
- * @param mesh Finite-element mesh over domain.
- * @param label Label for vertices marking boundary.
- */
- SubMesh(const Mesh& mesh,
- const char* label);
-
- /// Default destructor
- ~SubMesh(void);
-
- /// Deallocate PETSc and local data structures.
- void deallocate(void);
-
- /** Create mesh.
- *
- * @param mesh Finite-element mesh over domain.
- * @param label Label for vertices marking boundary.
- */
- void createSubMesh(const Mesh& mesh,
- const char* label);
-
- /** Get DMPlex mesh.
- *
- * @returns DMPlex mesh.
- */
- PetscDM dmMesh(void) const;
-
- /** Set DMPlex mesh.
- *
- * @param DMPlex mesh.
- * @param label Label for mesh.
- */
- void dmMesh(PetscDM dm,
- const char* label ="domain");
-
- /** Get sizes for all point types.
- *
- * @param numNormalCells
- * @param numCohesiveCells
- * @param numNormalVertices
- * @param numShadowVertices
- * @param numLagrangeVertices.
- */
- void getPointTypeSizes(PetscInt *numNormalCells,
- PetscInt *numCohesiveCells,
- PetscInt *numNormalVertices,
- PetscInt *numShadowVertices,
- PetscInt *numLagrangeVertices) const;
-
- /** Set coordinate system using mesh.
- *
- * @param mesh Finite-element mesh over domain.
- */
- void coordsys(const Mesh& mesh);
-
- /** Get coordinate system.
- *
- * @returns Coordinate system.
- */
- const spatialdata::geocoords::CoordSys* coordsys(void) const;
-
- /** Set debug flag.
- *
- * @param value Turn on debugging if true.
- */
- void debug(const bool value);
-
- /** Get debug flag.
- *
- * @param Get debugging flag.
- */
- bool debug(void) const;
-
- /** Get dimension of mesh.
- *
- * @returns Dimension of mesh.
- */
- int dimension(void) const;
-
- /** Get representative cone size for mesh.
- *
- * @returns Representative cone size for mesh.
- */
- int coneSize(void) const;
-
- /** Get number of vertices in mesh.
- *
- * @returns Number of vertices in mesh.
- */
- int numVertices(void) const;
-
- /** Get number of cells in mesh.
- *
- * @returns Number of cells in mesh.
- */
- int numCells(void) const;
-
- /** Get MPI communicator associated with mesh.
- *
- * @returns MPI communicator.
- */
- const MPI_Comm comm(void) const;
-
- /// Initialize the finite-element mesh.
- void initialize(void);
-
- /** Print mesh to stdout.
- *
- * @param label Label for mesh.
- */
- void view(const char* label) const;
-
-// PRIVATE MEMBERS //////////////////////////////////////////////////////
-private :
-
- PetscDM _newMesh;
- spatialdata::geocoords::CoordSys* _coordsys; ///< Coordinate system.
- bool _debug; ///< Debugging flag for mesh.
-
-// NOT IMPLEMENTED //////////////////////////////////////////////////////
-private :
-
- SubMesh(const SubMesh&); ///< Not implemented
- const SubMesh& operator=(const SubMesh&); ///< Not implemented
-
-}; // SubMesh
-
-#include "SubMesh.icc"
-
-#endif // pylith_topology_submesh_hh
-
-
-// End of file
Deleted: short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.icc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.icc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.icc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,153 +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) 2010-2013 University of California, Davis
-//
-// See COPYING for license information.
-//
-// ======================================================================
-//
-
-#if !defined(pylith_topology_submesh_hh)
-#error "SubMesh.icc must be included only from SubMesh.hh"
-#else
-
-#include "pylith/utils/error.h" // USES PYLITH_CHECK_ERROR
-
-// Get DMComplex mesh.
-inline
-PetscDM
-pylith::topology::SubMesh::dmMesh(void) const {
- return _newMesh;
-}
-
-// Set DMComplex mesh.
-inline
-void
-pylith::topology::SubMesh::dmMesh(PetscDM dm,
- const char* label) {
- PetscErrorCode err;
- err = DMDestroy(&_newMesh);PYLITH_CHECK_ERROR(err);
- _newMesh = dm;
- err = PetscObjectSetName((PetscObject) _newMesh, label);PYLITH_CHECK_ERROR(err);
-}
-
-// Get point type sizes.
-inline
-void
-pylith::topology::SubMesh::getPointTypeSizes(PetscInt *numNormalCells,
- PetscInt *numCohesiveCells,
- PetscInt *numNormalVertices,
- PetscInt *numShadowVertices,
- PetscInt *numLagrangeVertices) const {
- *numNormalCells = 0;
- *numCohesiveCells = 0;
- *numNormalVertices = 0;
- *numShadowVertices = 0;
- *numLagrangeVertices = 0;
-}
-
-// Get coordinate system.
-inline
-const spatialdata::geocoords::CoordSys*
-pylith::topology::SubMesh::coordsys(void) const {
- return _coordsys;
-}
-
-// Set debug flag.
-inline
-void
-pylith::topology::SubMesh::debug(const bool value) {
- _debug = value;
-}
-
-// Get debug flag.
-inline
-bool
-pylith::topology::SubMesh::debug(void) const {
- return _debug;
-}
-
-// Get dimension of mesh.
-inline
-int
-pylith::topology::SubMesh::dimension(void) const {
- PetscInt dim = 0;
- if (_newMesh) {
- PetscErrorCode err = DMPlexGetDimension(_newMesh, &dim);PYLITH_CHECK_ERROR(err);
- } // if
- return dim;
-}
-
-// Get representative cone size for mesh.
-inline
-int
-pylith::topology::SubMesh::coneSize(void) const {
- PetscInt coneSize = 0;
- if (_newMesh) {
- PetscErrorCode err;
- PetscInt cStart = 0;
- err = DMPlexGetHeightStratum(_newMesh, 1, &cStart, NULL);PYLITH_CHECK_ERROR(err);
- err = DMPlexGetConeSize(_newMesh, cStart, &coneSize);PYLITH_CHECK_ERROR(err);
- } // if
- return coneSize;
-}
-
-// Get number of vertices in mesh.
-inline
-int
-pylith::topology::SubMesh::numVertices(void) const {
- PetscInt nvertices = 0;
- if (_newMesh) {
- PetscInt begin=0, end=0;
- PetscErrorCode err = DMPlexGetDepthStratum(_newMesh, 0, &begin, &end);PYLITH_CHECK_ERROR(err);
- nvertices = end-begin;
- } // if
- return nvertices;
-}
-
-// Get number of cells in mesh.
-inline
-int
-pylith::topology::SubMesh::numCells(void) const {
- PetscInt ncells = 0;
- if (_newMesh) {
- PetscInt begin=0, end=0;
- PetscErrorCode err = DMPlexGetHeightStratum(_newMesh, 1, &begin, &end);PYLITH_CHECK_ERROR(err);
- ncells = end-begin;
- } // if
- return ncells;
-}
-
-// Get MPI communicator associated with mesh.
-inline
-const MPI_Comm
-pylith::topology::SubMesh::comm(void) const {
- MPI_Comm comm;
- if (_newMesh) {
- PetscErrorCode err = PetscObjectGetComm((PetscObject)_newMesh, &comm);
- } // if
- return comm;
-} // if
-
-// Print mesh to stdout.
-inline
-void
-pylith::topology::SubMesh::view(const char* label) const {
- assert(_newMesh);
- PetscErrorCode err = DMView(_newMesh, PETSC_VIEWER_STDOUT_WORLD);PYLITH_CHECK_ERROR(err);
-}
-
-
-#endif
-
-
-// End of file
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorMesh.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -50,12 +50,6 @@
*/
VecVisitorMesh(const Field<Mesh>& field);
- /** Constructor with field over a submesh.
- *
- * @param field Field over a submesh.
- */
- VecVisitorMesh(const Field<SubMesh>& field);
-
/// Default destructor
~VecVisitorMesh(void);
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorMesh.icc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorMesh.icc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorMesh.icc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -21,7 +21,6 @@
#else
#include "Mesh.hh" // USES Mesh
-#include "SubMesh.hh" // USES SubMesh
#include "Field.hh" // USES Field
#include "pylith/utils/error.h" // USES PYLITH_CHECK_ERROR
@@ -40,19 +39,6 @@
} // constructor
// ----------------------------------------------------------------------
-// Constructor with field over a submesh.
-inline
-pylith::topology::VecVisitorMesh::VecVisitorMesh(const Field<SubMesh>& field) :
- _dm(NULL),
- _localVec(NULL),
- _section(NULL),
- _localArray(NULL)
-{ // constructor
- _dm = field.mesh().dmMesh();assert(_dm);
- initialize<Field<SubMesh> >(field);
-} // constructor
-
-// ----------------------------------------------------------------------
// Default destructor
inline
pylith::topology::VecVisitorMesh::~VecVisitorMesh(void)
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorSubMesh.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorSubMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorSubMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -247,7 +247,7 @@
*
* @param submesh Submesh associated with index set.
*/
- SubMeshIS(const SubMesh& submesh);
+ SubMeshIS(const Mesh& submesh);
/// Default destructor.
~SubMeshIS(void);
@@ -259,7 +259,7 @@
*
* @returns Submesh.
*/
- const SubMesh& submesh(void) const;
+ const Mesh& submesh(void) const;
/** Get PETSc index set.
*
@@ -282,7 +282,7 @@
// PRIVATE MEMBERS //////////////////////////////////////////////////////
private :
- const SubMesh& _submesh;
+ const Mesh& _submesh;
PetscIS _indexSet; ///< PETSc index set.
PetscInt _size; ///< Size of index set.
const PetscInt* _points; ///< Array of points in index set.
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorSubMesh.icc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorSubMesh.icc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/VisitorSubMesh.icc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -270,7 +270,7 @@
// ----------------------------------------------------------------------
// Default constructor.
inline
-pylith::topology::SubMeshIS::SubMeshIS(const SubMesh& submesh) :
+pylith::topology::SubMeshIS::SubMeshIS(const Mesh& submesh) :
_submesh(submesh),
_indexSet(NULL)
{ // constructor
@@ -305,7 +305,7 @@
// ----------------------------------------------------------------------
// Get the submesh.
inline
-const pylith::topology::SubMesh&
+const pylith::topology::Mesh&
pylith::topology::SubMeshIS::submesh(void) const
{ // submesh
return _submesh;
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/topologyfwd.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/topologyfwd.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/topologyfwd.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -29,6 +29,7 @@
#include "pylith/utils/types.hh"
+#if 0 // :TODO: Update this for PETSc DM.
namespace ALE {
template<typename cellrefiner_type> class MeshRefiner;
class RefineEdges2;
@@ -43,12 +44,12 @@
class MeshOrder;
} // ALE
+#endif
namespace pylith {
namespace topology {
class Mesh;
- class SubMesh;
class MeshOps;
class CoordsVisitor;
class SubMeshIS;
Modified: short/3D/PyLith/trunk/modulesrc/bc/BCIntegratorSubMesh.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/bc/BCIntegratorSubMesh.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/bc/BCIntegratorSubMesh.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -25,7 +25,7 @@
namespace bc {
class pylith::bc::BCIntegratorSubMesh : public BoundaryCondition,
- public pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::SubMesh> >
+ public pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::Mesh> >
{ // class BoundaryCondition
// PUBLIC METHODS /////////////////////////////////////////////////
@@ -52,7 +52,7 @@
*
* @return Boundary mesh.
*/
- const pylith::topology::SubMesh& boundaryMesh(void) const;
+ const pylith::topology::Mesh& boundaryMesh(void) const;
/** Get mesh labels for submesh associated with applied forces.
*
Modified: short/3D/PyLith/trunk/modulesrc/bc/DirichletBoundary.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/bc/DirichletBoundary.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/bc/DirichletBoundary.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -52,7 +52,7 @@
*
* @return Boundary mesh.
*/
- const pylith::topology::SubMesh& boundaryMesh(void) const;
+ const pylith::topology::Mesh& boundaryMesh(void) const;
/** Get vertex field with BC information.
*
@@ -61,7 +61,7 @@
*
* @returns Field over vertices.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>&
+ const pylith::topology::Field<pylith::topology::Mesh>&
vertexField(const char* name,
const pylith::topology::SolutionFields& fields);
Modified: short/3D/PyLith/trunk/modulesrc/bc/Neumann.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/bc/Neumann.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/bc/Neumann.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -85,7 +85,7 @@
*
* @returns Traction vector at integration points.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>&
+ const pylith::topology::Field<pylith::topology::Mesh>&
cellField(const char* name,
pylith::topology::SolutionFields* const fields =0);
Modified: short/3D/PyLith/trunk/modulesrc/bc/bc.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/bc/bc.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/bc/bc.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -61,7 +61,6 @@
// template instantiation
%template(MeshIntegrator) pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::Mesh> >;
-%template(SubMeshIntegrator) pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::SubMesh> >;
%include "BoundaryCondition.i"
%include "BoundaryConditionPoints.i"
Modified: short/3D/PyLith/trunk/modulesrc/faults/BruneSlipFn.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/BruneSlipFn.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/BruneSlipFn.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -65,7 +65,7 @@
* @param normalizer Nondimensionalization of scales.
* @param originTime Origin time for earthquake source.
*/
- void initialize(const pylith::topology::SubMesh& faultMesh,
+ void initialize(const pylith::topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime =0.0);
@@ -76,20 +76,20 @@
*
* @returns Slip vector as left-lateral/reverse/normal.
*/
- void slip(pylith::topology::Field<pylith::topology::SubMesh>* const slipField,
+ void slip(pylith::topology::Field<pylith::topology::Mesh>* const slipField,
const PylithScalar t);
/** Get final slip.
*
* @returns Final slip.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>& finalSlip(void);
+ const pylith::topology::Field<pylith::topology::Mesh>& finalSlip(void);
/** Get time when slip begins at each point.
*
* @returns Time when slip begins.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>& slipTime(void);
+ const pylith::topology::Field<pylith::topology::Mesh>& slipTime(void);
}; // class BruneSlipFn
Modified: short/3D/PyLith/trunk/modulesrc/faults/ConstRateSlipFn.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/ConstRateSlipFn.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/ConstRateSlipFn.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -59,7 +59,7 @@
* @param normalizer Nondimensionalization of scales.
* @param originTime Origin time for earthquake source.
*/
- void initialize(const pylith::topology::SubMesh& faultMesh,
+ void initialize(const pylith::topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime =0.0);
@@ -70,20 +70,20 @@
*
* @returns Slip vector as left-lateral/reverse/normal.
*/
- void slip(pylith::topology::Field<pylith::topology::SubMesh>* const slipField,
+ void slip(pylith::topology::Field<pylith::topology::Mesh>* const slipField,
const PylithScalar t);
/** Get final slip.
*
* @returns Final slip.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>& finalSlip(void);
+ const pylith::topology::Field<pylith::topology::Mesh>& finalSlip(void);
/** Get time when slip begins at each point.
*
* @returns Time when slip begins.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>& slipTime(void);
+ const pylith::topology::Field<pylith::topology::Mesh>& slipTime(void);
}; // class ConstRateSlipFn
Modified: short/3D/PyLith/trunk/modulesrc/faults/EqKinSrc.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/EqKinSrc.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/EqKinSrc.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -63,7 +63,7 @@
* @param faultMesh Finite-element mesh of fault.
* @param normalizer Nondimensionalization of scales.
*/
- void initialize(const pylith::topology::SubMesh& faultMesh,
+ void initialize(const pylith::topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer);
/** Get slip on fault surface at time t.
@@ -71,20 +71,20 @@
* @param slipField Slip field over fault mesh.
* @param t Time t.
*/
- void slip(pylith::topology::Field<pylith::topology::SubMesh>* const slipField,
+ void slip(pylith::topology::Field<pylith::topology::Mesh>* const slipField,
const PylithScalar t);
/** Get final slip.
*
* @returns Final slip.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>& finalSlip(void) const;
+ const pylith::topology::Field<pylith::topology::Mesh>& finalSlip(void) const;
/** Get time when slip begins at each point.
*
* @returns Time when slip begins.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>& slipTime(void) const;
+ const pylith::topology::Field<pylith::topology::Mesh>& slipTime(void) const;
}; // class EqKinSrc
Modified: short/3D/PyLith/trunk/modulesrc/faults/Fault.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/Fault.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/Fault.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -128,7 +128,7 @@
*
* @returns PETSc mesh object
*/
- const pylith::topology::SubMesh& faultMesh(void) const;
+ const pylith::topology::Mesh& faultMesh(void) const;
/** Get vertex field associated with integrator.
*
@@ -137,7 +137,7 @@
* @returns Vertex field.
*/
virtual
- const pylith::topology::Field<pylith::topology::SubMesh>&
+ const pylith::topology::Field<pylith::topology::Mesh>&
vertexField(const char* name,
const pylith::topology::SolutionFields* fields =0) = 0;
@@ -148,7 +148,7 @@
* @returns Cell field.
*/
virtual
- const pylith::topology::Field<pylith::topology::SubMesh>&
+ const pylith::topology::Field<pylith::topology::Mesh>&
cellField(const char* name,
const pylith::topology::SolutionFields* fields =0) = 0;
Modified: short/3D/PyLith/trunk/modulesrc/faults/FaultCohesive.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/FaultCohesive.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/FaultCohesive.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -25,7 +25,7 @@
namespace faults {
class FaultCohesive : public Fault,
- public pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::SubMesh> >
+ public pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::Mesh> >
{ // class FaultCohesive
// PUBLIC METHODS /////////////////////////////////////////////////
@@ -85,8 +85,7 @@
*
* @returns Fields associated with fault.
*/
- const pylith::topology::Fields<topology::Field<pylith::topology::SubMesh> >*
- fields(void) const;
+ const pylith::topology::Fields<topology::Field<pylith::topology::Mesh> >* fields(void) const;
}; // class FaultCohesive
Modified: short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveDyn.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveDyn.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveDyn.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -137,7 +137,7 @@
* @param fields Solution fields.
* @returns Vertex field.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>&
+ const pylith::topology::Field<pylith::topology::Mesh>&
vertexField(const char* name,
const pylith::topology::SolutionFields* fields =0);
@@ -147,7 +147,7 @@
* @param fields Solution fields.
* @returns Cell field.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>&
+ const pylith::topology::Field<pylith::topology::Mesh>&
cellField(const char* name,
const pylith::topology::SolutionFields* fields =0);
Modified: short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveImpulses.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveImpulses.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveImpulses.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -109,7 +109,7 @@
* @param fields Solution fields.
* @returns Vertex field.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>&
+ const pylith::topology::Field<pylith::topology::Mesh>&
vertexField(const char* name,
const pylith::topology::SolutionFields* fields =0);
@@ -119,7 +119,7 @@
* @param fields Solution fields.
* @returns Cell field.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>&
+ const pylith::topology::Field<pylith::topology::Mesh>&
cellField(const char* name,
const pylith::topology::SolutionFields* fields =0);
Modified: short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveKin.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveKin.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveKin.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -86,7 +86,7 @@
* @param fields Solution fields.
* @returns Vertex field.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>&
+ const pylith::topology::Field<pylith::topology::Mesh>&
vertexField(const char* name,
const pylith::topology::SolutionFields* fields =0);
@@ -96,7 +96,7 @@
* @param fields Solution fields.
* @returns Cell field.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>&
+ const pylith::topology::Field<pylith::topology::Mesh>&
cellField(const char* name,
const pylith::topology::SolutionFields* fields =0);
Modified: short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveTract.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveTract.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/FaultCohesiveTract.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -86,7 +86,7 @@
*
* @returns Vertex field.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>&
+ const pylith::topology::Field<pylith::topology::Mesh>&
vertexField(const char* name,
const pylith::topology::SolutionFields* fields =0);
@@ -97,7 +97,7 @@
*
* @returns Cell field.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>&
+ const pylith::topology::Field<pylith::topology::Mesh>&
cellField(const char* name,
const pylith::topology::SolutionFields* fields =0);
Modified: short/3D/PyLith/trunk/modulesrc/faults/LiuCosSlipFn.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/LiuCosSlipFn.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/LiuCosSlipFn.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -67,7 +67,7 @@
* @param normalizer Nondimensionalization of scales.
* @param originTime Origin time for earthquake source.
*/
- void initialize(const pylith::topology::SubMesh& faultMesh,
+ void initialize(const pylith::topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime =0.0);
@@ -78,20 +78,20 @@
*
* @returns Slip vector as left-lateral/reverse/normal.
*/
- void slip(pylith::topology::Field<pylith::topology::SubMesh>* const slipField,
+ void slip(pylith::topology::Field<pylith::topology::Mesh>* const slipField,
const PylithScalar t);
/** Get final slip.
*
* @returns Final slip.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>& finalSlip(void);
+ const pylith::topology::Field<pylith::topology::Mesh>& finalSlip(void);
/** Get time when slip begins at each point.
*
* @returns Time when slip begins.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>& slipTime(void);
+ const pylith::topology::Field<pylith::topology::Mesh>& slipTime(void);
}; // class LiuCosSlipFn
Modified: short/3D/PyLith/trunk/modulesrc/faults/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/Makefile.am 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/Makefile.am 2013-05-13 23:33:37 UTC (rev 22058)
@@ -40,7 +40,7 @@
FaultCohesiveDyn.i \
FaultCohesiveImpulses.i \
FaultCohesiveTract.i \
- ../topology/SubMesh.i \
+ ../topology/Mesh.i \
../feassemble/Quadrature.i \
../feassemble/Integrator.i
Modified: short/3D/PyLith/trunk/modulesrc/faults/SlipTimeFn.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/SlipTimeFn.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/SlipTimeFn.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -49,7 +49,7 @@
* @param originTime Origin time for earthquake source.
*/
virtual
- void initialize(const pylith::topology::SubMesh& faultMesh,
+ void initialize(const pylith::topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime =0.0) = 0;
@@ -61,7 +61,7 @@
* @returns Slip vector as left-lateral/reverse/normal.
*/
virtual
- void slip(pylith::topology::Field<pylith::topology::SubMesh>* const slipField,
+ void slip(pylith::topology::Field<pylith::topology::Mesh>* const slipField,
const PylithScalar t) = 0;
/** Get final slip.
@@ -69,20 +69,20 @@
* @returns Final slip.
*/
virtual
- const pylith::topology::Field<pylith::topology::SubMesh>& finalSlip(void) = 0;
+ const pylith::topology::Field<pylith::topology::Mesh>& finalSlip(void) = 0;
/** Get time when slip begins at each point.
*
* @returns Time when slip begins.
*/
virtual
- const pylith::topology::Field<pylith::topology::SubMesh>& slipTime(void) = 0;
+ const pylith::topology::Field<pylith::topology::Mesh>& slipTime(void) = 0;
/** Get parameter fields.
*
* @returns Parameter fields.
*/
- const pylith::topology::Fields<pylith::topology::Field<pylith::topology::SubMesh> >*
+ const pylith::topology::Fields<pylith::topology::Field<pylith::topology::Mesh> >*
parameterFields(void) const;
}; // class SlipTimeFn
Modified: short/3D/PyLith/trunk/modulesrc/faults/StepSlipFn.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/StepSlipFn.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/StepSlipFn.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -59,7 +59,7 @@
* @param normalizer Nondimensionalization of scales.
* @param originTime Origin time for earthquake source.
*/
- void initialize(const pylith::topology::SubMesh& faultMesh,
+ void initialize(const pylith::topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime =0.0);
@@ -70,20 +70,20 @@
*
* @returns Slip vector as left-lateral/reverse/normal.
*/
- void slip(pylith::topology::Field<pylith::topology::SubMesh>* const slipField,
+ void slip(pylith::topology::Field<pylith::topology::Mesh>* const slipField,
const PylithScalar t);
/** Get final slip.
*
* @returns Final slip.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>& finalSlip(void);
+ const pylith::topology::Field<pylith::topology::Mesh>& finalSlip(void);
/** Get time when slip begins at each point.
*
* @returns Time when slip begins.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>& slipTime(void);
+ const pylith::topology::Field<pylith::topology::Mesh>& slipTime(void);
}; // class StepSlipFn
Modified: short/3D/PyLith/trunk/modulesrc/faults/TimeHistorySlipFn.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/TimeHistorySlipFn.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/TimeHistorySlipFn.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -65,7 +65,7 @@
* @param normalizer Nondimensionalization of scales.
* @param originTime Origin time for earthquake source.
*/
- void initialize(const pylith::topology::SubMesh& faultMesh,
+ void initialize(const pylith::topology::Mesh& faultMesh,
const spatialdata::units::Nondimensional& normalizer,
const PylithScalar originTime =0.0);
@@ -76,20 +76,20 @@
*
* @returns Slip vector as left-lateral/reverse/normal.
*/
- void slip(pylith::topology::Field<pylith::topology::SubMesh>* const slipField,
+ void slip(pylith::topology::Field<pylith::topology::Mesh>* const slipField,
const PylithScalar t);
/** Get final slip.
*
* @returns Final slip.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>& finalSlip(void);
+ const pylith::topology::Field<pylith::topology::Mesh>& finalSlip(void);
/** Get time when slip begins at each point.
*
* @returns Time when slip begins.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>& slipTime(void);
+ const pylith::topology::Field<pylith::topology::Mesh>& slipTime(void);
}; // class TimeHistorySlipFn
Modified: short/3D/PyLith/trunk/modulesrc/faults/TractPerturbation.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/TractPerturbation.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/TractPerturbation.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -51,7 +51,7 @@
*
* @returns Parameter fields.
*/
- const pylith::topology::Fields<topology::Field<pylith::topology::SubMesh> >* parameterFields(void) const;
+ const pylith::topology::Fields<topology::Field<pylith::topology::Mesh> >* parameterFields(void) const;
/** Initialize slip time function.
*
@@ -59,8 +59,8 @@
* @param faultOrientation Orientation of fault.
* @param normalizer Nondimensionalization of scales.
*/
- void initialize(const pylith::topology::SubMesh& faultMesh,
- const pylith::topology::Field<pylith::topology::SubMesh>& faultOrientation,
+ void initialize(const pylith::topology::Mesh& faultMesh,
+ const pylith::topology::Field<pylith::topology::Mesh>& faultOrientation,
const spatialdata::units::Nondimensional& normalizer);
/** Calculate spatial and temporal variation of value.
@@ -83,7 +83,7 @@
*
* @returns Traction vector field.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>&
+ const pylith::topology::Field<pylith::topology::Mesh>&
vertexField(const char* name,
pylith::topology::SolutionFields* const fields =0);
Modified: short/3D/PyLith/trunk/modulesrc/faults/faults.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/faults/faults.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/faults/faults.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -37,7 +37,7 @@
#include "pylith/faults/FaultCohesiveImpulses.hh"
#include "pylith/faults/FaultCohesiveTract.hh"
-#include "pylith/topology/SubMesh.hh"
+#include "pylith/topology/Mesh.hh"
#include "pylith/feassemble/Quadrature.hh"
#include "pylith/feassemble/Integrator.hh"
%}
@@ -66,13 +66,13 @@
%}
// Interfaces
-%include "../topology/SubMesh.i" // ISA Integrator<Quadrature<SubMesh> >
-%include "../feassemble/Quadrature.i" // ISA Integrator<Quadrature<SubMesh> >
-%include "../feassemble/Integrator.i" // ISA Integrator<Quadrature<SubMesh> >
+%include "../topology/Mesh.i" // ISA Integrator<Quadrature<Mesh> >
+%include "../feassemble/Quadrature.i" // ISA Integrator<Quadrature<Mesh> >
+%include "../feassemble/Integrator.i" // ISA Integrator<Quadrature<Mesh> >
%include "../bc/TimeDependent.i" // ISA TimeDependent
// Template instatiation
-%template(SubMeshIntegrator) pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::SubMesh > >;
+%template(MeshIntegrator) pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::Mesh > >;
%include "SlipTimeFn.i"
%include "StepSlipFn.i"
Modified: short/3D/PyLith/trunk/modulesrc/feassemble/feassemble.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/feassemble/feassemble.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/feassemble/feassemble.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -37,7 +37,6 @@
#include "pylith/feassemble/QuadratureRefCell.hh"
#include "pylith/topology/Mesh.hh"
-#include "pylith/topology/SubMesh.hh"
#include "pylith/feassemble/Quadrature.hh"
#include "pylith/feassemble/ElasticityImplicit.hh"
#include "pylith/feassemble/ElasticityExplicit.hh"
@@ -103,7 +102,6 @@
// Template instatiation
%template(MeshQuadrature) pylith::feassemble::Quadrature<pylith::topology::Mesh>;
-%template(SubMeshQuadrature) pylith::feassemble::Quadrature<pylith::topology::SubMesh>;
// End of file
Modified: short/3D/PyLith/trunk/modulesrc/friction/FrictionModel.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/friction/FrictionModel.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/friction/FrictionModel.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -97,8 +97,8 @@
* @param quadrature Quadrature for finite-element integration
*/
virtual
- void initialize(const pylith::topology::SubMesh& mesh,
- pylith::feassemble::Quadrature<pylith::topology::SubMesh>* quadrature);
+ void initialize(const pylith::topology::Mesh& mesh,
+ pylith::feassemble::Quadrature<pylith::topology::Mesh>* quadrature);
/** Check whether friction model has a field as a property or
* state variable.
@@ -116,13 +116,13 @@
* @param name Name of field to retrieve.
* @returns Field over fault interface cells.
*/
- const pylith::topology::Field<pylith::topology::SubMesh>& getField(const char* name);
+ const pylith::topology::Field<pylith::topology::Mesh>& getField(const char* name);
/** Get the field with all properties and state variables.
*
* @returns Properties field.
*/
- const pylith::topology::Fields<pylith::topology::Field<pylith::topology::SubMesh> >& fieldsPropsStateVars() const;
+ const pylith::topology::Fields<pylith::topology::Field<pylith::topology::Mesh> >& fieldsPropsStateVars() const;
/** Retrieve parameters for physical properties and state variables
* for vertex.
Modified: short/3D/PyLith/trunk/modulesrc/include/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/modulesrc/include/Makefile.am 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/include/Makefile.am 2013-05-13 23:33:37 UTC (rev 22058)
@@ -24,8 +24,7 @@
chararray.i \
scalartypemaps.i \
eqkinsrcarray.i \
- integratorarray.i \
- submeshfield.i
+ integratorarray.i
# End of file
Modified: short/3D/PyLith/trunk/modulesrc/include/integratorarray.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/include/integratorarray.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/include/integratorarray.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -52,41 +52,4 @@
delete[] $1;
}
-// ----------------------------------------------------------------------
-// List of submesh integrators.
-%typemap(in) (pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::SubMesh> >** integrators,
- const int numIntegrators)
-{
- // Check to make sure input is a list.
- if (PyList_Check($input)) {
- const int size = PyList_Size($input);
- $2 = size;
- $1 = (size > 0) ? new pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::SubMesh> >*[size] : 0;
- for (int i = 0; i < size; i++) {
- PyObject* s = PyList_GetItem($input,i);
- pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::SubMesh> >* integrator = 0;
- int err = SWIG_ConvertPtr(s, (void**) &integrator,
- $descriptor(pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::SubMesh> >*),
- 0);
- if (SWIG_IsOK(err))
- $1[i] = (pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::SubMesh> >*) integrator;
- else {
- PyErr_SetString(PyExc_TypeError, "List must contain submesh integrators.");
- delete[] $1;
- return NULL;
- } // if
- } // for
- } else {
- PyErr_SetString(PyExc_TypeError, "Expected list of submesh integrators.");
- return NULL;
- } // if/else
-} // typemap(in) [List of submesh integrators.]
-
-// This cleans up the array we malloc'd before the function call
-%typemap(freearg) (pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::SubMesh> >** integrators,
- const int numIntegrators) {
- delete[] $1;
-}
-
-
// End of file
Deleted: short/3D/PyLith/trunk/modulesrc/include/submeshfield.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/include/submeshfield.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/include/submeshfield.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,43 +0,0 @@
-// -*- C++ -*-
-//
-// ======================================================================
-//
-// Brad T. Aagaard, U.S. Geological Survey
-// Charles A. Williams, GNS Science
-// Matthew G. Knepley, University of Chicago
-//
-// This code was developed as part of the Computational Infrastructure
-// for Geodynamics (http://geodynamics.org).
-//
-// Copyright (c) 2010-2013 University of California, Davis
-//
-// See COPYING for license information.
-//
-// ======================================================================
-//
-
-// ----------------------------------------------------------------------
-// const Field<SubMesh>::Mesh (SubMesh)
-%typemap(in) (const pylith::topology::Field<pylith::topology::SubMesh>::Mesh& mesh)
-{
- pylith::topology::Field<pylith::topology::SubMesh>::Mesh* submesh = 0;
- int err = SWIG_ConvertPtr($input, (void**) &submesh,
- $descriptor(pylith::topology::Field<pylith::topology::SubMesh>::Mesh*),
- 0);
- if (SWIG_IsOK(err))
- $1 = (pylith::topology::Field<pylith::topology::SubMesh>::Mesh*) submesh;
- else {
- err = SWIG_ConvertPtr($input, (void**) &submesh,
- $descriptor(pylith::topology::SubMesh*),
- 0);
- if (SWIG_IsOK(err))
- $1 = (pylith::topology::Field<pylith::topology::SubMesh>::Mesh*) submesh;
- else {
- PyErr_SetString(PyExc_TypeError, "Argument must be a submesh.");
- return NULL;
- } // if
- } // if/else
-} // typemap(in)
-
-
-// End of file
Modified: short/3D/PyLith/trunk/modulesrc/meshio/OutputSolnPoints.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/meshio/OutputSolnPoints.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/meshio/OutputSolnPoints.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -25,7 +25,7 @@
namespace pylith {
namespace meshio {
-%template(_MeshOutputManager) pylith::meshio::OutputManager<pylith::topology::Mesh, pylith::topology::Field<pylith::topology::Mesh> >;
+%template(_PointsOutputManager) pylith::meshio::OutputManager<pylith::topology::Mesh, pylith::topology::Field<pylith::topology::Mesh> >;
class pylith::meshio::OutputSolnPoints : public OutputManager<pylith::topology::Mesh, pylith::topology::Field<pylith::topology::Mesh> >
Modified: short/3D/PyLith/trunk/modulesrc/meshio/OutputSolnSubset.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/meshio/OutputSolnSubset.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/meshio/OutputSolnSubset.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -22,12 +22,12 @@
* @brief Python interface to C++ OutputSolnSubset object.
*/
-%template(_SubMeshOutputManager) pylith::meshio::OutputManager<pylith::topology::SubMesh, pylith::topology::Field<pylith::topology::Mesh> >;
+%template(_MeshOutputManager) pylith::meshio::OutputManager<pylith::topology::Mesh, pylith::topology::Field<pylith::topology::Mesh> >;
namespace pylith {
namespace meshio {
- class pylith::meshio::OutputSolnSubset : public OutputManager<pylith::topology::SubMesh, pylith::topology::Field<pylith::topology::Mesh> >
+ class pylith::meshio::OutputSolnSubset : public OutputManager<pylith::topology::Mesh, pylith::topology::Field<pylith::topology::Mesh> >
{ // OutputSolnSubset
// PUBLIC METHODS /////////////////////////////////////////////////
@@ -58,7 +58,7 @@
*
* @returns Mesh associated with subdomain.
*/
- const pylith::topology::SubMesh& subdomainMesh(const pylith::topology::Mesh& mesh);
+ const pylith::topology::Mesh& subdomainMesh(const pylith::topology::Mesh& mesh);
}; // OutputSolnSubset
Modified: short/3D/PyLith/trunk/modulesrc/meshio/meshio.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/meshio/meshio.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/meshio/meshio.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -92,35 +92,22 @@
// Template instatiation
%template(MeshVertexFilter) pylith::meshio::VertexFilter<pylith::topology::Field<pylith::topology::Mesh> >;
-%template(SubMeshVertexFilter) pylith::meshio::VertexFilter<pylith::topology::Field<pylith::topology::SubMesh> >;
%template(MeshVertexFilterVecNorm) pylith::meshio::VertexFilterVecNorm<pylith::topology::Field<pylith::topology::Mesh> >;
-%template(SubMeshVertexFilterVecNorm) pylith::meshio::VertexFilterVecNorm<pylith::topology::Field<pylith::topology::SubMesh> >;
%template(MeshCellFilter) pylith::meshio::CellFilter<pylith::topology::Mesh, pylith::topology::Field<pylith::topology::Mesh> >;
-%template(SubMeshCellFilter) pylith::meshio::CellFilter<pylith::topology::SubMesh, pylith::topology::Field<pylith::topology::SubMesh> >;
%template(MeshCellFilterAvg) pylith::meshio::CellFilterAvg<pylith::topology::Mesh, pylith::topology::Field<pylith::topology::Mesh> >;
-%template(SubMeshCellFilterAvg) pylith::meshio::CellFilterAvg<pylith::topology::SubMesh, pylith::topology::Field<pylith::topology::SubMesh> >;
%template(MeshDataWriter) pylith::meshio::DataWriter<pylith::topology::Mesh, pylith::topology::Field<pylith::topology::Mesh> >;
-%template(SubMeshDataWriter) pylith::meshio::DataWriter<pylith::topology::SubMesh, pylith::topology::Field<pylith::topology::Mesh> >;
-%template(SubSubMeshDataWriter) pylith::meshio::DataWriter<pylith::topology::SubMesh, pylith::topology::Field<pylith::topology::SubMesh> >;
%template(MeshDataWriterVTK) pylith::meshio::DataWriterVTK<pylith::topology::Mesh, pylith::topology::Field<pylith::topology::Mesh> >;
-%template(SubMeshDataWriterVTK) pylith::meshio::DataWriterVTK<pylith::topology::SubMesh, pylith::topology::Field<pylith::topology::Mesh> >;
-%template(SubSubMeshDataWriterVTK) pylith::meshio::DataWriterVTK<pylith::topology::SubMesh, pylith::topology::Field<pylith::topology::SubMesh> >;
%template(PointsDataWriterVTK) pylith::meshio::DataWriterVTK<pylith::topology::Mesh, pylith::topology::Field<pylith::topology::Mesh> >;
#if defined(ENABLE_HDF5)
%template(MeshDataWriterHDF5) pylith::meshio::DataWriterHDF5<pylith::topology::Mesh, pylith::topology::Field<pylith::topology::Mesh> >;
-%template(SubMeshDataWriterHDF5) pylith::meshio::DataWriterHDF5<pylith::topology::SubMesh, pylith::topology::Field<pylith::topology::Mesh> >;
-%template(SubSubMeshDataWriterHDF5) pylith::meshio::DataWriterHDF5<pylith::topology::SubMesh, pylith::topology::Field<pylith::topology::SubMesh> >;
%template(MeshDataWriterHDF5Ext) pylith::meshio::DataWriterHDF5Ext<pylith::topology::Mesh, pylith::topology::Field<pylith::topology::Mesh> >;
-%template(SubMeshDataWriterHDF5Ext) pylith::meshio::DataWriterHDF5Ext<pylith::topology::SubMesh, pylith::topology::Field<pylith::topology::Mesh> >;
-%template(SubSubMeshDataWriterHDF5Ext) pylith::meshio::DataWriterHDF5Ext<pylith::topology::SubMesh, pylith::topology::Field<pylith::topology::SubMesh> >;
#endif
%template(MeshOutputManager) pylith::meshio::OutputManager<pylith::topology::Mesh, pylith::topology::Field<pylith::topology::Mesh> >;
-%template(SubMeshOutputManager) pylith::meshio::OutputManager<pylith::topology::SubMesh, pylith::topology::Field<pylith::topology::SubMesh> >;
// End of file
Modified: short/3D/PyLith/trunk/modulesrc/problems/Formulation.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/problems/Formulation.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/problems/Formulation.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -103,7 +103,7 @@
* @param integrators Integrators over lower-dimension meshes.
* @param numIntegrators Number of integrators.
*/
- void submeshIntegrators(pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::SubMesh> >** integrators,
+ void submeshIntegrators(pylith::feassemble::Integrator<pylith::feassemble::Quadrature<pylith::topology::Mesh> >** integrators,
const int numIntegrators);
/** Update handles and parameters for reforming the Jacobian and
Modified: short/3D/PyLith/trunk/modulesrc/topology/Jacobian.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/topology/Jacobian.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/topology/Jacobian.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -42,17 +42,6 @@
const char* matrixType ="aij",
const bool blockOkay =false);
- /** Constructor with field for submesh.
- *
- * @param field Fields associated with submesh and solution of the problem.
- * @param matrixType Type of PETSc sparse matrix.
- * @param blockOkay True if okay to use block size equal to fiberDim
- * (all or none of the DOF at each point are constrained).
- */
- Jacobian(const Field<SubMesh>& field,
- const char* matrixType ="aij",
- const bool blockOkay =true);
-
/// Destructor.
~Jacobian(void);
Modified: short/3D/PyLith/trunk/modulesrc/topology/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/modulesrc/topology/Makefile.am 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/topology/Makefile.am 2013-05-13 23:33:37 UTC (rev 22058)
@@ -26,7 +26,6 @@
swig_sources = \
topology.i \
Mesh.i \
- SubMesh.i \
MeshOps.i \
FieldBase.i \
Field.i \
Modified: short/3D/PyLith/trunk/modulesrc/topology/Mesh.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/topology/Mesh.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/topology/Mesh.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -106,12 +106,6 @@
*/
int numCells(void) const;
- /** Set MPI communicator associated with mesh.
- *
- * @param value MPI communicator.
- */
- void comm(const MPI_Comm value);
-
/** Get MPI communicator associated with mesh.
*
* @returns MPI communicator.
Deleted: short/3D/PyLith/trunk/modulesrc/topology/SubMesh.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/topology/SubMesh.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/topology/SubMesh.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,123 +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) 2010-2013 University of California, Davis
-//
-// See COPYING for license information.
-//
-// ======================================================================
-//
-
-/**
- * @file modulesrc/topology/SubMesh.i
- *
- * @brief Python interface to C++ Mesh object.
- */
-
-namespace pylith {
- namespace topology {
-
- class SubMesh
- { // SubMesh
-
- // PUBLIC METHODS /////////////////////////////////////////////////
- public :
-
- /// Default constructor.
- SubMesh(void);
-
- /** Constructor with mesh and label for vertices marking boundary.
- *
- * @param mesh Finite-element mesh over domain.
- * @param label Label for vertices marking boundary.
- */
- SubMesh(const pylith::topology::Mesh& mesh,
- const char* label);
-
- /// Default destructor
- ~SubMesh(void);
-
- /// Deallocate PETSc and local data structures.
- virtual
- void deallocate(void);
-
- /** Create Sieve mesh.
- *
- * @param mesh Finite-element mesh over domain.
- * @param label Label for vertices marking boundary.
- */
- void createSubMesh(const pylith::topology::Mesh& mesh,
- const char* label);
-
- /** Get coordinate system.
- *
- * @returns Coordinate system.
- */
- const spatialdata::geocoords::CoordSys* coordsys(void) const;
-
- /** Set debug flag.
- *
- * @param value Turn on debugging if true.
- */
- void debug(const bool value);
-
- /** Get debug flag.
- *
- * @param Get debugging flag.
- */
- bool debug(void) const;
-
- /** Get dimension of mesh.
- *
- * @returns Dimension of mesh.
- */
- int dimension(void) const;
-
- /** Get representative cone size for mesh.
- *
- * @returns Representative cone size for mesh.
- */
- int coneSize(void) const;
-
- /** Get number of vertices in mesh.
- *
- * @returns Number of vertices in mesh.
- */
- int numVertices(void) const;
-
- /** Get number of cells in mesh.
- *
- * @returns Number of cells in mesh.
- */
- int numCells(void) const;
-
- /** Get MPI communicator associated with mesh.
- *
- * @returns MPI communicator.
- */
- const MPI_Comm comm(void) const;
-
- /// Initialize the finite-element mesh.
- void initialize(void);
-
- /** Print mesh to stdout.
- *
- * @param label Label for mesh.
- */
- void view(const char* label);
-
- }; // SubMesh
-
- } // topology
-} // pylith
-
-
-// End of file
Modified: short/3D/PyLith/trunk/modulesrc/topology/topology.i
===================================================================
--- short/3D/PyLith/trunk/modulesrc/topology/topology.i 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/modulesrc/topology/topology.i 2013-05-13 23:33:37 UTC (rev 22058)
@@ -22,7 +22,6 @@
// Header files for module C++ code
%{
#include "pylith/topology/Mesh.hh"
-#include "pylith/topology/SubMesh.hh"
#include "pylith/topology/MeshOps.hh"
#include "pylith/topology/FieldBase.hh"
#include "pylith/topology/Field.hh"
@@ -45,7 +44,6 @@
%include "typemaps.i"
%include "../include/chararray.i"
-%include "../include/submeshfield.i"
%include "../include/scalartypemaps.i"
// Numpy interface stuff
@@ -59,7 +57,6 @@
// Interfaces
%include "Mesh.i"
-%include "SubMesh.i"
%include "MeshOps.i"
%include "FieldBase.i"
%include "Field.i"
@@ -73,16 +70,11 @@
// Template instatiation
%template(MeshField) pylith::topology::Field<pylith::topology::Mesh>;
-%template(SubMeshField) pylith::topology::Field<pylith::topology::SubMesh>;
%template(MeshFields) pylith::topology::Fields<pylith::topology::Field<pylith::topology::Mesh> >;
-%template(SubMeshFields) pylith::topology::Fields<pylith::topology::Field<pylith::topology::SubMesh> >;
%extend pylith::topology::Field<pylith::topology::Mesh> {
%template(createScatterMesh) createScatter<pylith::topology::Mesh>;
}
-%extend pylith::topology::Field<pylith::topology::Mesh> {
- %template(createScatterSubMesh) createScatter<pylith::topology::SubMesh>;
- }
// End of file
Modified: short/3D/PyLith/trunk/pylith/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/pylith/Makefile.am 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/Makefile.am 2013-05-13 23:33:37 UTC (rev 22058)
@@ -93,12 +93,9 @@
meshio/__init__.py \
meshio/CellFilter.py \
meshio/CellFilterAvgMesh.py \
- meshio/CellFilterAvgSubMesh.py \
meshio/DataWriter.py \
meshio/DataWriterVTK.py \
meshio/DataWriterVTKMesh.py \
- meshio/DataWriterVTKSubMesh.py \
- meshio/DataWriterVTKSubSubMesh.py \
meshio/DataWriterVTKPoints.py \
meshio/MeshIOObj.py \
meshio/MeshIOAscii.py \
@@ -106,7 +103,6 @@
meshio/OutputDirichlet.py \
meshio/OutputManager.py \
meshio/OutputManagerMesh.py \
- meshio/OutputManagerSubMesh.py \
meshio/OutputSoln.py \
meshio/OutputFaultKin.py \
meshio/OutputFaultDyn.py \
@@ -119,7 +115,6 @@
meshio/SingleOutput.py \
meshio/VertexFilter.py \
meshio/VertexFilterVecNormMesh.py \
- meshio/VertexFilterVecNormSubMesh.py \
mpi/__init__.py \
mpi/Communicator.py \
perf/__init__.py \
@@ -155,7 +150,6 @@
topology/__init__.py \
topology/Distributor.py \
topology/Mesh.py \
- topology/SubMesh.py \
topology/Field.py \
topology/Fields.py \
topology/SolutionFields.py \
@@ -193,12 +187,8 @@
nobase_pkgpyexec_PYTHON += \
meshio/DataWriterHDF5.py \
meshio/DataWriterHDF5Mesh.py \
- meshio/DataWriterHDF5SubMesh.py \
- meshio/DataWriterHDF5SubSubMesh.py \
meshio/DataWriterHDF5Ext.py \
meshio/DataWriterHDF5ExtMesh.py \
- meshio/DataWriterHDF5ExtSubMesh.py \
- meshio/DataWriterHDF5ExtSubSubMesh.py \
meshio/Xdmf.py
endif
Modified: short/3D/PyLith/trunk/pylith/bc/AbsorbingDampers.py
===================================================================
--- short/3D/PyLith/trunk/pylith/bc/AbsorbingDampers.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/bc/AbsorbingDampers.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -55,9 +55,9 @@
import pyre.inventory
- from pylith.feassemble.Quadrature import SubMeshQuadrature
+ from pylith.feassemble.Quadrature import MeshQuadrature
quadrature = pyre.inventory.facility("quadrature",
- factory=SubMeshQuadrature)
+ factory=MeshQuadrature)
quadrature.meta['tip'] = "Quadrature object for numerical integration."
from spatialdata.spatialdb.SimpleDB import SimpleDB
Modified: short/3D/PyLith/trunk/pylith/bc/Neumann.py
===================================================================
--- short/3D/PyLith/trunk/pylith/bc/Neumann.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/bc/Neumann.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -44,9 +44,9 @@
import pyre.inventory
- from pylith.feassemble.Quadrature import SubMeshQuadrature
+ from pylith.feassemble.Quadrature import MeshQuadrature
bcQuadrature = pyre.inventory.facility("quadrature",
- factory=SubMeshQuadrature)
+ factory=MeshQuadrature)
bcQuadrature.meta['tip'] = "Quadrature object for numerical integration."
from pylith.meshio.OutputNeumann import OutputNeumann
Modified: short/3D/PyLith/trunk/pylith/faults/Fault.py
===================================================================
--- short/3D/PyLith/trunk/pylith/faults/Fault.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/faults/Fault.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -97,8 +97,8 @@
"with fault normal; applies to fault surfaces " \
"in 2-D and 3-D)."
- from pylith.feassemble.Quadrature import SubMeshQuadrature
- faultQuadrature = pyre.inventory.facility("quadrature", factory=SubMeshQuadrature)
+ from pylith.feassemble.Quadrature import MeshQuadrature
+ faultQuadrature = pyre.inventory.facility("quadrature", factory=MeshQuadrature)
faultQuadrature.meta['tip'] = "Quadrature object for numerical integration."
from pylith.perf.MemoryLogger import MemoryLogger
Modified: short/3D/PyLith/trunk/pylith/feassemble/Quadrature.py
===================================================================
--- short/3D/PyLith/trunk/pylith/feassemble/Quadrature.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/feassemble/Quadrature.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -157,50 +157,4 @@
return
-# ----------------------------------------------------------------------
-from feassemble import SubMeshQuadrature as ModuleSubMeshQuadrature
-
-# SubMeshQuadrature class
-class SubMeshQuadrature(QuadratureBase, ModuleSubMeshQuadrature):
- """
- Python object for integrating over finite-elements using quadrature.
- """
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, name="submeshquadrature"):
- """
- Constructor.
- """
- QuadratureBase.__init__(self, name)
- ModuleSubMeshQuadrature.__init__(self)
- return
-
-
- # PRIVATE METHODS ////////////////////////////////////////////////////
-
- def _initialize(self, cell):
- """
- Initialize C++ quadrature object.
- """
- import numpy
- from pylith.utils.utils import sizeofPylithScalar
- size = sizeofPylithScalar()
- if 8 == size:
- ModuleSubMeshQuadrature.initialize(self, cell.basis,
- cell.basisDeriv,
- cell.quadPts,
- cell.quadWts,
- cell.geometry.spaceDim())
- elif 4 == size:
- ModuleSubMeshQuadrature.initialize(self, numpy.float32(cell.basis),
- numpy.float32(cell.basisDeriv),
- numpy.float32(cell.quadPts),
- numpy.float32(cell.quadWts),
- cell.geometry.spaceDim())
- else:
- raise ValueError("Unknown size for PylithScalar")
- return
-
-
# End of file
Deleted: short/3D/PyLith/trunk/pylith/meshio/CellFilterAvgSubMesh.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/CellFilterAvgSubMesh.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/CellFilterAvgSubMesh.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,76 +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) 2010-2013 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ----------------------------------------------------------------------
-#
-
-## @file pyre/meshio/CellFilterAvgSubMesh.py
-##
-## @brief Python class for averageing cell fields over each cell's
-## quadrature points when writing finite-element data.
-##
-## Factory: output_cell_filter
-
-from CellFilter import CellFilter
-from meshio import SubMeshCellFilterAvg as ModuleCellFilterAvg
-
-# CellFilterAvgSubMesh class
-class CellFilterAvgSubMesh(CellFilter, ModuleCellFilterAvg):
- """
- Python class for average cell fields over each cell's quadrature
- points when writing finite-element data.
-
- Factory: output_cell_filter
- """
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, name="cellfilteravgsubmesh"):
- """
- Constructor.
- """
- CellFilter.__init__(self, name)
- ModuleCellFilterAvg.__init__(self)
- return
-
-
- def initialize(self, quadrature):
- """
- Initialize output manager.
- """
- self.quadrature(quadrature)
- return
-
-
- # PRIVATE METHODS ///////////////////////////////////////////////////
-
- def _modelMemoryUse(self):
- """
- Model memory allocation.
- """
- self.perfLogger.logFields('Output', self.fieldAvg())
- return
-
-
-# FACTORIES ////////////////////////////////////////////////////////////
-
-def output_cell_filter():
- """
- Factory associated with CellFilter.
- """
- return CellFilterAvgSubMesh()
-
-
-# End of file
Deleted: short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5ExtSubMesh.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5ExtSubMesh.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5ExtSubMesh.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,69 +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) 2010-2013 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ----------------------------------------------------------------------
-#
-
-## @file pyre/meshio/DataWriterHDF5ExtSubMesh.py
-##
-## @brief Python object for writing finite-element data to HDF5Ext file.
-
-from DataWriterHDF5Ext import DataWriterHDF5Ext
-from meshio import SubMeshDataWriterHDF5Ext as ModuleDataWriterHDF5Ext
-
-# DataWriterHDF5ExtSubMesh class
-class DataWriterHDF5ExtSubMesh(DataWriterHDF5Ext, ModuleDataWriterHDF5Ext):
- """
- Python object for writing finite-element data to HDF5Ext file.
-
- Inventory
-
- Factory: output_data_writer
- """
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, name="datawriterhdf5submesh"):
- """
- Constructor.
- """
- DataWriterHDF5Ext.__init__(self, name)
- ModuleDataWriterHDF5Ext.__init__(self)
- return
-
-
- def initialize(self, normalizer):
- """
- Initialize writer.
- """
- DataWriterHDF5Ext.initialize(self, normalizer)
-
- timeScale = normalizer.timeScale()
-
- ModuleDataWriterHDF5Ext.filename(self, self.filename)
- ModuleDataWriterHDF5Ext.timeScale(self, timeScale.value)
- return
-
-
-# FACTORIES ////////////////////////////////////////////////////////////
-
-def data_writer():
- """
- Factory associated with DataWriter.
- """
- return DataWriterHDF5ExtSubMesh()
-
-
-# End of file
Deleted: short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5ExtSubSubMesh.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5ExtSubSubMesh.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5ExtSubSubMesh.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,69 +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) 2010-2013 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ----------------------------------------------------------------------
-#
-
-## @file pyre/meshio/DataWriterHDF5ExtSubSubMesh.py
-##
-## @brief Python object for writing finite-element data to HDF5Ext file.
-
-from DataWriterHDF5Ext import DataWriterHDF5Ext
-from meshio import SubSubMeshDataWriterHDF5Ext as ModuleDataWriterHDF5Ext
-
-# DataWriterHDF5ExtSubSubMesh class
-class DataWriterHDF5ExtSubSubMesh(DataWriterHDF5Ext, ModuleDataWriterHDF5Ext):
- """
- Python object for writing finite-element data to HDF5Ext file.
-
- Inventory
-
- Factory: output_data_writer
- """
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, name="datawriterhdf5submesh"):
- """
- Constructor.
- """
- DataWriterHDF5Ext.__init__(self, name)
- ModuleDataWriterHDF5Ext.__init__(self)
- return
-
-
- def initialize(self, normalizer):
- """
- Initialize writer.
- """
- DataWriterHDF5Ext.initialize(self, normalizer)
-
- timeScale = normalizer.timeScale()
-
- ModuleDataWriterHDF5Ext.filename(self, self.filename)
- ModuleDataWriterHDF5Ext.timeScale(self, timeScale.value)
- return
-
-
-# FACTORIES ////////////////////////////////////////////////////////////
-
-def data_writer():
- """
- Factory associated with DataWriter.
- """
- return DataWriterHDF5ExtSubSubMesh()
-
-
-# End of file
Deleted: short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5SubMesh.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5SubMesh.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5SubMesh.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,69 +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) 2010-2013 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ----------------------------------------------------------------------
-#
-
-## @file pyre/meshio/DataWriterHDF5SubMesh.py
-##
-## @brief Python object for writing finite-element data to HDF5 file.
-
-from DataWriterHDF5 import DataWriterHDF5
-from meshio import SubMeshDataWriterHDF5 as ModuleDataWriterHDF5
-
-# DataWriterHDF5SubMesh class
-class DataWriterHDF5SubMesh(DataWriterHDF5, ModuleDataWriterHDF5):
- """
- Python object for writing finite-element data to HDF5 file.
-
- Inventory
-
- Factory: output_data_writer
- """
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, name="datawriterhdf5submesh"):
- """
- Constructor.
- """
- DataWriterHDF5.__init__(self, name)
- ModuleDataWriterHDF5.__init__(self)
- return
-
-
- def initialize(self, normalizer):
- """
- Initialize writer.
- """
- DataWriterHDF5.initialize(self, normalizer)
-
- timeScale = normalizer.timeScale()
-
- ModuleDataWriterHDF5.filename(self, self.filename)
- ModuleDataWriterHDF5.timeScale(self, timeScale.value)
- return
-
-
-# FACTORIES ////////////////////////////////////////////////////////////
-
-def data_writer():
- """
- Factory associated with DataWriter.
- """
- return DataWriterHDF5SubMesh()
-
-
-# End of file
Deleted: short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5SubSubMesh.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5SubSubMesh.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/DataWriterHDF5SubSubMesh.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,69 +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) 2010-2013 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ----------------------------------------------------------------------
-#
-
-## @file pyre/meshio/DataWriterHDF5SubSubMesh.py
-##
-## @brief Python object for writing finite-element data to HDF5 file.
-
-from DataWriterHDF5 import DataWriterHDF5
-from meshio import SubSubMeshDataWriterHDF5 as ModuleDataWriterHDF5
-
-# DataWriterHDF5SubSubMesh class
-class DataWriterHDF5SubSubMesh(DataWriterHDF5, ModuleDataWriterHDF5):
- """
- Python object for writing finite-element data to HDF5 file.
-
- Inventory
-
- Factory: output_data_writer
- """
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, name="datawriterhdf5submesh"):
- """
- Constructor.
- """
- DataWriterHDF5.__init__(self, name)
- ModuleDataWriterHDF5.__init__(self)
- return
-
-
- def initialize(self, normalizer):
- """
- Initialize writer.
- """
- DataWriterHDF5.initialize(self, normalizer)
-
- timeScale = normalizer.timeScale()
-
- ModuleDataWriterHDF5.filename(self, self.filename)
- ModuleDataWriterHDF5.timeScale(self, timeScale.value)
- return
-
-
-# FACTORIES ////////////////////////////////////////////////////////////
-
-def data_writer():
- """
- Factory associated with DataWriter.
- """
- return DataWriterHDF5SubSubMesh()
-
-
-# End of file
Deleted: short/3D/PyLith/trunk/pylith/meshio/DataWriterVTKSubMesh.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/DataWriterVTKSubMesh.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/DataWriterVTKSubMesh.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,74 +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) 2010-2013 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ----------------------------------------------------------------------
-#
-
-## @file pyre/meshio/DataWriterVTKSubMesh.py
-##
-## @brief Python object for writing finite-element data to VTK file.
-
-from DataWriterVTK import DataWriterVTK
-from meshio import SubMeshDataWriterVTK as ModuleDataWriterVTK
-
-# DataWriterVTKSubMesh class
-class DataWriterVTKSubMesh(DataWriterVTK, ModuleDataWriterVTK):
- """
- Python object for writing finite-element data to VTK file.
-
- Inventory
-
- Factory: output_data_writer
- """
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, name="datawritervtksubmesh"):
- """
- Constructor.
- """
- DataWriterVTK.__init__(self, name)
- ModuleDataWriterVTK.__init__(self)
- return
-
-
- def initialize(self, normalizer):
- """
- Initialize writer.
- """
- DataWriterVTK.initialize(self, normalizer)
-
- timeScale = normalizer.timeScale()
- timeConstantN = normalizer.nondimensionalize(self.timeConstant,
- timeScale)
-
- ModuleDataWriterVTK.filename(self, self.filename)
- ModuleDataWriterVTK.timeScale(self, timeScale.value)
- ModuleDataWriterVTK.timeFormat(self, self.timeFormat)
- ModuleDataWriterVTK.timeConstant(self, timeConstantN)
- ModuleDataWriterVTK.precision(self, self.precision)
- return
-
-
-# FACTORIES ////////////////////////////////////////////////////////////
-
-def data_writer():
- """
- Factory associated with DataWriter.
- """
- return DataWriterVTKSubMesh()
-
-
-# End of file
Deleted: short/3D/PyLith/trunk/pylith/meshio/DataWriterVTKSubSubMesh.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/DataWriterVTKSubSubMesh.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/DataWriterVTKSubSubMesh.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,74 +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) 2010-2013 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ----------------------------------------------------------------------
-#
-
-## @file pyre/meshio/DataWriterVTKSubSubMesh.py
-##
-## @brief Python object for writing finite-element data to VTK file.
-
-from DataWriterVTK import DataWriterVTK
-from meshio import SubSubMeshDataWriterVTK as ModuleDataWriterVTK
-
-# DataWriterVTKSubSubMesh class
-class DataWriterVTKSubSubMesh(DataWriterVTK, ModuleDataWriterVTK):
- """
- Python object for writing finite-element data to VTK file.
-
- Inventory
-
- Factory: output_data_writer
- """
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, name="datawritervtksubmesh"):
- """
- Constructor.
- """
- DataWriterVTK.__init__(self, name)
- ModuleDataWriterVTK.__init__(self)
- return
-
-
- def initialize(self, normalizer):
- """
- Initialize writer.
- """
- DataWriterVTK.initialize(self, normalizer)
-
- timeScale = normalizer.timeScale()
- timeConstantN = normalizer.nondimensionalize(self.timeConstant,
- timeScale)
-
- ModuleDataWriterVTK.filename(self, self.filename)
- ModuleDataWriterVTK.timeScale(self, timeScale.value)
- ModuleDataWriterVTK.timeFormat(self, self.timeFormat)
- ModuleDataWriterVTK.timeConstant(self, timeConstantN)
- ModuleDataWriterVTK.precision(self, self.precision)
- return
-
-
-# FACTORIES ////////////////////////////////////////////////////////////
-
-def data_writer():
- """
- Factory associated with DataWriter.
- """
- return DataWriterVTKSubSubMesh()
-
-
-# End of file
Modified: short/3D/PyLith/trunk/pylith/meshio/MeshIOObj.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/MeshIOObj.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/MeshIOObj.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -64,8 +64,7 @@
from pylith.mpi.Communicator import petsc_comm_world
from pylith.topology.Mesh import Mesh
- mesh = Mesh()
- mesh.setComm(petsc_comm_world())
+ mesh = Mesh(dim=self.coordsys.spaceDim(), comm=petsc_comm_world())
mesh.coordsys(self.coordsys)
# Read mesh
Modified: short/3D/PyLith/trunk/pylith/meshio/OutputDirichlet.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/OutputDirichlet.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/OutputDirichlet.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -23,10 +23,10 @@
##
## Factory: output_manager
-from OutputManagerSubMesh import OutputManagerSubMesh
+from OutputManagerMesh import OutputManagerMesh
# OutputDirichlet class
-class OutputDirichlet(OutputManagerSubMesh):
+class OutputDirichlet(OutputManagerMesh):
"""
Python object for managing output of finite-element information for
Dirichlet boundary conditions.
@@ -36,7 +36,7 @@
# INVENTORY //////////////////////////////////////////////////////////
- class Inventory(OutputManagerSubMesh.Inventory):
+ class Inventory(OutputManagerMesh.Inventory):
"""
Python object for managing OutputDirichlet facilities and properties.
"""
@@ -63,7 +63,7 @@
"""
Constructor.
"""
- OutputManagerSubMesh.__init__(self, name)
+ OutputManagerMesh.__init__(self, name)
return
@@ -73,7 +73,7 @@
"""
Set members based using inventory.
"""
- OutputManagerSubMesh._configure(self)
+ OutputManagerMesh._configure(self)
self.vertexInfoFields = self.inventory.vertexInfoFields
self.vertexDataFields = []
self.cellInfoFields = []
Modified: short/3D/PyLith/trunk/pylith/meshio/OutputFaultDyn.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/OutputFaultDyn.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/OutputFaultDyn.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -23,10 +23,10 @@
##
## Factory: output_manager
-from OutputManagerSubMesh import OutputManagerSubMesh
+from OutputManagerMesh import OutputManagerMesh
# OutputFaultDyn class
-class OutputFaultDyn(OutputManagerSubMesh):
+class OutputFaultDyn(OutputManagerMesh):
"""
Python object for managing output of finite-element information for
faults with dynamic ruptures.
@@ -69,7 +69,7 @@
"""
Constructor.
"""
- OutputManagerSubMesh.__init__(self, name)
+ OutputManagerMesh.__init__(self, name)
return
@@ -79,7 +79,7 @@
"""
Set members based using inventory.
"""
- OutputManagerSubMesh._configure(self)
+ OutputManagerMesh._configure(self)
self.vertexInfoFields = self.inventory.vertexInfoFields
self.vertexDataFields = self.inventory.vertexDataFields
self.cellInfoFields = self.inventory.cellInfoFields
Modified: short/3D/PyLith/trunk/pylith/meshio/OutputFaultImpulses.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/OutputFaultImpulses.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/OutputFaultImpulses.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -23,10 +23,10 @@
##
## Factory: output_manager
-from OutputManagerSubMesh import OutputManagerSubMesh
+from OutputManagerMesh import OutputManagerMesh
# OutputFaultImpulses class
-class OutputFaultImpulses(OutputManagerSubMesh):
+class OutputFaultImpulses(OutputManagerMesh):
"""
Python object for managing output of finite-element information for
faults with Green's function slip impulses.
@@ -70,7 +70,7 @@
"""
Constructor.
"""
- OutputManagerSubMesh.__init__(self, name)
+ OutputManagerMesh.__init__(self, name)
return
@@ -80,7 +80,7 @@
"""
Set members based using inventory.
"""
- OutputManagerSubMesh._configure(self)
+ OutputManagerMesh._configure(self)
self.vertexInfoFields = self.inventory.vertexInfoFields
self.vertexDataFields = self.inventory.vertexDataFields
self.cellInfoFields = self.inventory.cellInfoFields
Modified: short/3D/PyLith/trunk/pylith/meshio/OutputFaultKin.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/OutputFaultKin.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/OutputFaultKin.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -23,10 +23,10 @@
##
## Factory: output_manager
-from OutputManagerSubMesh import OutputManagerSubMesh
+from OutputManagerMesh import OutputManagerMesh
# OutputFaultKin class
-class OutputFaultKin(OutputManagerSubMesh):
+class OutputFaultKin(OutputManagerMesh):
"""
Python object for managing output of finite-element information for
faults with kinematic ruptures.
@@ -71,7 +71,7 @@
"""
Constructor.
"""
- OutputManagerSubMesh.__init__(self, name)
+ OutputManagerMesh.__init__(self, name)
return
@@ -81,7 +81,7 @@
"""
Set members based using inventory.
"""
- OutputManagerSubMesh._configure(self)
+ OutputManagerMesh._configure(self)
self.vertexInfoFields = self.inventory.vertexInfoFields
self.vertexDataFields = self.inventory.vertexDataFields
self.cellInfoFields = self.inventory.cellInfoFields
Deleted: short/3D/PyLith/trunk/pylith/meshio/OutputManagerSubMesh.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/OutputManagerSubMesh.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/OutputManagerSubMesh.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,155 +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) 2010-2013 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ----------------------------------------------------------------------
-#
-
-## @file pyre/meshio/OutputManagerSubMesh.py
-##
-## @brief Python abstract base class for managing output of
-## finite-element information.
-##
-## Factory: output_manager
-
-from OutputManager import OutputManager
-from meshio import SubMeshOutputManager as ModuleOutputManager
-
-# OutputManagerSubMsh class
-class OutputManagerSubMesh(OutputManager, ModuleOutputManager):
- """
- Python abstract base class for managing output of finite-element
- information.
-
- \b Properties
- @li None
-
- \b Facilities
- @li \b writer Writer for data.
-
- Factory: output_manager
- """
-
- # INVENTORY //////////////////////////////////////////////////////////
-
- import pyre.inventory
-
- from DataWriterVTKSubSubMesh import DataWriterVTKSubSubMesh
- writer = pyre.inventory.facility("writer", factory=DataWriterVTKSubSubMesh,
- family="data_writer")
- writer.meta['tip'] = "Writer for data."
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, name="outputmanagersubmesh"):
- """
- Constructor.
- """
- OutputManager.__init__(self, name)
- return
-
-
- # PRIVATE METHODS ////////////////////////////////////////////////////
-
- def _configure(self):
- """
- Set members based using inventory.
- """
- from pylith.utils.NullComponent import NullComponent
-
- OutputManager._configure(self)
- ModuleOutputManager.coordsys(self, self.inventory.coordsys)
- ModuleOutputManager.writer(self, self.inventory.writer)
- if not isinstance(self.inventory.vertexFilter, NullComponent):
- ModuleOutputManager.vertexFilter(self, self.inventory.vertexFilter)
- if not isinstance(self.inventory.cellFilter, NullComponent):
- ModuleOutputManager.cellFilter(self, self.inventory.cellFilter)
- return
-
-
- def _createModuleObj(self):
- """
- Create handle to C++ object.
- """
- ModuleOutputManager.__init__(self)
- return
-
-
- def _open(self, mesh, nsteps, label, labelId):
- """
- Call C++ open();
- """
- if label != None and labelId != None:
- ModuleOutputManager.open(self, mesh, nsteps, label, labelId)
- else:
- ModuleOutputManager.open(self, mesh, nsteps)
- return
-
-
- def _openTimeStep(self, t, mesh, label, labelId):
- """
- Call C++ openTimeStep();
- """
- if label != None and labelId != None:
- ModuleOutputManager.openTimeStep(self, t, mesh, label, labelId)
- else:
- ModuleOutputManager.openTimeStep(self, t, mesh)
- return
-
-
- def _appendVertexField(self, t, field, mesh):
- """
- Call C++ appendVertexField();
- """
- ModuleOutputManager.appendVertexField(self, t, field, mesh)
- return
-
-
- def _appendCellField(self, t, field, label, labelId):
- """
- Call C++ appendCellField();
- """
- if label != None and labelId != None:
- ModuleOutputManager.appendCellField(self, t, field, label, labelId)
- else:
- ModuleOutputManager.appendCellField(self, t, field)
- return
-
-
- def _closeTimeStep(self):
- """
- Call C++ closeTimeStep().
- """
- ModuleOutputManager.closeTimeStep(self)
- return
-
-
- def _close(self):
- """
- Call C++ close().
- """
- ModuleOutputManager.close(self)
- return
-
-
-# FACTORIES ////////////////////////////////////////////////////////////
-
-def output_manager():
- """
- Factory associated with OutputManager.
- """
- return OutputManagerSubMesh()
-
-
-# End of file
Modified: short/3D/PyLith/trunk/pylith/meshio/OutputNeumann.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/OutputNeumann.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/OutputNeumann.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -23,10 +23,10 @@
##
## Factory: output_manager
-from OutputManagerSubMesh import OutputManagerSubMesh
+from OutputManagerMesh import OutputManagerMesh
# OutputNeumann class
-class OutputNeumann(OutputManagerSubMesh):
+class OutputNeumann(OutputManagerMesh):
"""
Python object for managing output of finite-element information for
Neumann boundary conditions.
@@ -36,7 +36,7 @@
# INVENTORY //////////////////////////////////////////////////////////
- class Inventory(OutputManagerSubMesh.Inventory):
+ class Inventory(OutputManagerMesh.Inventory):
"""
Python object for managing OutputNeumann facilities and properties.
"""
@@ -63,7 +63,7 @@
"""
Constructor.
"""
- OutputManagerSubMesh.__init__(self, name)
+ OutputManagerMesh.__init__(self, name)
return
@@ -73,7 +73,7 @@
"""
Set members based using inventory.
"""
- OutputManagerSubMesh._configure(self)
+ OutputManagerMesh._configure(self)
self.vertexInfoFields = []
self.vertexDataFields = []
self.cellInfoFields = self.inventory.cellInfoFields
Modified: short/3D/PyLith/trunk/pylith/meshio/OutputSolnSubset.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/OutputSolnSubset.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/OutputSolnSubset.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -66,8 +66,8 @@
label = pyre.inventory.str("label", default="", validator=validateLabel)
label.meta['tip'] = "Label identifier for subdomain."
- from DataWriterVTKSubMesh import DataWriterVTKSubMesh
- writer = pyre.inventory.facility("writer", factory=DataWriterVTKSubMesh,
+ from DataWriterVTKMesh import DataWriterVTKMesh
+ writer = pyre.inventory.facility("writer", factory=DataWriterVTKMesh,
family="data_writer")
writer.meta['tip'] = "Writer for data."
Deleted: short/3D/PyLith/trunk/pylith/meshio/VertexFilterVecNormSubMesh.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/VertexFilterVecNormSubMesh.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/VertexFilterVecNormSubMesh.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,59 +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) 2010-2013 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ----------------------------------------------------------------------
-#
-
-## @file pyre/meshio/VertexFilterVecNormSubMesh.py
-##
-## @brief Python class for computing vector norm for each vertex for
-## field over vertices when writing finite-element data.
-##
-## Factory: output_vertex_filter
-
-from VertexFilter import VertexFilter
-from meshio import SubMeshVertexFilterVecNorm as ModuleVertexFilterVecNorm
-
-# VertexFilterVecNormSubMesh class
-class VertexFilterVecNormSubMesh(VertexFilter, ModuleVertexFilterVecNorm):
- """
- Python class for computing vector norm for each vertex for field
- over vertices when writing finite-element data.
-
- Factory: output_vertex_filter
- """
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, name="vertexfiltervecnormsubmesh"):
- """
- Constructor.
- """
- VertexFilter.__init__(self, name)
- ModuleVertexFilterVecNorm.__init__(self)
- self.filter = True
- return
-
-
-# FACTORIES ////////////////////////////////////////////////////////////
-
-def output_vertex_filter():
- """
- Factory associated with VertexFilter.
- """
- return VertexFilterVecNormSubMesh()
-
-
-# End of file
Modified: short/3D/PyLith/trunk/pylith/meshio/__init__.py
===================================================================
--- short/3D/PyLith/trunk/pylith/meshio/__init__.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/meshio/__init__.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -22,12 +22,9 @@
__all__ = ['CellFilter',
'CellFilterAvgMesh',
- 'CellFilterAvgSubMesh',
'DataWriter',
'DataWriterVTK',
'DataWriterVTKMesh',
- 'DataWriterVTKSubMesh',
- 'DataWriterVTKSubSubMesh',
'DataWriterVTKPoints',
'MeshIOObj',
'MeshIOAscii',
@@ -37,7 +34,6 @@
'OutputFaultKin',
'OutputManager',
'OutputManagerMesh',
- 'OutputManagerSubMesh',
'OutputMatElastic',
'OutputNeumann'
'OutputSoln',
@@ -47,7 +43,6 @@
'SingleOutput',
'VertexFilter',
'VertexFilterVecNormMesh',
- 'VertexFilterVecNormSubMesh',
]
Modified: short/3D/PyLith/trunk/pylith/problems/TimeStep.py
===================================================================
--- short/3D/PyLith/trunk/pylith/problems/TimeStep.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/problems/TimeStep.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -187,7 +187,7 @@
if dt < dtStable:
dtStable = dt
import pylith.mpi.mpi as mpi
- comm = mesh.getComm()
+ comm = mesh.comm()
dtStableAll = mpi.allreduce_scalar_double(dtStable, mpi.mpi_min(), comm.handle)
return dtStableAll
Modified: short/3D/PyLith/trunk/pylith/topology/Field.py
===================================================================
--- short/3D/PyLith/trunk/pylith/topology/Field.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/topology/Field.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -22,7 +22,6 @@
## cells of a finite-element mesh.
from topology import MeshField as ModuleMeshField
-from topology import SubMeshField as ModuleSubMeshField
# ----------------------------------------------------------------------
# MeshField class
@@ -50,30 +49,4 @@
return
-# ----------------------------------------------------------------------
-# SubMeshField class
-class SubMeshField(ModuleSubMeshField):
- """
- Python object for managing a vector field over vertices or cells of
- a lower-dimension finite-element mesh.
- """
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, mesh):
- """
- Constructor.
- """
- ModuleSubMeshField.__init__(self, mesh)
- return
-
-
- def cleanup(self):
- """
- Deallocate PETSc and local data structures.
- """
- self.deallocate()
- return
-
-
# End of file
Modified: short/3D/PyLith/trunk/pylith/topology/Fields.py
===================================================================
--- short/3D/PyLith/trunk/pylith/topology/Fields.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/topology/Fields.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -22,7 +22,6 @@
## cells of a finite-element mesh.
from topology import MeshFields as ModuleMeshFields
-from topology import SubMeshFields as ModuleSubMeshFields
# ----------------------------------------------------------------------
# MeshFields class
@@ -50,30 +49,4 @@
return
-# ----------------------------------------------------------------------
-# SubMeshFields class
-class SubMeshFields(ModuleSubMeshFields):
- """
- Python object for managing vector fields over vertices or cells of
- a lower-dimension finite-element mesh.
- """
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, mesh):
- """
- Constructor.
- """
- ModuleSubMeshFields.__init__(self, mesh)
- return
-
-
- def cleanup(self):
- """
- Deallocate PETSc and local data structures.
- """
- self.deallocate()
- return
-
-
# End of file
Modified: short/3D/PyLith/trunk/pylith/topology/Mesh.py
===================================================================
--- short/3D/PyLith/trunk/pylith/topology/Mesh.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/topology/Mesh.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,16 +30,19 @@
# PUBLIC METHODS /////////////////////////////////////////////////////
- def __init__(self, dim=None, comm=None):
+ def __init__(self, dim=None, comm=None, mesh=None, label=None, isSubMesh=False):
"""
Constructor.
"""
- if comm is None and dim is None:
- ModuleMesh.__init__(self)
- elif comm is None:
+ if comm is None and dim is None and label is None:
+ ModuleMesh.__init__(self, isSubMesh)
+ elif comm is None and mesh is None and label is None:
ModuleMesh.__init__(self, dim)
- else:
+ elif label is None:
ModuleMesh.__init__(self, dim, comm.handle)
+ else:
+ assert(not mesh is None and not label is None)
+ ModuleMesh.__init__(self, mesh, label)
# Name of logging stage for mesh. We progress through various
# stages as we read, distribute, and refine mesh.
@@ -47,16 +50,8 @@
return
- def setComm(self, comm):
+ def comm(self):
"""
- Set communicator.
- """
- ModuleMesh.comm(self, comm.handle)
- return
-
-
- def getComm(self):
- """
Get communicator.
"""
# Use Communicator object to wrap C++ MPI_Comm* returned by
Modified: short/3D/PyLith/trunk/pylith/topology/MeshImporter.py
===================================================================
--- short/3D/PyLith/trunk/pylith/topology/MeshImporter.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/topology/MeshImporter.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -89,8 +89,8 @@
Hook for creating mesh.
"""
from pylith.utils.profiling import resourceUsageString
- from pylith.mpi.Communicator import mpi_comm_world
- comm = mpi_comm_world()
+ from pylith.mpi.Communicator import petsc_comm_world
+ comm = petsc_comm_world()
self._setupLogging()
logEvent = "%screate" % self._loggingPrefix
@@ -120,7 +120,7 @@
self._adjustTopology(mesh, faults)
# Distribute mesh
- if mesh.getComm().size > 1:
+ if comm.size > 1:
if 0 == comm.rank:
self._info.log("Distributing mesh.")
mesh = self.distributor.distribute(mesh, normalizer)
Modified: short/3D/PyLith/trunk/pylith/topology/RefineUniform.py
===================================================================
--- short/3D/PyLith/trunk/pylith/topology/RefineUniform.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/topology/RefineUniform.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -63,7 +63,7 @@
self._eventLogger.eventBegin(logEvent)
from Mesh import Mesh
- newMesh = Mesh(mesh.dimension(), mesh.getComm())
+ newMesh = Mesh(dim=mesh.dimension(), comm=mesh.comm())
newMesh.debug(mesh.debug())
newMesh.coordsys(mesh.coordsys())
ModuleRefineUniform.refine(self, newMesh, mesh, self.levels)
Deleted: short/3D/PyLith/trunk/pylith/topology/SubMesh.py
===================================================================
--- short/3D/PyLith/trunk/pylith/topology/SubMesh.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/pylith/topology/SubMesh.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,57 +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) 2010-2013 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ----------------------------------------------------------------------
-#
-
-## @file pylith/topology/SubMesh.py
-##
-## @brief Python Mesh for lower-dimension finite-element topology
-## information.
-
-from topology import SubMesh as ModuleSubMesh
-
-# SubMesh class
-class SubMesh(ModuleSubMesh):
- """
- Python Mesh for lower-dimension finite-element topology information.
- """
-
- # PUBLIC METHODS /////////////////////////////////////////////////////
-
- def __init__(self, mesh=None, label=None):
- """
- Constructor.
- """
- if mesh is None:
- ModuleSubMesh.__init__(self)
- else:
- if label is None:
- raise ValueError("SubMesh constructor with mesh requires label.")
- ModuleSubMesh.__init__(self, mesh, label)
- return
-
-
- def comm(self):
- """
- Get communicator.
- """
- # Use Communicator object to wrap C++ MPI_Comm* returned by
- # module.
- from pylith.mpi.Communicator import Communicator
- return Communicator(ModuleSubMesh.comm(self))
-
-
-# End of file
Modified: short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -27,7 +27,6 @@
#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/SolutionFields.hh" // USES SolutionFields
#include "pylith/topology/Jacobian.hh" // USES Jacobian
@@ -50,7 +49,7 @@
PYLITH_METHOD_BEGIN;
_data = 0;
- _quadrature = new feassemble::Quadrature<topology::SubMesh>();
+ _quadrature = new feassemble::Quadrature<topology::Mesh>();
CPPUNIT_ASSERT(_quadrature);
PYLITH_METHOD_END;
@@ -113,7 +112,7 @@
CPPUNIT_ASSERT(_data);
- const topology::SubMesh& boundaryMesh = *bc._boundaryMesh;
+ const topology::Mesh& boundaryMesh = *bc._boundaryMesh;
PetscDM subMesh = boundaryMesh.dmMesh();CPPUNIT_ASSERT(subMesh);
@@ -193,7 +192,7 @@
topology::SolutionFields fields(mesh);
_initialize(&mesh, &bc, &fields);
- const topology::SubMesh& boundaryMesh = *bc._boundaryMesh;
+ const topology::Mesh& boundaryMesh = *bc._boundaryMesh;
PetscDM subMesh = boundaryMesh.dmMesh();
PetscErrorCode err;
@@ -250,7 +249,7 @@
topology::SolutionFields fields(mesh);
_initialize(&mesh, &bc, &fields);
- const topology::SubMesh& boundaryMesh = *bc._boundaryMesh;
+ const topology::Mesh& boundaryMesh = *bc._boundaryMesh;
PetscDM subMesh = boundaryMesh.dmMesh();CPPUNIT_ASSERT(subMesh);
topology::Field<topology::Mesh>& solution = fields.solution();
@@ -334,7 +333,7 @@
jacobian.newSection(topology::FieldBase::VERTICES_FIELD, _data->spaceDim);
jacobian.allocate();
- const topology::SubMesh& boundaryMesh = *bc._boundaryMesh;
+ const topology::Mesh& boundaryMesh = *bc._boundaryMesh;
PetscDM subMesh = boundaryMesh.dmMesh();CPPUNIT_ASSERT(subMesh);
const PylithScalar t = 1.0;
Modified: short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -84,7 +84,7 @@
protected :
AbsorbingDampersData* _data; ///< Data for testing
- feassemble::Quadrature<topology::SubMesh>* _quadrature; ///< Used in testing.
+ feassemble::Quadrature<topology::Mesh>* _quadrature; ///< Used in testing.
// PRIVATE METHODS ////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampersCases.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampersCases.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampersCases.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,7 +20,7 @@
#include "TestAbsorbingDampersCases.hh" // Implementation of cases
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
// ----------------------------------------------------------------------
Modified: short/3D/PyLith/trunk/unittests/libtests/bc/TestBoundaryMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/bc/TestBoundaryMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/bc/TestBoundaryMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -25,7 +25,6 @@
#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
#include "pylith/topology/Field.hh" // USES Field
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Stratum.hh" // USES Stratum
#include "pylith/topology/VisitorSubMesh.hh" // USES SubMeshIS
#include "pylith/meshio/MeshIOAscii.hh" // USES MeshIOAscii
@@ -80,7 +79,7 @@
topology::MeshOps::nondimensionalize(&mesh, normalizer);
// Create submesh
- topology::SubMesh submesh(mesh, _data->bcLabel);
+ topology::Mesh submesh(mesh, _data->bcLabel);
PetscDM dmMesh = submesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
// Check vertices
@@ -152,7 +151,7 @@
fault.adjustTopology(&mesh, &firstFaultVertex, &firstLagrangeVertex, &firstFaultCell, _flipFault);
// Create submesh
- topology::SubMesh submesh(mesh, _data->bcLabel);
+ topology::Mesh submesh(mesh, _data->bcLabel);
PetscDM dmMesh = submesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
// Check vertices
Modified: short/3D/PyLith/trunk/unittests/libtests/bc/TestDirichletBoundary.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/bc/TestDirichletBoundary.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/bc/TestDirichletBoundary.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -26,7 +26,6 @@
#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Stratum.hh" // USES Stratum
#include "pylith/meshio/MeshIOAscii.hh" // USES MeshIOAscii
Modified: short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumann.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumann.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumann.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -27,7 +27,6 @@
#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Stratum.hh" // USES Stratum
#include "pylith/topology/VisitorMesh.hh" // USES VecVisitorMesh
@@ -94,7 +93,7 @@
static
void _checkValues(const PylithScalar* valuesE,
const int fiberDimE,
- const topology::Field<topology::SubMesh>& field);
+ const topology::Field<topology::Mesh>& field);
} // _TestNeumann
} // bc
} // pylith
@@ -107,7 +106,7 @@
PYLITH_METHOD_BEGIN;
_data = 0;
- _quadrature = new feassemble::Quadrature<topology::SubMesh>();
+ _quadrature = new feassemble::Quadrature<topology::Mesh>();
CPPUNIT_ASSERT(_quadrature);
PYLITH_METHOD_END;
@@ -168,7 +167,7 @@
topology::SolutionFields fields(mesh);
_initialize(&mesh, &bc, &fields);
- const topology::SubMesh& boundaryMesh = *bc._boundaryMesh;
+ const topology::Mesh& boundaryMesh = *bc._boundaryMesh;
PetscDM subMesh = boundaryMesh.dmMesh();assert(subMesh);
topology::Stratum verticesStratum(subMesh, topology::Stratum::DEPTH, 0);
@@ -337,23 +336,23 @@
// bc._parameters->view("PARAMETERS"); // DEBUGGING
// Check initial values.
- const topology::Field<topology::SubMesh>& initial = bc._parameters->get("initial");
+ const topology::Field<topology::Mesh>& initial = bc._parameters->get("initial");
_TestNeumann::_checkValues(_TestNeumann::initial, numQuadPts*spaceDim, initial);
// Check rate values.
- const topology::Field<topology::SubMesh>& rate = bc._parameters->get("rate");
+ const topology::Field<topology::Mesh>& rate = bc._parameters->get("rate");
_TestNeumann::_checkValues(_TestNeumann::rate, numQuadPts*spaceDim, rate);
// Check rate start time.
- const topology::Field<topology::SubMesh>& rateTime = bc._parameters->get("rate time");
+ const topology::Field<topology::Mesh>& rateTime = bc._parameters->get("rate time");
_TestNeumann::_checkValues(_TestNeumann::rateTime, numQuadPts, rateTime);
// Check change values.
- const topology::Field<topology::SubMesh>& change = bc._parameters->get("change");
+ const topology::Field<topology::Mesh>& change = bc._parameters->get("change");
_TestNeumann::_checkValues(_TestNeumann::change, numQuadPts*spaceDim, change);
// Check change start time.
- const topology::Field<topology::SubMesh>& changeTime = bc._parameters->get("change time");
+ const topology::Field<topology::Mesh>& changeTime = bc._parameters->get("change time");
_TestNeumann::_checkValues(_TestNeumann::changeTime, numQuadPts, changeTime);
th.close();
@@ -419,7 +418,7 @@
valuesE[i+0] = _TestNeumann::initial[i+0]; // x
valuesE[i+1] = -_TestNeumann::initial[i+1]; // y
} // for
- const topology::Field<topology::SubMesh>& initial = bc._parameters->get("initial");
+ const topology::Field<topology::Mesh>& initial = bc._parameters->get("initial");
_TestNeumann::_checkValues(&valuesE[0], numQuadPts*spaceDim, initial);
// Check rate values.
@@ -427,7 +426,7 @@
valuesE[i+0] = _TestNeumann::rate[i+0]; // x
valuesE[i+1] = -_TestNeumann::rate[i+1]; // y
} // for
- const topology::Field<topology::SubMesh>& rate = bc._parameters->get("rate");
+ const topology::Field<topology::Mesh>& rate = bc._parameters->get("rate");
_TestNeumann::_checkValues(&valuesE[0], numQuadPts*spaceDim, rate);
// Check change values.
@@ -435,7 +434,7 @@
valuesE[i+0] = _TestNeumann::change[i+0]; // x
valuesE[i+1] = -_TestNeumann::change[i+1]; // y
} // for
- const topology::Field<topology::SubMesh>& change = bc._parameters->get("change");
+ const topology::Field<topology::Mesh>& change = bc._parameters->get("change");
_TestNeumann::_checkValues(&valuesE[0], numQuadPts*spaceDim, change);
PYLITH_METHOD_END;
@@ -475,7 +474,7 @@
CPPUNIT_ASSERT(bc._parameters);
// Check values.
- const topology::Field<topology::SubMesh>& value = bc._parameters->get("value");
+ const topology::Field<topology::Mesh>& value = bc._parameters->get("value");
_TestNeumann::_checkValues(_TestNeumann::initial, numQuadPts*spaceDim, value);
PYLITH_METHOD_END;
@@ -515,7 +514,7 @@
CPPUNIT_ASSERT(bc._parameters);
// Check values.
- const topology::Field<topology::SubMesh>& value = bc._parameters->get("value");
+ const topology::Field<topology::Mesh>& value = bc._parameters->get("value");
_TestNeumann::_checkValues(_TestNeumann::valuesRate, numQuadPts*spaceDim, value);
PYLITH_METHOD_END;
@@ -555,7 +554,7 @@
CPPUNIT_ASSERT(bc._parameters);
// Check values.
- const topology::Field<topology::SubMesh>& value = bc._parameters->get("value");
+ const topology::Field<topology::Mesh>& value = bc._parameters->get("value");
_TestNeumann::_checkValues(_TestNeumann::valuesChange, numQuadPts*spaceDim, value);
PYLITH_METHOD_END;
@@ -599,7 +598,7 @@
CPPUNIT_ASSERT(bc._parameters);
// Check values.
- const topology::Field<topology::SubMesh>& value = bc._parameters->get("value");
+ const topology::Field<topology::Mesh>& value = bc._parameters->get("value");
_TestNeumann::_checkValues(_TestNeumann::valuesChangeTH, numQuadPts*spaceDim, value);
PYLITH_METHOD_END;
@@ -665,7 +664,7 @@
_TestNeumann::valuesRate[i] +
_TestNeumann::valuesChangeTH[i];
- const topology::Field<topology::SubMesh>& value = bc._parameters->get("value");
+ const topology::Field<topology::Mesh>& value = bc._parameters->get("value");
_TestNeumann::_checkValues(&valuesE[0], numQuadPts*spaceDim, value);
PYLITH_METHOD_END;
@@ -767,13 +766,13 @@
void
pylith::bc::_TestNeumann::_checkValues(const PylithScalar* valuesE,
const int fiberDimE,
- const topology::Field<topology::SubMesh>& field)
+ const topology::Field<topology::Mesh>& field)
{ // _checkValues
PYLITH_METHOD_BEGIN;
CPPUNIT_ASSERT(valuesE);
- const topology::SubMesh& boundaryMesh = field.mesh();
+ const topology::Mesh& boundaryMesh = field.mesh();
const PetscInt ncells = _TestNeumann::ncells;
PetscDM subMesh = boundaryMesh.dmMesh();CPPUNIT_ASSERT(subMesh);
Modified: short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumann.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumann.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumann.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -110,7 +110,7 @@
protected :
NeumannData* _data; ///< Data for testing
- feassemble::Quadrature<topology::SubMesh>* _quadrature; ///< Used in testing.
+ feassemble::Quadrature<topology::Mesh>* _quadrature; ///< Used in testing.
// PRIVATE METHODS ////////////////////////////////////////////////////
private :
Modified: short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumannCases.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumannCases.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumannCases.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,7 +20,7 @@
#include "TestNeumannCases.hh" // Implementation of class methods
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
// ----------------------------------------------------------------------
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestBruneSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestBruneSlipFn.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestBruneSlipFn.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -25,7 +25,6 @@
#include "TestFaultMesh.hh" // USES createFaultMesh()
#include "pylith/topology/Mesh.hh" // USES Mesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Stratum.hh" // USES Stratum
@@ -258,14 +257,14 @@
const PylithScalar originTime = 5.064;
topology::Mesh mesh;
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
BruneSlipFn slipfn;
_initialize(&mesh, &faultMesh, &slipfn, originTime);
const spatialdata::geocoords::CoordSys* cs = faultMesh.coordsys();CPPUNIT_ASSERT(cs);
const int spaceDim = cs->spaceDim();
- topology::Field<topology::SubMesh> slip(faultMesh);
+ topology::Field<topology::Mesh> slip(faultMesh);
slip.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim);
slip.allocate();
@@ -337,7 +336,7 @@
// Initialize BruneSlipFn.
void
pylith::faults::TestBruneSlipFn::_initialize(topology::Mesh* mesh,
- topology::SubMesh* faultMesh,
+ topology::Mesh* faultMesh,
BruneSlipFn* slipfn,
const PylithScalar originTime)
{ // _initialize
@@ -423,7 +422,7 @@
mesh.coordsys(&cs);
// Create fault mesh
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
TestFaultMesh::createFaultMesh(&faultMesh, &mesh, data.faultLabel, data.faultId);
// Setup databases
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestBruneSlipFn.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestBruneSlipFn.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestBruneSlipFn.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include <cppunit/extensions/HelperMacros.h>
#include "pylith/faults/faultsfwd.hh" // USES BruneSlipFn
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh
+#include "pylith/topology/topologyfwd.hh" // USES Mesh
/// Namespace for pylith package
namespace pylith {
@@ -104,7 +104,7 @@
*/
static
void _initialize(topology::Mesh* mesh,
- topology::SubMesh* faultMesh,
+ topology::Mesh* faultMesh,
BruneSlipFn* slipfn,
const PylithScalar originTime);
@@ -115,14 +115,6 @@
static
void _testInitialize(const _TestBruneSlipFn::DataStruct& data);
- /** Setup fault coordinates
- *
- * @param mesh Finite-element mesh of domain.
- * @param faultMesh Finite-element mesh of fault.
- */
- static
- void _setupFaultCoordinates(topology::Mesh *mesh, topology::SubMesh *faultMesh);
-
}; // class TestBruneSlipFn
#endif // pylith_faults_testbruneslipfn_hh
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestConstRateSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestConstRateSlipFn.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestConstRateSlipFn.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -25,7 +25,6 @@
#include "TestFaultMesh.hh" // USES createFaultMesh()
#include "pylith/topology/Mesh.hh" // USES Mesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Stratum.hh" // USES Stratum
@@ -220,14 +219,14 @@
const PylithScalar originTime = 5.064;
topology::Mesh mesh;
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
ConstRateSlipFn slipfn;
_initialize(&mesh, &faultMesh, &slipfn, originTime);
const spatialdata::geocoords::CoordSys* cs = faultMesh.coordsys();CPPUNIT_ASSERT(cs);
const int spaceDim = cs->spaceDim();
- topology::Field<topology::SubMesh> slip(faultMesh);
+ topology::Field<topology::Mesh> slip(faultMesh);
slip.newSection(topology::Field<topology::Mesh>::VERTICES_FIELD, spaceDim);
slip.allocate();
@@ -262,7 +261,7 @@
// Initialize ConstRateSlipFn.
void
pylith::faults::TestConstRateSlipFn::_initialize(topology::Mesh* mesh,
- topology::SubMesh* faultMesh,
+ topology::Mesh* faultMesh,
ConstRateSlipFn* slipfn,
const PylithScalar originTime)
{ // _initialize
@@ -341,7 +340,7 @@
mesh.coordsys(&cs);
// Create fault mesh
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
TestFaultMesh::createFaultMesh(&faultMesh, &mesh, data.faultLabel, data.faultId);
// Setup databases
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestConstRateSlipFn.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestConstRateSlipFn.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestConstRateSlipFn.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include <cppunit/extensions/HelperMacros.h>
#include "pylith/faults/faultsfwd.hh" // USES ConstRateSlipFn
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh
+#include "pylith/topology/topologyfwd.hh" // USES Mesh
/// Namespace for pylith package
namespace pylith {
@@ -96,7 +96,7 @@
*/
static
void _initialize(topology::Mesh* mesh,
- topology::SubMesh* faultMesh,
+ topology::Mesh* faultMesh,
ConstRateSlipFn* slipfn,
const PylithScalar originTime);
@@ -107,14 +107,6 @@
static
void _testInitialize(const _TestConstRateSlipFn::DataStruct& data);
- /** Setup fault coordinates
- *
- * @param mesh Finite-element mesh of domain.
- * @param faultMesh Finite-element mesh of fault.
- */
- static
- void _setupFaultCoordinates(topology::Mesh *mesh, topology::SubMesh *faultMesh);
-
}; // class TestConstRateSlipFn
#endif // pylith_faults_testconstrateslipfn_hh
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestEqKinSrc.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestEqKinSrc.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestEqKinSrc.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -28,7 +28,6 @@
#include "pylith/faults/CohesiveTopology.hh" // USES CohesiveTopology
#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Stratum.hh" // USES Stratum
#include "pylith/topology/VisitorMesh.hh" // USES VecVisitorMesh
@@ -93,7 +92,7 @@
PYLITH_METHOD_BEGIN;
topology::Mesh mesh;
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
EqKinSrc eqsrc;
BruneSlipFn slipfn;
const PylithScalar originTime = 2.45;
@@ -120,7 +119,7 @@
const PylithScalar originTime = 2.42 / _TestEqKinSrc::timeScale;
topology::Mesh mesh;
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
EqKinSrc eqsrc;
BruneSlipFn slipfn;
_initialize(&mesh, &faultMesh, &eqsrc, &slipfn, originTime);
@@ -128,7 +127,7 @@
const spatialdata::geocoords::CoordSys* cs = faultMesh.coordsys();CPPUNIT_ASSERT(cs);
const int spaceDim = cs->spaceDim();
- topology::Field<topology::SubMesh> slip(faultMesh);
+ topology::Field<topology::Mesh> slip(faultMesh);
slip.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim);
slip.allocate();
@@ -169,7 +168,7 @@
// Initialize EqKinSrc.
void
pylith::faults::TestEqKinSrc::_initialize(topology::Mesh* mesh,
- topology::SubMesh* faultMesh,
+ topology::Mesh* faultMesh,
EqKinSrc* eqsrc,
BruneSlipFn* slipfn,
const PylithScalar originTime)
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestEqKinSrc.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestEqKinSrc.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestEqKinSrc.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -83,19 +83,11 @@
*/
static
void _initialize(topology::Mesh* mesh,
- topology::SubMesh* faultMesh,
+ topology::Mesh* faultMesh,
EqKinSrc* eqsrc,
BruneSlipFn* slipfn,
const PylithScalar originTime);
- /** Setup fault coordinates
- *
- * @param mesh Finite-element mesh of domain.
- * @param faultMesh Finite-element mesh of fault.
- */
- static
- void _setupFaultCoordinates(topology::Mesh *mesh, topology::SubMesh *faultMesh);
-
}; // class TestEqKinSrc
#endif // pylith_faults_testeqkinsrc_hh
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDyn.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDyn.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDyn.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -27,7 +27,6 @@
#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
#include "pylith/topology/SolutionFields.hh" // USES SolutionFields
#include "pylith/topology/Jacobian.hh" // USES Jacobian
@@ -54,7 +53,7 @@
PYLITH_METHOD_BEGIN;
_data = 0;
- _quadrature = new feassemble::Quadrature<topology::SubMesh>();
+ _quadrature = new feassemble::Quadrature<topology::Mesh>();
CPPUNIT_ASSERT(_quadrature);
_tractPerturbation = 0;
_dbInitialTract = 0;
@@ -533,7 +532,7 @@
_setFieldsJacobian(&mesh, &fault, &fields, &jacobian, _data->fieldIncrStick);
const int spaceDim = _data->spaceDim;
- topology::Field<topology::SubMesh> tractions(*fault._faultMesh);
+ topology::Field<topology::Mesh> tractions(*fault._faultMesh);
tractions.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim);
tractions.allocate();
tractions.zero();
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDyn.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDyn.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDyn.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include <cppunit/extensions/HelperMacros.h>
#include "pylith/faults/faultsfwd.hh" // forward declarations
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh
+#include "pylith/topology/topologyfwd.hh" // USES Mesh
#include "pylith/feassemble/feassemblefwd.hh" // HOLDSA Quadrature
#include "pylith/friction/frictionfwd.hh" // HOLDSA FrictionModel
#include "spatialdata/spatialdb/spatialdbfwd.hh" // HOLDSA SpatialDB
@@ -70,7 +70,7 @@
protected:
CohesiveDynData* _data; ///< Data for testing
- feassemble::Quadrature<topology::SubMesh>* _quadrature; ///< Fault quad.
+ feassemble::Quadrature<topology::Mesh>* _quadrature; ///< Fault quad.
TractPerturbation* _tractPerturbation; ///< Initial tractions.
spatialdata::spatialdb::SpatialDB* _dbInitialTract; ///< Initial tractions.
friction::FrictionModel* _friction; ///< Friction model
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDynCases.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDynCases.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDynCases.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,8 +20,8 @@
#include "TestFaultCohesiveDynCases.hh" // Implementation of class methods
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
-#include "pylith/feassemble/Quadrature.hh" // USES Quadrature<SubMesh>
+#include "pylith/topology/Mesh.hh" // USES Mesh
+#include "pylith/feassemble/Quadrature.hh" // USES Quadrature<Mesh>
#include "pylith/feassemble/GeometryLine2D.hh" // USES GeometryLine2D
#include "pylith/feassemble/GeometryTri3D.hh" // USES GeometryTri3D
#include "pylith/feassemble/GeometryQuad3D.hh" // USES GeometryQuad3D
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulses.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulses.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulses.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -26,7 +26,6 @@
#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Stratum.hh" // USES Stratum
#include "pylith/topology/VisitorMesh.hh" // USES VecVisitorMesh
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
@@ -50,7 +49,7 @@
PYLITH_METHOD_BEGIN;
_data = 0;
- _quadrature = new feassemble::Quadrature<topology::SubMesh>();
+ _quadrature = new feassemble::Quadrature<topology::Mesh>();
CPPUNIT_ASSERT(_quadrature);
_dbImpulseAmp = 0;
_flipFault = false;
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulses.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulses.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulses.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include <cppunit/extensions/HelperMacros.h>
#include "pylith/faults/faultsfwd.hh" // forward declarations
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh
+#include "pylith/topology/topologyfwd.hh" // USES Mesh
#include "pylith/feassemble/feassemblefwd.hh" // HOLDSA Quadrature
#include "pylith/friction/frictionfwd.hh" // HOLDSA FrictionModel
#include "spatialdata/spatialdb/spatialdbfwd.hh" // HOLDSA SpatialDB
@@ -67,7 +67,7 @@
protected:
CohesiveImpulsesData* _data; ///< Data for testing
- feassemble::Quadrature<topology::SubMesh>* _quadrature; ///< Fault quad.
+ feassemble::Quadrature<topology::Mesh>* _quadrature; ///< Fault quad.
spatialdata::spatialdb::SpatialDB* _dbImpulseAmp; ///< Initial tractions.
bool _flipFault; ///< If true, flip fault orientation.
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulsesCases.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulsesCases.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulsesCases.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,8 +20,8 @@
#include "TestFaultCohesiveImpulsesCases.hh" // Implementation of class methods
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
-#include "pylith/feassemble/Quadrature.hh" // USES Quadrature<SubMesh>
+#include "pylith/topology/Mesh.hh" // USES Mesh
+#include "pylith/feassemble/Quadrature.hh" // USES Quadrature<Mesh>
#include "pylith/feassemble/GeometryLine2D.hh" // USES GeometryLine2D
#include "pylith/feassemble/GeometryTri3D.hh" // USES GeometryTri3D
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -28,7 +28,6 @@
#include "pylith/faults/BruneSlipFn.hh" // USES BruneSlipFn
#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Stratum.hh" // USES Stratum
#include "pylith/topology/VisitorMesh.hh" // USES VecVisitorMesh
#include "pylith/topology/VisitorSubMesh.hh" // USES SubMeshIS
@@ -54,7 +53,7 @@
PYLITH_METHOD_BEGIN;
_data = 0;
- _quadrature = new feassemble::Quadrature<topology::SubMesh>();
+ _quadrature = new feassemble::Quadrature<topology::Mesh>();
CPPUNIT_ASSERT(_quadrature);
const int nsrcs = 1;
_eqsrcs.resize(nsrcs);
@@ -603,7 +602,7 @@
} // setup disp
CPPUNIT_ASSERT(fault._faultMesh);
- topology::Field<topology::SubMesh> tractions(*fault._faultMesh);
+ topology::Field<topology::Mesh> tractions(*fault._faultMesh);
tractions.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim);
tractions.allocate();
tractions.zero();
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include <cppunit/extensions/HelperMacros.h>
#include "pylith/faults/faultsfwd.hh" // forward declarations
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh
+#include "pylith/topology/topologyfwd.hh" // USES Mesh
#include "pylith/feassemble/feassemblefwd.hh" // HOLDSA Quadrature
#include <vector> // HASA std::vector
@@ -62,7 +62,7 @@
protected :
CohesiveKinData* _data; ///< Data for testing
- feassemble::Quadrature<topology::SubMesh>* _quadrature; ///< Fault quad.
+ feassemble::Quadrature<topology::Mesh>* _quadrature; ///< Fault quad.
std::vector<EqKinSrc*> _eqsrcs; ///< Array of Kinematic earthquake sources.
std::vector<BruneSlipFn*> _slipfns; ///< Slip time function.
bool _flipFault; ///< If true, flip fault orientation.
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKinCases.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKinCases.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKinCases.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,8 +20,8 @@
#include "TestFaultCohesiveKinCases.hh" // Implementation of class methods
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
-#include "pylith/feassemble/Quadrature.hh" // USES Quadrature<SubMesh>
+#include "pylith/topology/Mesh.hh" // USES Mesh
+#include "pylith/feassemble/Quadrature.hh" // USES Quadrature<Mesh>
#include "pylith/feassemble/GeometryPoint1D.hh" // USES GeometryPoint1D
#include "pylith/feassemble/GeometryLine2D.hh" // USES GeometryLine2D
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKinSrcsCases.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKinSrcsCases.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKinSrcsCases.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -21,8 +21,8 @@
#include "TestFaultCohesiveKinSrcsCases.hh" // Implementation of class methods
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
-#include "pylith/feassemble/Quadrature.hh" // USES Quadrature<SubMesh>
+#include "pylith/topology/Mesh.hh" // USES Mesh
+#include "pylith/feassemble/Quadrature.hh" // USES Quadrature<Mesh>
#include "pylith/feassemble/GeometryPoint1D.hh" // USES GeometryPoint1D
#include "pylith/feassemble/GeometryLine2D.hh" // USES GeometryLine2D
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKinSrcsTet4.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKinSrcsTet4.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKinSrcsTet4.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -22,8 +22,8 @@
#include "data/CohesiveKinSrcsDataTet4.hh" // USES CohesiveKinDataTet4
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
-#include "pylith/feassemble/Quadrature.hh" // USES Quadrature<SubMesh>
+#include "pylith/topology/Mesh.hh" // USES Mesh
+#include "pylith/feassemble/Quadrature.hh" // USES Quadrature<Mesh>
#include "pylith/feassemble/GeometryTri3D.hh" // USES GeometryTri3D
// ----------------------------------------------------------------------
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -22,11 +22,10 @@
#include "pylith/faults/CohesiveTopology.hh" // USES CohesiveTopology
#include "pylith/topology/Mesh.hh" // USES Mesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
// ----------------------------------------------------------------------
void
-pylith::faults::TestFaultMesh::createFaultMesh(topology::SubMesh* faultMesh,
+pylith::faults::TestFaultMesh::createFaultMesh(topology::Mesh* faultMesh,
topology::Mesh* mesh,
const char* faultLabel,
const int faultId)
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -34,7 +34,7 @@
} // faults
} // pylith
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh
+#include "pylith/topology/topologyfwd.hh" // USES Mesh
/// C++ object for constructing fault mesh.
class pylith::faults::TestFaultMesh
@@ -51,7 +51,7 @@
* @param faultId Material id for fault.
*/
static
- void createFaultMesh(topology::SubMesh* faultMesh,
+ void createFaultMesh(topology::Mesh* faultMesh,
topology::Mesh* mesh,
const char* faultLabel,
const int faultId);
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestLiuCosSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestLiuCosSlipFn.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestLiuCosSlipFn.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -25,7 +25,6 @@
#include "TestFaultMesh.hh" // USES createFaultMesh()
#include "pylith/topology/Mesh.hh" // USES Mesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Stratum.hh" // USES Stratum
@@ -256,14 +255,14 @@
const PylithScalar originTime = 5.064;
topology::Mesh mesh;
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
LiuCosSlipFn slipfn;
_initialize(&mesh, &faultMesh, &slipfn, originTime);
const spatialdata::geocoords::CoordSys* cs = faultMesh.coordsys();CPPUNIT_ASSERT(cs);
const int spaceDim = cs->spaceDim();
- topology::Field<topology::SubMesh> slip(faultMesh);
+ topology::Field<topology::Mesh> slip(faultMesh);
slip.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim);
slip.allocate();
@@ -332,7 +331,7 @@
// Initialize LiuCosSlipFn.
void
pylith::faults::TestLiuCosSlipFn::_initialize(topology::Mesh* mesh,
- topology::SubMesh* faultMesh,
+ topology::Mesh* faultMesh,
LiuCosSlipFn* slipfn,
const PylithScalar originTime)
{ // _initialize
@@ -416,7 +415,7 @@
mesh.coordsys(&cs);
// Create fault mesh
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
TestFaultMesh::createFaultMesh(&faultMesh, &mesh, data.faultLabel, data.faultId);
// Setup databases
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestLiuCosSlipFn.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestLiuCosSlipFn.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestLiuCosSlipFn.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include <cppunit/extensions/HelperMacros.h>
#include "pylith/faults/faultsfwd.hh" // USES LiuCosSlipFn
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh
+#include "pylith/topology/topologyfwd.hh" // USES Mesh
/// Namespace for pylith package
namespace pylith {
@@ -104,7 +104,7 @@
*/
static
void _initialize(topology::Mesh* mesh,
- topology::SubMesh* faultMesh,
+ topology::Mesh* faultMesh,
LiuCosSlipFn* slipfn,
const PylithScalar originTime);
@@ -126,14 +126,6 @@
const PylithScalar finalSlip,
const PylithScalar riseTime);
- /** Setup fault coordinates
- *
- * @param mesh Finite-element mesh of domain.
- * @param faultMesh Finite-element mesh of fault.
- */
- static
- void _setupFaultCoordinates(topology::Mesh *mesh, topology::SubMesh *faultMesh);
-
}; // class TestLiuCosSlipFn
#endif // pylith_faults_testliucosslipfn_hh
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestSlipFn.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestSlipFn.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -22,11 +22,10 @@
#include "pylith/faults/CohesiveTopology.hh" // USES CohesiveTopology
#include "pylith/topology/Mesh.hh" // USES Mesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
// ----------------------------------------------------------------------
void
-pylith::faults::TestSlipFn::_createFaultMesh(topology::SubMesh* faultMesh,
+pylith::faults::TestSlipFn::_createFaultMesh(topology::Mesh* faultMesh,
topology::Mesh* mesh,
const char* faultLabel,
const int faultId)
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestSlipFn.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestSlipFn.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestSlipFn.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -27,7 +27,7 @@
#if !defined(pylith_faults_testslipfn_hh)
#define pylith_faults_testslipfn_hh
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh
+#include "pylith/topology/topologyfwd.hh" // USES Mesh
#include <cppunit/extensions/HelperMacros.h>
@@ -54,7 +54,7 @@
*/
static
void
- _createFaultMesh(topology::SubMesh* faultMesh,
+ _createFaultMesh(topology::Mesh* faultMesh,
topology::Mesh* mesh,
const char* faultLabel,
const int faultId);
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestStepSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestStepSlipFn.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestStepSlipFn.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -25,7 +25,6 @@
#include "TestFaultMesh.hh" // USES createFaultMesh()
#include "pylith/topology/Mesh.hh" // USES Mesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Stratum.hh" // USES Stratum
@@ -219,14 +218,14 @@
const PylithScalar originTime = 5.064;
topology::Mesh mesh;
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
StepSlipFn slipfn;
_initialize(&mesh, &faultMesh, &slipfn, originTime);
const spatialdata::geocoords::CoordSys* cs = faultMesh.coordsys();CPPUNIT_ASSERT(cs);
const int spaceDim = cs->spaceDim();
- topology::Field<topology::SubMesh> slip(faultMesh);
+ topology::Field<topology::Mesh> slip(faultMesh);
slip.newSection(topology::Field<topology::Mesh>::VERTICES_FIELD, spaceDim);
slip.allocate();
@@ -258,7 +257,7 @@
// Initialize StepSlipFn.
void
pylith::faults::TestStepSlipFn::_initialize(topology::Mesh* mesh,
- topology::SubMesh* faultMesh,
+ topology::Mesh* faultMesh,
StepSlipFn* slipfn,
const PylithScalar originTime)
{ // _initialize
@@ -337,7 +336,7 @@
mesh.coordsys(&cs);
// Create fault mesh
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
TestFaultMesh::createFaultMesh(&faultMesh, &mesh, data.faultLabel, data.faultId);
// Setup databases
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestStepSlipFn.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestStepSlipFn.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestStepSlipFn.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include <cppunit/extensions/HelperMacros.h>
#include "pylith/faults/faultsfwd.hh" // USES StepSlipFn
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh
+#include "pylith/topology/topologyfwd.hh" // USES Mesh
/// Namespace for pylith package
namespace pylith {
@@ -96,7 +96,7 @@
*/
static
void _initialize(topology::Mesh* mesh,
- topology::SubMesh* faultMesh,
+ topology::Mesh* faultMesh,
StepSlipFn* slipfn,
const PylithScalar originTime);
@@ -107,14 +107,6 @@
static
void _testInitialize(const _TestStepSlipFn::DataStruct& data);
- /** Setup fault coordinates
- *
- * @param mesh Finite-element mesh of domain.
- * @param faultMesh Finite-element mesh of fault.
- */
- static
- void _setupFaultCoordinates(topology::Mesh *mesh, topology::SubMesh *faultMesh);
-
}; // class TestStepSlipFn
#endif // pylith_faults_teststepslipfn_hh
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestTimeHistorySlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestTimeHistorySlipFn.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestTimeHistorySlipFn.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -25,7 +25,6 @@
#include "TestFaultMesh.hh" // USES createFaultMesh()
#include "pylith/topology/Mesh.hh" // USES Mesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Stratum.hh" // USES Stratum
@@ -251,7 +250,7 @@
const PylithScalar originTime = 5.064;
topology::Mesh mesh;
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
TimeHistorySlipFn slipfn;
spatialdata::spatialdb::TimeHistory th;
_initialize(&mesh, &faultMesh, &slipfn, &th, originTime);
@@ -259,7 +258,7 @@
const spatialdata::geocoords::CoordSys* cs = faultMesh.coordsys();CPPUNIT_ASSERT(cs);
const int spaceDim = cs->spaceDim();
- topology::Field<topology::SubMesh> slip(faultMesh);
+ topology::Field<topology::Mesh> slip(faultMesh);
slip.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim);
slip.allocate();
@@ -291,7 +290,7 @@
// Initialize TimeHistorySlipFn.
void
pylith::faults::TestTimeHistorySlipFn::_initialize(topology::Mesh* mesh,
- topology::SubMesh* faultMesh,
+ topology::Mesh* faultMesh,
TimeHistorySlipFn* slipfn,
spatialdata::spatialdb::TimeHistory* th,
const PylithScalar originTime)
@@ -374,7 +373,7 @@
mesh.coordsys(&cs);
// Create fault mesh
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
TestFaultMesh::createFaultMesh(&faultMesh, &mesh, data.faultLabel, data.faultId);
// Setup databases
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestTimeHistorySlipFn.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestTimeHistorySlipFn.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestTimeHistorySlipFn.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include <cppunit/extensions/HelperMacros.h>
#include "pylith/faults/faultsfwd.hh" // USES TimeHistorySlipFn
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh
+#include "pylith/topology/topologyfwd.hh" // USES Mesh
#include "spatialdata/spatialdb/spatialdbfwd.hh" // USES TimeHistory
/// Namespace for pylith package
@@ -102,7 +102,7 @@
*/
static
void _initialize(topology::Mesh* mesh,
- topology::SubMesh* faultMesh,
+ topology::Mesh* faultMesh,
TimeHistorySlipFn* slipfn,
spatialdata::spatialdb::TimeHistory* th,
const PylithScalar originTime);
@@ -125,14 +125,6 @@
const PylithScalar finalSlip,
const PylithScalar riseTime);
- /** Setup fault coordinates
- *
- * @param mesh Finite-element mesh of domain.
- * @param faultMesh Finite-element mesh of fault.
- */
- static
- void _setupFaultCoordinates(topology::Mesh *mesh, topology::SubMesh *faultMesh);
-
}; // class TestTimeHistorySlipFn
#endif // pylith_faults_testtimehistoryslipfn_hh
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestTractPerturbation.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestTractPerturbation.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestTractPerturbation.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -27,7 +27,6 @@
#include "pylith/faults/CohesiveTopology.hh" // USES CohesiveTopology
#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Stratum.hh" // USES Stratum
@@ -138,7 +137,7 @@
PYLITH_METHOD_BEGIN;
topology::Mesh mesh;
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
TractPerturbation tract;
_initialize(&mesh, &faultMesh, &tract);
@@ -160,7 +159,7 @@
};
topology::Mesh mesh;
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
TractPerturbation tract;
_initialize(&mesh, &faultMesh, &tract);
@@ -209,11 +208,11 @@
CPPUNIT_ASSERT_EQUAL(fiberDimE, spaceDim+spaceDim+spaceDim+1);
topology::Mesh mesh;
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
TractPerturbation tract;
_initialize(&mesh, &faultMesh, &tract);
- const topology::Fields<topology::Field<topology::SubMesh> >* parameters = tract.parameterFields();CPPUNIT_ASSERT(parameters);
+ const topology::Fields<topology::Field<topology::Mesh> >* parameters = tract.parameterFields();CPPUNIT_ASSERT(parameters);
PetscDM faultDMMesh = faultMesh.dmMesh();CPPUNIT_ASSERT(faultDMMesh);
topology::Stratum verticesStratum(faultDMMesh, topology::Stratum::DEPTH, 0);
@@ -280,11 +279,11 @@
const char* label = "traction_change_start_time";
topology::Mesh mesh;
- topology::SubMesh faultMesh;
+ topology::Mesh faultMesh;
TractPerturbation tract;
_initialize(&mesh, &faultMesh, &tract);
- const topology::Field<topology::SubMesh>& field = tract.vertexField(label);
+ const topology::Field<topology::Mesh>& field = tract.vertexField(label);
PetscDM faultDMMesh = faultMesh.dmMesh();CPPUNIT_ASSERT(faultDMMesh);
topology::Stratum verticesStratum(faultDMMesh, topology::Stratum::DEPTH, 0);
@@ -311,7 +310,7 @@
// Initialize TractPerturbation.
void
pylith::faults::TestTractPerturbation::_initialize(topology::Mesh* mesh,
- topology::SubMesh* faultMesh,
+ topology::Mesh* faultMesh,
TractPerturbation* tract)
{ // _initialize
PYLITH_METHOD_BEGIN;
@@ -366,7 +365,7 @@
dbChange.ioHandler(&ioChange);
// Setup fault orientation
- topology::Field<topology::SubMesh> faultOrientation(*faultMesh);
+ topology::Field<topology::Mesh> faultOrientation(*faultMesh);
faultOrientation.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim*spaceDim);
faultOrientation.allocate();
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestTractPerturbation.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestTractPerturbation.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestTractPerturbation.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -91,17 +91,9 @@
*/
static
void _initialize(topology::Mesh* mesh,
- topology::SubMesh* faultMesh,
+ topology::Mesh* faultMesh,
TractPerturbation* tract);
- /** Setup fault coordinates
- *
- * @param mesh Finite-element mesh of domain.
- * @param faultMesh Finite-element mesh of fault.
- */
- static
- void _setupFaultCoordinates(topology::Mesh *mesh, topology::SubMesh *faultMesh);
-
}; // class TestTractPerturbation
#endif // pylith_faults_testtractperturbation_hh
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicit.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicit.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicit.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -27,7 +27,6 @@
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Stratum.hh" // USES Stratum
#include "pylith/topology/VisitorMesh.hh" // USES VecVisitorMesh
#include "pylith/topology/SolutionFields.hh" // USES SolutionFields
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitLgDeform.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitLgDeform.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitLgDeform.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -29,7 +29,6 @@
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
#include "pylith/topology/Stratum.hh" // USES Stratum
#include "pylith/topology/VisitorMesh.hh" // USES VecVisitorMesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/SolutionFields.hh" // USES SolutionFields
#include "pylith/topology/Jacobian.hh" // USES Jacobian
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTet4.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTet4.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTet4.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -28,7 +28,6 @@
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Stratum.hh" // USES Stratum
#include "pylith/topology/VisitorMesh.hh" // USES VecVisitorMesh
#include "pylith/topology/SolutionFields.hh" // USES SolutionFields
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTri3.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTri3.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTri3.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -28,7 +28,6 @@
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Stratum.hh" // USES Stratum
#include "pylith/topology/VisitorMesh.hh" // USES VecVisitorMesh
#include "pylith/topology/SolutionFields.hh" // USES SolutionFields
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicit.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicit.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicit.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -28,7 +28,6 @@
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Stratum.hh" // USES Stratum
#include "pylith/topology/VisitorMesh.hh" // USES VecVisitorMesh
#include "pylith/topology/SolutionFields.hh" // USES SolutionFields
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicitLgDeform.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicitLgDeform.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicitLgDeform.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -27,7 +27,6 @@
#include "pylith/feassemble/Quadrature.hh" // USES Quadrature
#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Stratum.hh" // USES Stratum
#include "pylith/topology/VisitorMesh.hh" // USES VecVisitorMesh
#include "pylith/topology/SolutionFields.hh" // USES SolutionFields
Modified: short/3D/PyLith/trunk/unittests/libtests/friction/TestFrictionModel.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/friction/TestFrictionModel.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/friction/TestFrictionModel.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -26,7 +26,7 @@
#include "pylith/friction/StaticFriction.hh" // USES StaticFriction
#include "pylith/friction/SlipWeakening.hh" // USES SlipWeakening
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::nondimensionalize()
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Fields.hh" // USES Fields
@@ -176,7 +176,7 @@
for(PetscInt v = vStart; v < vEnd; ++v) {
for (int i = 0; i < numProperties; ++i, ++index) {
const materials::Metadata::ParamDescription& property = metadata.getProperty(i);
- topology::Field<topology::SubMesh>& prop = friction._fieldsPropsStateVars->get(property.name.c_str());
+ topology::Field<topology::Mesh>& prop = friction._fieldsPropsStateVars->get(property.name.c_str());
topology::VecVisitorMesh propVisitor(prop);
const PetscScalar* propArray = propVisitor.localArray();CPPUNIT_ASSERT(propArray);
@@ -213,7 +213,7 @@
StaticFrictionData data;
_initialize(&mesh, &fault, &friction, &data);
- const topology::Field<topology::SubMesh>& frictionField = friction.getField("friction_coefficient");
+ const topology::Field<topology::Mesh>& frictionField = friction.getField("friction_coefficient");
topology::VecVisitorMesh frictionVisitor(frictionField);
PetscScalar *frictionArray = frictionVisitor.localArray();CPPUNIT_ASSERT(frictionArray);
@@ -402,7 +402,7 @@
CPPUNIT_ASSERT(friction._fieldsPropsStateVars);
for(PetscInt i = 0; i < numStateVars; ++i) {
const materials::Metadata::ParamDescription& stateVar = metadata.getStateVar(i);
- topology::Field<topology::SubMesh>& stateVarField = friction._fieldsPropsStateVars->get(stateVar.name.c_str());
+ topology::Field<topology::Mesh>& stateVarField = friction._fieldsPropsStateVars->get(stateVar.name.c_str());
topology::VecVisitorMesh stateVarVisitor(stateVarField);
PetscScalar *fieldsArray = stateVarVisitor.localArray();CPPUNIT_ASSERT(fieldsArray);
@@ -834,7 +834,7 @@
topology::MeshOps::nondimensionalize(mesh, normalizer);
// Setup quadrature
- feassemble::Quadrature<topology::SubMesh> quadrature;
+ feassemble::Quadrature<topology::Mesh> quadrature;
feassemble::GeometryLine2D geometry;
quadrature.refGeometry(&geometry);
const int cellDim = 1;
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestCellFilterAvg.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestCellFilterAvg.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestCellFilterAvg.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -33,7 +33,6 @@
// ----------------------------------------------------------------------
typedef pylith::topology::Field<pylith::topology::Mesh> MeshField;
-typedef pylith::topology::Field<pylith::topology::SubMesh> SubMeshField;
// ----------------------------------------------------------------------
// Test constructor
@@ -198,10 +197,10 @@
iohandler.filename(filename);
iohandler.read(&mesh);
- topology::SubMesh submesh(mesh, group);
+ topology::Mesh submesh(mesh, group);
// Set cell field
- SubMeshField field(submesh);
+ MeshField field(submesh);
field.newSection(topology::FieldBase::FACES_FIELD, fiberDim);
field.allocate();
field.vectorFieldType(fieldType);
@@ -223,17 +222,17 @@
} // for
} // for
- feassemble::Quadrature<topology::SubMesh> quadrature;
+ feassemble::Quadrature<topology::Mesh> quadrature;
quadrature.initialize(basis, numQuadPts, numBasis,
basisDerivRef, numQuadPts, numBasis, cellDim,
quadPtsRef, numQuadPts, cellDim,
quadWts, numQuadPts,
spaceDim);
- CellFilterAvg<topology::SubMesh, SubMeshField> filter;
+ CellFilterAvg<topology::Mesh, MeshField> filter;
filter.quadrature(&quadrature);
- const SubMeshField& fieldF = filter.filter(field);
+ const MeshField& fieldF = filter.filter(field);
CPPUNIT_ASSERT_EQUAL(fieldTypeE, fieldF.vectorFieldType());
CPPUNIT_ASSERT_EQUAL(label, std::string(fieldF.label()));
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterBCMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterBCMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterBCMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -36,7 +36,7 @@
#include "spatialdata/geocoords/CSCart.hh" // USES CSCart
// ----------------------------------------------------------------------
-typedef pylith::topology::Field<pylith::topology::SubMesh> SubMeshField;
+typedef pylith::topology::Field<pylith::topology::Mesh> MeshField;
// ----------------------------------------------------------------------
// Setup testing data.
@@ -100,7 +100,7 @@
fault.adjustTopology(_mesh, &firstFaultVertex, &firstLagrangeVertex, &firstFaultCell, _flipFault);
} // if
- delete _submesh; _submesh = new topology::SubMesh(*_mesh, _data->bcLabel);CPPUNIT_ASSERT(_submesh);
+ delete _submesh; _submesh = new topology::Mesh(*_mesh, _data->bcLabel);CPPUNIT_ASSERT(_submesh);
PYLITH_METHOD_END;
} // _initialize
@@ -108,7 +108,7 @@
// ----------------------------------------------------------------------
// Create vertex fields.
void
-pylith::meshio::TestDataWriterBCMesh::_createVertexFields(topology::Fields<SubMeshField>* fields) const
+pylith::meshio::TestDataWriterBCMesh::_createVertexFields(topology::Fields<MeshField>* fields) const
{ // _createVertexFields
PYLITH_METHOD_BEGIN;
@@ -128,7 +128,7 @@
const char* name = _data->vertexFieldsInfo[i].name;
const int fiberDim = _data->vertexFieldsInfo[i].fiber_dim;
fields->add(name, name);
- SubMeshField& field = fields->get(name);
+ MeshField& field = fields->get(name);
field.newSection(topology::FieldBase::VERTICES_FIELD, fiberDim);
field.allocate();
field.vectorFieldType(_data->vertexFieldsInfo[i].field_type);
@@ -152,7 +152,7 @@
// ----------------------------------------------------------------------
// Create cell fields.
void
-pylith::meshio::TestDataWriterBCMesh::_createCellFields(topology::Fields<SubMeshField>* fields) const
+pylith::meshio::TestDataWriterBCMesh::_createCellFields(topology::Fields<MeshField>* fields) const
{ // _createCellFields
PYLITH_METHOD_BEGIN;
@@ -174,7 +174,7 @@
const char* name = _data->cellFieldsInfo[i].name;
const int fiberDim = _data->cellFieldsInfo[i].fiber_dim;
fields->add(name, name);
- SubMeshField& field = fields->get(name);
+ MeshField& field = fields->get(name);
field.newSection(topology::FieldBase::CELLS_FIELD, fiberDim, height);
field.allocate();
field.vectorFieldType(_data->cellFieldsInfo[i].field_type);
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterBCMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterBCMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterBCMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -27,7 +27,7 @@
#if !defined(pylith_meshio_testdatawriterbcmesh_hh)
#define pylith_meshio_testdatawriterbcmesh_hh
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh, Field
+#include "pylith/topology/topologyfwd.hh" // USES Mesh, Field
/// Namespace for pylith package
namespace pylith {
@@ -59,21 +59,21 @@
* @param fields Vertex fields.
*/
void
- _createVertexFields(topology::Fields<topology::Field<topology::SubMesh> >* fields) const;
+ _createVertexFields(topology::Fields<topology::Field<topology::Mesh> >* fields) const;
/** Create cell fields.
*
* @param fields Cell fields.
*/
void
- _createCellFields(topology::Fields<topology::Field<topology::SubMesh> >* fields) const;
+ _createCellFields(topology::Fields<topology::Field<topology::Mesh> >* fields) const;
// PROTECTED MEMBERS //////////////////////////////////////////////////
protected :
DataWriterData* _data; ///< Data for testing
topology::Mesh* _mesh; ///< Mesh for domain
- topology::SubMesh* _submesh; ///< Mesh for subdomain.
+ topology::Mesh* _submesh; ///< Mesh for subdomain.
bool _flipFault; ///< If true, flip fault orientation.
}; // class TestDataWriterBCMesh
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterFaultMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterFaultMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterFaultMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -39,7 +39,7 @@
#include <map> // USES std::map
// ----------------------------------------------------------------------
-typedef pylith::topology::Field<pylith::topology::SubMesh> MeshField;
+typedef pylith::topology::Field<pylith::topology::Mesh> MeshField;
// ----------------------------------------------------------------------
// Setup testing data.
@@ -50,7 +50,8 @@
_data = 0;
_mesh = new topology::Mesh();
- _faultMesh = new topology::SubMesh();
+ const bool isSubMesh = true;
+ _faultMesh = new topology::Mesh(isSubMesh);
_flipFault = false;
PYLITH_METHOD_END;
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterFaultMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterFaultMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterFaultMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -27,7 +27,7 @@
#if !defined(pylith_meshio_testdatawriterfaultmesh_hh)
#define pylith_meshio_testdatawriterfaultmesh_hh
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh, Field
+#include "pylith/topology/topologyfwd.hh" // USES Mesh, Field
/// Namespace for pylith package
namespace pylith {
@@ -59,21 +59,21 @@
* @param fields Vertex fields.
*/
void
- _createVertexFields(topology::Fields<topology::Field<topology::SubMesh> >* fields) const;
+ _createVertexFields(topology::Fields<topology::Field<topology::Mesh> >* fields) const;
/** Create cell fields.
*
* @param fields Cell fields.
*/
void
- _createCellFields(topology::Fields<topology::Field<topology::SubMesh> >* fields) const;
+ _createCellFields(topology::Fields<topology::Field<topology::Mesh> >* fields) const;
// PROTECTED MEMBERS //////////////////////////////////////////////////
protected :
DataWriterData* _data; ///< Data for testing
topology::Mesh* _mesh; ///< Mesh for domain
- topology::SubMesh* _faultMesh; ///< Fault mesh.
+ topology::Mesh* _faultMesh; ///< Fault mesh.
bool _flipFault; ///< If true, flip fault orientation.
}; // class TestDataWriterFaultMesh
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5BCMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5BCMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5BCMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -33,7 +33,7 @@
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5BCMesh );
// ----------------------------------------------------------------------
-typedef pylith::topology::Field<pylith::topology::SubMesh> SubMeshField;
+typedef pylith::topology::Field<pylith::topology::Mesh> MeshField;
// ----------------------------------------------------------------------
// Setup testing data.
@@ -66,7 +66,7 @@
{ // testConstructor
PYLITH_METHOD_BEGIN;
- DataWriterHDF5<topology::SubMesh, SubMeshField> writer;
+ DataWriterHDF5<topology::Mesh, MeshField> writer;
CPPUNIT_ASSERT(!writer._viewer);
@@ -83,7 +83,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5<topology::SubMesh, SubMeshField> writer;
+ DataWriterHDF5<topology::Mesh, MeshField> writer;
writer.filename(_data->timestepFilename);
@@ -117,9 +117,9 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5<topology::SubMesh, SubMeshField> writer;
+ DataWriterHDF5<topology::Mesh, MeshField> writer;
- topology::Fields<SubMeshField> vertexFields(*_submesh);
+ topology::Fields<MeshField> vertexFields(*_submesh);
_createVertexFields(&vertexFields);
writer.filename(_data->vertexFilename);
@@ -140,7 +140,7 @@
writer.openTimeStep(t, *_submesh, label, id);
} // else
for (int i=0; i < nfields; ++i) {
- SubMeshField& field = vertexFields.get(_data->vertexFieldsInfo[i].name);
+ MeshField& field = vertexFields.get(_data->vertexFieldsInfo[i].name);
writer.writeVertexField(t, field, *_submesh);
} // for
writer.closeTimeStep();
@@ -161,9 +161,9 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5<topology::SubMesh, SubMeshField> writer;
+ DataWriterHDF5<topology::Mesh, MeshField> writer;
- topology::Fields<SubMeshField> cellFields(*_submesh);
+ topology::Fields<MeshField> cellFields(*_submesh);
_createCellFields(&cellFields);
writer.filename(_data->cellFilename);
@@ -178,7 +178,7 @@
writer.open(*_submesh, numTimeSteps);
writer.openTimeStep(t, *_submesh);
for (int i=0; i < nfields; ++i) {
- SubMeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
+ MeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
writer.writeCellField(t, field);
} // for
} else {
@@ -187,7 +187,7 @@
writer.open(*_submesh, numTimeSteps, label, id);
writer.openTimeStep(t, *_submesh, label, id);
for (int i=0; i < nfields; ++i) {
- SubMeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
+ MeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
writer.writeCellField(t, field, label, id);
} // for
} // else
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5BCMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5BCMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5BCMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include "TestDataWriterHDF5.hh"
#include "TestDataWriterBCMesh.hh"
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh, Field
+#include "pylith/topology/topologyfwd.hh" // USES Mesh, Field
#include <cppunit/extensions/HelperMacros.h>
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5BCMeshCases.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5BCMeshCases.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5BCMeshCases.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,21 +20,12 @@
#include "TestDataWriterHDF5BCMeshCases.hh" // Implementation of class methods
-#include "data/DataWriterHDF5DataBCMeshTri3.hh"
-#include "data/DataWriterHDF5DataBCMeshQuad4.hh"
-#include "data/DataWriterHDF5DataBCMeshTet4.hh"
-#include "data/DataWriterHDF5DataBCMeshHex8.hh"
-
#include "pylith/utils/error.h" // USES PYLITH_METHOD_BEGIN/END
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataBCMeshTri3.hh"
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5BCMeshTri3 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5BCMeshQuad4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5BCMeshTet4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5BCMeshHex8 );
-
-// ----------------------------------------------------------------------
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5BCMeshTri3::setUp(void)
@@ -51,6 +42,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataBCMeshQuad4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5BCMeshQuad4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5BCMeshQuad4::setUp(void)
@@ -67,6 +61,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataBCMeshTet4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5BCMeshTet4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5BCMeshTet4::setUp(void)
@@ -83,6 +80,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataBCMeshHex8.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5BCMeshHex8 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5BCMeshHex8::setUp(void)
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtBCMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtBCMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtBCMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -33,7 +33,7 @@
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtBCMesh );
// ----------------------------------------------------------------------
-typedef pylith::topology::Field<pylith::topology::SubMesh> SubMeshField;
+typedef pylith::topology::Field<pylith::topology::Mesh> MeshField;
// ----------------------------------------------------------------------
// Setup testing data.
@@ -66,7 +66,7 @@
{ // testConstructor
PYLITH_METHOD_BEGIN;
- DataWriterHDF5Ext<topology::SubMesh, SubMeshField> writer;
+ DataWriterHDF5Ext<topology::Mesh, MeshField> writer;
PYLITH_METHOD_END;
} // testConstructor
@@ -81,7 +81,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5Ext<topology::SubMesh, SubMeshField> writer;
+ DataWriterHDF5Ext<topology::Mesh, MeshField> writer;
writer.filename(_data->timestepFilename);
@@ -115,9 +115,9 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5Ext<topology::SubMesh, SubMeshField> writer;
+ DataWriterHDF5Ext<topology::Mesh, MeshField> writer;
- topology::Fields<SubMeshField> vertexFields(*_submesh);
+ topology::Fields<MeshField> vertexFields(*_submesh);
_createVertexFields(&vertexFields);
writer.filename(_data->vertexFilename);
@@ -138,7 +138,7 @@
writer.openTimeStep(t, *_submesh, label, id);
} // else
for (int i=0; i < nfields; ++i) {
- SubMeshField& field = vertexFields.get(_data->vertexFieldsInfo[i].name);
+ MeshField& field = vertexFields.get(_data->vertexFieldsInfo[i].name);
writer.writeVertexField(t, field, *_submesh);
} // for
writer.closeTimeStep();
@@ -159,9 +159,9 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5Ext<topology::SubMesh, SubMeshField> writer;
+ DataWriterHDF5Ext<topology::Mesh, MeshField> writer;
- topology::Fields<SubMeshField> cellFields(*_submesh);
+ topology::Fields<MeshField> cellFields(*_submesh);
_createCellFields(&cellFields);
writer.filename(_data->cellFilename);
@@ -176,7 +176,7 @@
writer.open(*_submesh, numTimeSteps);
writer.openTimeStep(t, *_submesh);
for (int i=0; i < nfields; ++i) {
- SubMeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
+ MeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
writer.writeCellField(t, field);
} // for
} else {
@@ -185,7 +185,7 @@
writer.open(*_submesh, numTimeSteps, label, id);
writer.openTimeStep(t, *_submesh, label, id);
for (int i=0; i < nfields; ++i) {
- SubMeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
+ MeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
writer.writeCellField(t, field, label, id);
} // for
} // else
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtBCMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtBCMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtBCMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include "TestDataWriterHDF5.hh"
#include "TestDataWriterBCMesh.hh"
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh, Field
+#include "pylith/topology/topologyfwd.hh" // USES Mesh, Field
#include <cppunit/extensions/HelperMacros.h>
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtBCMeshCases.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtBCMeshCases.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtBCMeshCases.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,21 +20,13 @@
#include "TestDataWriterHDF5ExtBCMeshCases.hh" // Implementation of class methods
-#include "data/DataWriterHDF5DataBCMeshTri3.hh"
-#include "data/DataWriterHDF5DataBCMeshQuad4.hh"
-#include "data/DataWriterHDF5DataBCMeshTet4.hh"
-#include "data/DataWriterHDF5DataBCMeshHex8.hh"
-
#include "pylith/utils/error.h" // USES PYLITH_METHOD_BEGIN/END
+
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataBCMeshTri3.hh"
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtBCMeshTri3 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtBCMeshQuad4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtBCMeshTet4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtBCMeshHex8 );
-
-// ----------------------------------------------------------------------
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5ExtBCMeshTri3::setUp(void)
@@ -51,6 +43,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataBCMeshQuad4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtBCMeshQuad4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5ExtBCMeshQuad4::setUp(void)
@@ -67,6 +62,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataBCMeshTet4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtBCMeshTet4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5ExtBCMeshTet4::setUp(void)
@@ -83,6 +81,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataBCMeshHex8.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtBCMeshHex8 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5ExtBCMeshHex8::setUp(void)
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtFaultMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtFaultMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtFaultMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -36,7 +36,7 @@
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtFaultMesh );
// ----------------------------------------------------------------------
-typedef pylith::topology::Field<pylith::topology::SubMesh> MeshField;
+typedef pylith::topology::Field<pylith::topology::Mesh> MeshField;
// ----------------------------------------------------------------------
// Setup testing data.
@@ -69,7 +69,7 @@
{ // testConstructor
PYLITH_METHOD_BEGIN;
- DataWriterHDF5Ext<topology::SubMesh, MeshField> writer;
+ DataWriterHDF5Ext<topology::Mesh, MeshField> writer;
PYLITH_METHOD_END;
} // testConstructor
@@ -84,7 +84,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5Ext<topology::SubMesh, MeshField> writer;
+ DataWriterHDF5Ext<topology::Mesh, MeshField> writer;
writer.filename(_data->timestepFilename);
@@ -118,7 +118,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5Ext<topology::SubMesh, MeshField> writer;
+ DataWriterHDF5Ext<topology::Mesh, MeshField> writer;
topology::Fields<MeshField> vertexFields(*_faultMesh);
_createVertexFields(&vertexFields);
@@ -162,7 +162,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5Ext<topology::SubMesh, MeshField> writer;
+ DataWriterHDF5Ext<topology::Mesh, MeshField> writer;
topology::Fields<MeshField> cellFields(*_faultMesh);
_createCellFields(&cellFields);
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtFaultMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtFaultMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtFaultMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include "TestDataWriterHDF5.hh"
#include "TestDataWriterFaultMesh.hh"
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh, Field
+#include "pylith/topology/topologyfwd.hh" // USES Mesh, sField
#include <cppunit/extensions/HelperMacros.h>
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtFaultMeshCases.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtFaultMeshCases.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtFaultMeshCases.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,20 +20,10 @@
#include "TestDataWriterHDF5ExtFaultMeshCases.hh" // Implementation of class methods
-#include "data/DataWriterHDF5DataFaultMeshTri3.hh"
-#include "data/DataWriterHDF5DataFaultMeshQuad4.hh"
-#include "data/DataWriterHDF5DataFaultMeshTet4.hh"
-#include "data/DataWriterHDF5DataFaultMeshHex8.hh"
-
-
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataFaultMeshTri3.hh"
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtFaultMeshTri3 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtFaultMeshQuad4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtFaultMeshTet4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtFaultMeshHex8 );
-
-// ----------------------------------------------------------------------
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5ExtFaultMeshTri3::setUp(void)
@@ -47,6 +37,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataFaultMeshQuad4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtFaultMeshQuad4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5ExtFaultMeshQuad4::setUp(void)
@@ -60,6 +53,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataFaultMeshTet4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtFaultMeshTet4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5ExtFaultMeshTet4::setUp(void)
@@ -73,6 +69,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataFaultMeshHex8.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtFaultMeshHex8 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5ExtFaultMeshHex8::setUp(void)
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtSubMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtSubMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtSubMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -34,7 +34,6 @@
// ----------------------------------------------------------------------
typedef pylith::topology::Field<pylith::topology::Mesh> MeshField;
-typedef pylith::topology::Field<pylith::topology::SubMesh> SubMeshField;
// ----------------------------------------------------------------------
// Setup testing data.
@@ -67,7 +66,7 @@
{ // testConstructor
PYLITH_METHOD_BEGIN;
- DataWriterHDF5Ext<topology::SubMesh, SubMeshField> writer;
+ DataWriterHDF5Ext<topology::Mesh, MeshField> writer;
PYLITH_METHOD_END;
} // testConstructor
@@ -82,7 +81,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5Ext<topology::SubMesh, SubMeshField> writer;
+ DataWriterHDF5Ext<topology::Mesh, MeshField> writer;
writer.filename(_data->timestepFilename);
@@ -113,7 +112,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5Ext<topology::SubMesh, MeshField> writer;
+ DataWriterHDF5Ext<topology::Mesh, MeshField> writer;
topology::Fields<MeshField> vertexFields(*_mesh);
_createVertexFields(&vertexFields);
@@ -157,9 +156,9 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5Ext<topology::SubMesh, SubMeshField> writer;
+ DataWriterHDF5Ext<topology::Mesh, MeshField> writer;
- topology::Fields<SubMeshField> cellFields(*_submesh);
+ topology::Fields<MeshField> cellFields(*_submesh);
_createCellFields(&cellFields);
writer.filename(_data->cellFilename);
@@ -174,7 +173,7 @@
writer.open(*_submesh, numTimeSteps);
writer.openTimeStep(t, *_submesh);
for (int i=0; i < nfields; ++i) {
- SubMeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
+ MeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
writer.writeCellField(t, field);
} // for
} else {
@@ -183,7 +182,7 @@
writer.open(*_submesh, numTimeSteps, label, id);
writer.openTimeStep(t, *_submesh, label, id);
for (int i=0; i < nfields; ++i) {
- SubMeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
+ MeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
writer.writeCellField(t, field, label, id);
} // for
} // else
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtSubMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtSubMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtSubMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include "TestDataWriterHDF5.hh"
#include "TestDataWriterSubMesh.hh"
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh, Field
+#include "pylith/topology/topologyfwd.hh" // USES Mesh, Field
#include <cppunit/extensions/HelperMacros.h>
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtSubMeshCases.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtSubMeshCases.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5ExtSubMeshCases.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,23 +20,12 @@
#include "TestDataWriterHDF5ExtSubMeshCases.hh" // Implementation of class methods
-#include "data/DataWriterHDF5DataSubMeshLine2.hh"
-#include "data/DataWriterHDF5DataSubMeshTri3.hh"
-#include "data/DataWriterHDF5DataSubMeshQuad4.hh"
-#include "data/DataWriterHDF5DataSubMeshTet4.hh"
-#include "data/DataWriterHDF5DataSubMeshHex8.hh"
-
#include "pylith/utils/error.h" // USES PYLITH_METHOD_BEGIN/END
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataSubMeshLine2.hh"
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtSubMeshLine2 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtSubMeshTri3 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtSubMeshQuad4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtSubMeshTet4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtSubMeshHex8 );
-
-// ----------------------------------------------------------------------
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5ExtSubMeshLine2::setUp(void)
@@ -53,6 +42,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataSubMeshTri3.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtSubMeshTri3 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5ExtSubMeshTri3::setUp(void)
@@ -69,6 +61,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataSubMeshQuad4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtSubMeshQuad4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5ExtSubMeshQuad4::setUp(void)
@@ -85,6 +80,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataSubMeshTet4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtSubMeshTet4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5ExtSubMeshTet4::setUp(void)
@@ -101,6 +99,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataSubMeshHex8.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5ExtSubMeshHex8 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5ExtSubMeshHex8::setUp(void)
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5FaultMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5FaultMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5FaultMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -36,7 +36,7 @@
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5FaultMesh );
// ----------------------------------------------------------------------
-typedef pylith::topology::Field<pylith::topology::SubMesh> MeshField;
+typedef pylith::topology::Field<pylith::topology::Mesh> MeshField;
// ----------------------------------------------------------------------
// Setup testing data.
@@ -69,7 +69,7 @@
{ // testConstructor
PYLITH_METHOD_BEGIN;
- DataWriterHDF5<topology::SubMesh, MeshField> writer;
+ DataWriterHDF5<topology::Mesh, MeshField> writer;
CPPUNIT_ASSERT(!writer._viewer);
@@ -86,7 +86,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5<topology::SubMesh, MeshField> writer;
+ DataWriterHDF5<topology::Mesh, MeshField> writer;
writer.filename(_data->timestepFilename);
@@ -120,7 +120,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5<topology::SubMesh, MeshField> writer;
+ DataWriterHDF5<topology::Mesh, MeshField> writer;
topology::Fields<MeshField> vertexFields(*_faultMesh);
_createVertexFields(&vertexFields);
@@ -164,7 +164,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5<topology::SubMesh, MeshField> writer;
+ DataWriterHDF5<topology::Mesh, MeshField> writer;
topology::Fields<MeshField> cellFields(*_faultMesh);
_createCellFields(&cellFields);
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5FaultMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5FaultMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5FaultMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include "TestDataWriterHDF5.hh"
#include "TestDataWriterFaultMesh.hh"
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh, Field
+#include "pylith/topology/topologyfwd.hh" // USES Mesh, Field
#include <cppunit/extensions/HelperMacros.h>
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5FaultMeshCases.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5FaultMeshCases.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5FaultMeshCases.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,21 +20,13 @@
#include "TestDataWriterHDF5FaultMeshCases.hh" // Implementation of class methods
-#include "data/DataWriterHDF5DataFaultMeshTri3.hh"
-#include "data/DataWriterHDF5DataFaultMeshQuad4.hh"
-#include "data/DataWriterHDF5DataFaultMeshTet4.hh"
-#include "data/DataWriterHDF5DataFaultMeshHex8.hh"
-
#include "pylith/utils/error.h" // USES PYLITH_METHOD_BEGIN/END
+
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataFaultMeshTri3.hh"
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5FaultMeshTri3 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5FaultMeshQuad4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5FaultMeshTet4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5FaultMeshHex8 );
-
-// ----------------------------------------------------------------------
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5FaultMeshTri3::setUp(void)
@@ -52,6 +44,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataFaultMeshQuad4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5FaultMeshQuad4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5FaultMeshQuad4::setUp(void)
@@ -69,6 +64,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataFaultMeshTet4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5FaultMeshTet4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5FaultMeshTet4::setUp(void)
@@ -86,6 +84,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataFaultMeshHex8.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5FaultMeshHex8 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5FaultMeshHex8::setUp(void)
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5SubMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5SubMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5SubMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -34,7 +34,6 @@
// ----------------------------------------------------------------------
typedef pylith::topology::Field<pylith::topology::Mesh> MeshField;
-typedef pylith::topology::Field<pylith::topology::SubMesh> SubMeshField;
// ----------------------------------------------------------------------
// Setup testing data.
@@ -67,7 +66,7 @@
{ // testConstructor
PYLITH_METHOD_BEGIN;
- DataWriterHDF5<topology::SubMesh, MeshField> writer;
+ DataWriterHDF5<topology::Mesh, MeshField> writer;
CPPUNIT_ASSERT(!writer._viewer);
@@ -84,7 +83,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5<topology::SubMesh, MeshField> writer;
+ DataWriterHDF5<topology::Mesh, MeshField> writer;
writer.filename(_data->timestepFilename);
@@ -115,7 +114,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5<topology::SubMesh, MeshField> writer;
+ DataWriterHDF5<topology::Mesh, MeshField> writer;
topology::Fields<MeshField> vertexFields(*_mesh);
_createVertexFields(&vertexFields);
@@ -159,9 +158,9 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterHDF5<topology::SubMesh, SubMeshField> writer;
+ DataWriterHDF5<topology::Mesh, MeshField> writer;
- topology::Fields<SubMeshField> cellFields(*_submesh);
+ topology::Fields<MeshField> cellFields(*_submesh);
_createCellFields(&cellFields);
writer.filename(_data->cellFilename);
@@ -176,7 +175,7 @@
writer.open(*_submesh, numTimeSteps);
writer.openTimeStep(t, *_submesh);
for (int i=0; i < nfields; ++i) {
- SubMeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
+ MeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
writer.writeCellField(t, field);
} // for
} else {
@@ -185,7 +184,7 @@
writer.open(*_submesh, numTimeSteps, label, id);
writer.openTimeStep(t, *_submesh, label, id);
for (int i=0; i < nfields; ++i) {
- SubMeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
+ MeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
writer.writeCellField(t, field, label, id);
} // for
} // else
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5SubMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5SubMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5SubMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include "TestDataWriterHDF5.hh"
#include "TestDataWriterSubMesh.hh"
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh, Field
+#include "pylith/topology/topologyfwd.hh" // USES Mesh, Field
#include <cppunit/extensions/HelperMacros.h>
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5SubMeshCases.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5SubMeshCases.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterHDF5SubMeshCases.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,23 +20,13 @@
#include "TestDataWriterHDF5SubMeshCases.hh" // Implementation of class methods
-#include "data/DataWriterHDF5DataSubMeshLine2.hh"
-#include "data/DataWriterHDF5DataSubMeshTri3.hh"
-#include "data/DataWriterHDF5DataSubMeshQuad4.hh"
-#include "data/DataWriterHDF5DataSubMeshTet4.hh"
-#include "data/DataWriterHDF5DataSubMeshHex8.hh"
-
#include "pylith/utils/error.h" // USES PYLITH_METHOD_BEGIN/END
+
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataSubMeshLine2.hh"
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5SubMeshLine2 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5SubMeshTri3 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5SubMeshQuad4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5SubMeshTet4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5SubMeshHex8 );
-
-// ----------------------------------------------------------------------
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5SubMeshLine2::setUp(void)
@@ -53,6 +43,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataSubMeshTri3.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5SubMeshTri3 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5SubMeshTri3::setUp(void)
@@ -69,6 +62,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataSubMeshQuad4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5SubMeshQuad4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5SubMeshQuad4::setUp(void)
@@ -85,6 +81,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataSubMeshTet4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5SubMeshTet4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5SubMeshTet4::setUp(void)
@@ -101,6 +100,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterHDF5DataSubMeshHex8.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterHDF5SubMeshHex8 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterHDF5SubMeshHex8::setUp(void)
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterSubMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterSubMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterSubMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -37,7 +37,6 @@
// ----------------------------------------------------------------------
typedef pylith::topology::Field<pylith::topology::Mesh> MeshField;
-typedef pylith::topology::Field<pylith::topology::SubMesh> SubMeshField;
// ----------------------------------------------------------------------
// Setup testing data.
@@ -102,7 +101,7 @@
} // if
CPPUNIT_ASSERT(_data->bcLabel);
- delete _submesh; _submesh = new topology::SubMesh(*_mesh, _data->bcLabel);CPPUNIT_ASSERT(_submesh);
+ delete _submesh; _submesh = new topology::Mesh(*_mesh, _data->bcLabel);CPPUNIT_ASSERT(_submesh);
PYLITH_METHOD_END;
} // _initialize
@@ -154,7 +153,7 @@
// ----------------------------------------------------------------------
// Create cell fields.
void
-pylith::meshio::TestDataWriterSubMesh::_createCellFields(topology::Fields<SubMeshField>* fields) const
+pylith::meshio::TestDataWriterSubMesh::_createCellFields(topology::Fields<MeshField>* fields) const
{ // _createCellFields
PYLITH_METHOD_BEGIN;
@@ -175,7 +174,7 @@
const char* name = _data->cellFieldsInfo[i].name;
const int fiberDim = _data->cellFieldsInfo[i].fiber_dim;
fields->add(name, name);
- SubMeshField& field = fields->get(name);
+ MeshField& field = fields->get(name);
field.newSection(topology::FieldBase::CELLS_FIELD, fiberDim, 1);
field.allocate();
field.vectorFieldType(_data->cellFieldsInfo[i].field_type);
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterSubMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterSubMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterSubMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -27,7 +27,7 @@
#if !defined(pylith_meshio_testdatawritersubmesh_hh)
#define pylith_meshio_testdatawritersubmesh_hh
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh, Field
+#include "pylith/topology/topologyfwd.hh" // USES Mesh, Field
/// Namespace for pylith package
namespace pylith {
@@ -66,14 +66,14 @@
* @param fields Cell fields.
*/
void
- _createCellFields(topology::Fields<topology::Field<topology::SubMesh> >* fields) const;
+ _createCellFields(topology::Fields<topology::Field<topology::Mesh> >* fields) const;
// PROTECTED MEMBERS //////////////////////////////////////////////////
protected :
DataWriterData* _data; ///< Data for testing
topology::Mesh* _mesh; ///< Mesh for domain
- topology::SubMesh* _submesh; ///< Mesh for subdomain.
+ topology::Mesh* _submesh; ///< Mesh for subdomain.
bool _flipFault; ///< If true, flip fault orientation.
}; // class TestDataWriterSubMesh
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKBCMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKBCMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKBCMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -33,7 +33,7 @@
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKBCMesh );
// ----------------------------------------------------------------------
-typedef pylith::topology::Field<pylith::topology::SubMesh> SubMeshField;
+typedef pylith::topology::Field<pylith::topology::Mesh> MeshField;
// ----------------------------------------------------------------------
// Setup testing data.
@@ -66,7 +66,7 @@
{ // testConstructor
PYLITH_METHOD_BEGIN;
- DataWriterVTK<topology::SubMesh, SubMeshField> writer;
+ DataWriterVTK<topology::Mesh, MeshField> writer;
CPPUNIT_ASSERT(!writer._viewer);
CPPUNIT_ASSERT_EQUAL(false, writer._wroteVertexHeader);
@@ -85,7 +85,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterVTK<topology::SubMesh, SubMeshField> writer;
+ DataWriterVTK<topology::Mesh, MeshField> writer;
writer.filename(_data->timestepFilename);
writer.timeFormat(_data->timeFormat);
@@ -129,9 +129,9 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterVTK<topology::SubMesh, SubMeshField> writer;
+ DataWriterVTK<topology::Mesh, MeshField> writer;
- topology::Fields<SubMeshField> vertexFields(*_submesh);
+ topology::Fields<MeshField> vertexFields(*_submesh);
_createVertexFields(&vertexFields);
writer.filename(_data->vertexFilename);
@@ -151,7 +151,7 @@
writer.openTimeStep(t, *_submesh, label, id);
} // else
for (int i=0; i < nfields; ++i) {
- SubMeshField& field = vertexFields.get(_data->vertexFieldsInfo[i].name);
+ MeshField& field = vertexFields.get(_data->vertexFieldsInfo[i].name);
writer.writeVertexField(t, field, *_submesh);
CPPUNIT_ASSERT(writer._wroteVertexHeader);
CPPUNIT_ASSERT_EQUAL(false, writer._wroteCellHeader);
@@ -176,9 +176,9 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterVTK<topology::SubMesh, SubMeshField> writer;
+ DataWriterVTK<topology::Mesh, MeshField> writer;
- topology::Fields<SubMeshField> cellFields(*_submesh);
+ topology::Fields<MeshField> cellFields(*_submesh);
_createCellFields(&cellFields);
writer.filename(_data->cellFilename);
@@ -192,7 +192,7 @@
writer.open(*_submesh, numTimeSteps);
writer.openTimeStep(t, *_submesh);
for (int i=0; i < nfields; ++i) {
- SubMeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
+ MeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
writer.writeCellField(t, field);
CPPUNIT_ASSERT_EQUAL(false, writer._wroteVertexHeader);
CPPUNIT_ASSERT(writer._wroteCellHeader);
@@ -203,7 +203,7 @@
writer.open(*_submesh, numTimeSteps, label, id);
writer.openTimeStep(t, *_submesh, label, id);
for (int i=0; i < nfields; ++i) {
- SubMeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
+ MeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
writer.writeCellField(t, field, label, id);
CPPUNIT_ASSERT_EQUAL(false, writer._wroteVertexHeader);
CPPUNIT_ASSERT(writer._wroteCellHeader);
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKBCMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKBCMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKBCMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include "TestDataWriterVTK.hh"
#include "TestDataWriterBCMesh.hh"
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh, Field
+#include "pylith/topology/topologyfwd.hh" // USES Mesh, Field
#include <cppunit/extensions/HelperMacros.h>
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKBCMeshCases.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKBCMeshCases.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKBCMeshCases.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -22,20 +22,11 @@
#include "pylith/utils/error.h" // USES PYLITH_METHOD_BEGIN/END
-#include "data/DataWriterVTKDataBCMeshTri3.hh"
-#include "data/DataWriterVTKDataBCMeshQuad4.hh"
-#include "data/DataWriterVTKDataBCMeshTet4.hh"
-#include "data/DataWriterVTKDataBCMeshHex8.hh"
-
// ----------------------------------------------------------------------
+#include "data/DataWriterVTKDataBCMeshTri3.hh"
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKBCMeshTri3 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKBCMeshQuad4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKBCMeshTet4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKBCMeshHex8 );
-
-// ----------------------------------------------------------------------
// Setup testing data.
void
pylith::meshio::TestDataWriterVTKBCMeshTri3::setUp(void)
@@ -52,6 +43,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterVTKDataBCMeshQuad4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKBCMeshQuad4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterVTKBCMeshQuad4::setUp(void)
@@ -68,6 +62,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterVTKDataBCMeshTet4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKBCMeshTet4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterVTKBCMeshTet4::setUp(void)
@@ -84,6 +81,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterVTKDataBCMeshHex8.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKBCMeshHex8 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterVTKBCMeshHex8::setUp(void)
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKFaultMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKFaultMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKFaultMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -36,7 +36,7 @@
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKFaultMesh );
// ----------------------------------------------------------------------
-typedef pylith::topology::Field<pylith::topology::SubMesh> MeshField;
+typedef pylith::topology::Field<pylith::topology::Mesh> MeshField;
// ----------------------------------------------------------------------
// Setup testing data.
@@ -69,7 +69,7 @@
{ // testConstructor
PYLITH_METHOD_BEGIN;
- DataWriterVTK<topology::SubMesh, MeshField> writer;
+ DataWriterVTK<topology::Mesh, MeshField> writer;
CPPUNIT_ASSERT(!writer._viewer);
CPPUNIT_ASSERT_EQUAL(false, writer._wroteVertexHeader);
@@ -88,7 +88,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterVTK<topology::SubMesh, MeshField> writer;
+ DataWriterVTK<topology::Mesh, MeshField> writer;
writer.filename(_data->timestepFilename);
writer.timeFormat(_data->timeFormat);
@@ -132,7 +132,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterVTK<topology::SubMesh, MeshField> writer;
+ DataWriterVTK<topology::Mesh, MeshField> writer;
topology::Fields<MeshField> vertexFields(*_faultMesh);
_createVertexFields(&vertexFields);
@@ -179,7 +179,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterVTK<topology::SubMesh, MeshField> writer;
+ DataWriterVTK<topology::Mesh, MeshField> writer;
topology::Fields<MeshField> cellFields(*_faultMesh);
_createCellFields(&cellFields);
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKFaultMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKFaultMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKFaultMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include "TestDataWriterVTK.hh"
#include "TestDataWriterFaultMesh.hh"
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh, Field
+#include "pylith/topology/topologyfwd.hh" // USES Mesh, Field
#include <cppunit/extensions/HelperMacros.h>
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKFaultMeshCases.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKFaultMeshCases.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKFaultMeshCases.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -22,20 +22,10 @@
#include "pylith/utils/error.h" // USES PYLITH_METHOD_BEGIN/END
-#include "data/DataWriterVTKDataFaultMeshTri3.hh"
-#include "data/DataWriterVTKDataFaultMeshQuad4.hh"
-#include "data/DataWriterVTKDataFaultMeshTet4.hh"
-#include "data/DataWriterVTKDataFaultMeshHex8.hh"
-
-
// ----------------------------------------------------------------------
+#include "data/DataWriterVTKDataFaultMeshTri3.hh"
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKFaultMeshTri3 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKFaultMeshQuad4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKFaultMeshTet4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKFaultMeshHex8 );
-
-// ----------------------------------------------------------------------
// Setup testing data.
void
pylith::meshio::TestDataWriterVTKFaultMeshTri3::setUp(void)
@@ -53,6 +43,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterVTKDataFaultMeshQuad4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKFaultMeshQuad4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterVTKFaultMeshQuad4::setUp(void)
@@ -70,6 +63,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterVTKDataFaultMeshTet4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKFaultMeshTet4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterVTKFaultMeshTet4::setUp(void)
@@ -87,6 +83,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterVTKDataFaultMeshHex8.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKFaultMeshHex8 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterVTKFaultMeshHex8::setUp(void)
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKSubMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKSubMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKSubMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -34,7 +34,6 @@
// ----------------------------------------------------------------------
typedef pylith::topology::Field<pylith::topology::Mesh> MeshField;
-typedef pylith::topology::Field<pylith::topology::SubMesh> SubMeshField;
// ----------------------------------------------------------------------
// Setup testing data.
@@ -67,7 +66,7 @@
{ // testConstructor
PYLITH_METHOD_BEGIN;
- DataWriterVTK<topology::SubMesh, MeshField> writer;
+ DataWriterVTK<topology::Mesh, MeshField> writer;
CPPUNIT_ASSERT(!writer._viewer);
CPPUNIT_ASSERT_EQUAL(false, writer._wroteVertexHeader);
@@ -86,7 +85,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterVTK<topology::SubMesh, MeshField> writer;
+ DataWriterVTK<topology::Mesh, MeshField> writer;
writer.filename(_data->timestepFilename);
writer.timeFormat(_data->timeFormat);
@@ -130,7 +129,7 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterVTK<topology::SubMesh, MeshField> writer;
+ DataWriterVTK<topology::Mesh, MeshField> writer;
topology::Fields<MeshField> vertexFields(*_mesh);
_createVertexFields(&vertexFields);
@@ -177,9 +176,9 @@
CPPUNIT_ASSERT(_mesh);
CPPUNIT_ASSERT(_data);
- DataWriterVTK<topology::SubMesh, SubMeshField> writer;
+ DataWriterVTK<topology::Mesh, MeshField> writer;
- topology::Fields<SubMeshField> cellFields(*_submesh);
+ topology::Fields<MeshField> cellFields(*_submesh);
_createCellFields(&cellFields);
writer.filename(_data->cellFilename);
@@ -193,7 +192,7 @@
writer.open(*_submesh, numTimeSteps);
writer.openTimeStep(t, *_submesh);
for (int i=0; i < nfields; ++i) {
- SubMeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
+ MeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
writer.writeCellField(t, field);
CPPUNIT_ASSERT_EQUAL(false, writer._wroteVertexHeader);
CPPUNIT_ASSERT(writer._wroteCellHeader);
@@ -204,7 +203,7 @@
writer.open(*_submesh, numTimeSteps, label, id);
writer.openTimeStep(t, *_submesh, label, id);
for (int i=0; i < nfields; ++i) {
- SubMeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
+ MeshField& field = cellFields.get(_data->cellFieldsInfo[i].name);
writer.writeCellField(t, field, label, id);
CPPUNIT_ASSERT_EQUAL(false, writer._wroteVertexHeader);
CPPUNIT_ASSERT(writer._wroteCellHeader);
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKSubMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKSubMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKSubMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -30,7 +30,7 @@
#include "TestDataWriterVTK.hh"
#include "TestDataWriterSubMesh.hh"
-#include "pylith/topology/topologyfwd.hh" // USES Mesh, SubMesh, Field
+#include "pylith/topology/topologyfwd.hh" // USES Mesh, Field
#include <cppunit/extensions/HelperMacros.h>
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKSubMeshCases.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKSubMeshCases.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterVTKSubMeshCases.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -22,22 +22,11 @@
#include "pylith/utils/error.h" // USES PYLITH_METHOD_BEGIN/END
-#include "data/DataWriterVTKDataSubMeshLine2.hh"
-#include "data/DataWriterVTKDataSubMeshTri3.hh"
-#include "data/DataWriterVTKDataSubMeshQuad4.hh"
-#include "data/DataWriterVTKDataSubMeshTet4.hh"
-#include "data/DataWriterVTKDataSubMeshHex8.hh"
-
// ----------------------------------------------------------------------
+#include "data/DataWriterVTKDataSubMeshLine2.hh"
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKSubMeshLine2 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKSubMeshTri3 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKSubMeshQuad4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKSubMeshTet4 );
-CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKSubMeshHex8 );
-
-// ----------------------------------------------------------------------
// Setup testing data.
void
pylith::meshio::TestDataWriterVTKSubMeshLine2::setUp(void)
@@ -54,6 +43,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterVTKDataSubMeshTri3.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKSubMeshTri3 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterVTKSubMeshTri3::setUp(void)
@@ -70,6 +62,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterVTKDataSubMeshQuad4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKSubMeshQuad4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterVTKSubMeshQuad4::setUp(void)
@@ -86,6 +81,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterVTKDataSubMeshTet4.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKSubMeshTet4 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterVTKSubMeshTet4::setUp(void)
@@ -102,6 +100,9 @@
// ----------------------------------------------------------------------
+#include "data/DataWriterVTKDataSubMeshHex8.hh"
+CPPUNIT_TEST_SUITE_REGISTRATION( pylith::meshio::TestDataWriterVTKSubMeshHex8 );
+
// Setup testing data.
void
pylith::meshio::TestDataWriterVTKSubMeshHex8::setUp(void)
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestOutputSolnSubset.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestOutputSolnSubset.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestOutputSolnSubset.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -23,7 +23,6 @@
#include "pylith/meshio/OutputSolnSubset.hh"
#include "pylith/topology/Mesh.hh" // USES Mesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Stratum.hh" // USES Stratum
#include "pylith/meshio/MeshIOAscii.hh" // USES MeshIOAscii
Modified: short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldSubMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldSubMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldSubMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -21,7 +21,7 @@
#include "TestFieldSubMesh.hh" // Implementation of class methods
#include "pylith/topology/Field.hh" // USES Field
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/MeshOps.hh" // USES MeshOps::createDMMesh()
#include "pylith/topology/Stratum.hh" // USES Stratum
#include "pylith/topology/VisitorMesh.hh" // USES VecVisitorMesh
@@ -71,10 +71,11 @@
PYLITH_METHOD_BEGIN;
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
- Field<SubMesh> field(submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
+ Field<Mesh> field(submesh);
+
PYLITH_METHOD_END;
} // testConstructor
@@ -86,9 +87,9 @@
PYLITH_METHOD_BEGIN;
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
- Field<SubMesh> field(submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
+ Field<Mesh> field(submesh);
PetscSection section = field.petscSection();
CPPUNIT_ASSERT(section);
@@ -104,11 +105,11 @@
PYLITH_METHOD_BEGIN;
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
- Field<SubMesh> field(submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
+ Field<Mesh> field(submesh);
- const SubMesh& mesh2 = field.mesh();
+ const Mesh& mesh2 = field.mesh();
CPPUNIT_ASSERT_EQUAL(_TestFieldSubMesh::cellDim-1, mesh2.dimension());
PYLITH_METHOD_END;
@@ -122,9 +123,9 @@
PYLITH_METHOD_BEGIN;
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
- Field<SubMesh> field(submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
+ Field<Mesh> field(submesh);
CPPUNIT_ASSERT_EQUAL(_TestFieldSubMesh::cellDim, field.spaceDim());
@@ -139,9 +140,9 @@
PYLITH_METHOD_BEGIN;
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
- Field<SubMesh> field(submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
+ Field<Mesh> field(submesh);
field.newSection();
PetscSection section = field.petscSection();
@@ -160,10 +161,10 @@
const int fiberDim = 2;
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
- Field<SubMesh> field(submesh);
+ Field<Mesh> field(submesh);
field.newSection(topology::FieldBase::VERTICES_FIELD, fiberDim);
field.allocate();
@@ -190,11 +191,11 @@
const int fiberDim = 2;
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
- Field<SubMesh> field(submesh);
- field.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ Field<Mesh> field(submesh);
+ field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
field.allocate();
PetscDM dmMesh = submesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
@@ -220,16 +221,16 @@
const int fiberDim = 3;
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
// Create field with atlas to use to create new field
- Field<SubMesh> fieldSrc(submesh);
- fieldSrc.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ Field<Mesh> fieldSrc(submesh);
+ fieldSrc.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
fieldSrc.allocate();
const int fiberDim2 = 4;
- Field<SubMesh> field(submesh);
+ Field<Mesh> field(submesh);
field.newSection(fieldSrc, fiberDim2);
field.allocate();
@@ -263,8 +264,8 @@
};
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
PetscDM dmMesh = submesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
PetscErrorCode err = 0;
@@ -272,9 +273,9 @@
err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);PYLITH_CHECK_ERROR(err);
// Create field with atlas to use to create new field
- Field<SubMesh> fieldSrc(submesh);
+ Field<Mesh> fieldSrc(submesh);
{ // Setup source field
- fieldSrc.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ fieldSrc.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
PetscSection section = fieldSrc.petscSection();CPPUNIT_ASSERT(section);
int iV=0;
for(PetscInt v = vStart; v < vEnd; ++v) {
@@ -290,7 +291,7 @@
fieldSrc.zero();
} // Setup source field
- Field<SubMesh> field(submesh);
+ Field<Mesh> field(submesh);
field.cloneSection(fieldSrc);
PetscSection section = field.petscSection();CPPUNIT_ASSERT(section);
PetscVec vec = field.localVector();CPPUNIT_ASSERT(vec);
@@ -315,18 +316,18 @@
PYLITH_METHOD_BEGIN;
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
- Field<SubMesh> field(submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
+ Field<Mesh> field(submesh);
field.scale(2.0);
- field.vectorFieldType(Field<SubMesh>::TENSOR);
+ field.vectorFieldType(Field<Mesh>::TENSOR);
field.addDimensionOkay(true);
field.clear();
CPPUNIT_ASSERT_EQUAL(PylithScalar(1.0), field._metadata["default"].scale);
- CPPUNIT_ASSERT_EQUAL(Field<SubMesh>::OTHER, field._metadata["default"].vectorFieldType);
+ CPPUNIT_ASSERT_EQUAL(Field<Mesh>::OTHER, field._metadata["default"].vectorFieldType);
CPPUNIT_ASSERT_EQUAL(false, field._metadata["default"].dimsOkay);
PYLITH_METHOD_END;
@@ -348,11 +349,11 @@
};
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
- Field<SubMesh> field(submesh);
- field.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ Field<Mesh> field(submesh);
+ field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
field.allocate();
PetscDM dmMesh = submesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
@@ -399,11 +400,11 @@
};
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
- Field<SubMesh> field(submesh);
- field.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ Field<Mesh> field(submesh);
+ field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
field.allocate();
PetscDM dmMesh = submesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
@@ -452,17 +453,17 @@
};
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
PetscDM dmMesh = submesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
Stratum depthStratum(dmMesh, Stratum::DEPTH, 0);
const PetscInt vStart = depthStratum.begin();
const PetscInt vEnd = depthStratum.end();
- Field<SubMesh> field(submesh);
+ Field<Mesh> field(submesh);
{ // setup field
- field.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
field.allocate();
VecVisitorMesh fieldVisitor(field);
PetscScalar* fieldArray = fieldVisitor.localArray();
@@ -505,17 +506,17 @@
};
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
PetscDM dmMesh = submesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
Stratum depthStratum(dmMesh, Stratum::DEPTH, 0);
const PetscInt vStart = depthStratum.begin();
const PetscInt vEnd = depthStratum.end();
- Field<SubMesh> fieldSrc(submesh);
+ Field<Mesh> fieldSrc(submesh);
{ // setup source field
- fieldSrc.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ fieldSrc.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
fieldSrc.allocate();
VecVisitorMesh fieldVisitor(fieldSrc);
PetscScalar* fieldArray = fieldVisitor.localArray();
@@ -527,8 +528,8 @@
} // for
} // setup source field
- Field<SubMesh> field(submesh);
- field.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ Field<Mesh> field(submesh);
+ field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
field.allocate();
field.copy(fieldSrc);
@@ -566,17 +567,17 @@
};
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
PetscDM dmMesh = submesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
Stratum depthStratum(dmMesh, Stratum::DEPTH, 0);
const PetscInt vStart = depthStratum.begin();
const PetscInt vEnd = depthStratum.end();
- Field<SubMesh> fieldSrc(submesh);
+ Field<Mesh> fieldSrc(submesh);
{ // setup source field
- fieldSrc.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ fieldSrc.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
fieldSrc.allocate();
VecVisitorMesh fieldVisitor(fieldSrc);
PetscScalar* fieldArray = fieldVisitor.localArray();
@@ -588,9 +589,9 @@
} // for
} // setup source field
- Field<SubMesh> field(submesh);
+ Field<Mesh> field(submesh);
{ // setup destination field
- field.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
field.allocate();
VecVisitorMesh fieldVisitor(field);
PetscScalar* fieldArray = fieldVisitor.localArray();
@@ -633,17 +634,17 @@
};
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
PetscDM dmMesh = submesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
Stratum depthStratum(dmMesh, Stratum::DEPTH, 0);
const PetscInt vStart = depthStratum.begin();
const PetscInt vEnd = depthStratum.end();
- Field<SubMesh> field(submesh);
+ Field<Mesh> field(submesh);
{ // setup field
- field.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
field.allocate();
VecVisitorMesh fieldVisitor(field);
PetscScalar* fieldArray = fieldVisitor.localArray();
@@ -688,16 +689,16 @@
};
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
PetscDM dmMesh = submesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
Stratum depthStratum(dmMesh, Stratum::DEPTH, 0);
const PetscInt vStart = depthStratum.begin();
const PetscInt vEnd = depthStratum.end();
- Field<SubMesh> field(submesh);
- field.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ Field<Mesh> field(submesh);
+ field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
field.allocate();
VecVisitorMesh fieldVisitor(field);
PetscScalar* fieldArray = fieldVisitor.localArray();
@@ -722,10 +723,10 @@
const int fiberDim = 3;
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
- Field<SubMesh> field(submesh);
+ Field<Mesh> field(submesh);
field.newSection(FieldBase::VERTICES_FIELD, fiberDim);
field.allocate();
@@ -738,7 +739,7 @@
const PetscInt vEnd = depthStratum.end();
CPPUNIT_ASSERT_EQUAL(size_t(1), field._scatters.size());
- const Field<SubMesh>::ScatterInfo& sinfo = field._getScatter("");
+ const Field<Mesh>::ScatterInfo& sinfo = field._getScatter("");
CPPUNIT_ASSERT(sinfo.dm);
CPPUNIT_ASSERT(sinfo.vector);
@@ -754,19 +755,19 @@
// Create another scatter.
field.createScatter(submesh, "B");
CPPUNIT_ASSERT_EQUAL(size_t(2), field._scatters.size());
- const Field<SubMesh>::ScatterInfo& sinfoB = field._getScatter("B");
+ const Field<Mesh>::ScatterInfo& sinfoB = field._getScatter("B");
CPPUNIT_ASSERT(sinfoB.dm);
CPPUNIT_ASSERT(sinfoB.vector);
- Field<SubMesh> field2(submesh);
+ Field<Mesh> field2(submesh);
field2.cloneSection(field);
CPPUNIT_ASSERT_EQUAL(size_t(2), field2._scatters.size());
- const Field<SubMesh>::ScatterInfo& sinfo2 = field2._getScatter("");
+ const Field<Mesh>::ScatterInfo& sinfo2 = field2._getScatter("");
CPPUNIT_ASSERT(sinfo2.dm);
CPPUNIT_ASSERT(sinfo2.vector);
- const Field<SubMesh>::ScatterInfo& sinfo2B = field2._getScatter("B");
+ const Field<Mesh>::ScatterInfo& sinfo2B = field2._getScatter("B");
CPPUNIT_ASSERT(sinfo2B.dm);
CPPUNIT_ASSERT(sinfo2B.vector);
@@ -783,10 +784,10 @@
const int fiberDim = 3;
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
- Field<SubMesh> field(submesh);
+ Field<Mesh> field(submesh);
field.newSection(FieldBase::VERTICES_FIELD, fiberDim);
field.allocate();
@@ -799,7 +800,7 @@
const PetscInt vStart = depthStratum.begin();
const PetscInt vEnd = depthStratum.end();
- const Field<SubMesh>::ScatterInfo& sinfo = field._getScatter("");
+ const Field<Mesh>::ScatterInfo& sinfo = field._getScatter("");
CPPUNIT_ASSERT(sinfo.dm);
CPPUNIT_ASSERT(sinfo.vector);
@@ -815,19 +816,19 @@
// Create another scatter.
field.createScatterWithBC(submesh, "B");
CPPUNIT_ASSERT_EQUAL(size_t(2), field._scatters.size());
- const Field<SubMesh>::ScatterInfo& sinfoB = field._getScatter("B");
+ const Field<Mesh>::ScatterInfo& sinfoB = field._getScatter("B");
CPPUNIT_ASSERT(sinfoB.dm);
CPPUNIT_ASSERT(sinfoB.vector);
- Field<SubMesh> field2(submesh);
+ Field<Mesh> field2(submesh);
field2.cloneSection(field);
CPPUNIT_ASSERT_EQUAL(size_t(2), field2._scatters.size());
- const Field<SubMesh>::ScatterInfo& sinfo2 = field2._getScatter("");
+ const Field<Mesh>::ScatterInfo& sinfo2 = field2._getScatter("");
CPPUNIT_ASSERT(sinfo2.dm);
CPPUNIT_ASSERT(sinfo2.vector);
- const Field<SubMesh>::ScatterInfo& sinfo2B = field2._getScatter("B");
+ const Field<Mesh>::ScatterInfo& sinfo2B = field2._getScatter("B");
CPPUNIT_ASSERT(sinfo2B.dm);
CPPUNIT_ASSERT(sinfo2B.vector);
@@ -844,17 +845,17 @@
const int fiberDim = 3;
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
- Field<SubMesh> field(submesh);
+ Field<Mesh> field(submesh);
field.newSection(FieldBase::VERTICES_FIELD, fiberDim);
field.allocate();
CPPUNIT_ASSERT_EQUAL(size_t(0), field._scatters.size());
field.createScatter(submesh);
CPPUNIT_ASSERT_EQUAL(size_t(1), field._scatters.size());
- const Field<SubMesh>::ScatterInfo& sinfo = field._getScatter("");
+ const Field<Mesh>::ScatterInfo& sinfo = field._getScatter("");
CPPUNIT_ASSERT(sinfo.dm);
CPPUNIT_ASSERT(sinfo.vector);
@@ -888,17 +889,17 @@
};
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
PetscDM dmMesh = submesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
Stratum depthStratum(dmMesh, Stratum::DEPTH, 0);
const PetscInt vStart = depthStratum.begin();
const PetscInt vEnd = depthStratum.end();
- Field<SubMesh> field(submesh);
+ Field<Mesh> field(submesh);
{ // setup field
- field.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
field.allocate();
VecVisitorMesh fieldVisitor(field);
PetscScalar* fieldArray = fieldVisitor.localArray();
@@ -946,16 +947,16 @@
};
Mesh mesh;
- SubMesh submesh;
- _buildMesh(&mesh, &submesh);
+ _buildMesh(&mesh);
+ Mesh submesh(mesh, _TestFieldSubMesh::label);
PetscDM dmMesh = submesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
Stratum depthStratum(dmMesh, Stratum::DEPTH, 0);
const PetscInt vStart = depthStratum.begin();
const PetscInt vEnd = depthStratum.end();
- Field<SubMesh> field(submesh);
- field.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ Field<Mesh> field(submesh);
+ field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
field.allocate();
field.createScatter(submesh, context);
@@ -989,13 +990,11 @@
// ----------------------------------------------------------------------
void
-pylith::topology::TestFieldSubMesh::_buildMesh(Mesh* mesh,
- SubMesh* submesh)
+pylith::topology::TestFieldSubMesh::_buildMesh(Mesh* mesh)
{ // _buildMesh
PYLITH_METHOD_BEGIN;
assert(mesh);
- assert(submesh);
const int cellDim = _TestFieldSubMesh::cellDim;
const int ncells = _TestFieldSubMesh::ncells;
@@ -1064,8 +1063,6 @@
cs.initialize();
mesh->coordsys(&cs);
- submesh->createSubMesh(*mesh, _TestFieldSubMesh::label);
-
PYLITH_METHOD_END;
} // _buildMesh
Modified: short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldSubMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldSubMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldSubMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -146,11 +146,9 @@
/** Build mesh.
*
* @param mesh Finite-element mesh.
- * @param submesh Boundary mesh.
*/
static
- void _buildMesh(Mesh* mesh,
- SubMesh* submesh);
+ void _buildMesh(Mesh* mesh);
}; // class TestFieldSubMesh
Modified: short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsSubMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsSubMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsSubMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -20,7 +20,7 @@
#include "TestFieldsSubMesh.hh" // Implementation of class methods
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
+#include "pylith/topology/Mesh.hh" // USES Mesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/Fields.hh" // USES Fields
#include "pylith/topology/Stratum.hh" // USES Stratum
@@ -32,7 +32,7 @@
CPPUNIT_TEST_SUITE_REGISTRATION( pylith::topology::TestFieldsSubMesh );
// ----------------------------------------------------------------------
-typedef pylith::topology::Fields<pylith::topology::Field<pylith::topology::SubMesh> > FieldsSubMesh;
+typedef pylith::topology::Fields<pylith::topology::Field<pylith::topology::Mesh> > FieldsMesh;
// ----------------------------------------------------------------------
void
@@ -45,7 +45,7 @@
importer.filename("data/tri3.mesh");
importer.read(_mesh);
- _submesh = new SubMesh(*_mesh, "bc");
+ _submesh = new Mesh(*_mesh, "bc");
PYLITH_METHOD_END;
} // setUp
@@ -70,7 +70,7 @@
PYLITH_METHOD_BEGIN;
CPPUNIT_ASSERT(_submesh);
- FieldsSubMesh fields(*_submesh);
+ FieldsMesh fields(*_submesh);
PYLITH_METHOD_END;
} // testConstructor
@@ -83,7 +83,7 @@
PYLITH_METHOD_BEGIN;
CPPUNIT_ASSERT(_submesh);
- FieldsSubMesh fields(*_submesh);
+ FieldsMesh fields(*_submesh);
const char* label = "field";
fields.add(label, "displacement");
@@ -103,14 +103,14 @@
const int fiberDim = 3;
CPPUNIT_ASSERT(_submesh);
- FieldsSubMesh fields(*_submesh);
+ FieldsMesh fields(*_submesh);
const char* label = "field";
- fields.add(label, "velocity", Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ fields.add(label, "velocity", Field<Mesh>::VERTICES_FIELD, fiberDim);
const size_t size = 1;
CPPUNIT_ASSERT_EQUAL(size, fields._fields.size());
- Field<SubMesh>& field = fields.get(label);
+ Field<Mesh>& field = fields.get(label);
field.allocate();
PetscDM dmMesh = _submesh->dmMesh();CPPUNIT_ASSERT(dmMesh);
@@ -134,7 +134,7 @@
PYLITH_METHOD_BEGIN;
CPPUNIT_ASSERT(_submesh);
- FieldsSubMesh fields(*_submesh);
+ FieldsMesh fields(*_submesh);
const char* labelA = "field A";
fields.add(labelA, "displacement");
@@ -147,7 +147,7 @@
fields.del(labelA);
size = 1;
CPPUNIT_ASSERT_EQUAL(size, fields._fields.size());
- const Field<SubMesh>& field = fields.get(labelB);
+ const Field<Mesh>& field = fields.get(labelB);
PYLITH_METHOD_END;
} // testDelete
@@ -160,11 +160,11 @@
PYLITH_METHOD_BEGIN;
CPPUNIT_ASSERT(_submesh);
- FieldsSubMesh fields(*_submesh);
+ FieldsMesh fields(*_submesh);
const char* label = "field";
fields.add(label, "displacement");
- const Field<SubMesh>& field = fields.get(label);
+ const Field<Mesh>& field = fields.get(label);
PYLITH_METHOD_END;
} // testGet
@@ -177,14 +177,14 @@
PYLITH_METHOD_BEGIN;
CPPUNIT_ASSERT(_submesh);
- FieldsSubMesh fields(*_submesh);
+ FieldsMesh fields(*_submesh);
const char* label = "field";
fields.add(label, "displacement");
- const FieldsSubMesh* fieldsPtr = &fields;
+ const FieldsMesh* fieldsPtr = &fields;
CPPUNIT_ASSERT(fieldsPtr);
- const Field<SubMesh>& field = fieldsPtr->get(label);
+ const Field<Mesh>& field = fieldsPtr->get(label);
PYLITH_METHOD_END;
} // testGetConst
@@ -197,7 +197,7 @@
PYLITH_METHOD_BEGIN;
CPPUNIT_ASSERT(_submesh);
- FieldsSubMesh fields(*_submesh);
+ FieldsMesh fields(*_submesh);
fields.add("field A", "velocity");
@@ -224,21 +224,21 @@
const int fiberDim = 3;
CPPUNIT_ASSERT(_submesh);
- FieldsSubMesh fields(*_submesh);
+ FieldsMesh fields(*_submesh);
const char* labelA = "field A";
- fields.add(labelA, "velocity", Field<SubMesh>::VERTICES_FIELD, fiberDim);
+ fields.add(labelA, "velocity", Field<Mesh>::VERTICES_FIELD, fiberDim);
const char* labelB = "field B";
fields.add(labelB, "displacement");
- Field<SubMesh>& fieldA = fields.get(labelA);
+ Field<Mesh>& fieldA = fields.get(labelA);
fieldA.allocate();
fields.copyLayout(labelA);
const size_t size = 2;
CPPUNIT_ASSERT_EQUAL(size, fields._fields.size());
- const Field<SubMesh>& field = fields.get(labelB);
+ const Field<Mesh>& field = fields.get(labelB);
PetscDM dmMesh = _submesh->dmMesh();CPPUNIT_ASSERT(dmMesh);
Stratum depthStratum(dmMesh, Stratum::DEPTH, 0);
Modified: short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsSubMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsSubMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsSubMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -35,7 +35,6 @@
class TestFieldsSubMesh;
class Mesh;
- class SubMesh;
} // topology
} // pylith
@@ -95,7 +94,7 @@
private :
Mesh* _mesh;
- SubMesh* _submesh;
+ Mesh* _submesh;
}; // class TestFieldsSubMesh
Modified: short/3D/PyLith/trunk/unittests/libtests/topology/TestJacobian.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/topology/TestJacobian.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/topology/TestJacobian.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -23,7 +23,6 @@
#include "pylith/topology/Jacobian.hh" // USES Jacobian
#include "pylith/topology/Mesh.hh" // USES Mesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Field.hh" // USES Field
#include "pylith/topology/SolutionFields.hh" // USES SolutionFields
@@ -65,8 +64,8 @@
Field<Mesh> field(mesh);
_initializeField(&mesh, &field);
- SubMesh submesh(mesh, "bc");
- Field<SubMesh> subfield(submesh);
+ Mesh submesh(mesh, "bc");
+ Field<Mesh> subfield(submesh);
subfield.newSection(FieldBase::VERTICES_FIELD, submesh.dimension());
subfield.allocate();
subfield.zero();
Modified: short/3D/PyLith/trunk/unittests/libtests/topology/TestMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/topology/TestMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/topology/TestMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -52,7 +52,7 @@
CPPUNIT_ASSERT(mesh2._dmMesh);
CPPUNIT_ASSERT_EQUAL(dim, mesh2.dimension());
MPI_Comm_compare(PETSC_COMM_WORLD, mesh2.comm(), &result);
- CPPUNIT_ASSERT_EQUAL(int(MPI_IDENT), result);
+ CPPUNIT_ASSERT_EQUAL(int(MPI_CONGRUENT), result);
dim = 1;
Mesh mesh3(dim, PETSC_COMM_SELF);
@@ -142,11 +142,16 @@
PYLITH_METHOD_BEGIN;
Mesh mesh;
- CPPUNIT_ASSERT_EQUAL(PETSC_COMM_WORLD, mesh.comm());
+ int result = 0;
+ MPI_Comm_compare(PETSC_COMM_WORLD, mesh.comm(), &result);
+ CPPUNIT_ASSERT_EQUAL(int(MPI_IDENT), result);
- mesh.comm(PETSC_COMM_SELF);
- CPPUNIT_ASSERT_EQUAL(PETSC_COMM_SELF, mesh.comm());
+ Mesh mesh2(2, PETSC_COMM_SELF);
+ result = 0;
+ MPI_Comm_compare(PETSC_COMM_SELF, mesh2.comm(), &result);
+ CPPUNIT_ASSERT_EQUAL(int(MPI_CONGRUENT), result);
+
PYLITH_METHOD_END;
} // testComm
Modified: short/3D/PyLith/trunk/unittests/libtests/topology/TestSubMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/topology/TestSubMesh.cc 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/topology/TestSubMesh.cc 2013-05-13 23:33:37 UTC (rev 22058)
@@ -21,7 +21,6 @@
#include "TestSubMesh.hh" // Implementation of class methods
#include "pylith/topology/Mesh.hh" // USES Mesh
-#include "pylith/topology/SubMesh.hh" // USES SubMesh
#include "pylith/topology/Stratum.hh" // USES Stratum
#include "pylith/topology/MeshOps.hh" // USES MeshOps::createDMMesh()
@@ -73,9 +72,9 @@
{ // testConstructor
PYLITH_METHOD_BEGIN;
- SubMesh mesh;
- CPPUNIT_ASSERT_EQUAL(0, mesh.dimension());
- CPPUNIT_ASSERT_EQUAL(false, mesh.debug());
+ Mesh submesh;
+ CPPUNIT_ASSERT_EQUAL(0, submesh.dimension());
+ CPPUNIT_ASSERT_EQUAL(false, submesh.debug());
PYLITH_METHOD_END;
} // testConstructor
@@ -90,15 +89,15 @@
Mesh mesh2D;
_buildMesh(&mesh2D);
- SubMesh mesh(mesh2D, _TestSubMesh::label);
- CPPUNIT_ASSERT_EQUAL(_TestSubMesh::cellDim-1, mesh.dimension());
+ Mesh submesh(mesh2D, _TestSubMesh::label);
+ CPPUNIT_ASSERT_EQUAL(_TestSubMesh::cellDim-1, submesh.dimension());
int result = 0;
- MPI_Comm_compare(PETSC_COMM_WORLD, mesh.comm(), &result);
+ MPI_Comm_compare(PETSC_COMM_WORLD, submesh.comm(), &result);
CPPUNIT_ASSERT_EQUAL(int(MPI_CONGRUENT), result);
// Check vertices
- const PetscDM dmMesh = mesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
+ const PetscDM dmMesh = submesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
Stratum depthStratum(dmMesh, Stratum::DEPTH, 0);
const PetscInt vStart = depthStratum.begin();
const PetscInt vEnd = depthStratum.end();
@@ -124,50 +123,6 @@
} // testConstructorMesh
// ----------------------------------------------------------------------
-// Test createSubMesh().
-void
-pylith::topology::TestSubMesh::testCreateSubMesh(void)
-{ // testCreateSubMesh
- PYLITH_METHOD_BEGIN;
-
- Mesh mesh2D;
- _buildMesh(&mesh2D);
-
- SubMesh mesh;
- mesh.createSubMesh(mesh2D, _TestSubMesh::label);
- CPPUNIT_ASSERT_EQUAL(_TestSubMesh::cellDim-1, mesh.dimension());
-
- int result = 0;
- MPI_Comm_compare(PETSC_COMM_WORLD, mesh.comm(), &result);
- CPPUNIT_ASSERT_EQUAL(int(MPI_CONGRUENT), result);
-
- // Check vertices
- const PetscDM dmMesh = mesh.dmMesh();CPPUNIT_ASSERT(dmMesh);
- Stratum depthStratum(dmMesh, Stratum::DEPTH, 0);
- const PetscInt vStart = depthStratum.begin();
- const PetscInt vEnd = depthStratum.end();
-
- const PetscInt nvertices = _TestSubMesh::submeshNumVertices;
- CPPUNIT_ASSERT_EQUAL(nvertices, depthStratum.size());
- for (PetscInt v = vStart, iV=0; v < vEnd; ++v, ++iV) {
- CPPUNIT_ASSERT_EQUAL(_TestSubMesh::submeshVertices[iV], v);
- } // for
-
- // Check cells
- Stratum heightStratum(dmMesh, Stratum::HEIGHT, 0);
- const PetscInt cStart = heightStratum.begin();
- const PetscInt cEnd = heightStratum.end();
-
- const PetscInt ncells = _TestSubMesh::submeshNumCells;
- CPPUNIT_ASSERT_EQUAL(ncells, heightStratum.size());
- for (PetscInt c = cStart, iC=0; c < cEnd; ++c, ++iC) {
- CPPUNIT_ASSERT_EQUAL(_TestSubMesh::submeshCells[iC], c);
- } // for
-
- PYLITH_METHOD_END;
-} // testCreateSubMesh
-
-// ----------------------------------------------------------------------
// Test coordsys().
void
pylith::topology::TestSubMesh::testCoordsys(void)
@@ -177,9 +132,9 @@
Mesh mesh2D;
_buildMesh(&mesh2D);
- SubMesh mesh(mesh2D, _TestSubMesh::label);
+ Mesh submesh(mesh2D, _TestSubMesh::label);
- CPPUNIT_ASSERT_EQUAL(_TestSubMesh::cellDim, mesh.coordsys()->spaceDim());
+ CPPUNIT_ASSERT_EQUAL(_TestSubMesh::cellDim, submesh.coordsys()->spaceDim());
PYLITH_METHOD_END;
} // testCoordsys
@@ -191,12 +146,15 @@
{ // testDebug
PYLITH_METHOD_BEGIN;
- SubMesh mesh;
- CPPUNIT_ASSERT_EQUAL(false, mesh.debug());
+ Mesh mesh2D;
+ _buildMesh(&mesh2D);
- mesh.debug(true);
- CPPUNIT_ASSERT_EQUAL(true, mesh.debug());
+ Mesh submesh(mesh2D, _TestSubMesh::label);
+ CPPUNIT_ASSERT_EQUAL(false, submesh.debug());
+ submesh.debug(true);
+ CPPUNIT_ASSERT_EQUAL(true, submesh.debug());
+
PYLITH_METHOD_END;
} // testDebug
@@ -207,13 +165,13 @@
{ // testDimension
PYLITH_METHOD_BEGIN;
- SubMesh mesh;
- CPPUNIT_ASSERT_EQUAL(0, mesh.dimension());
+ Mesh submesh;
+ CPPUNIT_ASSERT_EQUAL(0, submesh.dimension());
Mesh mesh2D;
_buildMesh(&mesh2D);
- SubMesh mesh2(mesh2D, _TestSubMesh::label);
- CPPUNIT_ASSERT_EQUAL(_TestSubMesh::cellDim-1, mesh2.dimension());
+ Mesh submesh2(mesh2D, _TestSubMesh::label);
+ CPPUNIT_ASSERT_EQUAL(_TestSubMesh::cellDim-1, submesh2.dimension());
PYLITH_METHOD_END;
} // testDimension
@@ -228,7 +186,7 @@
Mesh mesh;
_buildMesh(&mesh);
- SubMesh submesh(mesh, _TestSubMesh::label);
+ Mesh submesh(mesh, _TestSubMesh::label);
CPPUNIT_ASSERT_EQUAL(_TestSubMesh::submeshNumCorners, submesh.coneSize());
PYLITH_METHOD_END;
@@ -243,7 +201,7 @@
Mesh mesh;
_buildMesh(&mesh);
- SubMesh submesh(mesh, _TestSubMesh::label);
+ Mesh submesh(mesh, _TestSubMesh::label);
CPPUNIT_ASSERT_EQUAL(_TestSubMesh::submeshNumVertices, submesh.numVertices());
PYLITH_METHOD_END;
@@ -258,7 +216,7 @@
Mesh mesh;
_buildMesh(&mesh);
- SubMesh submesh(mesh, _TestSubMesh::label);
+ Mesh submesh(mesh, _TestSubMesh::label);
CPPUNIT_ASSERT_EQUAL(_TestSubMesh::submeshNumCells, submesh.numCells());
PYLITH_METHOD_END;
@@ -271,14 +229,13 @@
{ // testComm
PYLITH_METHOD_BEGIN;
- SubMesh mesh;
-
Mesh mesh2D;
_buildMesh(&mesh2D);
- mesh.createSubMesh(mesh2D, _TestSubMesh::label);
+ Mesh submesh(mesh2D, _TestSubMesh::label);
+
int result = 0;
- MPI_Comm_compare(PETSC_COMM_WORLD, mesh.comm(), &result);
+ MPI_Comm_compare(PETSC_COMM_WORLD, submesh.comm(), &result);
CPPUNIT_ASSERT_EQUAL(int(MPI_CONGRUENT), result);
PYLITH_METHOD_END;
Modified: short/3D/PyLith/trunk/unittests/libtests/topology/TestSubMesh.hh
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/topology/TestSubMesh.hh 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/libtests/topology/TestSubMesh.hh 2013-05-13 23:33:37 UTC (rev 22058)
@@ -48,7 +48,6 @@
CPPUNIT_TEST( testConstructor );
CPPUNIT_TEST( testConstructorMesh );
- CPPUNIT_TEST( testCreateSubMesh );
CPPUNIT_TEST( testCoordsys );
CPPUNIT_TEST( testDebug );
CPPUNIT_TEST( testDimension );
@@ -68,9 +67,6 @@
/// Test constructor w/mesh.
void testConstructorMesh(void);
- /// Test createSubMesh.
- void testCreateSubMesh(void);
-
/// Test coordsys().
void testCoordsys(void);
Modified: short/3D/PyLith/trunk/unittests/pytests/bc/TestAbsorbingDampers.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/bc/TestAbsorbingDampers.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/bc/TestAbsorbingDampers.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -193,8 +193,8 @@
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
- from pylith.feassemble.Quadrature import SubMeshQuadrature
- quadrature = SubMeshQuadrature()
+ from pylith.feassemble.Quadrature import MeshQuadrature
+ quadrature = MeshQuadrature()
quadrature.inventory.cell = cell
quadrature._configure()
Modified: short/3D/PyLith/trunk/unittests/pytests/bc/TestNeumann.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/bc/TestNeumann.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/bc/TestNeumann.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -191,8 +191,8 @@
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
- from pylith.feassemble.Quadrature import SubMeshQuadrature
- quadrature = SubMeshQuadrature()
+ from pylith.feassemble.Quadrature import MeshQuadrature
+ quadrature = MeshQuadrature()
quadrature.inventory.cell = cell
quadrature._configure()
Modified: short/3D/PyLith/trunk/unittests/pytests/faults/TestFaultCohesiveDyn.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/faults/TestFaultCohesiveDyn.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/faults/TestFaultCohesiveDyn.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -263,8 +263,8 @@
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
- from pylith.feassemble.Quadrature import SubMeshQuadrature
- quadrature = SubMeshQuadrature()
+ from pylith.feassemble.Quadrature import MeshQuadrature
+ quadrature = MeshQuadrature()
quadrature.inventory.cell = cell
quadrature._configure()
Modified: short/3D/PyLith/trunk/unittests/pytests/faults/TestFaultCohesiveImpulses.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/faults/TestFaultCohesiveImpulses.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/faults/TestFaultCohesiveImpulses.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -277,8 +277,8 @@
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
- from pylith.feassemble.Quadrature import SubMeshQuadrature
- quadrature = SubMeshQuadrature()
+ from pylith.feassemble.Quadrature import MeshQuadrature
+ quadrature = MeshQuadrature()
quadrature.inventory.cell = cell
quadrature._configure()
Modified: short/3D/PyLith/trunk/unittests/pytests/faults/TestFaultCohesiveKin.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/faults/TestFaultCohesiveKin.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/faults/TestFaultCohesiveKin.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -277,8 +277,8 @@
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
- from pylith.feassemble.Quadrature import SubMeshQuadrature
- quadrature = SubMeshQuadrature()
+ from pylith.feassemble.Quadrature import MeshQuadrature
+ quadrature = MeshQuadrature()
quadrature.inventory.cell = cell
quadrature._configure()
Modified: short/3D/PyLith/trunk/unittests/pytests/feassemble/Makefile.am
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/feassemble/Makefile.am 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/feassemble/Makefile.am 2013-05-13 23:33:37 UTC (rev 22058)
@@ -31,7 +31,6 @@
TestFIATSimplex.py \
TestCellGeometry.py \
TestMeshQuadrature.py \
- TestSubMeshQuadrature.py \
TestElasticityExplicit.py \
TestElasticityImplicit.py \
TestElasticityExplicitLgDeform.py \
Deleted: short/3D/PyLith/trunk/unittests/pytests/feassemble/TestSubMeshQuadrature.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/feassemble/TestSubMeshQuadrature.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/feassemble/TestSubMeshQuadrature.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -1,234 +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) 2010-2013 University of California, Davis
-#
-# See COPYING for license information.
-#
-# ======================================================================
-#
-
-## @file unittests/pytests/feassemble/TestSubMeshQuadrature.py
-
-## @brief Unit testing of Python SubMeshQuadrature object.
-
-import unittest
-import numpy
-
-from pylith.feassemble.Quadrature import SubMeshQuadrature
-from pylith.feassemble.FIATSimplex import FIATSimplex
-from pylith.feassemble.FIATLagrange import FIATLagrange
-
-# ----------------------------------------------------------------------
-def N0(p):
- return -0.5*p*(1.0-p)
-
-def N0p(p):
- return -0.5*(1.0-p) + 0.5*p
-
-def N1(p):
- return 0.5*p*(1.0+p)
-
-def N1p(p):
- return +0.5*(1.0+p) + 0.5*p
-
-def N2(p):
- return (1.0-p**2)
-
-def N2p(p):
- return -2.0*p
-
-# ----------------------------------------------------------------------
-class TestSubMeshQuadrature(unittest.TestCase):
- """
- Unit testing of Python SubMeshQuadrature object.
- """
-
- def test_minJacobian(self):
- """
- Test minJacobian().
- """
- minJacobian = 4.0e-02;
- q = SubMeshQuadrature()
- q.minJacobian(minJacobian)
- self.assertAlmostEqual(minJacobian, q.minJacobian(), places=5)
- return
-
-
- def test_checkConditioning(self):
- """
- Test checkConditioning().
- """
- q = SubMeshQuadrature()
-
- flag = False # default
- self.assertEqual(flag, q.checkConditioning())
-
- flag = True
- q.checkConditioning(flag)
- self.assertEqual(flag, q.checkConditioning())
-
- flag = False
- q.checkConditioning(flag)
- self.assertEqual(flag, q.checkConditioning())
-
- return
-
-
- def test_initialize(self):
- """
- Test initialize().
- """
- cell = FIATSimplex()
- cell.inventory.dimension = 1
- cell.inventory.degree = 2
- cell.inventory.order = 2
- cell._configure()
-
- scalarType = None
- from pylith.utils.utils import sizeofPylithScalar
- if 8 == sizeofPylithScalar():
- scalarType = numpy.float64
- elif 4 == sizeofPylithScalar():
- scalarType = numpy.float32
- else:
- raise ValueError("Unknown size for PylithScalar.")
-
- verticesE = numpy.array([ [-1.0], [1.0], [0.0] ])
- quadPtsE = numpy.array( [[-1.0/3**0.5],
- [+1.0/3**0.5]],
- dtype=scalarType )
- quadWtsE = numpy.array( [1.0, 1.0], dtype=scalarType )
-
- # Compute basis functions and derivatives at quadrature points
- basisE = numpy.zeros( (2, 3), dtype=scalarType)
- basisDerivE = numpy.zeros( (2, 3, 1), dtype=scalarType)
- iQuad = 0
- for q in quadPtsE:
- basisE[iQuad] = numpy.array([N0(q), N1(q), N2(q)],
- dtype=scalarType).reshape( (3,) )
- deriv = numpy.array([[N0p(q)], [N1p(q)], [N2p(q)]],
- dtype=scalarType)
- basisDerivE[iQuad] = deriv.reshape((3, 1))
- iQuad += 1
-
- quadrature = SubMeshQuadrature()
- quadrature.inventory.cell = cell
- quadrature._configure()
-
- quadrature.preinitialize(spaceDim=2)
- quadrature.initialize()
-
- self.assertEqual(1, quadrature.cellDim())
- self.assertEqual(2, quadrature.spaceDim())
- self.assertEqual(3, quadrature.numBasis())
- self.assertEqual(2, quadrature.numQuadPts())
-
- from pylith.utils.utils import TestArray_checkScalar
-
- self.failUnless(TestArray_checkScalar(basisE.ravel(),
- quadrature.basis()))
- self.failUnless(TestArray_checkScalar(basisDerivE.ravel(),
- quadrature.basisDerivRef()))
- self.failUnless(TestArray_checkScalar(quadPtsE.ravel(),
- quadrature.quadPtsRef()))
- self.failUnless(TestArray_checkScalar(quadWtsE.ravel(),
- quadrature.quadWts()))
-
- quadrature.initializeGeometry()
- return
-
-
- def test_simplex1D(self):
- """
- Test setup of quadrature for simplex cells for a 1-D problem in 2-D space.
- """
- spaceDim = 2
-
- cell = FIATSimplex()
- cell.inventory.dimension = 1
- cell._configure()
-
- quadrature = SubMeshQuadrature()
- quadrature.inventory.cell = cell
- quadrature._configure()
-
- quadrature.preinitialize(spaceDim)
- self.assertEqual(1, quadrature.cellDim())
- self.assertEqual(spaceDim, quadrature.spaceDim())
- self.assertEqual(2, quadrature.numBasis())
- return
-
-
- def test_simplex2D(self):
- """
- Test setup of quadrature for simplex cells for a 2-D problem in 3-D space.
- """
- spaceDim = 3
-
- cell = FIATSimplex()
- cell.inventory.dimension = 2
- cell._configure()
-
- quadrature = SubMeshQuadrature()
- quadrature.inventory.cell = cell
- quadrature._configure()
-
- quadrature.preinitialize(spaceDim)
- self.assertEqual(2, quadrature.cellDim())
- self.assertEqual(spaceDim, quadrature.spaceDim())
- self.assertEqual(3, quadrature.numBasis())
- return
-
-
- def test_lagrange1D(self):
- """
- Test setup of quadrature for Lagrange cells for a 1-D problem in 2-D space.
- """
- spaceDim = 2
-
- cell = FIATLagrange()
- cell.inventory.dimension = 1
- cell._configure()
-
- quadrature = SubMeshQuadrature()
- quadrature.inventory.cell = cell
- quadrature._configure()
-
- quadrature.preinitialize(spaceDim)
- self.assertEqual(1, quadrature.cellDim())
- self.assertEqual(spaceDim, quadrature.spaceDim())
- self.assertEqual(2, quadrature.numBasis())
- return
-
-
- def test_lagrange2D(self):
- """
- Test setup of quadrature for Lagrange cells for a 2-D problem in 3-D space.
- """
- spaceDim = 3
-
- cell = FIATLagrange()
- cell.inventory.dimension = 2
- cell._configure()
-
- quadrature = SubMeshQuadrature()
- quadrature.inventory.cell = cell
- quadrature._configure()
-
- quadrature.preinitialize(spaceDim)
- self.assertEqual(2, quadrature.cellDim())
- self.assertEqual(spaceDim, quadrature.spaceDim())
- self.assertEqual(4, quadrature.numBasis())
- return
-
-
-# End of file
Modified: short/3D/PyLith/trunk/unittests/pytests/feassemble/testfeassemble.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/feassemble/testfeassemble.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/feassemble/testfeassemble.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -75,9 +75,6 @@
from TestMeshQuadrature import TestMeshQuadrature
suite.addTest(unittest.makeSuite(TestMeshQuadrature))
- from TestSubMeshQuadrature import TestSubMeshQuadrature
- suite.addTest(unittest.makeSuite(TestSubMeshQuadrature))
-
from TestElasticityImplicit import TestElasticityImplicit
suite.addTest(unittest.makeSuite(TestElasticityImplicit))
Modified: short/3D/PyLith/trunk/unittests/pytests/meshio/TestCellFilterAvg.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/meshio/TestCellFilterAvg.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/meshio/TestCellFilterAvg.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -23,7 +23,6 @@
import unittest
from pylith.meshio.CellFilterAvgMesh import CellFilterAvgMesh
-from pylith.meshio.CellFilterAvgSubMesh import CellFilterAvgSubMesh
# ----------------------------------------------------------------------
class TestCellFilterAvgMesh(unittest.TestCase):
@@ -76,54 +75,4 @@
return
-# ----------------------------------------------------------------------
-class TestCellFilterAvgSubMesh(unittest.TestCase):
- """
- Unit testing of Python CellFilterAvg object.
- """
-
- def test_constructor(self):
- """
- Test constructor.
- """
- filter = CellFilterAvgSubMesh()
- filter._configure()
- return
-
-
- def test_initialize(self):
- """
- Test constructor.
- """
- spaceDim = 2
-
- from pylith.feassemble.FIATSimplex import FIATSimplex
- cell = FIATSimplex()
- cell.inventory.dimension = 1
- cell.inventory.degree = 2
- cell.inventory.order = 2
- cell._configure()
-
- from pylith.feassemble.Quadrature import SubMeshQuadrature
- quadrature = SubMeshQuadrature()
- quadrature.inventory.cell = cell
- quadrature._configure()
- quadrature.preinitialize(spaceDim)
- quadrature.initialize()
-
- filter = CellFilterAvgSubMesh()
- filter._configure()
- filter.initialize(quadrature)
- return
-
-
- def test_factory(self):
- """
- Test factory method.
- """
- from pylith.meshio.CellFilterAvgSubMesh import output_cell_filter
- filter = output_cell_filter()
- return
-
-
# End of file
Modified: short/3D/PyLith/trunk/unittests/pytests/meshio/TestDataWriterHDF5.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/meshio/TestDataWriterHDF5.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/meshio/TestDataWriterHDF5.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -23,8 +23,6 @@
import unittest
from pylith.meshio.DataWriterHDF5Mesh import DataWriterHDF5Mesh
-from pylith.meshio.DataWriterHDF5SubMesh import DataWriterHDF5SubMesh
-from pylith.meshio.DataWriterHDF5SubSubMesh import DataWriterHDF5SubSubMesh
# ----------------------------------------------------------------------
class TestDataWriterHDF5Mesh(unittest.TestCase):
@@ -63,78 +61,4 @@
return
-# ----------------------------------------------------------------------
-class TestDataWriterHDF5SubMesh(unittest.TestCase):
- """
- Unit testing of Python DataWriterHDF5 object.
- """
-
- def test_constructor(self):
- """
- Test constructor.
- """
- filter = DataWriterHDF5SubMesh()
- filter._configure()
- return
-
-
- def test_initialize(self):
- """
- Test constructor.
- """
- filter = DataWriterHDF5SubMesh()
- filter._configure()
-
- from spatialdata.units.Nondimensional import Nondimensional
- normalizer = Nondimensional()
- filter.initialize(normalizer)
- return
-
-
- def test_factory(self):
- """
- Test factory method.
- """
- from pylith.meshio.DataWriterHDF5SubMesh import data_writer
- filter = data_writer()
- return
-
-
-# ----------------------------------------------------------------------
-class TestDataWriterHDF5SubSubMesh(unittest.TestCase):
- """
- Unit testing of Python DataWriterHDF5 object.
- """
-
- def test_constructor(self):
- """
- Test constructor.
- """
- filter = DataWriterHDF5SubSubMesh()
- filter._configure()
- return
-
-
- def test_initialize(self):
- """
- Test constructor.
- """
- filter = DataWriterHDF5SubSubMesh()
- filter._configure()
-
- from spatialdata.units.Nondimensional import Nondimensional
- normalizer = Nondimensional()
- filter.initialize(normalizer)
- return
-
-
- def test_factory(self):
- """
- Test factory method.
- """
- from pylith.meshio.DataWriterHDF5SubSubMesh import data_writer
- filter = data_writer()
- return
-
-
# End of file
Modified: short/3D/PyLith/trunk/unittests/pytests/meshio/TestDataWriterHDF5Ext.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/meshio/TestDataWriterHDF5Ext.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/meshio/TestDataWriterHDF5Ext.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -23,8 +23,6 @@
import unittest
from pylith.meshio.DataWriterHDF5ExtMesh import DataWriterHDF5ExtMesh
-from pylith.meshio.DataWriterHDF5ExtSubMesh import DataWriterHDF5ExtSubMesh
-from pylith.meshio.DataWriterHDF5ExtSubSubMesh import DataWriterHDF5ExtSubSubMesh
# ----------------------------------------------------------------------
class TestDataWriterHDF5ExtMesh(unittest.TestCase):
@@ -63,78 +61,4 @@
return
-# ----------------------------------------------------------------------
-class TestDataWriterHDF5ExtSubMesh(unittest.TestCase):
- """
- Unit testing of Python DataWriterHDF5Ext object.
- """
-
- def test_constructor(self):
- """
- Test constructor.
- """
- filter = DataWriterHDF5ExtSubMesh()
- filter._configure()
- return
-
-
- def test_initialize(self):
- """
- Test constructor.
- """
- filter = DataWriterHDF5ExtSubMesh()
- filter._configure()
-
- from spatialdata.units.Nondimensional import Nondimensional
- normalizer = Nondimensional()
- filter.initialize(normalizer)
- return
-
-
- def test_factory(self):
- """
- Test factory method.
- """
- from pylith.meshio.DataWriterHDF5ExtSubMesh import data_writer
- filter = data_writer()
- return
-
-
-# ----------------------------------------------------------------------
-class TestDataWriterHDF5ExtSubSubMesh(unittest.TestCase):
- """
- Unit testing of Python DataWriterHDF5Ext object.
- """
-
- def test_constructor(self):
- """
- Test constructor.
- """
- filter = DataWriterHDF5ExtSubSubMesh()
- filter._configure()
- return
-
-
- def test_initialize(self):
- """
- Test constructor.
- """
- filter = DataWriterHDF5ExtSubSubMesh()
- filter._configure()
-
- from spatialdata.units.Nondimensional import Nondimensional
- normalizer = Nondimensional()
- filter.initialize(normalizer)
- return
-
-
- def test_factory(self):
- """
- Test factory method.
- """
- from pylith.meshio.DataWriterHDF5ExtSubSubMesh import data_writer
- filter = data_writer()
- return
-
-
# End of file
Modified: short/3D/PyLith/trunk/unittests/pytests/meshio/TestDataWriterVTK.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/meshio/TestDataWriterVTK.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/meshio/TestDataWriterVTK.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -23,8 +23,6 @@
import unittest
from pylith.meshio.DataWriterVTKMesh import DataWriterVTKMesh
-from pylith.meshio.DataWriterVTKSubMesh import DataWriterVTKSubMesh
-from pylith.meshio.DataWriterVTKSubSubMesh import DataWriterVTKSubSubMesh
# ----------------------------------------------------------------------
class TestDataWriterVTKMesh(unittest.TestCase):
@@ -63,78 +61,4 @@
return
-# ----------------------------------------------------------------------
-class TestDataWriterVTKSubMesh(unittest.TestCase):
- """
- Unit testing of Python DataWriterVTK object.
- """
-
- def test_constructor(self):
- """
- Test constructor.
- """
- filter = DataWriterVTKSubMesh()
- filter._configure()
- return
-
-
- def test_initialize(self):
- """
- Test constructor.
- """
- filter = DataWriterVTKSubMesh()
- filter._configure()
-
- from spatialdata.units.Nondimensional import Nondimensional
- normalizer = Nondimensional()
- filter.initialize(normalizer)
- return
-
-
- def test_factory(self):
- """
- Test factory method.
- """
- from pylith.meshio.DataWriterVTKSubMesh import data_writer
- filter = data_writer()
- return
-
-
-# ----------------------------------------------------------------------
-class TestDataWriterVTKSubSubMesh(unittest.TestCase):
- """
- Unit testing of Python DataWriterVTK object.
- """
-
- def test_constructor(self):
- """
- Test constructor.
- """
- filter = DataWriterVTKSubSubMesh()
- filter._configure()
- return
-
-
- def test_initialize(self):
- """
- Test constructor.
- """
- filter = DataWriterVTKSubSubMesh()
- filter._configure()
-
- from spatialdata.units.Nondimensional import Nondimensional
- normalizer = Nondimensional()
- filter.initialize(normalizer)
- return
-
-
- def test_factory(self):
- """
- Test factory method.
- """
- from pylith.meshio.DataWriterVTKSubSubMesh import data_writer
- filter = data_writer()
- return
-
-
# End of file
Modified: short/3D/PyLith/trunk/unittests/pytests/meshio/TestOutputManagerSubMesh.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/meshio/TestOutputManagerSubMesh.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/meshio/TestOutputManagerSubMesh.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -22,7 +22,7 @@
import unittest
-from pylith.meshio.OutputManagerSubMesh import OutputManagerSubMesh
+from pylith.meshio.OutputManagerMesh import OutputManagerMesh
# ----------------------------------------------------------------------
class TestProvider(object):
@@ -54,11 +54,11 @@
normalizer._configure()
mesh = iohandler.read(debug=False, interpolate=False)
- from pylith.topology.SubMesh import SubMesh
- submesh = SubMesh(mesh, "4")
+ from pylith.topology.Mesh import Mesh
+ submesh = Mesh(mesh=mesh, label="4")
- from pylith.topology.Fields import SubMeshFields
- fields = SubMeshFields(submesh)
+ from pylith.topology.Fields import MeshFields
+ fields = MeshFields(submesh)
self.mesh = mesh
self.submesh = submesh
@@ -139,7 +139,7 @@
"""
Test constructor.
"""
- output = OutputManagerSubMesh()
+ output = OutputManagerMesh()
output.inventory.writer._configure()
output._configure()
return
@@ -150,7 +150,7 @@
Test preinitialize().
"""
dataProvider = TestProvider()
- output = OutputManagerSubMesh()
+ output = OutputManagerMesh()
output.preinitialize(dataProvider)
self.failIf(output.dataProvider is None)
@@ -162,7 +162,7 @@
Test verifyConfiguration().
"""
dataProvider = TestProvider()
- output = OutputManagerSubMesh()
+ output = OutputManagerMesh()
output.preinitialize(dataProvider)
output.vertexInfoFields = ["vertex info"]
@@ -178,7 +178,7 @@
Test initialize().
"""
# No quadrature
- output = OutputManagerSubMesh()
+ output = OutputManagerMesh()
output.inventory.writer.inventory.filename = "test.vtk"
output.inventory.writer._configure()
output._configure()
@@ -188,18 +188,18 @@
# With quadrature
from pylith.feassemble.FIATLagrange import FIATLagrange
- from pylith.feassemble.Quadrature import SubMeshQuadrature
+ from pylith.feassemble.Quadrature import MeshQuadrature
cell = FIATLagrange()
cell.inventory.dimension = 2
cell.inventory.degree = 2
cell.inventory.order = 2
cell._configure()
- quadrature = SubMeshQuadrature()
+ quadrature = MeshQuadrature()
quadrature.inventory.cell = cell
quadrature._configure()
- output = OutputManagerSubMesh()
+ output = OutputManagerMesh()
output.inventory.writer.inventory.filename = "test.vtk"
output.inventory.writer._configure()
output._configure()
@@ -213,7 +213,7 @@
"""
Test open() and close().
"""
- output = OutputManagerSubMesh()
+ output = OutputManagerMesh()
output.inventory.writer.inventory.filename = "output.vtk"
output.inventory.writer._configure()
output._configure()
@@ -230,7 +230,7 @@
"""
Test writeInfo().
"""
- output = OutputManagerSubMesh()
+ output = OutputManagerMesh()
output.inventory.writer.inventory.filename = "output.vtk"
output.inventory.writer._configure()
output.inventory.vertexInfoFields = ["vertex info"]
@@ -251,7 +251,7 @@
"""
Test writeData().
"""
- output = OutputManagerSubMesh()
+ output = OutputManagerMesh()
output.inventory.writer.inventory.filename = "output.vtk"
output.inventory.writer.inventory.timeFormat = "%3.1f"
output.inventory.writer._configure()
@@ -277,7 +277,7 @@
dataProvider = TestProvider()
# Default values should be true
- output = OutputManagerSubMesh()
+ output = OutputManagerMesh()
output.inventory.writer._configure()
output._configure()
output.preinitialize(dataProvider)
@@ -286,7 +286,7 @@
self.assertEqual(True, output._checkWrite(3.234e+8))
# Check writing based on time
- output = OutputManagerSubMesh()
+ output = OutputManagerMesh()
output.inventory.writer._configure()
output._configure()
output.preinitialize(dataProvider)
@@ -304,7 +304,7 @@
self.assertEqual(True, output._checkWrite(t))
# Check writing based on number of steps
- output = OutputManagerSubMesh()
+ output = OutputManagerMesh()
output.inventory.writer._configure()
output.inventory.outputFreq = "skip"
output.inventory.skip = 1
@@ -333,7 +333,7 @@
"""
Test factory method.
"""
- from pylith.meshio.OutputManagerSubMesh import output_manager
+ from pylith.meshio.OutputManagerMesh import output_manager
o = output_manager()
return
Modified: short/3D/PyLith/trunk/unittests/pytests/meshio/TestVertexFilterVecNorm.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/meshio/TestVertexFilterVecNorm.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/meshio/TestVertexFilterVecNorm.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -23,7 +23,6 @@
import unittest
from pylith.meshio.VertexFilterVecNormMesh import VertexFilterVecNormMesh
-from pylith.meshio.VertexFilterVecNormSubMesh import VertexFilterVecNormSubMesh
# ----------------------------------------------------------------------
class TestVertexFilterVecNormMesh(unittest.TestCase):
@@ -60,38 +59,4 @@
return
-# ----------------------------------------------------------------------
-class TestVertexFilterVecNormSubMesh(unittest.TestCase):
- """
- Unit testing of Python VertexFilterVecNorm object.
- """
-
- def test_constructor(self):
- """
- Test constructor.
- """
- filter = VertexFilterVecNormSubMesh()
- filter._configure()
- return
-
-
- def test_initialize(self):
- """
- Test constructor.
- """
- filter = VertexFilterVecNormSubMesh()
- filter._configure()
- filter.initialize()
- return
-
-
- def test_factory(self):
- """
- Test factory method.
- """
- from pylith.meshio.VertexFilterVecNormSubMesh import output_vertex_filter
- filter = output_vertex_filter()
- return
-
-
# End of file
Modified: short/3D/PyLith/trunk/unittests/pytests/meshio/testhdf5.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/meshio/testhdf5.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/meshio/testhdf5.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -66,21 +66,9 @@
from TestDataWriterHDF5 import TestDataWriterHDF5Mesh
suite.addTest(unittest.makeSuite(TestDataWriterHDF5Mesh))
- from TestDataWriterHDF5 import TestDataWriterHDF5SubMesh
- suite.addTest(unittest.makeSuite(TestDataWriterHDF5SubMesh))
-
- from TestDataWriterHDF5 import TestDataWriterHDF5SubSubMesh
- suite.addTest(unittest.makeSuite(TestDataWriterHDF5SubSubMesh))
-
from TestDataWriterHDF5Ext import TestDataWriterHDF5ExtMesh
suite.addTest(unittest.makeSuite(TestDataWriterHDF5ExtMesh))
- from TestDataWriterHDF5Ext import TestDataWriterHDF5ExtSubMesh
- suite.addTest(unittest.makeSuite(TestDataWriterHDF5ExtSubMesh))
-
- from TestDataWriterHDF5Ext import TestDataWriterHDF5ExtSubSubMesh
- suite.addTest(unittest.makeSuite(TestDataWriterHDF5ExtSubSubMesh))
-
from TestXdmf import TestXdmf
suite.addTest(unittest.makeSuite(TestXdmf))
Modified: short/3D/PyLith/trunk/unittests/pytests/meshio/testmeshio.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/meshio/testmeshio.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/meshio/testmeshio.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -72,24 +72,12 @@
from TestVertexFilterVecNorm import TestVertexFilterVecNormMesh
suite.addTest(unittest.makeSuite(TestVertexFilterVecNormMesh))
- from TestVertexFilterVecNorm import TestVertexFilterVecNormSubMesh
- suite.addTest(unittest.makeSuite(TestVertexFilterVecNormSubMesh))
-
from TestCellFilterAvg import TestCellFilterAvgMesh
suite.addTest(unittest.makeSuite(TestCellFilterAvgMesh))
- from TestCellFilterAvg import TestCellFilterAvgSubMesh
- suite.addTest(unittest.makeSuite(TestCellFilterAvgSubMesh))
-
from TestDataWriterVTK import TestDataWriterVTKMesh
suite.addTest(unittest.makeSuite(TestDataWriterVTKMesh))
- from TestDataWriterVTK import TestDataWriterVTKSubMesh
- suite.addTest(unittest.makeSuite(TestDataWriterVTKSubMesh))
-
- from TestDataWriterVTK import TestDataWriterVTKSubSubMesh
- suite.addTest(unittest.makeSuite(TestDataWriterVTKSubSubMesh))
-
from TestOutputManagerMesh import TestOutputManagerMesh
suite.addTest(unittest.makeSuite(TestOutputManagerMesh))
Modified: short/3D/PyLith/trunk/unittests/pytests/problems/TestTimeStepAdapt.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/problems/TestTimeStepAdapt.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/problems/TestTimeStepAdapt.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -93,9 +93,7 @@
Integrator(0.5)]
from pylith.topology.Mesh import Mesh
- from pylith.mpi.Communicator import petsc_comm_world
mesh = Mesh()
- mesh.setComm(petsc_comm_world())
# Set time step
dt = 0.5 / 2.0
@@ -151,9 +149,7 @@
Integrator(2.4)]
from pylith.topology.Mesh import Mesh
- from pylith.mpi.Communicator import petsc_comm_world
mesh = Mesh()
- mesh.setComm(petsc_comm_world())
dt = 2.4 / 2.0
tstep.timeStep(mesh, integrators)
Modified: short/3D/PyLith/trunk/unittests/pytests/problems/TestTimeStepUniform.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/problems/TestTimeStepUniform.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/problems/TestTimeStepUniform.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -85,9 +85,7 @@
Integrator(8.0)]
from pylith.topology.Mesh import Mesh
- from pylith.mpi.Communicator import petsc_comm_world
mesh = Mesh()
- mesh.setComm(petsc_comm_world())
self.assertEqual(1.0, tstep.timeStep(mesh, integrators))
Modified: short/3D/PyLith/trunk/unittests/pytests/problems/TestTimeStepUser.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/problems/TestTimeStepUser.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/problems/TestTimeStepUser.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -110,9 +110,7 @@
Integrator(80.0)]
from pylith.topology.Mesh import Mesh
- from pylith.mpi.Communicator import petsc_comm_world
mesh = Mesh()
- #mesh.setComm(petsc_comm_world())
self.assertEqual(step1, tstep.timeStep(mesh, integrators))
self.assertEqual(step2, tstep.timeStep(mesh, integrators))
Modified: short/3D/PyLith/trunk/unittests/pytests/topology/TestJacobian.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/topology/TestJacobian.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/topology/TestJacobian.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -144,11 +144,8 @@
self.jacobian = Jacobian(self.fields.solution(), "aij")
self.jacobian.assemble("final_assembly")
- from pylith.mpi.Communicator import Communicator
- comm = Communicator(self.mesh.comm())
+ self.jacobian.write("jacobian.mat", self.mesh.comm())
- self.jacobian.write("jacobian.mat", comm)
-
# No testing of result.
return
Modified: short/3D/PyLith/trunk/unittests/pytests/topology/TestMesh.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/topology/TestMesh.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/topology/TestMesh.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -105,9 +105,8 @@
Test comm().
"""
from pylith.mpi.Communicator import petsc_comm_self
- mesh = Mesh()
- mesh.setComm(petsc_comm_self())
- comm = mesh.getComm()
+ mesh = Mesh(dim=3, comm=petsc_comm_self())
+ comm = mesh.comm()
self.assertEqual(0, comm.rank)
self.assertEqual(1, comm.size)
return
Modified: short/3D/PyLith/trunk/unittests/pytests/topology/TestSubMesh.py
===================================================================
--- short/3D/PyLith/trunk/unittests/pytests/topology/TestSubMesh.py 2013-05-13 18:43:34 UTC (rev 22057)
+++ short/3D/PyLith/trunk/unittests/pytests/topology/TestSubMesh.py 2013-05-13 23:33:37 UTC (rev 22058)
@@ -22,19 +22,19 @@
import unittest
-from pylith.topology.SubMesh import SubMesh
+from pylith.topology.Mesh import Mesh
# ----------------------------------------------------------------------
class TestSubMesh(unittest.TestCase):
"""
- Unit testing of SubMesh object.
+ Unit testing of Mesh object.
"""
def test_constructorA(self):
"""
Test constructor.
"""
- mesh = SubMesh()
+ mesh = Mesh()
self.assertEqual(0, mesh.dimension())
self.assertEqual(False, mesh.debug())
return
@@ -45,29 +45,18 @@
Test constructor.
"""
mesh = self._getMesh()
- submesh = SubMesh(mesh, "bc")
+ submesh = Mesh(mesh=mesh, label="bc")
self.assertEqual(1, submesh.dimension())
self.assertEqual(False, mesh.debug())
return
- def test_createSubMesh(self):
- """
- Test createSeiveMesh().
- """
- mesh = self._getMesh()
- submesh = SubMesh()
- submesh.createSubMesh(mesh, "bc")
- self.assertEqual(1, submesh.dimension())
- return
-
-
def test_coordsys(self):
"""
Test coordsys().
"""
mesh = self._getMesh()
- submesh = SubMesh(mesh, "bc")
+ submesh = Mesh(mesh=mesh, label="bc")
self.assertEqual(2, submesh.coordsys().spaceDim())
return
@@ -77,7 +66,7 @@
Test debug().
"""
mesh = self._getMesh()
- submesh = SubMesh(mesh, "bc")
+ submesh = Mesh(mesh=mesh, label="bc")
self.assertEqual(False, submesh.debug())
@@ -91,7 +80,7 @@
Test debug().
"""
mesh = self._getMesh()
- submesh = SubMesh(mesh, "bc")
+ submesh = Mesh(mesh=mesh, label="bc")
self.assertEqual(1, submesh.dimension())
return
@@ -102,7 +91,7 @@
Test comm().
"""
mesh = self._getMesh()
- submesh = SubMesh(mesh, "bc")
+ submesh = Mesh(mesh=mesh, label="bc")
comm = submesh.comm()
self.assertEqual(0, comm.rank)
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