[cig-commits] r21207 - in short/3D/PyLith/trunk: libsrc/pylith/bc libsrc/pylith/faults libsrc/pylith/feassemble libsrc/pylith/materials libsrc/pylith/meshio libsrc/pylith/problems libsrc/pylith/topology unittests/libtests/bc unittests/libtests/faults unittests/libtests/feassemble unittests/libtests/friction unittests/libtests/materials unittests/libtests/meshio unittests/libtests/topology
knepley at geodynamics.org
knepley at geodynamics.org
Sat Jan 5 09:40:23 PST 2013
Author: knepley
Date: 2013-01-05 09:40:22 -0800 (Sat, 05 Jan 2013)
New Revision: 21207
Modified:
short/3D/PyLith/trunk/libsrc/pylith/bc/AbsorbingDampers.cc
short/3D/PyLith/trunk/libsrc/pylith/bc/Neumann.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/CohesiveTopology.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveImpulses.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.cc
short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.cc
short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicit.cc
short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicitLgDeform.cc
short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicitTet4.cc
short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicitTri3.cc
short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityImplicit.cc
short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityImplicitLgDeform.cc
short/3D/PyLith/trunk/libsrc/pylith/feassemble/IntegratorElasticity.cc
short/3D/PyLith/trunk/libsrc/pylith/materials/ElasticMaterial.cc
short/3D/PyLith/trunk/libsrc/pylith/materials/Material.cc
short/3D/PyLith/trunk/libsrc/pylith/meshio/CellFilterAvg.cc
short/3D/PyLith/trunk/libsrc/pylith/meshio/DataWriterHDF5.cc
short/3D/PyLith/trunk/libsrc/pylith/meshio/DataWriterHDF5Ext.cc
short/3D/PyLith/trunk/libsrc/pylith/meshio/DataWriterVTK.cc
short/3D/PyLith/trunk/libsrc/pylith/meshio/MeshBuilder.cc
short/3D/PyLith/trunk/libsrc/pylith/meshio/MeshIO.cc
short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnPoints.cc
short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnPoints.hh
short/3D/PyLith/trunk/libsrc/pylith/meshio/VertexFilterVecNorm.cc
short/3D/PyLith/trunk/libsrc/pylith/problems/Implicit.cc
short/3D/PyLith/trunk/libsrc/pylith/problems/Solver.cc
short/3D/PyLith/trunk/libsrc/pylith/topology/Distributor.cc
short/3D/PyLith/trunk/libsrc/pylith/topology/Field.cc
short/3D/PyLith/trunk/libsrc/pylith/topology/Field.hh
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/SubMesh.cc
short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.hh
short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.cc
short/3D/PyLith/trunk/unittests/libtests/bc/TestDirichletBC.cc
short/3D/PyLith/trunk/unittests/libtests/bc/TestDirichletBCMulti.cc
short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumann.cc
short/3D/PyLith/trunk/unittests/libtests/bc/TestPointForce.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestBruneSlipFn.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestConstRateSlipFn.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestEqKinSrc.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDyn.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulses.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestLiuCosSlipFn.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestStepSlipFn.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestTimeHistorySlipFn.cc
short/3D/PyLith/trunk/unittests/libtests/faults/TestTractPerturbation.cc
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/materials/TestElasticMaterial.cc
short/3D/PyLith/trunk/unittests/libtests/materials/TestMaterial.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/TestDataWriterFaultMesh.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterMesh.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterPoints.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterSubMesh.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestMeshIO.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestOutputManager.cc
short/3D/PyLith/trunk/unittests/libtests/meshio/TestVertexFilterVecNorm.cc
short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldMesh.cc
short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldSubMesh.cc
short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsMesh.cc
short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsNewMesh.cc
short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsSubMesh.cc
short/3D/PyLith/trunk/unittests/libtests/topology/TestSolutionFields.cc
short/3D/PyLith/trunk/unittests/libtests/topology/TestSubMesh.cc
Log:
Updated to DMPlex, point interpolation tests pass
Modified: short/3D/PyLith/trunk/libsrc/pylith/bc/AbsorbingDampers.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/bc/AbsorbingDampers.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/bc/AbsorbingDampers.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -96,7 +96,7 @@
PetscErrorCode err;
assert(subMesh);
- err = DMComplexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
// Get damping constants at each quadrature point and rotate to
// global coordinate frame using orientation information
@@ -148,7 +148,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(subMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -180,10 +180,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, c);
- err = DMComplexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
PetscInt ddof, doff;
@@ -286,8 +286,8 @@
PetscErrorCode err;
assert(subMesh);
- err = DMComplexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(subMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(subMesh, &subpointMap);CHECK_PETSC_ERROR(err);
// Get sections
PetscSection valueSection = _parameters->get("damping constants").petscSection();
@@ -310,7 +310,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(subMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
#endif
@@ -331,10 +331,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, c);
- err = DMComplexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
#if defined(DETAILED_EVENT_LOGGING)
@@ -353,7 +353,7 @@
err = PetscSectionGetDof(valueSection, c, &ddof);CHECK_PETSC_ERROR(err);
err = PetscSectionGetOffset(valueSection, c, &doff);CHECK_PETSC_ERROR(err);
assert(ddof == numQuadPts*spaceDim);
- err = DMComplexVecGetClosure(subMesh, velSubsection, velVec, c, &velSize, &velArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(subMesh, velSubsection, velVec, c, &velSize, &velArray);CHECK_PETSC_ERROR(err);
assert(velSize == numBasis*spaceDim);
#if defined(DETAILED_EVENT_LOGGING)
@@ -380,8 +380,8 @@
} // for
} // for
} // for
- err = DMComplexVecRestoreClosure(subMesh, velSubsection, velVec, c, &velSize, &velArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(subMesh, residualSubsection, residualVec, c, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(subMesh, velSubsection, velVec, c, &velSize, &velArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(subMesh, residualSubsection, residualVec, c, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
#if defined(DETAILED_EVENT_LOGGING)
PetscLogFlops(numQuadPts*(1+numBasis*(1+numBasis*(3*spaceDim))));
@@ -442,8 +442,8 @@
PetscErrorCode err;
assert(subMesh);
- err = DMComplexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(subMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(subMesh, &subpointMap);CHECK_PETSC_ERROR(err);
// Get sections
PetscSection valueSection = _parameters->get("damping constants").petscSection();
@@ -466,7 +466,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(subMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
#endif
@@ -487,10 +487,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, c);
- err = DMComplexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
#if defined(DETAILED_EVENT_LOGGING)
@@ -509,7 +509,7 @@
err = PetscSectionGetDof(valueSection, c, &ddof);CHECK_PETSC_ERROR(err);
err = PetscSectionGetOffset(valueSection, c, &doff);CHECK_PETSC_ERROR(err);
assert(ddof == numQuadPts*spaceDim);
- err = DMComplexVecGetClosure(subMesh, velSubsection, velVec, c, &velSize, &velArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(subMesh, velSubsection, velVec, c, &velSize, &velArray);CHECK_PETSC_ERROR(err);
assert(velSize == numBasis*spaceDim);
#if defined(DETAILED_EVENT_LOGGING)
@@ -537,8 +537,8 @@
valIJ * velArray[iBasis*spaceDim+iDim];
} // for
} // for
- err = DMComplexVecRestoreClosure(subMesh, velSubsection, velVec, c, &velSize, &velArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(subMesh, residualSubsection, residualVec, c, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(subMesh, velSubsection, velVec, c, &velSize, &velArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(subMesh, residualSubsection, residualVec, c, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
#if defined(DETAILED_EVENT_LOGGING)
PetscLogFlops(numQuadPts*(1+numBasis+numBasis*(1+spaceDim*3)));
_logger->eventEnd(computeEvent);
@@ -595,8 +595,8 @@
PetscErrorCode err;
assert(subMesh);
- err = DMComplexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(subMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(subMesh, &subpointMap);CHECK_PETSC_ERROR(err);
// Get sections
PetscSection valueSection = _parameters->get("damping constants").petscSection();
@@ -629,7 +629,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(subMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
#endif
@@ -650,10 +650,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, c);
- err = DMComplexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
#if defined(DETAILED_EVENT_LOGGING)
_logger->eventEnd(geometryEvent);
@@ -702,7 +702,7 @@
#endif
// Assemble cell contribution into PETSc Matrix
- err = DMComplexMatSetClosure(subMesh, solutionSubsection, solutionGlobalSubsection, jacobianMat, c, &_cellMatrix[0], ADD_VALUES);
+ err = DMPlexMatSetClosure(subMesh, solutionSubsection, solutionGlobalSubsection, jacobianMat, c, &_cellMatrix[0], ADD_VALUES);
CHECK_PETSC_ERROR_MSG(err, "Update to PETSc Mat failed.");
#if defined(DETAILED_EVENT_LOGGING)
@@ -758,8 +758,8 @@
PetscErrorCode err;
assert(subMesh);
- err = DMComplexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(subMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(subMesh, &subpointMap);CHECK_PETSC_ERROR(err);
// Get parameters used in integration.
const PylithScalar dt = _dt;
@@ -784,7 +784,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(subMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
#endif
@@ -805,10 +805,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, c);
- err = DMComplexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
#if defined(DETAILED_EVENT_LOGGING)
_logger->eventEnd(geometryEvent);
@@ -849,7 +849,7 @@
* dampingArray[doff+iQuad * spaceDim + iDim];
} // for
} // for
- err = DMComplexVecSetClosure(subMesh, jacobianSubsection, jacobianVec, c, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(subMesh, jacobianSubsection, jacobianVec, c, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
#if defined(DETAILED_EVENT_LOGGING)
PetscLogFlops(numQuadPts*(4+numBasis+numBasis*(1+spaceDim*2)));
_logger->eventEnd(computeEvent);
Modified: short/3D/PyLith/trunk/libsrc/pylith/bc/Neumann.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/bc/Neumann.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/bc/Neumann.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -112,8 +112,8 @@
PetscErrorCode err;
assert(subMesh);
- err = DMComplexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(subMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(subMesh, &subpointMap);CHECK_PETSC_ERROR(err);
// Get sections
_calculateValue(t);
@@ -131,7 +131,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(subMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
#endif
@@ -144,10 +144,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, c);
- err = DMComplexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
// Reset element vector to zero
@@ -177,7 +177,7 @@
} // for
} // for
} // for
- err = DMComplexVecSetClosure(subMesh, residualSubsection, residualVec, c, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(subMesh, residualSubsection, residualVec, c, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
PetscLogFlops(numQuadPts*(1+numBasis*(1+numBasis*(1+2*spaceDim))));
} // for
err = VecRestoreArray(valueVec, &tractionsArray);CHECK_PETSC_ERROR(err);
@@ -403,7 +403,7 @@
PetscErrorCode err;
assert(subMesh);
- err = DMComplexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
const int cellDim = _quadrature->cellDim() > 0 ? _quadrature->cellDim() : 1;
const int numBasis = _quadrature->numBasis();
@@ -419,7 +419,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(subMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -449,10 +449,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, c);
- err = DMComplexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
const scalar_array& quadPtsNondim = _quadrature->quadPts();
quadPtsGlobal = quadPtsNondim;
@@ -506,7 +506,7 @@
PetscErrorCode err;
assert(subMesh);
- err = DMComplexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
// Quadrature related values.
const feassemble::CellGeometry& cellGeometry = _quadrature->refGeometry();
@@ -528,7 +528,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(subMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(subMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -575,10 +575,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, c);
- err = DMComplexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(subMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
for(int iQuad=0, iRef=0, iSpace=0; iQuad < numQuadPts; ++iQuad, iRef+=cellDim, iSpace+=spaceDim) {
// Compute Jacobian and determinant at quadrature point, then get orientation.
@@ -678,7 +678,7 @@
PetscErrorCode err;
assert(subMesh);
- err = DMComplexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
const int spaceDim = _quadrature->spaceDim();
const int numQuadPts = _quadrature->numQuadPts();
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/BruneSlipFn.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -92,7 +92,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
logger.stagePush("Fault");
@@ -173,7 +173,7 @@
PetscSection coordSection;
Vec coordVec;
PetscScalar *coordArray;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -267,7 +267,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Get sections
const topology::Field<topology::SubMesh>& finalSlip = _parameters->get("final slip");
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/CohesiveTopology.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/CohesiveTopology.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/CohesiveTopology.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -30,7 +30,7 @@
#include "pylith/utils/petscerror.h" // USES CHECK_PETSC_ERROR
-extern PetscErrorCode DMComplexGetOrientedFace(DM dm, PetscInt cell, PetscInt faceSize, const PetscInt face[], PetscInt numCorners, PetscInt indices[], PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented);
+extern PetscErrorCode DMPlexGetOrientedFace(DM dm, PetscInt cell, PetscInt faceSize, const PetscInt face[], PetscInt numCorners, PetscInt indices[], PetscInt origVertices[], PetscInt faceVertices[], PetscBool *posOriented);
// ----------------------------------------------------------------------
typedef pylith::topology::Mesh::SieveMesh SieveMesh;
@@ -129,7 +129,7 @@
ALE::ISieveConverter::convertMesh(*fault, &dm, renumbering, true);
// Have to make subpointMap here: renumbering[original] = fault
- err = DMComplexGetChart(dm, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetChart(dm, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
assert(renumbering.size() == pEnd-pStart);
err = PetscMalloc((pEnd-pStart) * sizeof(PetscInt), &renum);CHECK_PETSC_ERROR(err);
for(SieveSubMesh::renumbering_type::const_iterator p_iter = renumbering.begin(); p_iter != renumbering.end(); ++p_iter) {
@@ -142,7 +142,7 @@
assert(renum[p] > renum[p-1]);
}
err = ISCreateGeneral(fault->comm(), pEnd-pStart, renum, PETSC_OWN_POINTER, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexSetSubpointMap(dm, subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetSubpointMap(dm, subpointMap);CHECK_PETSC_ERROR(err);
renumbering.clear();
faultMesh->setDMMesh(dm);
}
@@ -176,7 +176,7 @@
const ALE::Obj<SieveMesh>& sieveMesh = mesh->sieveMesh();
assert(!sieveMesh.isNull());
- /* DMComplex */
+ /* DMPlex */
DM complexMesh = mesh->dmMesh();
assert(complexMesh);
const ALE::Obj<SieveSubMesh>& faultSieveMesh = faultMesh.sieveMesh();
@@ -193,7 +193,7 @@
PetscInt cStart, cEnd;
#define USE_DMCOMPLEX_ON
#ifdef USE_DMCOMPLEX_ON
- err = DMComplexGetHeightStratum(complexMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(complexMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
assert(numCells == cEnd - cStart);
#endif
int numCorners = 0; // The number of vertices in a mesh cell
@@ -220,7 +220,7 @@
#ifdef USE_DMCOMPLEX_ON
PetscInt numCornersDM;
- err = DMComplexGetConeSize(complexMesh, cStart, &numCornersDM);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetConeSize(complexMesh, cStart, &numCornersDM);CHECK_PETSC_ERROR(err);
assert(numCorners == numCornersDM);
err = PetscMalloc(faceSize * sizeof(PetscInt), &indicesDM);CHECK_PETSC_ERROR(err);
#endif
@@ -237,7 +237,7 @@
assert(!vertices.isNull());
#ifdef USE_DMCOMPLEX_ON
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(complexMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(complexMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
assert(vertices->size() == vEnd - vStart);
#endif
const ALE::Obj<std::set<std::string> >& groupNames = sieveMesh->getIntSections();
@@ -275,29 +275,29 @@
#ifdef USE_DMCOMPLEX_ON
PetscInt pStart, pEnd;
- err = DMComplexGetChart(complexMesh, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetChart(complexMesh, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
assert(firstFaultVertex == pEnd - pStart);
#endif
}
#ifdef USE_DMCOMPLEX_ON
- /* DMComplex */
+ /* DMPlex */
DM newMesh;
PetscInt *newCone;
PetscInt maxConeSize = 0;
err = DMCreate(sieveMesh->comm(), &newMesh);CHECK_PETSC_ERROR(err);
- err = DMSetType(newMesh, DMCOMPLEX);CHECK_PETSC_ERROR(err);
- err = DMComplexSetDimension(newMesh, sieveMesh->getDimension());CHECK_PETSC_ERROR(err);
- err = DMComplexSetChart(newMesh, 0, firstFaultVertexDM + extraVertices);CHECK_PETSC_ERROR(err);
+ err = DMSetType(newMesh, DMPLEX);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetDimension(newMesh, sieveMesh->getDimension());CHECK_PETSC_ERROR(err);
+ err = DMPlexSetChart(newMesh, 0, firstFaultVertexDM + extraVertices);CHECK_PETSC_ERROR(err);
for(PetscInt c = cStart; c < cEnd; ++c) {
PetscInt coneSize;
- err = DMComplexGetConeSize(complexMesh, c, &coneSize);CHECK_PETSC_ERROR(err);
- err = DMComplexSetConeSize(newMesh, c, coneSize);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetConeSize(complexMesh, c, &coneSize);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetConeSize(newMesh, c, coneSize);CHECK_PETSC_ERROR(err);
maxConeSize = PetscMax(maxConeSize, coneSize);
}
for(PetscInt c = cEnd; c < cEnd+numFaultFaces; ++c) {
- err = DMComplexSetConeSize(newMesh, c, constraintCell ? faceSize*3 : faceSize*2);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetConeSize(newMesh, c, constraintCell ? faceSize*3 : faceSize*2);CHECK_PETSC_ERROR(err);
}
err = DMSetUp(newMesh);CHECK_PETSC_ERROR(err);
err = PetscMalloc(maxConeSize * sizeof(PetscInt), &newCone);CHECK_PETSC_ERROR(err);
@@ -305,21 +305,21 @@
const PetscInt *cone;
PetscInt coneSize, cp;
- err = DMComplexGetCone(complexMesh, c, &cone);CHECK_PETSC_ERROR(err);
- err = DMComplexGetConeSize(complexMesh, c, &coneSize);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCone(complexMesh, c, &cone);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetConeSize(complexMesh, c, &coneSize);CHECK_PETSC_ERROR(err);
for(cp = 0; cp < coneSize; ++cp) {
newCone[cp] = cone[cp] + extraCells;
}
- err = DMComplexSetCone(newMesh, c, newCone);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetCone(newMesh, c, newCone);CHECK_PETSC_ERROR(err);
}
err = PetscFree(newCone);CHECK_PETSC_ERROR(err);
PetscInt cMax, vMax;
- err = DMComplexGetVTKBounds(newMesh, &cMax, &vMax);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetVTKBounds(newMesh, &cMax, &vMax);CHECK_PETSC_ERROR(err);
if (cMax < 0) {
- err = DMComplexSetVTKBounds(newMesh, firstFaultCellDM, PETSC_DETERMINE);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetVTKBounds(newMesh, firstFaultCellDM, PETSC_DETERMINE);CHECK_PETSC_ERROR(err);
}
- err = DMComplexSetVTKBounds(newMesh, PETSC_DETERMINE, firstLagrangeVertexDM);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetVTKBounds(newMesh, PETSC_DETERMINE, firstLagrangeVertexDM);CHECK_PETSC_ERROR(err);
// Renumber labels
std::set<std::string> names(groupNames->begin(), groupNames->end());
@@ -331,10 +331,10 @@
PetscBool hasLabel;
const PetscInt *ids;
- err = DMComplexHasLabel(complexMesh, lname, &hasLabel);CHECK_PETSC_ERROR(err);
+ err = DMPlexHasLabel(complexMesh, lname, &hasLabel);CHECK_PETSC_ERROR(err);
if (!hasLabel) continue;
- err = DMComplexGetLabelSize(complexMesh, lname, &n);CHECK_PETSC_ERROR(err);
- err = DMComplexGetLabelIdIS(complexMesh, lname, &idIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetLabelSize(complexMesh, lname, &n);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetLabelIdIS(complexMesh, lname, &idIS);CHECK_PETSC_ERROR(err);
err = ISGetIndices(idIS, &ids);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < n; ++i) {
const PetscInt id = ids[i];
@@ -342,14 +342,14 @@
IS sIS;
PetscInt size;
- err = DMComplexGetStratumSize(complexMesh, lname, id, &size);CHECK_PETSC_ERROR(err);
- err = DMComplexGetStratumIS(complexMesh, lname, id, &sIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumSize(complexMesh, lname, id, &size);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(complexMesh, lname, id, &sIS);CHECK_PETSC_ERROR(err);
err = ISGetIndices(sIS, &points);CHECK_PETSC_ERROR(err);
for(PetscInt s = 0; s < size; ++s) {
if ((points[s] >= vStart) && (points[s] < vEnd)) {
- err = DMComplexSetLabelValue(newMesh, lname, points[s]+extraCells, id);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(newMesh, lname, points[s]+extraCells, id);CHECK_PETSC_ERROR(err);
} else {
- err = DMComplexSetLabelValue(newMesh, lname, points[s], id);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(newMesh, lname, points[s], id);CHECK_PETSC_ERROR(err);
}
}
err = ISRestoreIndices(sIS, &points);CHECK_PETSC_ERROR(err);
@@ -371,7 +371,7 @@
// Add shadow and constraint vertices (if they exist) to group
// associated with fault
groupField->addPoint(firstFaultVertex, 1);
- err = DMComplexSetLabelValue(newMesh, groupField->getName().c_str(), firstFaultVertexDM, 1);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(newMesh, groupField->getName().c_str(), firstFaultVertexDM, 1);CHECK_PETSC_ERROR(err);
#if defined(FAST_STRATIFY)
// OPTIMIZATION
sieveMesh->setHeight(firstFaultVertex, 1);
@@ -381,7 +381,7 @@
vertexLagrangeRenumber[*v_iter] = firstLagrangeVertex;
vertexLagrangeRenumberDM[*v_iter+faultVertexOffsetDM] = firstLagrangeVertexDM;
groupField->addPoint(firstLagrangeVertex, 1);
- err = DMComplexSetLabelValue(newMesh, groupField->getName().c_str(), firstLagrangeVertexDM, 1);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(newMesh, groupField->getName().c_str(), firstLagrangeVertexDM, 1);CHECK_PETSC_ERROR(err);
#if defined(FAST_STRATIFY)
// OPTIMIZATION
sieveMesh->setHeight(firstLagrangeVertex, 1);
@@ -406,9 +406,9 @@
PetscInt vertexDM = *v_iter+faultVertexOffsetDM;
PetscInt value;
//assert(extraCells == faultVertexOffsetDM);
- err = DMComplexGetLabelValue(complexMesh, (*name).c_str(), vertexDM, &value);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetLabelValue(complexMesh, (*name).c_str(), vertexDM, &value);CHECK_PETSC_ERROR(err);
if (value) {
- err = DMComplexSetLabelValue(newMesh, (*name).c_str(), vertexRenumberDM[vertexDM], value);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(newMesh, (*name).c_str(), vertexRenumberDM[vertexDM], value);CHECK_PETSC_ERROR(err);
}
} // for
} // for
@@ -487,7 +487,7 @@
assert(faceVertices.size() == coneSize);
faceSet.clear();
#ifdef USE_DMCOMPLEX_ON
- err = DMComplexGetOrientedFace(complexMesh, cell, coneSize, faceConeDM, numCorners, indicesDM, origVerticesDM, faceVerticesDM, PETSC_NULL);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetOrientedFace(complexMesh, cell, coneSize, faceConeDM, numCorners, indicesDM, origVerticesDM, faceVerticesDM, PETSC_NULL);CHECK_PETSC_ERROR(err);
for(PetscInt c = 0; c < coneSize; ++c) {
assert(faceVertices[c]+faultVertexOffsetDM == faceVerticesDM[c]);
}
@@ -568,11 +568,11 @@
} // for
} // if
#ifdef USE_DMCOMPLEX_ON
- err = DMComplexSetCone(newMesh, firstFaultCellDM, cohesiveCone);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetCone(newMesh, firstFaultCellDM, cohesiveCone);CHECK_PETSC_ERROR(err);
#endif
// TODO: Need to reform the material label when sieve is reallocated
sieveMesh->setValue(material, firstFaultCell, materialId);
- err = DMComplexSetLabelValue(newMesh, "material-id", firstFaultCellDM, materialId);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(newMesh, "material-id", firstFaultCellDM, materialId);CHECK_PETSC_ERROR(err);
logger.stagePop();
logger.stagePush("SerialFaultStratification");
#if defined(FAST_STRATIFY)
@@ -586,7 +586,7 @@
cV2.clear();
} // for over fault faces
// This completes the set of cells scheduled to be replaced
- // TODO: Convert to DMComplex
+ // TODO: Convert to DMPlex
TopologyOps::PointSet replaceCellsBase(replaceCells);
const ALE::Obj<SieveFlexMesh::label_sequence>& faultBdVerts = faultBoundary->depthStratum(0);
@@ -629,8 +629,8 @@
const PetscInt *cone;
PetscInt coneSize;
- err = DMComplexGetCone(complexMesh, cell, &cone);CHECK_PETSC_ERROR(err);
- err = DMComplexGetConeSize(complexMesh, cell, &coneSize);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCone(complexMesh, cell, &cone);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetConeSize(complexMesh, cell, &coneSize);CHECK_PETSC_ERROR(err);
if (replaceCells.find(cell) != replaceCells.end()) {
for(PetscInt c = 0; c < coneSize; ++c) {
PetscBool replaced = PETSC_FALSE;
@@ -651,15 +651,15 @@
cohesiveCone[c] = cone[c] + extraCells;
}
}
- err = DMComplexSetCone(newMesh, cell, cohesiveCone);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetCone(newMesh, cell, cohesiveCone);CHECK_PETSC_ERROR(err);
}
#endif
err = PetscFree3(origVerticesDM, faceVerticesDM, cohesiveCone);CHECK_PETSC_ERROR(err);
sieve->reallocate();
#ifdef USE_DMCOMPLEX_ON
- /* DMComplex */
- err = DMComplexSymmetrize(newMesh);CHECK_PETSC_ERROR(err);
- err = DMComplexStratify(newMesh);CHECK_PETSC_ERROR(err);
+ /* DMPlex */
+ err = DMPlexSymmetrize(newMesh);CHECK_PETSC_ERROR(err);
+ err = DMPlexStratify(newMesh);CHECK_PETSC_ERROR(err);
#endif
// More checking
@@ -806,8 +806,8 @@
PetscInt coordSize;
#ifdef USE_DMCOMPLEX_ON
- err = DMComplexGetCoordinateSection(complexMesh, &coordSection);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(newMesh, &newCoordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(complexMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(newMesh, &newCoordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(complexMesh, &coordinatesVec);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(newCoordSection, vStart+extraCells, vEnd+extraCells+extraVertices);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
@@ -1104,10 +1104,10 @@
PetscInt pvStart, pvEnd, fvStart, fvEnd, n;
PetscErrorCode err;
- err = DMComplexGetDepthStratum(dmMesh, 0, &pvStart, &pvEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(dmFaultMesh, 0, &fvStart, &fvEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmFaultMesh, &faultCoordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &pvStart, &pvEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmFaultMesh, 0, &fvStart, &fvEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmFaultMesh, &faultCoordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(faultCoordSection, fvStart, fvEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = pvStart; v < pvEnd; ++v) {
PetscInt sievePoint = convertDMToSievePointNumbering(v, numNormalCells, numCohesiveCells, numNormalVertices, numShadowVertices, numLagrangeVertices);
@@ -1145,8 +1145,8 @@
PetscInt *renum;
PetscInt pStart, pEnd;
- err = DMComplexGetChart(dmFaultMesh, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(dmFaultMesh, 0, &fvStart, &fvEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetChart(dmFaultMesh, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmFaultMesh, 0, &fvStart, &fvEnd);CHECK_PETSC_ERROR(err);
assert(convertRenumbering.size() == pEnd-pStart);
err = PetscMalloc((pEnd-pStart) * sizeof(PetscInt), &renum);CHECK_PETSC_ERROR(err);
std::cout << std::endl;
@@ -1168,7 +1168,7 @@
assert(renum[p] > renum[p-1]);
}
err = ISCreateGeneral(faultMesh->comm(), pEnd-pStart, renum, PETSC_OWN_POINTER, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexSetSubpointMap(dmFaultMesh, subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetSubpointMap(dmFaultMesh, subpointMap);CHECK_PETSC_ERROR(err);
// Update dimensioned coordinates if they exist.
if (sieveMesh->hasRealSection("coordinates_dimensioned")) {
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/ConstRateSlipFn.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -90,7 +90,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
logger.stagePush("Fault");
@@ -156,7 +156,7 @@
PetscSection coordSection;
Vec coordVec;
PetscScalar *coordArray;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -233,7 +233,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Get sections
const topology::Field<topology::SubMesh>& slipRate = _parameters->get("slip rate");
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveDyn.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -2020,8 +2020,8 @@
PetscInt numCohesiveCells, vStart, vEnd;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetStratumIS(dmMesh, "material-id", id(), &cellsCohesiveIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", id(), &cellsCohesiveIS);CHECK_PETSC_ERROR(err);
err = ISGetLocalSize(cellsCohesiveIS, &numCohesiveCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellsCohesiveIS, &cellsCohesive);CHECK_PETSC_ERROR(err);
@@ -2058,7 +2058,7 @@
// Get cone for cohesive cell
PetscInt *closure = PETSC_NULL;
PetscInt closureSize, q = 0;
- err = DMComplexGetTransitiveClosure(dmMesh, cellsCohesive[c], PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetTransitiveClosure(dmMesh, cellsCohesive[c], PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
// Filter out non-vertices
for(PetscInt p = 0; p < closureSize*2; p += 2) {
if ((closure[p] >= vStart) && (closure[p] < vEnd)) {
@@ -2081,7 +2081,7 @@
indicesGlobal[iB+iDim] = gind + iDim;
} // for
} // for
- err = DMComplexRestoreTransitiveClosure(dmMesh, cellsCohesive[c], PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexRestoreTransitiveClosure(dmMesh, cellsCohesive[c], PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
for (int i=0; i < subnrows; ++i) {
indicesPerm[i] = i;
@@ -2106,7 +2106,7 @@
// Insert cell contribution into PETSc Matrix
PetscInt c_fault = _cohesiveToFault[cellsCohesive[c]];
- err = DMComplexMatSetClosure(faultDMMesh, solutionFaultSection, solutionFaultGlobalSection, jacobianFaultMatrix, c_fault, &jacobianSubCell[0], INSERT_VALUES);
+ err = DMPlexMatSetClosure(faultDMMesh, solutionFaultSection, solutionFaultGlobalSection, jacobianFaultMatrix, c_fault, &jacobianSubCell[0], INSERT_VALUES);
CHECK_PETSC_ERROR_MSG(err, "Update to PETSc Mat failed.");
// Destory IS for cohesiveCell
@@ -2157,14 +2157,14 @@
PetscErrorCode err;
assert(faultDMMesh);
- err = DMComplexGetHeightStratum(faultDMMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(faultDMMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
const int numCells = cEnd-cStart;
// Get sections
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(faultDMMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(faultDMMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(faultDMMesh, &coordVec);CHECK_PETSC_ERROR(err);
PetscSection dLagrangeSection = _fields->get("sensitivity dLagrange").petscSection();
@@ -2183,15 +2183,15 @@
// Compute geometry
const PetscScalar *coords = PETSC_NULL;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(faultDMMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(faultDMMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, c);
- err = DMComplexVecRestoreClosure(faultDMMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(faultDMMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
// Restrict input fields to cell
const PetscScalar *dLagrangeArray = PETSC_NULL;
PetscInt dLagrangeSize;
- err = DMComplexVecGetClosure(faultDMMesh, dLagrangeSection, dLagrangeVec, c, &dLagrangeSize, &dLagrangeArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(faultDMMesh, dLagrangeSection, dLagrangeVec, c, &dLagrangeSize, &dLagrangeArray);CHECK_PETSC_ERROR(err);
// Get cell geometry information that depends on cell
const scalar_array& basis = _quadrature->basis();
@@ -2223,10 +2223,10 @@
} // for
} // for
} // for
- err = DMComplexVecRestoreClosure(faultDMMesh, dLagrangeSection, dLagrangeVec, c, &dLagrangeSize, &dLagrangeArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(faultDMMesh, dLagrangeSection, dLagrangeVec, c, &dLagrangeSize, &dLagrangeArray);CHECK_PETSC_ERROR(err);
// Assemble cell contribution into field
- err = DMComplexVecSetClosure(faultDMMesh, residualSection, residualVec, c, &residualCell[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(faultDMMesh, residualSection, residualVec, c, &residualCell[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
} // for
} // _sensitivityReformResidual
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveImpulses.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveImpulses.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveImpulses.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -313,7 +313,7 @@
PetscSection coordSection;
Vec coordVec;
PetscScalar *coords;
- err = DMComplexGetCoordinateSection(faultDMMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(faultDMMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(faultDMMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(_dbImpulseAmp);
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/FaultCohesiveLagrange.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -977,8 +977,8 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexHasLabel(dmMesh, label(), &hasLabel);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexHasLabel(dmMesh, label(), &hasLabel);CHECK_PETSC_ERROR(err);
if (!hasLabel) {
std::ostringstream msg;
msg << "Mesh missing group of vertices '" << label() << " for boundary condition.";
@@ -1026,7 +1026,7 @@
IS cellIS;
const PetscInt *cells;
PetscInt numCells;
- err = DMComplexGetStratumIS(dmMesh, "material-id", id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", id(), &cellIS);CHECK_PETSC_ERROR(err);
assert(cellIS);
err = ISGetLocalSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -1034,7 +1034,7 @@
PetscInt *closure = PETSC_NULL;
PetscInt cellNumCorners = 0, closureSize;
- err = DMComplexGetTransitiveClosure(dmMesh, cells[c], PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetTransitiveClosure(dmMesh, cells[c], PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
for(PetscInt p = 0; p < closureSize*2; p += 2) {
const PetscInt point = closure[p];
if ((point >= vStart) && (point < vEnd)) {
@@ -1049,7 +1049,7 @@
<< "'.";
throw std::runtime_error(msg.str());
} // if
- err = DMComplexRestoreTransitiveClosure(dmMesh, cells[c], PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexRestoreTransitiveClosure(dmMesh, cells[c], PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
} // for
err = ISRestoreIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
} // verifyConfiguration
@@ -1110,8 +1110,8 @@
PetscInt numCells, vStart, vEnd;
PetscErrorCode err;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetStratumIS(dmMesh, "material-id", id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", id(), &cellIS);CHECK_PETSC_ERROR(err);
assert(cellIS);
err = ISGetLocalSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
const int numConstraintVert = _quadrature->numBasis();
@@ -1123,9 +1123,9 @@
PetscInt numPoints, fcStart, fcEnd, fvStart, fvEnd;
assert(faultDMMesh);
- err = DMComplexGetHeightStratum(faultDMMesh, 0, &fcStart, &fcEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(faultDMMesh, 0, &fvStart, &fvEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(faultDMMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(faultDMMesh, 0, &fcStart, &fcEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(faultDMMesh, 0, &fvStart, &fvEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(faultDMMesh, &subpointMap);CHECK_PETSC_ERROR(err);
err = ISGetLocalSize(subpointMap, &numPoints);CHECK_PETSC_ERROR(err);
assert(numCells == fcEnd-fcStart);
@@ -1144,7 +1144,7 @@
PetscInt *closure = PETSC_NULL;
PetscInt closureSize, q = 0;
- err = DMComplexGetTransitiveClosure(dmMesh, cells[c], PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetTransitiveClosure(dmMesh, cells[c], PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
for(PetscInt p = 0; p < closureSize*2; p += 2) {
const PetscInt point = closure[p];
if ((point >= vStart) && (point < vEnd)) {
@@ -1184,7 +1184,7 @@
++index;
} // if
} // for
- err = DMComplexRestoreTransitiveClosure(dmMesh, cells[c], PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexRestoreTransitiveClosure(dmMesh, cells[c], PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
} // for
err = ISRestoreIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
err = ISRestoreIndices(subpointMap, &points);CHECK_PETSC_ERROR(err);
@@ -1257,7 +1257,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
err = VecGetArray(fieldVec, &fieldArray);CHECK_PETSC_ERROR(err);
err = VecGetArray(orientationVec, &orientationArray);CHECK_PETSC_ERROR(err);
@@ -1320,7 +1320,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
err = VecGetArray(fieldVec, &fieldArray);CHECK_PETSC_ERROR(err);
err = VecGetArray(orientationVec, &orientationArray);CHECK_PETSC_ERROR(err);
@@ -1371,8 +1371,8 @@
PetscErrorCode err;
assert(faultDMMesh);
- err = DMComplexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetHeightStratum(faultDMMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(faultDMMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
// Containers for orientation information.
const int cohesiveDim = _faultMesh->dimension();
@@ -1413,7 +1413,7 @@
// Get section containing coordinates of vertices
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(faultDMMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(faultDMMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(faultDMMesh, &coordVec);CHECK_PETSC_ERROR(err);
// Set orientation function
@@ -1432,8 +1432,8 @@
scalar_array coordinatesCell(numBasis * spaceDim);
// Get orientations at fault cell's vertices.
- err = DMComplexVecGetClosure(faultDMMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
- err = DMComplexGetTransitiveClosure(faultDMMesh, c, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(faultDMMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetTransitiveClosure(faultDMMesh, c, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
// Filter out non-vertices
@@ -1461,8 +1461,8 @@
orientationArray[off+d] += orientationVertex[d];
}
} // for
- err = DMComplexVecRestoreClosure(faultDMMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
- err = DMComplexRestoreTransitiveClosure(faultDMMesh, c, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(faultDMMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexRestoreTransitiveClosure(faultDMMesh, c, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
} // for
err = VecRestoreArray(orientationVec, &orientationArray);CHECK_PETSC_ERROR(err);
@@ -1668,8 +1668,8 @@
PetscErrorCode err;
assert(faultDMMesh);
- err = DMComplexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetHeightStratum(faultDMMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(faultDMMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
logger.stagePush("FaultFields");
@@ -1694,7 +1694,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(faultDMMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(faultDMMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(faultDMMesh, &coordVec);CHECK_PETSC_ERROR(err);
// Loop over cells in fault mesh, compute area
@@ -1707,10 +1707,10 @@
#else
const PetscScalar *coords = PETSC_NULL;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(faultDMMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(faultDMMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, c);
- err = DMComplexVecRestoreClosure(faultDMMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(faultDMMesh, coordSection, coordVec, c, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
// Get cell geometry information that depends on cell
@@ -1725,7 +1725,7 @@
areaCell[iBasis] += dArea;
} // for
} // for
- err = DMComplexVecSetClosure(faultDMMesh, areaSection, areaVec, c, &areaCell[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(faultDMMesh, areaSection, areaVec, c, &areaCell[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
PetscLogFlops(numQuadPts*(1+numBasis*2));
} // for
@@ -1982,7 +1982,7 @@
PetscErrorCode err;
assert(faultDMMesh);
- err = DMComplexGetHeightStratum(faultDMMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(faultDMMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
logger.stagePush("OutputFields");
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/LiuCosSlipFn.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -92,7 +92,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
logger.stagePush("Fault");
@@ -173,7 +173,7 @@
PetscSection coordSection;
Vec coordVec;
PetscScalar *coordArray;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -267,7 +267,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Get sections
const topology::Field<topology::SubMesh>& finalSlip = _parameters->get("final slip");
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/StepSlipFn.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -92,7 +92,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
delete _parameters; _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
assert(0 != _parameters);
@@ -156,7 +156,7 @@
PetscSection coordSection;
Vec coordVec;
PetscScalar *coordArray;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -233,7 +233,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Get sections
const topology::Field<topology::SubMesh>& finalSlip = _parameters->get("final slip");
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/TimeHistorySlipFn.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -98,7 +98,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
delete _parameters; _parameters = new topology::Fields<topology::Field<topology::SubMesh> >(faultMesh);
assert(0 != _parameters);
@@ -162,7 +162,7 @@
PetscSection coordSection;
Vec coordVec;
PetscScalar *coordArray;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -242,7 +242,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Get sections
const topology::Field<topology::SubMesh>& finalSlip = _parameters->get("slip amplitude");
Modified: short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/faults/TractPerturbation.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -262,7 +262,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const spatialdata::geocoords::CoordSys* cs = _parameters->mesh().coordsys();
assert(cs);
@@ -464,7 +464,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const spatialdata::geocoords::CoordSys* cs = _parameters->mesh().coordsys();
assert(cs);
@@ -481,7 +481,7 @@
PetscSection coordSection;
Vec coordVec;
PetscScalar *coordArray;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
Modified: short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicit.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicit.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicit.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -188,7 +188,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -215,7 +215,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -250,10 +250,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, cell);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
#if defined(DETAILED_EVENT_LOGGING)
_logger->eventEnd(geometryEvent);
@@ -274,9 +274,9 @@
// Restrict input fields to cell
const PetscScalar *accArray, *velArray, *dispTArray;
PetscInt accSize, velSize, dispTSize;
- err = DMComplexVecGetClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecGetClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
assert(velSize == accSize);
assert(dispTSize == accSize);
@@ -350,9 +350,9 @@
// Numerical damping. Compute displacements adjusted by velocity
// times normalized viscosity.
for(PetscInt i = 0; i < dispTSize; ++i) {dispAdjCell[i] = dispTArray[i] + viscosity * velArray[i];}
- err = DMComplexVecRestoreClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecRestoreClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
// Compute B(transpose) * sigma, first computing strains
calcTotalStrainFn(&strainCell, basisDeriv, dispAdjCell, numBasis, numQuadPts);
@@ -372,7 +372,7 @@
#endif
// Assemble cell contribution into field
- err = DMComplexVecSetClosure(dmMesh, residualSection, residualVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, residualSection, residualVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
#if defined(DETAILED_EVENT_LOGGING)
_logger->eventEnd(updateEvent);
@@ -440,7 +440,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -457,7 +457,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -477,10 +477,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, cell);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
#if defined(DETAILED_EVENT_LOGGING)
@@ -531,7 +531,7 @@
#endif
// Assemble cell contribution into lumped matrix.
- err = DMComplexVecSetClosure(dmMesh, jacSection, jacVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, jacSection, jacVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
#if defined(DETAILED_EVENT_LOGGING)
_logger->eventEnd(updateEvent);
Modified: short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicitLgDeform.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicitLgDeform.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicitLgDeform.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -185,7 +185,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -212,7 +212,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -242,10 +242,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, cell);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
// Get state variables for cell.
@@ -257,10 +257,10 @@
// Restrict input fields to cell
const PetscScalar *accArray, *velArray, *dispTArray;
PetscInt accSize, velSize, dispTSize;
- err = DMComplexVecGetClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecGetClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
assert(velSize == accSize);
- err = DMComplexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
assert(dispTSize == accSize);
// Get cell geometry information that depends on cell
@@ -326,10 +326,10 @@
for (PetscInt i = 0; i < dispTSize; ++i) {
dispAdjCell[i] = dispTArray[i] + viscosity * velArray[i];
} // for
- err = DMComplexVecRestoreClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecRestoreClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
// Compute B(transpose) * sigma, first computing strains
_calcDeformation(&deformCell, basisDeriv, coordinatesCell, dispAdjCell, numBasis, numQuadPts, spaceDim);
@@ -339,7 +339,7 @@
CALL_MEMBER_FN(*this, elasticityResidualFn)(stressCell, dispAdjCell);
// Assemble cell contribution into field
- err = DMComplexVecSetClosure(dmMesh, residualSection, residualVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, residualSection, residualVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
} // for
err = ISRestoreIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
err = ISDestroy(&cellIS);CHECK_PETSC_ERROR(err);
@@ -401,7 +401,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -417,7 +417,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -433,10 +433,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, cell);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
// Get state variables for cell.
@@ -472,7 +472,7 @@
_lumpCellMatrix();
// Assemble cell contribution into lumped matrix.
- err = DMComplexVecSetClosure(dmMesh, jacSection, jacVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, jacSection, jacVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
} // for
err = ISRestoreIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
err = ISDestroy(&cellIS);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicitTet4.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicitTet4.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicitTet4.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -174,7 +174,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -201,7 +201,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -234,9 +234,9 @@
// Restrict input fields to cell
const PetscScalar *accArray, *velArray, *dispTArray;
PetscInt accSize, velSize, dispTSize;
- err = DMComplexVecGetClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecGetClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
assert(velSize == accSize);
assert(dispTSize == accSize);
@@ -248,11 +248,11 @@
// Compute geometry information for current cell
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
const PylithScalar volume = _volume(coordinatesCell);
assert(volume > 0.0);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#if defined(DETAILED_EVENT_LOGGING)
_logger->eventEnd(geometryEvent);
@@ -314,9 +314,9 @@
// Numerical damping. Compute displacements adjusted by velocity
// times normalized viscosity.
for(PetscInt i = 0; i < dispTSize; ++i) {dispAdjCell[i] = dispTArray[i] + viscosity * velArray[i];}
- err = DMComplexVecRestoreClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecRestoreClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
// Compute B(transpose) * sigma, first computing strains
const PylithScalar x0 = coordinatesCell[0];
@@ -420,7 +420,7 @@
#endif
// Assemble cell contribution into field
- err = DMComplexVecSetClosure(dmMesh, residualSection, residualVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, residualSection, residualVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
#if defined(DETAILED_EVENT_LOGGING)
_logger->eventEnd(updateEvent);
@@ -488,7 +488,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -504,7 +504,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -521,11 +521,11 @@
#endif
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
const PylithScalar volume = _volume(coordinatesCell);
assert(volume > 0.0);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#if defined(DETAILED_EVENT_LOGGING)
_logger->eventEnd(geometryEvent);
@@ -552,7 +552,7 @@
#endif
// Assemble cell contribution into lumped matrix.
- err = DMComplexVecSetClosure(dmMesh, jacSection, jacVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, jacSection, jacVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
#if defined(DETAILED_EVENT_LOGGING)
_logger->eventEnd(updateEvent);
Modified: short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicitTri3.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicitTri3.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityExplicitTri3.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -173,7 +173,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -200,7 +200,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -233,9 +233,9 @@
// Restrict input fields to cell
const PetscScalar *accArray, *velArray, *dispTArray;
PetscInt accSize, velSize, dispTSize;
- err = DMComplexVecGetClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecGetClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
assert(velSize == accSize);
assert(dispTSize == accSize);
@@ -247,11 +247,11 @@
// Compute geometry information for current cell
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
const PylithScalar area = _area(coordinatesCell);
assert(area > 0.0);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#if defined(DETAILED_EVENT_LOGGING)
_logger->eventEnd(geometryEvent);
@@ -313,9 +313,9 @@
// Numerical damping. Compute displacements adjusted by velocity
// times normalized viscosity.
for(PetscInt i = 0; i < dispTSize; ++i) {dispAdjCell[i] = dispTArray[i] + viscosity * velArray[i];}
- err = DMComplexVecRestoreClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecRestoreClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, accSection, accVec, cell, &accSize, &accArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, velSection, velVec, cell, &velSize, &velArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
// Compute B(transpose) * sigma, first computing strains
const PylithScalar x0 = coordinatesCell[0];
@@ -369,7 +369,7 @@
#endif
// Assemble cell contribution into field
- err = DMComplexVecSetClosure(dmMesh, residualSection, residualVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, residualSection, residualVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
#if defined(DETAILED_EVENT_LOGGING)
_logger->eventEnd(updateEvent);
@@ -437,7 +437,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -453,7 +453,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -470,11 +470,11 @@
#endif
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
const PylithScalar area = _area(coordinatesCell);
assert(area > 0.0);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#if defined(DETAILED_EVENT_LOGGING)
_logger->eventEnd(geometryEvent);
@@ -500,7 +500,7 @@
#endif
// Assemble cell contribution into lumped matrix.
- err = DMComplexVecSetClosure(dmMesh, jacSection, jacVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, jacSection, jacVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
#if defined(DETAILED_EVENT_LOGGING)
_logger->eventEnd(updateEvent);
Modified: short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityImplicit.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityImplicit.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityImplicit.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -171,7 +171,7 @@
const PetscInt *cells;
PetscInt numCells;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -193,7 +193,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
#endif
@@ -216,10 +216,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, cell);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
// Get state variables for cell.
@@ -231,8 +231,8 @@
// Restrict input fields to cell
const PetscScalar *dispTArray, *dispTIncrArray;
PetscInt dispTSize, dispTIncrSize;
- err = DMComplexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecGetClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
assert(dispTSize == dispTIncrSize);
// Get cell geometry information that depends on cell
@@ -243,8 +243,8 @@
// Compute current estimate of displacement at time t+dt using solution increment.
for(PetscInt i = 0; i < dispTSize; ++i) {dispTpdtCell[i] = dispTArray[i] + dispTIncrArray[i];}
- err = DMComplexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecRestoreClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
// Compute body force vector if gravity is being used.
if (0 != _gravityField) {
@@ -288,7 +288,7 @@
}
#endif
// Assemble cell contribution into field
- err = DMComplexVecSetClosure(dmMesh, residualSection, residualVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, residualSection, residualVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
}
err = ISRestoreIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
err = ISDestroy(&cellIS);CHECK_PETSC_ERROR(err);
@@ -369,7 +369,7 @@
PetscInt numCells;
assert(dmMesh);
const int materialId = _material->id();
- err = DMComplexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -395,7 +395,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -411,10 +411,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, cell);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
// Get physical properties and state variables for cell.
@@ -426,8 +426,8 @@
// Restrict input fields to cell
const PetscScalar *dispTArray, *dispTIncrArray;
PetscInt dispTSize, dispTIncrSize;
- err = DMComplexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecGetClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
assert(dispTSize == dispTIncrSize);
// Get cell geometry information that depends on cell
@@ -437,8 +437,8 @@
// Compute current estimate of displacement at time t+dt using solution increment.
for(PetscInt i = 0; i < dispTSize; ++i) {dispTpdtCell[i] = dispTArray[i] + dispTIncrArray[i];}
- err = DMComplexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecRestoreClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
// Compute strains
calcTotalStrainFn(&strainCell, basisDeriv, dispTpdtCell, numBasis, numQuadPts);
@@ -481,7 +481,7 @@
// Assemble cell contribution into PETSc matrix.
// Notice that we are using the default sections
- err = DMComplexMatSetClosure(dmMesh, dispTSection, PETSC_NULL, jacobianMat, cell, &_cellMatrix[0], ADD_VALUES);
+ err = DMPlexMatSetClosure(dmMesh, dispTSection, PETSC_NULL, jacobianMat, cell, &_cellMatrix[0], ADD_VALUES);
CHECK_PETSC_ERROR_MSG(err, "Update to PETSc Mat failed.");
} // for
err = ISRestoreIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityImplicitLgDeform.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityImplicitLgDeform.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/feassemble/ElasticityImplicitLgDeform.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -167,7 +167,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -188,7 +188,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -210,10 +210,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, cell);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
// Get state variables for cell.
@@ -225,8 +225,8 @@
// Restrict input fields to cell
const PetscScalar *dispTArray, *dispTIncrArray;
PetscInt dispTSize, dispTIncrSize;
- err = DMComplexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecGetClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
assert(dispTSize == dispTIncrSize);
// Get cell geometry information that depends on cell
@@ -238,8 +238,8 @@
// Compute current estimate of displacement at time t+dt using
// solution increment.
for(PetscInt i = 0; i < dispTSize; ++i) {dispTpdtCell[i] = dispTArray[i] + dispTIncrArray[i];}
- err = DMComplexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecRestoreClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
// Compute body force vector if gravity is being used.
if (0 != _gravityField) {
@@ -290,7 +290,7 @@
}
#endif
// Assemble cell contribution into field
- err = DMComplexVecSetClosure(dmMesh, residualSection, residualVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, residualSection, residualVec, cell, &_cellVector[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
} // for
err = ISRestoreIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
err = ISDestroy(&cellIS);CHECK_PETSC_ERROR(err);
@@ -376,7 +376,7 @@
assert(dmMesh);
const int materialId = _material->id();
- err = DMComplexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -402,7 +402,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
@@ -418,10 +418,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, cell);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
// Get state variables for cell.
@@ -433,8 +433,8 @@
// Restrict input fields to cell
const PetscScalar *dispTArray, *dispTIncrArray;
PetscInt dispTSize, dispTIncrSize;
- err = DMComplexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecGetClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
assert(dispTSize == dispTIncrSize);
// Get cell geometry information that depends on cell
@@ -445,8 +445,8 @@
// Compute current estimate of displacement at time t+dt using
// solution increment.
for(PetscInt i = 0; i < dispTSize; ++i) {dispTpdtCell[i] = dispTArray[i] + dispTIncrArray[i];}
- err = DMComplexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
- err = DMComplexVecRestoreClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, dispTIncrSection, dispTIncrVec, cell, &dispTIncrSize, &dispTIncrArray);CHECK_PETSC_ERROR(err);
// Compute deformation tensor, strains, and stresses
_calcDeformation(&deformCell, basisDeriv, coordinatesCell, dispTpdtCell,
@@ -495,7 +495,7 @@
} // if
// Assemble cell contribution into PETSc matrix.
- err = DMComplexMatSetClosure(dmMesh, dispTSection, PETSC_NULL, jacobianMat, cell, &_cellMatrix[0], ADD_VALUES);
+ err = DMPlexMatSetClosure(dmMesh, dispTSection, PETSC_NULL, jacobianMat, cell, &_cellMatrix[0], ADD_VALUES);
CHECK_PETSC_ERROR_MSG(err, "Update to PETSc Mat failed.");
} // for
Modified: short/3D/PyLith/trunk/libsrc/pylith/feassemble/IntegratorElasticity.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/feassemble/IntegratorElasticity.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/feassemble/IntegratorElasticity.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -188,7 +188,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -203,7 +203,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
#endif
@@ -217,10 +217,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, cell);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
// Get physical properties and state variables for cell.
@@ -229,9 +229,9 @@
// Restrict input fields to cell
const PetscScalar *dispTArray;
PetscInt dispTSize;
- err = DMComplexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < dispTSize; ++i) {dispTCell[i] = dispTArray[i];}
- err = DMComplexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
// Get cell geometry information that depends on cell
const scalar_array& basisDeriv = _quadrature->basisDeriv();
@@ -287,7 +287,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -295,7 +295,7 @@
const PetscInt cell = cells[c];
PetscInt cellNumCorners;
- err = DMComplexGetConeSize(dmMesh, cell, &cellNumCorners);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetConeSize(dmMesh, cell, &cellNumCorners);CHECK_PETSC_ERROR(err);
if (numCorners != cellNumCorners) {
std::ostringstream msg;
msg << "Quadrature is incompatible with cell in material '"
@@ -474,7 +474,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
int_array cellsTmp(cells, numCells);
@@ -550,7 +550,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -565,7 +565,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
#endif
@@ -583,18 +583,18 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
_quadrature->computeGeometry(coordinatesCell, cell);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
// Restrict input fields to cell
const PetscScalar *dispTArray;
PetscInt dispTSize;
- err = DMComplexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < dispTSize; ++i) {dispTCell[i] = dispTArray[i];}
- err = DMComplexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, dispTSection, dispTVec, cell, &dispTSize, &dispTArray);CHECK_PETSC_ERROR(err);
// Get cell geometry information that depends on cell
const scalar_array& basisDeriv = _quadrature->basisDeriv();
@@ -603,11 +603,11 @@
calcTotalStrainFn(&strainCell, basisDeriv, dispTCell, numBasis, numQuadPts);
if (!calcStress) {
- err = DMComplexVecSetClosure(dmMesh, fieldSection, fieldVec, cell, &strainCell[0], INSERT_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, fieldSection, fieldVec, cell, &strainCell[0], INSERT_VALUES);CHECK_PETSC_ERROR(err);
} else {
_material->retrievePropsAndVars(cell);
stressCell = _material->calcStress(strainCell);
- err = DMComplexVecSetClosure(dmMesh, fieldSection, fieldVec, cell, &stressCell[0], INSERT_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, fieldSection, fieldVec, cell, &stressCell[0], INSERT_VALUES);CHECK_PETSC_ERROR(err);
} // else
} // for
err = ISRestoreIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -643,7 +643,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _material->id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -658,13 +658,13 @@
PetscInt fieldSize;
const PetscScalar *fieldArray;
- err = DMComplexVecGetClosure(dmMesh, fieldSection, fieldVec, cell, &fieldSize, &fieldArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, fieldSection, fieldVec, cell, &fieldSize, &fieldArray);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < fieldSize; ++i) {strainCell[i] = fieldArray[i];}
- err = DMComplexVecRestoreClosure(dmMesh, fieldSection, fieldVec, cell, &fieldSize, &fieldArray);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, fieldSection, fieldVec, cell, &fieldSize, &fieldArray);CHECK_PETSC_ERROR(err);
_material->retrievePropsAndVars(cell);
stressCell = _material->calcStress(strainCell);
- err = DMComplexVecSetClosure(dmMesh, fieldSection, PETSC_NULL, cell, &stressCell[0], INSERT_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, fieldSection, PETSC_NULL, cell, &stressCell[0], INSERT_VALUES);CHECK_PETSC_ERROR(err);
} // for
err = ISRestoreIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
err = ISDestroy(&cellIS);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/libsrc/pylith/materials/ElasticMaterial.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/materials/ElasticMaterial.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/materials/ElasticMaterial.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -287,7 +287,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -578,7 +578,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -586,7 +586,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
#endif
@@ -654,10 +654,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
quadrature->computeGeometry(coordinatesCell, cell);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
// Dimensionalize coordinates for querying
@@ -687,7 +687,7 @@
_normalizer->nondimensionalize(&stressCell[0], stressCell.size(),
pressureScale);
- err = DMComplexVecSetClosure(dmMesh, initialStressSection, initialStressVec, cell, &stressCell[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, initialStressSection, initialStressVec, cell, &stressCell[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
} // for
// Close databases
@@ -731,7 +731,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", id(), &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", id(), &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -739,7 +739,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
Vec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
#endif
@@ -807,10 +807,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
quadrature->computeGeometry(coordinatesCell, cell);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
// Dimensionalize coordinates for querying
@@ -836,7 +836,7 @@
} // if
} // for
- err = DMComplexVecSetClosure(dmMesh, initialStrainSection, initialStrainVec, cell, &strainCell[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, initialStrainSection, initialStrainVec, cell, &strainCell[0], ADD_VALUES);CHECK_PETSC_ERROR(err);
} // for
// Close databases
Modified: short/3D/PyLith/trunk/libsrc/pylith/materials/Material.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/materials/Material.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/materials/Material.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -131,7 +131,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _id, &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _id, &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
const spatialdata::geocoords::CoordSys* cs = mesh.coordsys();
@@ -154,7 +154,7 @@
scalar_array coordinatesCell(numBasis*spaceDim);
PetscSection coordSection;
PetscVec coordVec;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
assert(coordSection);assert(coordVec);
#endif
@@ -221,10 +221,10 @@
#else
const PetscScalar *coords;
PetscInt coordsSize;
- err = DMComplexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
for(PetscInt i = 0; i < coordsSize; ++i) {coordinatesCell[i] = coords[i];}
quadrature->computeGeometry(coordinatesCell, cell);
- err = DMComplexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordSection, coordVec, cell, &coordsSize, &coords);CHECK_PETSC_ERROR(err);
#endif
const scalar_array& quadPtsNonDim = quadrature->quadPts();
@@ -373,7 +373,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", _id, &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", _id, &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
@@ -409,7 +409,7 @@
err = PetscSectionGetChart(fieldSection, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
if (pEnd < 0) {
- err = DMComplexGetHeightStratum(dmMesh, 0, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(fieldSection, pStart, pEnd);CHECK_PETSC_ERROR(err);
} else {
// check fiber dimension
Modified: short/3D/PyLith/trunk/libsrc/pylith/meshio/CellFilterAvg.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/meshio/CellFilterAvg.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/meshio/CellFilterAvg.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -106,14 +106,14 @@
if (!label) {
PetscInt cMax;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetVTKBounds(dmMesh, &cMax, PETSC_NULL);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetVTKBounds(dmMesh, &cMax, PETSC_NULL);CHECK_PETSC_ERROR(err);
if (cMax >= 0) {cEnd = PetscMin(cEnd, cMax);}
numCells = cEnd - cStart;
} else {
const PetscInt *cells;
- err = DMComplexGetStratumIS(dmMesh, label, 1, &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, label, 1, &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
cStart = cells[0];
Modified: short/3D/PyLith/trunk/libsrc/pylith/meshio/DataWriterHDF5.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/meshio/DataWriterHDF5.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/meshio/DataWriterHDF5.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -112,7 +112,7 @@
DM dmCoord;
PetscReal lengthScale;
- err = DMComplexGetScale(dmMesh, PETSC_UNIT_LENGTH, &lengthScale);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetScale(dmMesh, PETSC_UNIT_LENGTH, &lengthScale);CHECK_PETSC_ERROR(err);
err = DMGetCoordinateDM(dmMesh, &dmCoord);CHECK_PETSC_ERROR(err);
topology::Field<mesh_type> coordinates(mesh, dmCoord, topology::FieldBase::Metadata());
coordinates.label("vertices");
@@ -131,11 +131,11 @@
PetscInt vStart, vEnd, vMax, verticesSize, dim, dimLocal = 0;
/* TODO Get rid of this and use the createScatterWithBC(numbering) code */
- err = DMComplexGetScale(dmMesh, PETSC_UNIT_LENGTH, &lengthScale);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetScale(dmMesh, PETSC_UNIT_LENGTH, &lengthScale);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordinates);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetVTKBounds(dmMesh, PETSC_NULL, &vMax);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetVTKBounds(dmMesh, PETSC_NULL, &vMax);CHECK_PETSC_ERROR(err);
if (vMax >= 0) {vEnd = PetscMin(vEnd, vMax);}
for(PetscInt vertex = vStart; vertex < vEnd; ++vertex) {
err = PetscSectionGetDof(coordSection, vertex, &dimLocal);CHECK_PETSC_ERROR(err);
@@ -192,22 +192,22 @@
#endif
PetscInt cStart, cEnd, cMax, dof, conesSize, numCorners, numCornersLocal = 0;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetVTKBounds(dmMesh, &cMax, PETSC_NULL);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetVTKBounds(dmMesh, &cMax, PETSC_NULL);CHECK_PETSC_ERROR(err);
if (cMax >= 0) {cEnd = PetscMin(cEnd, cMax);}
for(PetscInt cell = cStart; cell < cEnd; ++cell) {
PetscInt *closure = PETSC_NULL;
PetscInt closureSize, v;
- err = DMComplexGetTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
numCornersLocal = 0;
for (v = 0; v < closureSize*2; v += 2) {
if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
++numCornersLocal;
}
}
- err = DMComplexRestoreTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexRestoreTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
if (numCornersLocal) break;
}
err = MPI_Allreduce(&numCornersLocal, &numCorners, 1, MPIU_INT, MPI_MAX, mesh.comm());CHECK_PETSC_ERROR(err);
@@ -216,7 +216,7 @@
for(PetscInt cell = cStart; cell < cEnd; ++cell) {
PetscInt value;
- err = DMComplexGetLabelValue(dmMesh, label, cell, &value);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetLabelValue(dmMesh, label, cell, &value);CHECK_PETSC_ERROR(err);
if (value == labelId) ++conesSize;
}
conesSize *= numCorners;
@@ -230,8 +230,8 @@
PetscVec cellVec;
PetscScalar *vertices;
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexGetVertexNumbering(dmMesh, &globalVertexNumbers);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetVertexNumbering(dmMesh, &globalVertexNumbers);CHECK_PETSC_ERROR(err);
if (subpointMap) {err = ISGetIndices(subpointMap, &gpoints);CHECK_PETSC_ERROR(err);}
err = ISGetIndices(globalVertexNumbers, &gvertex);CHECK_PETSC_ERROR(err);
err = VecCreate(mesh.comm(), &cellVec);CHECK_PETSC_ERROR(err);
@@ -247,10 +247,10 @@
if (label) {
PetscInt value;
- err = DMComplexGetLabelValue(dmMesh, label, cell, &value);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetLabelValue(dmMesh, label, cell, &value);CHECK_PETSC_ERROR(err);
if (value != labelId) continue;
}
- err = DMComplexGetTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
for(p = 0; p < closureSize*2; p += 2) {
if ((closure[p] >= vStart) && (closure[p] < vEnd)) {
//const PetscInt gv = gpoints ? gpoints[closure[p]] : gvertex[closure[p] - vStart];
@@ -258,7 +258,7 @@
vertices[v++] = gv < 0 ? -(gv+1) : gv;
}
}
- err = DMComplexRestoreTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexRestoreTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
//assert(v == (cell-cStart+1)*numCorners);
}
CHKMEMA;
Modified: short/3D/PyLith/trunk/libsrc/pylith/meshio/DataWriterHDF5Ext.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/meshio/DataWriterHDF5Ext.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/meshio/DataWriterHDF5Ext.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -145,11 +145,11 @@
PetscInt vStart, vEnd, vMax, verticesSize, globalSize, dim, dimLocal = 0;
/* TODO Get rid of this and use the createScatterWithBC(numbering) code */
- err = DMComplexGetScale(dmMesh, PETSC_UNIT_LENGTH, &lengthScale);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetScale(dmMesh, PETSC_UNIT_LENGTH, &lengthScale);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordinates);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetVTKBounds(dmMesh, PETSC_NULL, &vMax);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetVTKBounds(dmMesh, PETSC_NULL, &vMax);CHECK_PETSC_ERROR(err);
if (vMax >= 0) {vEnd = PetscMin(vEnd, vMax);}
for(PetscInt vertex = vStart; vertex < vEnd; ++vertex) {
err = PetscSectionGetDof(coordSection, vertex, &dimLocal);CHECK_PETSC_ERROR(err);
@@ -277,22 +277,22 @@
#else
PetscInt cStart, cEnd, cMax, dof, conesSize, numCells, numCorners, numCornersLocal = 0;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetVTKBounds(dmMesh, &cMax, PETSC_NULL);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetVTKBounds(dmMesh, &cMax, PETSC_NULL);CHECK_PETSC_ERROR(err);
if (cMax >= 0) {cEnd = PetscMin(cEnd, cMax);}
for(PetscInt cell = cStart; cell < cEnd; ++cell) {
PetscInt *closure = PETSC_NULL;
PetscInt closureSize, v;
- err = DMComplexGetTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
numCornersLocal = 0;
for (v = 0; v < closureSize*2; v += 2) {
if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
++numCornersLocal;
}
}
- err = DMComplexRestoreTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexRestoreTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
if (numCornersLocal) break;
}
err = MPI_Allreduce(&numCornersLocal, &numCorners, 1, MPIU_INT, MPI_MAX, mesh.comm());CHECK_PETSC_ERROR(err);
@@ -301,7 +301,7 @@
for(PetscInt cell = cStart; cell < cEnd; ++cell) {
PetscInt value;
- err = DMComplexGetLabelValue(dmMesh, label, cell, &value);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetLabelValue(dmMesh, label, cell, &value);CHECK_PETSC_ERROR(err);
if (value == labelId) ++conesSize;
}
conesSize *= numCorners;
@@ -315,8 +315,8 @@
PetscVec cellVec, elemVec;
PetscScalar *vertices;
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexGetVertexNumbering(dmMesh, &globalVertexNumbers);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetVertexNumbering(dmMesh, &globalVertexNumbers);CHECK_PETSC_ERROR(err);
if (subpointMap) {err = ISGetIndices(subpointMap, &gpoints);CHECK_PETSC_ERROR(err);}
err = ISGetIndices(globalVertexNumbers, &gvertex);CHECK_PETSC_ERROR(err);
err = VecCreate(mesh.comm(), &cellVec);CHECK_PETSC_ERROR(err);
@@ -332,10 +332,10 @@
if (label) {
PetscInt value;
- err = DMComplexGetLabelValue(dmMesh, label, cell, &value);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetLabelValue(dmMesh, label, cell, &value);CHECK_PETSC_ERROR(err);
if (value != labelId) continue;
}
- err = DMComplexGetTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
for(p = 0; p < closureSize*2; p += 2) {
if ((closure[p] >= vStart) && (closure[p] < vEnd)) {
//const PetscInt gv = gpoints ? gpoints[closure[p]] : gvertex[closure[p] - vStart];
@@ -343,7 +343,7 @@
vertices[v++] = gv < 0 ? -(gv+1) : gv;
}
}
- err = DMComplexRestoreTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
+ err = DMPlexRestoreTransitiveClosure(dmMesh, cell, PETSC_TRUE, &closureSize, &closure);CHECK_PETSC_ERROR(err);
//assert(v == (cell-cStart+1)*numCorners);
}
CHKMEMA;
@@ -470,8 +470,8 @@
IS globalVertexNumbers;
assert(section);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, PETSC_NULL);CHECK_PETSC_ERROR(err);
- err = DMComplexGetVertexNumbering(dmMesh, &globalVertexNumbers);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, PETSC_NULL);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetVertexNumbering(dmMesh, &globalVertexNumbers);CHECK_PETSC_ERROR(err);
err = ISGetSize(globalVertexNumbers, &n);CHECK_PETSC_ERROR(err);
if (n > 0) {
const PetscInt *indices;
@@ -605,12 +605,12 @@
IS globalCellNumbers;
assert(section);
- err = DMComplexGetVTKCellHeight(dmMesh, &cellHeight);CHECK_PETSC_ERROR(err);
- err = DMComplexGetHeightStratum(dmMesh, cellHeight, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetVTKCellHeight(dmMesh, &cellHeight);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, cellHeight, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
if (label) {
IS pointIS;
- DMComplexGetStratumIS(dmMesh, label, labelId, &pointIS);CHECK_PETSC_ERROR(err);
+ DMPlexGetStratumIS(dmMesh, label, labelId, &pointIS);CHECK_PETSC_ERROR(err);
err = ISGetLocalSize(pointIS, &n);CHECK_PETSC_ERROR(err);
if (n > 0) {
const PetscInt *indices;
@@ -624,7 +624,7 @@
err = ISRestoreIndices(pointIS, &indices);CHECK_PETSC_ERROR(err);
}
} else {
- err = DMComplexGetCellNumbering(dmMesh, &globalCellNumbers);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCellNumbering(dmMesh, &globalCellNumbers);CHECK_PETSC_ERROR(err);
err = ISGetLocalSize(globalCellNumbers, &n);CHECK_PETSC_ERROR(err);
if (n > 0) {
const PetscInt *indices;
Modified: short/3D/PyLith/trunk/libsrc/pylith/meshio/DataWriterVTK.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/meshio/DataWriterVTK.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/meshio/DataWriterVTK.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -19,13 +19,13 @@
#include <portinfo>
#include <petscdmmesh_viewers.hh> // USES VTKViewer
-#include <petscdmcomplex.h>
+#include <petscdmplex.h>
#include <cassert> // USES assert()
#include <sstream> // USES std::ostringstream
#include <stdexcept> // USES std::runtime_error
-extern PetscErrorCode DMComplexVTKWriteAll(PetscObject odm, PetscViewer viewer);
+extern PetscErrorCode DMPlexVTKWriteAll(PetscObject odm, PetscViewer viewer);
// ----------------------------------------------------------------------
// Constructor
@@ -122,7 +122,7 @@
DM complexMesh = mesh.dmMesh();
if (complexMesh) {
- /* DMComplex */
+ /* DMPlex */
err = PetscViewerCreate(mesh.comm(), &_viewer);CHECK_PETSC_ERROR(err);
err = PetscViewerSetType(_viewer, PETSCVIEWERVTK);CHECK_PETSC_ERROR(err);
err = PetscViewerSetFormat(_viewer, PETSC_VIEWER_ASCII_VTK);CHECK_PETSC_ERROR(err);
@@ -137,7 +137,7 @@
const typename mesh_type::SieveMesh::label_sequence::const_iterator cEnd = cells->end();
for(typename mesh_type::SieveMesh::label_sequence::const_iterator c_iter = cBegin; c_iter != cEnd; ++c_iter) {
- err = DMComplexSetLabelValue(complexMesh, "vtk", *c_iter, 1);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(complexMesh, "vtk", *c_iter, 1);CHECK_PETSC_ERROR(err);
}
}
} else {
@@ -197,8 +197,8 @@
PetscErrorCode err;
if (complexMesh) {
- err = DMComplexClearLabelStratum(complexMesh, "vtk", 1);CHECK_PETSC_ERROR(err);
- err = DMComplexClearLabelStratum(complexMesh, "vtk", 2);CHECK_PETSC_ERROR(err);
+ err = DMPlexClearLabelStratum(complexMesh, "vtk", 1);CHECK_PETSC_ERROR(err);
+ err = DMPlexClearLabelStratum(complexMesh, "vtk", 2);CHECK_PETSC_ERROR(err);
}
#endif
PetscViewerDestroy(&_viewer); _viewer = 0;
@@ -222,7 +222,7 @@
DM complexMesh = mesh.dmMesh();
if (complexMesh) {
- /* DMComplex */
+ /* DMPlex */
PetscContainer c;
PetscSection s = field.petscSection();
Vec v = field.localVector();
@@ -230,7 +230,7 @@
/* Will change to just VecView() once I setup the vectors correctly (use VecSetOperation() to change the view method) */
PetscViewerVTKFieldType ft = field.vectorFieldType() != topology::FieldBase::VECTOR ? PETSC_VTK_POINT_FIELD : PETSC_VTK_POINT_VECTOR_FIELD;
- PetscErrorCode err = PetscViewerVTKAddField(_viewer, (PetscObject) complexMesh, DMComplexVTKWriteAll, ft, (PetscObject) v);CHECK_PETSC_ERROR(err);
+ PetscErrorCode err = PetscViewerVTKAddField(_viewer, (PetscObject) complexMesh, DMPlexVTKWriteAll, ft, (PetscObject) v);CHECK_PETSC_ERROR(err);
err = PetscObjectReference((PetscObject) v);CHECK_PETSC_ERROR(err); /* Needed because viewer destroys the Vec */
err = PetscContainerCreate(((PetscObject) v)->comm, &c);CHECK_PETSC_ERROR(err);
err = PetscContainerSetPointer(c, s);CHECK_PETSC_ERROR(err);
@@ -309,7 +309,7 @@
DM complexMesh = field.mesh().dmMesh();
if (complexMesh) {
- /* DMComplex */
+ /* DMPlex */
PetscContainer c;
PetscSection s = field.petscSection();
Vec v = field.localVector();
@@ -317,7 +317,7 @@
/* Will change to just VecView() once I setup the vectors correctly (use VecSetOperation() to change the view) */
PetscViewerVTKFieldType ft = field.vectorFieldType() != topology::FieldBase::VECTOR ? PETSC_VTK_CELL_FIELD : PETSC_VTK_CELL_VECTOR_FIELD;
- PetscErrorCode err = PetscViewerVTKAddField(_viewer, (PetscObject) complexMesh, DMComplexVTKWriteAll, ft, (PetscObject) v); CHECK_PETSC_ERROR(err);
+ PetscErrorCode err = PetscViewerVTKAddField(_viewer, (PetscObject) complexMesh, DMPlexVTKWriteAll, ft, (PetscObject) v); CHECK_PETSC_ERROR(err);
err = PetscObjectReference((PetscObject) v);CHECK_PETSC_ERROR(err); /* Needed because viewer destroys the Vec */
err = PetscContainerCreate(((PetscObject) v)->comm, &c);CHECK_PETSC_ERROR(err);
err = PetscContainerSetPointer(c, s);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/libsrc/pylith/meshio/MeshBuilder.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/meshio/MeshBuilder.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/meshio/MeshBuilder.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -79,7 +79,7 @@
mesh->createSieveMesh(dim);
const ALE::Obj<SieveMesh>& sieveMesh = mesh->sieveMesh();
assert(!sieveMesh.isNull());
- /* DMComplex */
+ /* DMPlex */
mesh->createDMMesh(dim);
DM complexMesh = mesh->dmMesh();
assert(complexMesh);
@@ -122,10 +122,10 @@
delete[] coneO; coneO = 0;
// Symmetrize to fill up supports
sieve->symmetrize();
- /* DMComplex */
- err = DMComplexSetChart(complexMesh, 0, numCells+numVertices);CHECK_PETSC_ERROR(err);
+ /* DMPlex */
+ err = DMPlexSetChart(complexMesh, 0, numCells+numVertices);CHECK_PETSC_ERROR(err);
for(PetscInt c = 0; c < numCells; ++c) {
- err = DMComplexSetConeSize(complexMesh, c, numCorners);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetConeSize(complexMesh, c, numCorners);CHECK_PETSC_ERROR(err);
}
err = DMSetUp(complexMesh);CHECK_PETSC_ERROR(err);
PetscInt *cone2 = new PetscInt[numCorners];
@@ -133,11 +133,11 @@
for(PetscInt v = 0; v < numCorners; ++v) {
cone2[v] = cells[c*numCorners+v]+numCells;
}
- err = DMComplexSetCone(complexMesh, c, cone2);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetCone(complexMesh, c, cone2);CHECK_PETSC_ERROR(err);
} // for
delete [] cone2; cone2 = 0;
- err = DMComplexSymmetrize(complexMesh);CHECK_PETSC_ERROR(err);
- err = DMComplexStratify(complexMesh);CHECK_PETSC_ERROR(err);
+ err = DMPlexSymmetrize(complexMesh);CHECK_PETSC_ERROR(err);
+ err = DMPlexStratify(complexMesh);CHECK_PETSC_ERROR(err);
} else {
// Same old thing
ALE::Obj<SieveFlexMesh::sieve_type> s =
@@ -191,13 +191,13 @@
logger.stagePush("MeshCoordinates");
ALE::SieveBuilder<SieveMesh>::buildCoordinates(sieveMesh, spaceDim,
&(*coordinates)[0]);
- /* DMComplex */
+ /* DMPlex */
PetscSection coordSection;
Vec coordVec;
PetscScalar *coords;
PetscInt coordSize;
- err = DMComplexGetCoordinateSection(complexMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(complexMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHECK_PETSC_ERROR(err);
for(PetscInt v = numCells; v < numCells+numVertices; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/libsrc/pylith/meshio/MeshIO.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/meshio/MeshIO.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/meshio/MeshIO.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -245,10 +245,10 @@
}
PetscInt cStart, cEnd;
- err = DMComplexGetHeightStratum(complexMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(complexMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
assert(numCells == cEnd - cStart);
for(PetscInt c = cStart; c < cEnd; ++c) {
- err = DMComplexSetLabelValue(complexMesh, "material-id", c, materialIds[c-cStart]);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(complexMesh, "material-id", c, materialIds[c-cStart]);CHECK_PETSC_ERROR(err);
}
} // if
logger.stagePop();
@@ -332,11 +332,11 @@
if (CELL == type) {
for(PetscInt p = 0; p < numPoints; ++p) {
- err = DMComplexSetLabelValue(complexMesh, name.c_str(), points[p], 1);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(complexMesh, name.c_str(), points[p], 1);CHECK_PETSC_ERROR(err);
}
} else if (VERTEX == type) {
for(PetscInt p = 0; p < numPoints; ++p) {
- err = DMComplexSetLabelValue(complexMesh, name.c_str(), numCells+points[p], 1);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(complexMesh, name.c_str(), numCells+points[p], 1);CHECK_PETSC_ERROR(err);
}
}
logger.stagePop();
Modified: short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnPoints.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnPoints.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnPoints.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -53,15 +53,7 @@
OutputManager<topology::Mesh, topology::Field<topology::Mesh> >::deallocate();
if (_interpolator) {
- assert(_mesh);
- const ALE::Obj<SieveMesh>& sieveMesh = _mesh->sieveMesh();
- DM dm;
- PetscErrorCode err = 0;
-
- err = DMMeshCreate(sieveMesh->comm(), &dm);CHECK_PETSC_ERROR(err);
- err = DMMeshSetMesh(dm, sieveMesh);CHECK_PETSC_ERROR(err);
- err = DMMeshInterpolationDestroy(dm, &_interpolator);CHECK_PETSC_ERROR(err);
- err = DMDestroy(&dm);CHECK_PETSC_ERROR(err);
+ PetscErrorCode err = err = DMInterpolationDestroy(&_interpolator);CHECK_PETSC_ERROR(err);
} // if
_mesh = 0; // :TODO: Use shared pointer
@@ -116,25 +108,22 @@
assert(csMesh->spaceDim() == spaceDim);
// Setup interpolator object
- DM dm;
+ DM dm = _mesh->dmMesh();
PetscErrorCode err = 0;
- assert(!_mesh->sieveMesh().isNull());
- err = DMMeshCreate(_mesh->sieveMesh()->comm(), &dm);CHECK_PETSC_ERROR(err);
- err = DMMeshSetMesh(dm, _mesh->sieveMesh());CHECK_PETSC_ERROR(err);
- err = DMMeshInterpolationCreate(dm, &_interpolator);CHECK_PETSC_ERROR(err);
+ assert(dm);
+ err = DMInterpolationCreate(((PetscObject) dm)->comm, &_interpolator);CHECK_PETSC_ERROR(err);
- err = DMMeshInterpolationSetDim(dm, spaceDim, _interpolator);CHECK_PETSC_ERROR(err);
+ err = DMInterpolationSetDim(_interpolator, spaceDim);CHECK_PETSC_ERROR(err);
- err = DMMeshInterpolationAddPoints(dm, numPoints, (PetscReal*)&pointsNondim[0], _interpolator);CHECK_PETSC_ERROR(err);
+ err = DMInterpolationAddPoints(_interpolator, numPoints, (PetscReal*) &pointsNondim[0]);CHECK_PETSC_ERROR(err);
const PetscBool pointsAllProcs = PETSC_TRUE;
- err = DMMeshInterpolationSetUp(dm, _interpolator, pointsAllProcs);CHECK_PETSC_ERROR(err);
- err = DMDestroy(&dm);CHECK_PETSC_ERROR(err);
+ err = DMInterpolationSetUp(_interpolator, dm, pointsAllProcs);CHECK_PETSC_ERROR(err);
// Create mesh corresponding to points.
const int meshDim = 0;
delete _pointsMesh; _pointsMesh = new topology::Mesh(meshDim);
- _pointsMesh->createSieveMesh(meshDim);
+ _pointsMesh->createDMMesh(meshDim);
assert(_pointsMesh);
const int numPointsLocal = _interpolator->n;
@@ -161,17 +150,6 @@
_pointsMesh->coordsys(_mesh->coordsys());
_pointsMesh->nondimensionalize(normalizer);
- // Create empty overlaps. MATT - IS THIS OKAY?
- assert(!_pointsMesh->sieveMesh().isNull());
- ALE::Obj<SieveSubMesh::send_overlap_type> sendOverlap = _pointsMesh->sieveMesh()->getSendOverlap();
- assert(!sendOverlap.isNull());
- ALE::Obj<SieveSubMesh::recv_overlap_type> recvOverlap = _pointsMesh->sieveMesh()->getRecvOverlap();
- assert(!recvOverlap.isNull());
- SieveMesh::renumbering_type emptyRenumbering;
- ALE::SetFromMap<SieveMesh::renumbering_type> emptyPoints(emptyRenumbering);
- ALE::OverlapBuilder<>::constructOverlap(emptyPoints, emptyRenumbering, sendOverlap, recvOverlap);
- _pointsMesh->sieveMesh()->setCalculatedOverlap(true);
-
#if 0 // DEBUGGING
_pointsMesh->view("POINTS MESH");
#endif
@@ -225,70 +203,57 @@
assert(_mesh);
assert(_fields);
- const ALE::Obj<SieveMesh>& pointsSieveMesh = _pointsMesh->sieveMesh();
- assert(!pointsSieveMesh.isNull());
- const ALE::Obj<SieveMesh::label_sequence>& vertices =
- pointsSieveMesh->depthStratum(0);
- assert(!vertices.isNull());
+ DM pointsDMMesh = _pointsMesh->dmMesh();
+ PetscInt pvStart, pvEnd;
+ PetscErrorCode err;
- const ALE::Obj<SieveMesh>& sieveMesh = _mesh->sieveMesh();
- assert(!sieveMesh.isNull());
- const std::string labelName =
- (sieveMesh->hasLabel("censored depth")) ? "censored depth" : "depth";
- assert(!sieveMesh->getLabelStratum(labelName, 0).isNull());
- assert(!field.section().isNull());
- int fiberDimLocal =
- (sieveMesh->getLabelStratum(labelName, 0)->size() > 0) ?
- field.section()->getFiberDimension(*sieveMesh->getLabelStratum(labelName, 0)->begin()) : 0;
- int fiberDim = 0;
- MPI_Allreduce(&fiberDimLocal, &fiberDim, 1, MPI_INT, MPI_MAX,
- field.mesh().comm());
+ assert(pointsDMMesh);
+ err = DMPlexGetDepthStratum(pointsDMMesh, 0, &pvStart, &pvEnd);CHECK_PETSC_ERROR(err);
+
+ DM dmMesh = field.dmMesh();
+ PetscInt vStart, vEnd;
+
+ assert(dmMesh);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ PetscSection section = field.petscSection();
+ PetscInt fiberDimLocal = 0;
+ PetscInt fiberDim = 0;
+
+ if (vEnd > vStart) {err = PetscSectionGetDof(section, vStart, &fiberDimLocal);CHECK_PETSC_ERROR(err);}
+ MPI_Allreduce(&fiberDimLocal, &fiberDim, 1, MPIU_INT, MPI_MAX, field.mesh().comm());
assert(fiberDim > 0);
// Create field if necessary for interpolated values or recreate
// field if mismatch in size between buffer and field.
ALE::MemoryLogger& logger = ALE::MemoryLogger::singleton();
logger.stagePush("Output");
- if (!_fields->hasField("buffer (interpolated)")) {
- _fields->add("buffer (interpolated)", field.label());
- } // if
+ ostringstream fieldName;
+ const char *context = field.label();
+ fieldName << context << " (interpolated)" << std::endl;
- topology::Field<topology::Mesh>& fieldInterp =
- _fields->get("buffer (interpolated)");
- if (fieldInterp.section().isNull() || vertices->size()*fiberDim != fieldInterp.sectionSize()) {
- fieldInterp.newSection(vertices, fiberDim);
- fieldInterp.allocate();
+ if (_fields->hasField(fieldName.str().c_str())) {
+ ostringstream msg;
+ msg << "Field " << fieldName << "already present in manager" << std::endl;
+ throw std::logic_error(msg.str());
} // if
- logger.stagePop();
+ _fields->add(fieldName.str().c_str(), field.label());
+ topology::Field<topology::Mesh>& fieldInterp = _fields->get(fieldName.str().c_str());
+ fieldInterp.newSection(topology::FieldBase::VERTICES_FIELD, fiberDim);
+ fieldInterp.allocate();
fieldInterp.zero();
fieldInterp.label(field.label());
fieldInterp.vectorFieldType(field.vectorFieldType());
fieldInterp.scale(field.scale());
+ logger.stagePop();
- const char* context = field.label();
fieldInterp.createScatter(*_pointsMesh, context);
PetscVec fieldInterpVec = fieldInterp.vector(context);
assert(fieldInterpVec);
-
- DM dm;
- SectionReal section;
- PetscErrorCode err = 0;
- err = DMMeshCreate(sieveMesh->comm(), &dm);CHECK_PETSC_ERROR(err);
- err = DMMeshSetMesh(dm, sieveMesh);CHECK_PETSC_ERROR(err);
- err = DMMeshInterpolationSetDof(dm, fiberDim,
- _interpolator);CHECK_PETSC_ERROR(err);
+ err = DMInterpolationSetDof(_interpolator, fiberDim);CHECK_PETSC_ERROR(err);
+ err = DMInterpolationEvaluate(_interpolator, dmMesh, field.localVector(), fieldInterpVec);CHECK_PETSC_ERROR(err);
- err = SectionRealCreate(sieveMesh->comm(), §ion);CHECK_PETSC_ERROR(err);
- err = SectionRealSetSection(section, field.section());CHECK_PETSC_ERROR(err);
- err = SectionRealSetBundle(section, sieveMesh);CHECK_PETSC_ERROR(err);
-
- err = DMMeshInterpolationEvaluate(dm, section, fieldInterpVec,
- _interpolator);CHECK_PETSC_ERROR(err);
- err = SectionRealDestroy(§ion);CHECK_PETSC_ERROR(err);
- err = DMDestroy(&dm);CHECK_PETSC_ERROR(err);
-
fieldInterp.scatterVectorToSection(context);
OutputManager<topology::Mesh, topology::Field<topology::Mesh> >::appendVertexField(t, fieldInterp, *_pointsMesh);
Modified: short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnPoints.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnPoints.hh 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/meshio/OutputSolnPoints.hh 2013-01-05 17:40:22 UTC (rev 21207)
@@ -134,7 +134,7 @@
topology::Mesh* _mesh; ///< Domain mesh.
topology::Mesh* _pointsMesh; ///< Mesh for points (no cells).
- PetscDMMeshInterpolationInfo _interpolator; ///< Field interpolator.
+ DMInterpolationInfo _interpolator; ///< Field interpolator.
}; // OutputSolnPoints
Modified: short/3D/PyLith/trunk/libsrc/pylith/meshio/VertexFilterVecNorm.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/meshio/VertexFilterVecNorm.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/meshio/VertexFilterVecNorm.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -81,7 +81,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
PetscSection sectionIn = fieldIn.petscSection();
Vec vecIn = fieldIn.localVector();
Modified: short/3D/PyLith/trunk/libsrc/pylith/problems/Implicit.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/problems/Implicit.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/problems/Implicit.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -71,7 +71,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
err = VecGetArray(dispIncrVec, &dispIncrArray);CHECK_PETSC_ERROR(err);
err = VecGetArray(velVec, &velArray);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
Modified: short/3D/PyLith/trunk/libsrc/pylith/problems/Solver.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/problems/Solver.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/problems/Solver.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -220,7 +220,7 @@
const bool separateComponents = formulation->splitFieldComponents();
assert(solutionSection);
- err = DMComplexGetDimension(dmMesh, &spaceDim);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDimension(dmMesh, &spaceDim);CHECK_PETSC_ERROR(err);
err = PetscSectionGetNumFields(solutionSection, &numFields);CHECK_PETSC_ERROR(err);
err = PCSetDM(*pc, dmMesh);CHECK_PETSC_ERROR(err);
@@ -293,8 +293,8 @@
PetscInt dim = spaceDim, vStart, vEnd;
PetscVec mode[6];
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordinateSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordinateSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordinateVec);CHECK_PETSC_ERROR(err);
assert(coordinateSection);assert(coordinateVec);
if (dim > 1) {
@@ -309,7 +309,7 @@
values[d] = 1.0;
err = VecSet(solutionVec, 0.0);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
- err = DMComplexVecSetClosure(dmMesh, solutionSection, solutionVec, v, values, INSERT_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, solutionSection, solutionVec, v, values, INSERT_VALUES);CHECK_PETSC_ERROR(err);
} // for
err = DMLocalToGlobalBegin(dmMesh, solutionVec, INSERT_VALUES, mode[d]);CHECK_PETSC_ERROR(err);
err = DMLocalToGlobalEnd(dmMesh, solutionVec, INSERT_VALUES, mode[d]);CHECK_PETSC_ERROR(err);
@@ -322,14 +322,14 @@
PetscScalar values[3] = {0.0, 0.0, 0.0};
const PetscScalar *coords;
- err = DMComplexVecGetClosure(dmMesh, coordinateSection, coordinateVec, v, PETSC_NULL, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecGetClosure(dmMesh, coordinateSection, coordinateVec, v, PETSC_NULL, &coords);CHECK_PETSC_ERROR(err);
for(int i = 0; i < dim; ++i) {
for(int j = 0; j < dim; ++j) {
values[j] += _epsilon(i, j, k)*coords[i];
} // for
} // for
- err = DMComplexVecRestoreClosure(dmMesh, coordinateSection, coordinateVec, v, PETSC_NULL, &coords);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, solutionSection, solutionVec, v, values, INSERT_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecRestoreClosure(dmMesh, coordinateSection, coordinateVec, v, PETSC_NULL, &coords);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, solutionSection, solutionVec, v, values, INSERT_VALUES);CHECK_PETSC_ERROR(err);
}
err = DMLocalToGlobalBegin(dmMesh, solutionVec, INSERT_VALUES, mode[d]);CHECK_PETSC_ERROR(err);
err = DMLocalToGlobalEnd(dmMesh, solutionVec, INSERT_VALUES, mode[d]);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/Distributor.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/Distributor.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/Distributor.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -65,7 +65,7 @@
newMesh->coordsys(origMesh.coordsys());
DM newDM;
- PetscErrorCode err = DMComplexDistribute(origMesh.dmMesh(), partitioner, 0, &newDM);CHECK_PETSC_ERROR(err);
+ PetscErrorCode err = DMPlexDistribute(origMesh.dmMesh(), partitioner, 0, &newDM);CHECK_PETSC_ERROR(err);
newMesh->setDMMesh(newDM);
if (0 == strcasecmp(partitioner, "")) {
if (0 == commRank) {
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/Field.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/Field.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/Field.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -46,7 +46,7 @@
PetscSection s;
PetscErrorCode err;
- err = DMComplexClone(dm, &_dm);CHECK_PETSC_ERROR(err);
+ err = DMPlexClone(dm, &_dm);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dm, &coordVec);CHECK_PETSC_ERROR(err);
if (coordVec) {
DM coordDM, newCoordDM;
@@ -86,7 +86,7 @@
PetscSection s;
PetscErrorCode err;
- err = DMComplexClone(dm, &_dm);CHECK_PETSC_ERROR(err);
+ err = DMPlexClone(dm, &_dm);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dm, &coordVec);CHECK_PETSC_ERROR(err);
if (coordVec) {
err = DMGetCoordinateDM(dm, &coordDM);CHECK_PETSC_ERROR(err);
@@ -256,7 +256,16 @@
int
pylith::topology::Field<mesh_type, section_type>::sectionSize(void) const
{ // sectionSize
- return _section.isNull() ? 0 : _section->size();
+ PetscInt size = 0;
+ PetscErrorCode err;
+
+ if (_dm) {
+ PetscSection s;
+
+ err = DMGetDefaultSection(_dm, &s);CHECK_PETSC_ERROR(err);
+ err = PetscSectionGetStorageSize(s, &size);CHECK_PETSC_ERROR(err);
+ }
+ return size;
} // sectionSize
// ----------------------------------------------------------------------
@@ -318,6 +327,8 @@
if (_dm) {
PetscSection s;
err = DMGetDefaultSection(_dm, &s);CHECK_PETSC_ERROR(err);
+ err = PetscSectionReset(s);CHECK_PETSC_ERROR(err);
+ err = DMSetDefaultGlobalSection(_dm, PETSC_NULL);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(s, pointMin, pointMax+1);CHECK_PETSC_ERROR(err);
for(typename label_sequence::const_iterator p_iter = points->begin(); p_iter != points->end(); ++p_iter) {
@@ -329,6 +340,8 @@
if (_dm) {
PetscSection s;
err = DMGetDefaultSection(_dm, &s);CHECK_PETSC_ERROR(err);
+ err = PetscSectionReset(s);CHECK_PETSC_ERROR(err);
+ err = DMSetDefaultGlobalSection(_dm, PETSC_NULL);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(s, 0, 0);CHECK_PETSC_ERROR(err);
}
}
@@ -374,6 +387,8 @@
if (_dm) {
PetscSection s;
err = DMGetDefaultSection(_dm, &s);CHECK_PETSC_ERROR(err);
+ err = PetscSectionReset(s);CHECK_PETSC_ERROR(err);
+ err = DMSetDefaultGlobalSection(_dm, PETSC_NULL);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(s, pointMin, pointMax+1);CHECK_PETSC_ERROR(err);
for (int i=0; i < npts; ++i) {
@@ -385,6 +400,8 @@
if (_dm) {
PetscSection s;
err = DMGetDefaultSection(_dm, &s);CHECK_PETSC_ERROR(err);
+ err = PetscSectionReset(s);CHECK_PETSC_ERROR(err);
+ err = DMSetDefaultGlobalSection(_dm, PETSC_NULL);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(s, 0, 0);CHECK_PETSC_ERROR(err);
}
}
@@ -408,22 +425,24 @@
switch(domain) {
case VERTICES_FIELD:
- err = DMComplexGetDepthStratum(_dm, stratum, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(_dm, stratum, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
break;
case CELLS_FIELD:
- err = DMComplexGetHeightStratum(_dm, stratum, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(_dm, stratum, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
break;
case FACES_FIELD:
- err = DMComplexGetHeightStratum(_dm, stratum+1, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(_dm, stratum+1, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
break;
case POINTS_FIELD:
- err = DMComplexGetChart(_dm, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetChart(_dm, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
break;
default:
std::cerr << "Unknown value for DomainEnum: " << domain << std::endl;
throw std::logic_error("Bad domain enum in Field.");
}
err = DMGetDefaultSection(_dm, &s);CHECK_PETSC_ERROR(err);
+ err = PetscSectionReset(s);CHECK_PETSC_ERROR(err);
+ err = DMSetDefaultGlobalSection(_dm, PETSC_NULL);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(s, pStart, pEnd);CHECK_PETSC_ERROR(err);
for(PetscInt p = pStart; p < pEnd; ++p) {
@@ -494,6 +513,8 @@
PetscErrorCode err;
err = DMGetDefaultSection(_dm, &s);CHECK_PETSC_ERROR(err);
+ err = PetscSectionReset(s);CHECK_PETSC_ERROR(err);
+ err = DMSetDefaultGlobalSection(_dm, PETSC_NULL);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(s, pStart, pEnd);CHECK_PETSC_ERROR(err);
for(PetscInt p = pStart; p < pEnd; ++p) {
err = PetscSectionSetDof(s, p, fiberDim);CHECK_PETSC_ERROR(err);
@@ -506,6 +527,8 @@
err = DMGetDefaultSection(src._dm, &srcs);CHECK_PETSC_ERROR(err);
err = DMGetDefaultSection(_dm, &s);CHECK_PETSC_ERROR(err);
+ err = PetscSectionReset(s);CHECK_PETSC_ERROR(err);
+ err = DMSetDefaultGlobalSection(_dm, PETSC_NULL);CHECK_PETSC_ERROR(err);
err = PetscSectionGetChart(srcs, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(s, pStart, pEnd);CHECK_PETSC_ERROR(err);
for(PetscInt p = pStart; p < pEnd; ++p) {
@@ -645,7 +668,7 @@
} // cloneSection
// ----------------------------------------------------------------------
-// Get DMComplex section.
+// Get DMPlex section.
template<typename mesh_type, typename section_type>
void
pylith::topology::Field<mesh_type, section_type>::dmSection(PetscSection *s, Vec *v) const {
@@ -659,7 +682,7 @@
if (numNormalCells+numCohesiveCells+numNormalVertices+numShadowVertices+numLagrangeVertices > 0) {
PetscInt numFields, numComp, pMax, pStart, pEnd, qStart, qEnd;
- err = DMComplexGetChart(_mesh.dmMesh(), PETSC_NULL, &pMax);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetChart(_mesh.dmMesh(), PETSC_NULL, &pMax);CHECK_PETSC_ERROR(err);
err = PetscSectionCreate(_mesh.sieveMesh()->comm(), s);CHECK_PETSC_ERROR(err);
err = PetscSectionGetNumFields(section, &numFields);CHECK_PETSC_ERROR(err);
if (numFields) {
@@ -851,7 +874,7 @@
err = PetscSectionGetDof(section, p, &dof);CHECK_PETSC_ERROR(err);
if (dof > 0) {
assert(dof <= maxDof);
- err = DMComplexVecSetClosure(_dm, section, _localVec, p, &values[0], INSERT_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(_dm, section, _localVec, p, &values[0], INSERT_VALUES);CHECK_PETSC_ERROR(err);
} // if
} // for
}
@@ -1505,7 +1528,7 @@
PetscSection section, newSection, gsection;
PetscSF sf;
- err = DMComplexClone(_dm, &sinfo.dm);CHECK_PETSC_ERROR(err);
+ err = DMPlexClone(_dm, &sinfo.dm);CHECK_PETSC_ERROR(err);
err = DMGetDefaultSection(_dm, §ion);CHECK_PETSC_ERROR(err);
err = PetscSectionClone(section, &newSection);CHECK_PETSC_ERROR(err);
err = DMSetDefaultSection(sinfo.dm, newSection);CHECK_PETSC_ERROR(err);
@@ -1558,13 +1581,13 @@
PetscSection section, newSection, gsection;
PetscSF sf;
PetscInt cEnd, cMax, vEnd, vMax;
- err = DMComplexGetHeightStratum(_dm, 0, PETSC_NULL, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(_dm, 0, PETSC_NULL, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetVTKBounds(_dm, &cMax, &vMax);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(_dm, 0, PETSC_NULL, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(_dm, 0, PETSC_NULL, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetVTKBounds(_dm, &cMax, &vMax);CHECK_PETSC_ERROR(err);
PetscInt excludeRanges[4] = {cMax, cEnd, vMax, vEnd};
PetscInt numExcludes = (cMax >= 0 ? 1 : 0) + (vMax >= 0 ? 1 : 0);
- err = DMComplexClone(_dm, &sinfo.dm);CHECK_PETSC_ERROR(err);
+ err = DMPlexClone(_dm, &sinfo.dm);CHECK_PETSC_ERROR(err);
err = DMGetDefaultSection(_dm, §ion);CHECK_PETSC_ERROR(err);
err = PetscSectionClone(section, &newSection);CHECK_PETSC_ERROR(err);
err = DMSetDefaultSection(sinfo.dm, newSection);CHECK_PETSC_ERROR(err);
@@ -1574,7 +1597,7 @@
} else {
DMLabel label;
- err = DMComplexGetLabel(sinfo.dm, labelName.c_str(), &label);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetLabel(sinfo.dm, labelName.c_str(), &label);CHECK_PETSC_ERROR(err);
err = PetscSectionCreateGlobalSectionLabel(section, sf, PETSC_TRUE, label, labelValue, &gsection);CHECK_PETSC_ERROR(err);
}
err = DMSetDefaultGlobalSection(sinfo.dm, gsection);CHECK_PETSC_ERROR(err);
@@ -1853,7 +1876,7 @@
// Right now, we assume that the section covers the entire chart
PetscInt pStart, pEnd;
- err = DMComplexGetChart(_dm, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetChart(_dm, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(section, pStart, pEnd);CHECK_PETSC_ERROR(err);
#endif
}
@@ -1869,16 +1892,16 @@
assert(_dm);
switch(domain) {
case VERTICES_FIELD:
- err = DMComplexGetDepthStratum(_dm, 0, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(_dm, 0, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
break;
case CELLS_FIELD:
- err = DMComplexGetHeightStratum(_dm, 0, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(_dm, 0, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
break;
case FACES_FIELD:
- err = DMComplexGetHeightStratum(_dm, 1, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(_dm, 1, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
break;
case POINTS_FIELD:
- err = DMComplexGetChart(_dm, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetChart(_dm, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
break;
default:
std::cerr << "Unknown value for DomainEnum: " << domain << std::endl;
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/Field.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/Field.hh 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/Field.hh 2013-01-05 17:40:22 UTC (rev 21207)
@@ -106,9 +106,9 @@
*/
const ALE::Obj<section_type>& section(void) const;
- /** Get DMComplex section.
+ /** Get DMPlex section.
*
- * @returns DMComplex section.
+ * @returns DMPlex section.
*/
void dmSection(PetscSection *s, Vec *v) const;
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -89,15 +89,15 @@
} // createSieveMesh
// ----------------------------------------------------------------------
-// Create DMComplex mesh.
+// Create DMPlex mesh.
void
pylith::topology::Mesh::createDMMesh(const int dim)
{ // createDMMesh
PetscErrorCode err;
err = DMDestroy(&_newMesh);CHECK_PETSC_ERROR(err);
err = DMCreate(_comm, &_newMesh);CHECK_PETSC_ERROR(err);
- err = DMSetType(_newMesh, DMCOMPLEX);CHECK_PETSC_ERROR(err);
- err = DMComplexSetDimension(_newMesh, dim);CHECK_PETSC_ERROR(err);
+ err = DMSetType(_newMesh, DMPLEX);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetDimension(_newMesh, dim);CHECK_PETSC_ERROR(err);
err = PetscObjectSetName((PetscObject) _newMesh, "domain");CHECK_PETSC_ERROR(err);
} // createDMMesh
@@ -148,7 +148,7 @@
// There does not seem to be an advantage to calling nondimensionalize()
err = VecScale(coordVec, 1.0/lengthScale);CHECK_PETSC_ERROR(err);
- err = DMComplexSetScale(_newMesh, PETSC_UNIT_LENGTH, lengthScale);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetScale(_newMesh, PETSC_UNIT_LENGTH, lengthScale);CHECK_PETSC_ERROR(err);
PylithScalar coordsVertex[3];
for (SieveMesh::label_sequence::iterator v_iter=verticesBegin;
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.hh 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/Mesh.hh 2013-01-05 17:40:22 UTC (rev 21207)
@@ -107,21 +107,21 @@
*/
ALE::Obj<SieveMesh>& sieveMesh(void);
- /** Create DMComplex mesh.
+ /** Create DMPlex mesh.
*
* @param dim Dimension associated with mesh cells.
*/
void createDMMesh(const int dim=3);
- /** Get DMComplex mesh.
+ /** Get DMPlex mesh.
*
- * @returns DMComplex mesh.
+ * @returns DMPlex mesh.
*/
DM dmMesh(void) const;
- /** Set DMComplex mesh.
+ /** Set DMPlex mesh.
*
- * @param DMComplex mesh.
+ * @param DMPlex mesh.
*/
void setDMMesh(DM dm);
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.cc
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -87,7 +87,7 @@
PetscBool hasLabel;
PetscErrorCode err;
- err = DMComplexHasLabel(dmMesh, label, &hasLabel);CHECK_PETSC_ERROR(err);
+ err = DMPlexHasLabel(dmMesh, label, &hasLabel);CHECK_PETSC_ERROR(err);
if (!hasLabel) {
std::ostringstream msg;
msg << "Could not find group of points '" << label << "' in DM mesh.";
@@ -112,7 +112,7 @@
meshSieveMesh->getRealSection("coordinates_dimensioned"));
/* TODO: Add creation of pointSF for submesh */
- err = DMComplexCreateSubmesh(dmMesh, label, &_newMesh);CHECK_PETSC_ERROR(err);
+ err = DMPlexCreateSubmesh(dmMesh, label, &_newMesh);CHECK_PETSC_ERROR(err);
// Create the parallel overlap
const ALE::Obj<SieveMesh::sieve_type>& sieve = _mesh->getSieve();
Modified: short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.hh
===================================================================
--- short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.hh 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/libsrc/pylith/topology/SubMesh.hh 2013-01-05 17:40:22 UTC (rev 21207)
@@ -96,15 +96,15 @@
*/
ALE::Obj<SieveMesh>& sieveMesh(void);
- /** Get DMComplex mesh.
+ /** Get DMPlex mesh.
*
- * @returns DMComplex mesh.
+ * @returns DMPlex mesh.
*/
DM dmMesh(void) const;
- /** Set DMComplex mesh.
+ /** Set DMPlex mesh.
*
- * @param DMComplex mesh.
+ * @param DMPlex mesh.
*/
void setDMMesh(DM dm);
Modified: short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/bc/TestAbsorbingDampers.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -108,8 +108,8 @@
// Check boundary mesh
CPPUNIT_ASSERT(subMesh);
- err = DMComplexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(subMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(subMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const int cellDim = boundaryMesh.dimension();
const int numCorners = _data->numCorners;
@@ -128,9 +128,9 @@
PetscInt numCorners;
// Assume non-interpolated mesh
- err = DMComplexGetConeSize(subMesh, c, &numCorners);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetConeSize(subMesh, c, &numCorners);CHECK_PETSC_ERROR(err);
CPPUNIT_ASSERT_EQUAL(_data->numCorners, numCorners);
- err = DMComplexGetCone(subMesh, c, &cone);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCone(subMesh, c, &cone);CHECK_PETSC_ERROR(err);
for(PetscInt p = 0; p < numCorners; ++p, ++dp) {
CPPUNIT_ASSERT_EQUAL(_data->cells[dp], cone[p]);
}
@@ -188,7 +188,7 @@
const PylithScalar* valsE = _data->valsResidual;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const int totalNumVertices = vEnd - vStart;
const int sizeE = _data->spaceDim * totalNumVertices;
@@ -241,7 +241,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const PylithScalar* valsE = _data->valsJacobian;
const int totalNumVertices = vEnd - vStart;
const int nrowsE = totalNumVertices * _data->spaceDim;
@@ -317,7 +317,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const PylithScalar* valsMatrixE = _data->valsJacobian;
const int totalNumVertices = vEnd - vStart;
const int sizeE = totalNumVertices * _data->spaceDim;
@@ -428,7 +428,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
residual.newSection(pylith::topology::FieldBase::VERTICES_FIELD, _data->spaceDim);
residual.allocate();
residual.zero();
Modified: short/3D/PyLith/trunk/unittests/libtests/bc/TestDirichletBC.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/bc/TestDirichletBC.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/bc/TestDirichletBC.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -162,8 +162,8 @@
PetscInt cStart, cEnd, vStart, vEnd;
PetscErrorCode err;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const int fiberDim = _data->numDOF;
const int spaceDim = mesh.dimension();
@@ -219,8 +219,8 @@
PetscInt cStart, cEnd, vStart, vEnd;
PetscErrorCode err;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const int spaceDim = mesh.dimension();
const int fiberDim = _data->numDOF;
@@ -281,8 +281,8 @@
PetscInt cStart, cEnd, vStart, vEnd;
PetscErrorCode err;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const int fiberDim = _data->numDOF;
topology::Field<topology::Mesh> field(mesh);
@@ -383,8 +383,8 @@
PetscInt cStart, cEnd, vStart, vEnd;
PetscErrorCode err;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const int fiberDim = _data->numDOF;
topology::Field<topology::Mesh> field(mesh);
Modified: short/3D/PyLith/trunk/unittests/libtests/bc/TestDirichletBCMulti.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/bc/TestDirichletBCMulti.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/bc/TestDirichletBCMulti.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -70,8 +70,8 @@
PetscInt cStart, cEnd, vStart, vEnd;
PetscErrorCode err;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const int fiberDim = _data->numDOF;
topology::Field<topology::Mesh> field(mesh);
@@ -118,8 +118,8 @@
PetscInt cStart, cEnd, vStart, vEnd;
PetscErrorCode err;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const int fiberDim = _data->numDOF;
topology::Field<topology::Mesh> field(mesh);
@@ -176,8 +176,8 @@
PetscInt cStart, cEnd, vStart, vEnd;
PetscErrorCode err;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const int fiberDim = _data->numDOF;
topology::Field<topology::Mesh> field(mesh);
@@ -249,8 +249,8 @@
PetscInt cStart, cEnd, vStart, vEnd;
PetscErrorCode err;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const int fiberDim = _data->numDOF;
topology::Field<topology::Mesh> field(mesh);
Modified: short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumann.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumann.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/bc/TestNeumann.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -164,8 +164,8 @@
PetscErrorCode err;
assert(subMesh);
- err = DMComplexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetDepthStratum(subMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(subMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const int cellDim = boundaryMesh.dimension();
const int numCorners = _data->numCorners;
@@ -182,8 +182,8 @@
const PetscInt *cone;
PetscInt numCorners;
- err = DMComplexGetConeSize(subMesh, c, &numCorners);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCone(subMesh, c, &cone);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetConeSize(subMesh, c, &numCorners);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCone(subMesh, c, &cone);CHECK_PETSC_ERROR(err);
CPPUNIT_ASSERT_EQUAL(_data->numCorners, numCorners);
for(PetscInt p = 0; p < numCorners; ++p, ++dp) {
CPPUNIT_ASSERT_EQUAL(_data->cells[dp], cone[p]);
@@ -241,7 +241,7 @@
const PylithScalar* valsE = _data->valsResidual;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const int totalNumVertices = vEnd - vStart;
const int sizeE = _data->spaceDim * totalNumVertices;
@@ -759,7 +759,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(subMesh);
- err = DMComplexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(subMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
const PylithScalar scale = field.scale();
PetscSection section = field.petscSection();
Modified: short/3D/PyLith/trunk/unittests/libtests/bc/TestPointForce.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/bc/TestPointForce.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/bc/TestPointForce.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -97,7 +97,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
const int numCells = cEnd-cStart;
const int numForceDOF = _data->numForceDOF;
const size_t numPoints = _data->numForcePts;
@@ -178,7 +178,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const PylithScalar* valsE = _data->residual;
const int totalNumVertices = vEnd-vStart;
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestBruneSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestBruneSlipFn.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestBruneSlipFn.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -246,7 +246,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
topology::Field<topology::SubMesh> slip(faultMesh);
slip.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim);
slip.allocate();
@@ -373,9 +373,9 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, vStart, vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
@@ -483,9 +483,9 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, vStart, vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestConstRateSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestConstRateSlipFn.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestConstRateSlipFn.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -211,7 +211,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
topology::Field<topology::SubMesh> slip(faultMesh);
slip.newSection(topology::Field<topology::Mesh>::VERTICES_FIELD, spaceDim);
slip.allocate();
@@ -304,9 +304,9 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, vStart, vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
@@ -408,9 +408,9 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, vStart, vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestEqKinSrc.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestEqKinSrc.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestEqKinSrc.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -107,7 +107,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
topology::Field<topology::SubMesh> slip(faultMesh);
slip.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim);
slip.allocate();
@@ -210,9 +210,9 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, vStart, vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDyn.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDyn.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveDyn.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -144,8 +144,8 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
CPPUNIT_ASSERT(subpointMap);
err = ISGetSize(subpointMap, &numPoints);CHECK_PETSC_ERROR(err);
err = ISGetIndices(subpointMap, &points);CHECK_PETSC_ERROR(err);
@@ -242,7 +242,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Get section containing solution (disp + Lagrange multipliers)
PetscSection dispTIncrSection = fields.get("dispIncr(t->t+dt)").petscSection();
@@ -284,7 +284,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(faultDMMesh);
- err = DMComplexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Get section containing slip
PetscSection slipSection = fault.vertexField("slip").petscSection();
@@ -355,7 +355,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Get section containing solution (disp + Lagrange multipliers)
PetscSection dispIncrSection = fields.get("dispIncr(t->t+dt)").petscSection();
@@ -396,7 +396,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(faultDMMesh);
- err = DMComplexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Get section containing slip
PetscSection slipSection = fault.vertexField("slip").petscSection();
@@ -466,7 +466,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Get section containing solution (disp + Lagrange multipliers)
PetscSection dispIncrSection = fields.get("dispIncr(t->t+dt)").petscSection();
@@ -507,7 +507,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(faultDMMesh);
- err = DMComplexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Get section containing slip
PetscSection slipSection = fault.vertexField("slip").petscSection();
@@ -601,8 +601,8 @@
PetscErrorCode err;
CPPUNIT_ASSERT(faultDMMesh);
- err = DMComplexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(faultDMMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(faultDMMesh, &subpointMap);CHECK_PETSC_ERROR(err);
CPPUNIT_ASSERT(subpointMap);
err = ISGetSize(subpointMap, &numPoints);CHECK_PETSC_ERROR(err);
@@ -703,7 +703,7 @@
PetscInt labelSize;
PetscErrorCode err;
- err = DMComplexGetStratumSize(mesh->dmMesh(), _data->label, 1, &labelSize);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumSize(mesh->dmMesh(), _data->label, 1, &labelSize);CHECK_PETSC_ERROR(err);
PetscInt firstFaultVertex = 0;
PetscInt firstLagrangeVertex = labelSize;
@@ -769,7 +769,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Set displacement values
PetscSection dispSection = fields->get("disp(t)").petscSection();
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulses.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulses.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveImpulses.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -160,8 +160,8 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
CPPUNIT_ASSERT(subpointMap);
err = ISGetSize(subpointMap, &numPoints);CHECK_PETSC_ERROR(err);
err = ISGetIndices(subpointMap, &points);CHECK_PETSC_ERROR(err);
@@ -255,7 +255,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
int iVertex = 0;
err = VecGetArray(dispVec, &dispArray);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v, ++iVertex) {
@@ -342,7 +342,7 @@
PetscInt labelSize;
PetscErrorCode err;
- err = DMComplexGetStratumSize(mesh->dmMesh(), _data->label, 1, &labelSize);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumSize(mesh->dmMesh(), _data->label, 1, &labelSize);CHECK_PETSC_ERROR(err);
PetscInt firstFaultVertex = 0;
PetscInt firstLagrangeVertex = labelSize;
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestFaultCohesiveKin.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -146,8 +146,8 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
CPPUNIT_ASSERT(subpointMap);
err = ISGetSize(subpointMap, &numPoints);CHECK_PETSC_ERROR(err);
err = ISGetIndices(subpointMap, &points);CHECK_PETSC_ERROR(err);
@@ -262,7 +262,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
int iVertex = 0;
err = VecGetArray(dispVec, &dispArray);CHECK_PETSC_ERROR(err);
@@ -367,7 +367,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
int iVertex = 0;
err = VecGetArray(dispVec, &dispArray);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v, ++iVertex) {
@@ -476,13 +476,13 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
DM faultDMMesh = fault._faultMesh->dmMesh();
IS subpointMap;
CPPUNIT_ASSERT(faultDMMesh);
- err = DMComplexGetSubpointMap(faultDMMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(faultDMMesh, &subpointMap);CHECK_PETSC_ERROR(err);
CPPUNIT_ASSERT(subpointMap);
const PylithScalar tolerance = 1.0e-06;
@@ -545,7 +545,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
{ // setup disp
PetscSection dispSection = fields.get("disp(t)").petscSection();
@@ -679,7 +679,7 @@
PetscInt vStart, vEnd;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
int iVertex = 0;
err = VecGetArray(dispVec, &dispArray);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v, ++iVertex) {
@@ -717,8 +717,8 @@
PetscInt numPoints, vStart, vEnd;
CPPUNIT_ASSERT(faultDMMesh);
- err = DMComplexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(faultDMMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(faultDMMesh, &subpointMap);CHECK_PETSC_ERROR(err);
CPPUNIT_ASSERT(subpointMap);
err = ISGetSize(subpointMap, &numPoints);CHECK_PETSC_ERROR(err);
err = ISGetIndices(subpointMap, &points);CHECK_PETSC_ERROR(err);
@@ -795,7 +795,7 @@
PetscInt vStart, vEnd;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const int numFaultVertices = _data->numFaultVertices;
for(PetscInt v = vStart; v < vEnd; ++v) {
PetscInt dof, off, fdof;
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestLiuCosSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestLiuCosSlipFn.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestLiuCosSlipFn.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -246,7 +246,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
topology::Field<topology::SubMesh> slip(faultMesh);
slip.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim);
slip.allocate();
@@ -367,9 +367,9 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, vStart, vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
@@ -476,9 +476,9 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, vStart, vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestStepSlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestStepSlipFn.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestStepSlipFn.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -210,7 +210,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
topology::Field<topology::SubMesh> slip(faultMesh);
slip.newSection(topology::Field<topology::Mesh>::VERTICES_FIELD, spaceDim);
slip.allocate();
@@ -300,9 +300,9 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, vStart, vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
@@ -404,9 +404,9 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, vStart, vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestTimeHistorySlipFn.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestTimeHistorySlipFn.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestTimeHistorySlipFn.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -240,7 +240,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
topology::Field<topology::SubMesh> slip(faultMesh);
slip.newSection(topology::FieldBase::VERTICES_FIELD, spaceDim);
slip.allocate();
@@ -329,9 +329,9 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, vStart, vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
@@ -436,9 +436,9 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(dmMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, vStart, vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/unittests/libtests/faults/TestTractPerturbation.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/faults/TestTractPerturbation.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/faults/TestTractPerturbation.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -146,7 +146,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(faultDMMesh);
- err = DMComplexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
//traction.view("TRACTION"); // DEBUGGING
@@ -199,7 +199,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(faultDMMesh);
- err = DMComplexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
CPPUNIT_ASSERT(tract._parameters);
PetscSection valueSection = tract._parameters->get("value").petscSection();
@@ -295,7 +295,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(faultDMMesh);
- err = DMComplexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const PylithScalar tolerance = 1.0e-06;
int iPoint = 0;
@@ -349,7 +349,7 @@
PetscInt labelSize;
PetscErrorCode err;
- err = DMComplexGetStratumSize(mesh->dmMesh(), faultLabel, 1, &labelSize);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumSize(mesh->dmMesh(), faultLabel, 1, &labelSize);CHECK_PETSC_ERROR(err);
// Create fault mesh
PetscInt firstFaultVertex = 0;
@@ -382,9 +382,9 @@
PetscInt vStart, vEnd;
CPPUNIT_ASSERT(faultDMMesh);
- err = DMComplexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetSubpointMap(faultDMMesh, &subpointMap);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(faultDMMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(faultDMMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetSubpointMap(faultDMMesh, &subpointMap);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(faultDMMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, vStart, vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicit.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicit.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicit.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -293,8 +293,8 @@
CPPUNIT_ASSERT_DOUBLES_EQUAL(1.0, dtStable/_data->dtStableExplicit, tolerance);
} // testStableTimeStep
-extern PetscErrorCode DMComplexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]);
-extern PetscErrorCode DMComplexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]);
+extern PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]);
+extern PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]);
// ----------------------------------------------------------------------
// Initialize elasticity integrator.
@@ -343,8 +343,8 @@
_data->vertices);
PetscErrorCode err;
- err = DMComplexBuildFromCellList_Private(dmMesh, _data->numCells, _data->numVertices, _data->numBasis, _data->cells);CHECK_PETSC_ERROR(err);
- err = DMComplexBuildCoordinates_Private(dmMesh, _data->spaceDim, _data->numCells, _data->numVertices, _data->vertices);CHECK_PETSC_ERROR(err);
+ err = DMPlexBuildFromCellList_Private(dmMesh, _data->numCells, _data->numVertices, _data->numBasis, _data->cells);CHECK_PETSC_ERROR(err);
+ err = DMPlexBuildCoordinates_Private(dmMesh, _data->spaceDim, _data->numCells, _data->numVertices, _data->vertices);CHECK_PETSC_ERROR(err);
// Material ids
const ALE::Obj<SieveMesh::label_sequence>& cells =
@@ -360,9 +360,9 @@
sieveMesh->setValue(labelMaterials, *e_iter, _data->matId);
PetscInt cStart, cEnd, c;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
for(PetscInt c = cStart; c < cEnd; ++c) {
- err = DMComplexSetLabelValue(dmMesh, "material-id", c, _data->matId);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(dmMesh, "material-id", c, _data->matId);CHECK_PETSC_ERROR(err);
}
// Setup quadrature
@@ -443,11 +443,11 @@
_data->fieldT[iVertex*spaceDim+iDim] +
_data->fieldTmdt[iVertex*spaceDim+iDim]) / (dt*dt);
} // for
- err = DMComplexVecSetClosure(dmMesh, dispTSectionP, dispTVec, iVertex+offset, &_data->fieldT[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, dispTIncrSectionP, dispTIncrVec, iVertex+offset, &_data->fieldTIncr[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, dispTmdtSectionP, dispTmdtVec, iVertex+offset, &_data->fieldTmdt[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, velSectionP, velVec, iVertex+offset, &velVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, accSectionP, accVec, iVertex+offset, &accVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTSectionP, dispTVec, iVertex+offset, &_data->fieldT[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTIncrSectionP, dispTIncrVec, iVertex+offset, &_data->fieldTIncr[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTmdtSectionP, dispTmdtVec, iVertex+offset, &_data->fieldTmdt[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, velSectionP, velVec, iVertex+offset, &velVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, accSectionP, accVec, iVertex+offset, &accVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
} // for
} // _initialize
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitLgDeform.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitLgDeform.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitLgDeform.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -211,8 +211,8 @@
integrator.updateStateVars(t, &fields);
} // testUpdateStateVars
-extern PetscErrorCode DMComplexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]);
-extern PetscErrorCode DMComplexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]);
+extern PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]);
+extern PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]);
// ----------------------------------------------------------------------
// Initialize elasticity integrator.
@@ -265,8 +265,8 @@
_data->vertices);
PetscErrorCode err;
- err = DMComplexBuildFromCellList_Private(dmMesh, _data->numCells, _data->numVertices, _data->numBasis, _data->cells);CHECK_PETSC_ERROR(err);
- err = DMComplexBuildCoordinates_Private(dmMesh, _data->spaceDim, _data->numCells, _data->numVertices, _data->vertices);CHECK_PETSC_ERROR(err);
+ err = DMPlexBuildFromCellList_Private(dmMesh, _data->numCells, _data->numVertices, _data->numBasis, _data->cells);CHECK_PETSC_ERROR(err);
+ err = DMPlexBuildCoordinates_Private(dmMesh, _data->spaceDim, _data->numCells, _data->numVertices, _data->vertices);CHECK_PETSC_ERROR(err);
// Material ids
const ALE::Obj<SieveMesh::label_sequence>& cells =
@@ -282,9 +282,9 @@
sieveMesh->setValue(labelMaterials, *e_iter, _data->matId);
PetscInt cStart, cEnd, c;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
for(PetscInt c = cStart; c < cEnd; ++c) {
- err = DMComplexSetLabelValue(dmMesh, "material-id", c, _data->matId);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(dmMesh, "material-id", c, _data->matId);CHECK_PETSC_ERROR(err);
}
// Setup quadrature
@@ -358,11 +358,11 @@
_data->fieldT[iVertex*spaceDim+iDim] +
_data->fieldTmdt[iVertex*spaceDim+iDim]) / (dt*dt);
} // for
- err = DMComplexVecSetClosure(dmMesh, dispTSectionP, dispTVec, iVertex+offset, &_data->fieldT[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, dispTIncrSectionP, dispTIncrVec, iVertex+offset, &_data->fieldTIncr[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, dispTmdtSectionP, dispTmdtVec, iVertex+offset, &_data->fieldTmdt[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, velSectionP, velVec, iVertex+offset, &velVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, accSectionP, accVec, iVertex+offset, &accVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTSectionP, dispTVec, iVertex+offset, &_data->fieldT[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTIncrSectionP, dispTIncrVec, iVertex+offset, &_data->fieldTIncr[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTmdtSectionP, dispTmdtVec, iVertex+offset, &_data->fieldTmdt[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, velSectionP, velVec, iVertex+offset, &velVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, accSectionP, accVec, iVertex+offset, &accVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
} // for
} // _initialize
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTet4.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTet4.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTet4.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -287,8 +287,8 @@
CPPUNIT_ASSERT_DOUBLES_EQUAL(1.0, dtStable/_data->dtStableExplicit, tolerance);
} // testStableTimeStep
-extern PetscErrorCode DMComplexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]);
-extern PetscErrorCode DMComplexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]);
+extern PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]);
+extern PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]);
// ----------------------------------------------------------------------
// Initialize elasticity integrator.
@@ -337,8 +337,8 @@
_data->vertices);
PetscErrorCode err;
- err = DMComplexBuildFromCellList_Private(dmMesh, _data->numCells, _data->numVertices, _data->numBasis, _data->cells);CHECK_PETSC_ERROR(err);
- err = DMComplexBuildCoordinates_Private(dmMesh, _data->spaceDim, _data->numCells, _data->numVertices, _data->vertices);CHECK_PETSC_ERROR(err);
+ err = DMPlexBuildFromCellList_Private(dmMesh, _data->numCells, _data->numVertices, _data->numBasis, _data->cells);CHECK_PETSC_ERROR(err);
+ err = DMPlexBuildCoordinates_Private(dmMesh, _data->spaceDim, _data->numCells, _data->numVertices, _data->vertices);CHECK_PETSC_ERROR(err);
// Material ids
const ALE::Obj<SieveMesh::label_sequence>& cells =
@@ -354,9 +354,9 @@
sieveMesh->setValue(labelMaterials, *e_iter, _data->matId);
PetscInt cStart, cEnd, c;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
for(PetscInt c = cStart; c < cEnd; ++c) {
- err = DMComplexSetLabelValue(dmMesh, "material-id", c, _data->matId);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(dmMesh, "material-id", c, _data->matId);CHECK_PETSC_ERROR(err);
}
// Setup quadrature
@@ -435,11 +435,11 @@
_data->fieldT[iVertex*spaceDim+iDim] +
_data->fieldTmdt[iVertex*spaceDim+iDim]) / (dt*dt);
} // for
- err = DMComplexVecSetClosure(dmMesh, dispTSectionP, dispTVec, iVertex+offset, &_data->fieldT[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, dispTIncrSectionP, dispTIncrVec, iVertex+offset, &_data->fieldTIncr[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, dispTmdtSectionP, dispTmdtVec, iVertex+offset, &_data->fieldTmdt[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, velSectionP, velVec, iVertex+offset, &velVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, accSectionP, accVec, iVertex+offset, &accVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTSectionP, dispTVec, iVertex+offset, &_data->fieldT[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTIncrSectionP, dispTIncrVec, iVertex+offset, &_data->fieldTIncr[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTmdtSectionP, dispTmdtVec, iVertex+offset, &_data->fieldTmdt[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, velSectionP, velVec, iVertex+offset, &velVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, accSectionP, accVec, iVertex+offset, &accVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
} // for
} // _initialize
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTri3.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTri3.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityExplicitTri3.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -287,8 +287,8 @@
CPPUNIT_ASSERT_DOUBLES_EQUAL(1.0, dtStable/_data->dtStableExplicit, tolerance);
} // testStableTimeStep
-extern PetscErrorCode DMComplexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]);
-extern PetscErrorCode DMComplexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]);
+extern PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]);
+extern PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]);
// ----------------------------------------------------------------------
// Initialize elasticity integrator.
@@ -337,8 +337,8 @@
_data->vertices);
PetscErrorCode err;
- err = DMComplexBuildFromCellList_Private(dmMesh, _data->numCells, _data->numVertices, _data->numBasis, _data->cells);CHECK_PETSC_ERROR(err);
- err = DMComplexBuildCoordinates_Private(dmMesh, _data->spaceDim, _data->numCells, _data->numVertices, _data->vertices);CHECK_PETSC_ERROR(err);
+ err = DMPlexBuildFromCellList_Private(dmMesh, _data->numCells, _data->numVertices, _data->numBasis, _data->cells);CHECK_PETSC_ERROR(err);
+ err = DMPlexBuildCoordinates_Private(dmMesh, _data->spaceDim, _data->numCells, _data->numVertices, _data->vertices);CHECK_PETSC_ERROR(err);
// Material ids
const ALE::Obj<SieveMesh::label_sequence>& cells =
@@ -354,9 +354,9 @@
sieveMesh->setValue(labelMaterials, *e_iter, _data->matId);
PetscInt cStart, cEnd, c;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
for(PetscInt c = cStart; c < cEnd; ++c) {
- err = DMComplexSetLabelValue(dmMesh, "material-id", c, _data->matId);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(dmMesh, "material-id", c, _data->matId);CHECK_PETSC_ERROR(err);
}
// Setup quadrature
@@ -435,11 +435,11 @@
_data->fieldT[iVertex*spaceDim+iDim] +
_data->fieldTmdt[iVertex*spaceDim+iDim]) / (dt*dt);
} // for
- err = DMComplexVecSetClosure(dmMesh, dispTSectionP, dispTVec, iVertex+offset, &_data->fieldT[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, dispTIncrSectionP, dispTIncrVec, iVertex+offset, &_data->fieldTIncr[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, dispTmdtSectionP, dispTmdtVec, iVertex+offset, &_data->fieldTmdt[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, velSectionP, velVec, iVertex+offset, &velVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, accSectionP, accVec, iVertex+offset, &accVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTSectionP, dispTVec, iVertex+offset, &_data->fieldT[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTIncrSectionP, dispTIncrVec, iVertex+offset, &_data->fieldTIncr[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTmdtSectionP, dispTmdtVec, iVertex+offset, &_data->fieldTmdt[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, velSectionP, velVec, iVertex+offset, &velVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, accSectionP, accVec, iVertex+offset, &accVertex[0], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
} // for
} // _initialize
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicit.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicit.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicit.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -267,8 +267,8 @@
CPPUNIT_ASSERT_EQUAL(pylith::PYLITH_MAXSCALAR, stableTimeStep);
} // testStableTimeStep
-extern PetscErrorCode DMComplexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]);
-extern PetscErrorCode DMComplexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]);
+extern PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]);
+extern PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]);
// ----------------------------------------------------------------------
// Initialize elasticity integrator.
@@ -318,8 +318,8 @@
_data->vertices);
PetscErrorCode err;
- err = DMComplexBuildFromCellList_Private(dmMesh, _data->numCells, _data->numVertices, _data->numBasis, _data->cells);CHECK_PETSC_ERROR(err);
- err = DMComplexBuildCoordinates_Private(dmMesh, _data->spaceDim, _data->numCells, _data->numVertices, _data->vertices);CHECK_PETSC_ERROR(err);
+ err = DMPlexBuildFromCellList_Private(dmMesh, _data->numCells, _data->numVertices, _data->numBasis, _data->cells);CHECK_PETSC_ERROR(err);
+ err = DMPlexBuildCoordinates_Private(dmMesh, _data->spaceDim, _data->numCells, _data->numVertices, _data->vertices);CHECK_PETSC_ERROR(err);
// Material ids
const ALE::Obj<SieveMesh::label_sequence>& cells =
@@ -335,9 +335,9 @@
sieveMesh->setValue(labelMaterials, *e_iter, _data->matId);
PetscInt cStart, cEnd;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
for(PetscInt c = cStart; c < cEnd; ++c) {
- err = DMComplexSetLabelValue(dmMesh, "material-id", c, _data->matId);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(dmMesh, "material-id", c, _data->matId);CHECK_PETSC_ERROR(err);
}
// Setup quadrature
@@ -388,8 +388,8 @@
Vec dispTIncrVec = fields->get("dispIncr(t->t+dt)").localVector();
CPPUNIT_ASSERT(dispTIncrSectionP);CPPUNIT_ASSERT(dispTIncrVec);
for(int iVertex=0; iVertex < _data->numVertices; ++iVertex) {
- err = DMComplexVecSetClosure(dmMesh, dispTSectionP, dispTVec, iVertex+offset, &_data->fieldT[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, dispTIncrSectionP, dispTIncrVec, iVertex+offset, &_data->fieldTIncr[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTSectionP, dispTVec, iVertex+offset, &_data->fieldT[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTIncrSectionP, dispTIncrVec, iVertex+offset, &_data->fieldTIncr[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
} // for
} // _initialize
Modified: short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicitLgDeform.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicitLgDeform.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/feassemble/TestElasticityImplicitLgDeform.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -209,8 +209,8 @@
integrator.updateStateVars(t, &fields);
} // testUpdateStateVars
-extern PetscErrorCode DMComplexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]);
-extern PetscErrorCode DMComplexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]);
+extern PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]);
+extern PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]);
// ----------------------------------------------------------------------
// Initialize elasticity integrator.
@@ -260,8 +260,8 @@
_data->vertices);
PetscErrorCode err;
- err = DMComplexBuildFromCellList_Private(dmMesh, _data->numCells, _data->numVertices, _data->numBasis, _data->cells);CHECK_PETSC_ERROR(err);
- err = DMComplexBuildCoordinates_Private(dmMesh, _data->spaceDim, _data->numCells, _data->numVertices, _data->vertices);CHECK_PETSC_ERROR(err);
+ err = DMPlexBuildFromCellList_Private(dmMesh, _data->numCells, _data->numVertices, _data->numBasis, _data->cells);CHECK_PETSC_ERROR(err);
+ err = DMPlexBuildCoordinates_Private(dmMesh, _data->spaceDim, _data->numCells, _data->numVertices, _data->vertices);CHECK_PETSC_ERROR(err);
// Material ids
const ALE::Obj<SieveMesh::label_sequence>& cells =
@@ -277,9 +277,9 @@
sieveMesh->setValue(labelMaterials, *e_iter, _data->matId);
PetscInt cStart, cEnd;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
for(PetscInt c = cStart; c < cEnd; ++c) {
- err = DMComplexSetLabelValue(dmMesh, "material-id", c, _data->matId);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(dmMesh, "material-id", c, _data->matId);CHECK_PETSC_ERROR(err);
}
// Setup quadrature
@@ -330,8 +330,8 @@
Vec dispTIncrVec = fields->get("dispIncr(t->t+dt)").localVector();
CPPUNIT_ASSERT(dispTIncrSectionP);CPPUNIT_ASSERT(dispTIncrVec);
for(int iVertex=0; iVertex < _data->numVertices; ++iVertex) {
- err = DMComplexVecSetClosure(dmMesh, dispTSectionP, dispTVec, iVertex+offset, &_data->fieldT[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
- err = DMComplexVecSetClosure(dmMesh, dispTIncrSectionP, dispTIncrVec, iVertex+offset, &_data->fieldTIncr[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTSectionP, dispTVec, iVertex+offset, &_data->fieldT[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
+ err = DMPlexVecSetClosure(dmMesh, dispTIncrSectionP, dispTIncrVec, iVertex+offset, &_data->fieldTIncr[iVertex*_data->spaceDim], INSERT_ALL_VALUES);CHECK_PETSC_ERROR(err);
} // for
} // _initialize
Modified: short/3D/PyLith/trunk/unittests/libtests/friction/TestFrictionModel.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/friction/TestFrictionModel.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/friction/TestFrictionModel.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -228,7 +228,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
PetscSection fieldSection = field.petscSection();
Vec fieldVec = field.localVector();
Modified: short/3D/PyLith/trunk/unittests/libtests/materials/TestElasticMaterial.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/materials/TestElasticMaterial.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/materials/TestElasticMaterial.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -100,7 +100,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
PetscInt cell = cells[0];
@@ -203,7 +203,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
PetscInt cell = cells[0];
@@ -275,7 +275,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
PetscInt cell = cells[0];
@@ -316,7 +316,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
PetscInt cell = cells[0];
@@ -360,7 +360,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
PetscInt cell = cells[0];
@@ -430,7 +430,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
PetscInt cell = cells[0];
@@ -850,7 +850,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/unittests/libtests/materials/TestMaterial.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/materials/TestMaterial.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/materials/TestMaterial.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -216,7 +216,7 @@
PetscErrorCode err;
assert(dmMesh);
- err = DMComplexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, "material-id", materialId, &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestCellFilterAvg.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestCellFilterAvg.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestCellFilterAvg.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -105,7 +105,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
PetscSection section = field.petscSection();
Vec vec = field.localVector();
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterBCMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterBCMesh.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterBCMesh.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -115,7 +115,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Set vertex fields
for (int i=0; i < nfields; ++i) {
@@ -168,7 +168,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetHeightStratum(dmMesh, height, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, height, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
// Set cell fields
for (int i=0; i < nfields; ++i) {
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterFaultMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterFaultMesh.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterFaultMesh.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -110,7 +110,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Set vertex fields
for (int i=0; i < nfields; ++i) {
@@ -163,7 +163,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetHeightStratum(dmMesh, height, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, height, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
// Set cell fields
for (int i=0; i < nfields; ++i) {
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterMesh.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterMesh.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -103,7 +103,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Set vertex fields
for (int i=0; i < nfields; ++i) {
@@ -159,10 +159,10 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
numCells = cEnd - cStart;
if (_data->cellsLabel) {
- err = DMComplexGetStratumIS(dmMesh, _data->cellsLabel, _data->labelId, &cellIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, _data->cellsLabel, _data->labelId, &cellIS);CHECK_PETSC_ERROR(err);
err = ISGetSize(cellIS, &numCells);CHECK_PETSC_ERROR(err);
err = ISGetIndices(cellIS, &cells);CHECK_PETSC_ERROR(err);
}
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterPoints.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterPoints.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterPoints.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -103,7 +103,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Set vertex fields
for (int i=0; i < nfields; ++i) {
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterSubMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterSubMesh.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestDataWriterSubMesh.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -117,7 +117,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Set vertex fields
for (int i=0; i < nfields; ++i) {
@@ -171,7 +171,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetHeightStratum(dmMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 1, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
numCells = cEnd - cStart;
// Set cell fields
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestMeshIO.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestMeshIO.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestMeshIO.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -82,7 +82,7 @@
PetscBool interpolateMesh = interpolate ? PETSC_TRUE : PETSC_FALSE;
PetscErrorCode err;
- err = DMComplexCreateFromCellList(mesh->comm(), data.cellDim, data.numCells, data.numVertices, data.numCorners, interpolateMesh, data.cells, data.vertices, &dmMesh);CHECK_PETSC_ERROR(err);
+ err = DMPlexCreateFromCellList(mesh->comm(), data.cellDim, data.numCells, data.numVertices, data.numCorners, interpolateMesh, data.cells, data.vertices, &dmMesh);CHECK_PETSC_ERROR(err);
mesh->setDMMesh(dmMesh);
// Material ids
@@ -96,9 +96,9 @@
PetscInt cStart, cEnd;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
for(PetscInt c = cStart; c < cEnd; ++c) {
- err = DMComplexSetLabelValue(dmMesh, "material-id", c, data.materialIds[c-cStart]);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(dmMesh, "material-id", c, data.materialIds[c-cStart]);CHECK_PETSC_ERROR(err);
}
// Groups
@@ -107,7 +107,7 @@
CPPUNIT_ASSERT(!groupField.isNull());
groupField->setChart(sieveMesh->getSieve()->getChart());
- err = DMComplexCreateLabel(dmMesh, data.groupNames[iGroup]);CHECK_PETSC_ERROR(err);
+ err = DMPlexCreateLabel(dmMesh, data.groupNames[iGroup]);CHECK_PETSC_ERROR(err);
MeshIO::GroupPtType type;
const int numPoints = data.groupSizes[iGroup];
@@ -115,14 +115,14 @@
type = MeshIO::CELL;
for(int i=0; i < numPoints; ++i, ++index) {
groupField->setFiberDimension(data.groups[index], 1);
- err = DMComplexSetLabelValue(dmMesh, data.groupNames[iGroup], data.groups[index], 1);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(dmMesh, data.groupNames[iGroup], data.groups[index], 1);CHECK_PETSC_ERROR(err);
}
} else if (0 == strcasecmp("vertex", data.groupTypes[iGroup])) {
type = MeshIO::VERTEX;
const int numCells = sieveMesh->heightStratum(0)->size();
for(int i=0; i < numPoints; ++i, ++index) {
groupField->setFiberDimension(data.groups[index]+numCells, 1);
- err = DMComplexSetLabelValue(dmMesh, data.groupNames[iGroup], data.groups[index]+numCells, 1);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(dmMesh, data.groupNames[iGroup], data.groups[index]+numCells, 1);CHECK_PETSC_ERROR(err);
}
} else
throw std::logic_error("Could not parse group type.");
@@ -192,8 +192,8 @@
PetscInt vStart, vEnd;
PetscErrorCode err;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = DMGetCoordinatesLocal(dmMesh, &coordVec);CHECK_PETSC_ERROR(err);
CPPUNIT_ASSERT(coordSection);CPPUNIT_ASSERT(coordVec);
err = VecGetArray(coordVec, &coords);CHECK_PETSC_ERROR(err);
@@ -239,14 +239,14 @@
} // for
PetscInt cStart, cEnd;
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
CPPUNIT_ASSERT_EQUAL(data.numCells, cEnd-cStart);
for(PetscInt c = cStart; c < cEnd; ++c) {
const PetscInt *cone;
PetscInt coneSize;
- err = DMComplexGetConeSize(dmMesh, c, &coneSize);CHECK_PETSC_ERROR(err);
- err = DMComplexGetCone(dmMesh, c, &cone);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetConeSize(dmMesh, c, &coneSize);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCone(dmMesh, c, &cone);CHECK_PETSC_ERROR(err);
CPPUNIT_ASSERT_EQUAL(data.numCorners, coneSize);
for(PetscInt p = 0; p < coneSize; ++p) {
CPPUNIT_ASSERT_EQUAL(data.cells[(c-cStart)*coneSize+p], cone[p]-offset);
@@ -270,7 +270,7 @@
for(PetscInt c = cStart; c < cEnd; ++c) {
PetscInt matId;
- err = DMComplexGetLabelValue(dmMesh, "material-id", c, &matId);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetLabelValue(dmMesh, "material-id", c, &matId);CHECK_PETSC_ERROR(err);
CPPUNIT_ASSERT_EQUAL(data.materialIds[c-cStart], matId);
}
@@ -322,8 +322,8 @@
PetscInt numLabels, pStart, pEnd;
- err = DMComplexGetChart(dmMesh, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
- err = DMComplexGetNumLabels(dmMesh, &numLabels);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetChart(dmMesh, &pStart, &pEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetNumLabels(dmMesh, &numLabels);CHECK_PETSC_ERROR(err);
numLabels -= 2; /* Remove depth and material labels */
CPPUNIT_ASSERT_EQUAL(data.numGroups, numLabels);
PetscInt iGroup = 0;
@@ -332,12 +332,12 @@
const char *name;
PetscInt firstPoint;
- err = DMComplexGetLabelName(dmMesh, l, &name);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetLabelName(dmMesh, l, &name);CHECK_PETSC_ERROR(err);
CPPUNIT_ASSERT_EQUAL(std::string(data.groupNames[iGroup]), std::string(name));
for(PetscInt p = pStart; p < pEnd; ++p) {
PetscInt val;
- err = DMComplexGetLabelValue(dmMesh, name, p, &val);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetLabelValue(dmMesh, name, p, &val);CHECK_PETSC_ERROR(err);
if (val >= 0) {
firstPoint = p;
break;
@@ -346,12 +346,12 @@
std::string groupType = (firstPoint >= cStart && firstPoint < cEnd) ? "cell" : "vertex";
CPPUNIT_ASSERT_EQUAL(std::string(data.groupTypes[iGroup]), groupType);
PetscInt numPoints;
- err = DMComplexGetStratumSize(dmMesh, name, 1, &numPoints);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumSize(dmMesh, name, 1, &numPoints);CHECK_PETSC_ERROR(err);
CPPUNIT_ASSERT_EQUAL(data.groupSizes[iGroup], numPoints);
IS pointIS;
const PetscInt *points;
const PetscInt offset = ("vertex" == groupType) ? numCells : 0;
- err = DMComplexGetStratumIS(dmMesh, name, 1, &pointIS);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetStratumIS(dmMesh, name, 1, &pointIS);CHECK_PETSC_ERROR(err);
err = ISGetIndices(pointIS, &points);CHECK_PETSC_ERROR(err);
for(PetscInt p = 0; p < numPoints; ++p) {
CPPUNIT_ASSERT_EQUAL(data.groups[index++], points[p]-offset);
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestOutputManager.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestOutputManager.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestOutputManager.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -199,7 +199,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
MeshField field(mesh);
field.newSection(topology::FieldBase::VERTICES_FIELD, fiberDim);
@@ -288,7 +288,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetHeightStratum(dmMesh, 0, &cStart, &cEnd);CHECK_PETSC_ERROR(err);
numCells = cEnd - cStart;
MeshField field(mesh);
Modified: short/3D/PyLith/trunk/unittests/libtests/meshio/TestVertexFilterVecNorm.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/meshio/TestVertexFilterVecNorm.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/meshio/TestVertexFilterVecNorm.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -87,7 +87,7 @@
PetscErrorCode err;
CPPUNIT_ASSERT(dmMesh);
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
PetscSection section = field.petscSection();
Vec vec = field.localVector();
Modified: short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldMesh.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldMesh.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -170,7 +170,7 @@
field.label(label.c_str());
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
field.newSection(topology::FieldBase::VERTICES_FIELD, fiberDim);
field.allocate();
PetscSection section = field.petscSection();
@@ -205,7 +205,7 @@
field.label(label.c_str());
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const int npts = (vEnd-vStart) / 2;
int_array pointsIn(npts);
int_array pointsOut(vEnd-vStart - npts);
@@ -273,7 +273,7 @@
CPPUNIT_ASSERT(section);CPPUNIT_ASSERT(vec);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
PetscInt dof;
err = PetscSectionGetDof(section, v, &dof);CHECK_PETSC_ERROR(err);
@@ -312,7 +312,7 @@
Vec vec = field.localVector();
CPPUNIT_ASSERT(section);CPPUNIT_ASSERT(vec);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
PetscInt dof;
err = PetscSectionGetDof(section, v, &dof);CHECK_PETSC_ERROR(err);
@@ -344,7 +344,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Create field with atlas to use to create new field
Field<Mesh> fieldSrc(mesh);
@@ -432,7 +432,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<Mesh> field(mesh);
field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
@@ -488,7 +488,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<Mesh> field(mesh);
field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
@@ -553,7 +553,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Create field and set constraint sizes
Field<Mesh> field(mesh);
@@ -623,7 +623,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<Mesh> field(mesh);
field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
@@ -682,7 +682,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<Mesh> fieldSrc(mesh);
{ // Setup source field
@@ -756,7 +756,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<Mesh> fieldSrc(mesh);
{ // Setup source field
@@ -839,7 +839,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<Mesh> field(mesh);
field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
@@ -899,7 +899,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<Mesh> field(mesh);
field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
@@ -937,7 +937,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<Mesh> field(mesh);
const std::string& label = "field A";
@@ -1002,7 +1002,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<Mesh> field(mesh);
const std::string& label = "field A";
@@ -1067,7 +1067,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<Mesh> field(mesh);
field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
@@ -1109,7 +1109,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<Mesh> field(mesh);
field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
@@ -1168,7 +1168,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<Mesh> field(mesh);
field.newSection(Field<Mesh>::VERTICES_FIELD, fiberDim);
@@ -1229,7 +1229,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Create field with section to use to create new field
Field<Mesh> fieldSrc(mesh);
@@ -1320,7 +1320,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Create field with atlas to use to create new field
Field<Mesh> fieldSrc(mesh);
@@ -1430,9 +1430,9 @@
ALE::SieveBuilder<Mesh::SieveMesh>::buildCoordinates(sieveMesh, spaceDim,
coordinates);
- err = DMComplexSetChart(dmMesh, 0, ncells+nvertices);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetChart(dmMesh, 0, ncells+nvertices);CHECK_PETSC_ERROR(err);
for(PetscInt c = 0; c < ncells; ++c) {
- err = DMComplexSetConeSize(dmMesh, c, ncorners);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetConeSize(dmMesh, c, ncorners);CHECK_PETSC_ERROR(err);
}
err = DMSetUp(dmMesh);CHECK_PETSC_ERROR(err);
PetscInt *cone = new PetscInt[ncorners];
@@ -1440,17 +1440,17 @@
for(PetscInt v = 0; v < ncorners; ++v) {
cone[v] = cells[c*ncorners+v]+ncells;
}
- err = DMComplexSetCone(dmMesh, c, cone);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetCone(dmMesh, c, cone);CHECK_PETSC_ERROR(err);
} // for
delete [] cone; cone = 0;
- err = DMComplexSymmetrize(dmMesh);CHECK_PETSC_ERROR(err);
- err = DMComplexStratify(dmMesh);CHECK_PETSC_ERROR(err);
+ err = DMPlexSymmetrize(dmMesh);CHECK_PETSC_ERROR(err);
+ err = DMPlexStratify(dmMesh);CHECK_PETSC_ERROR(err);
PetscSection coordSection;
Vec coordVec;
PetscScalar *coords;
PetscInt coordSize;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, ncells, ncells+nvertices);CHECK_PETSC_ERROR(err);
for(PetscInt v = ncells; v < ncells+nvertices; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
Modified: short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldSubMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldSubMesh.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldSubMesh.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -146,7 +146,7 @@
Field<SubMesh> field(submesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
field.newSection(topology::FieldBase::VERTICES_FIELD, fiberDim);
field.allocate();
PetscSection section = field.petscSection();
@@ -181,7 +181,7 @@
CPPUNIT_ASSERT(section);CPPUNIT_ASSERT(vec);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
PetscInt dof;
err = PetscSectionGetDof(section, v, &dof);CHECK_PETSC_ERROR(err);
@@ -216,7 +216,7 @@
Vec vec = field.localVector();
CPPUNIT_ASSERT(section);CPPUNIT_ASSERT(vec);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
for(PetscInt v = vStart; v < vEnd; ++v) {
PetscInt dof;
err = PetscSectionGetDof(section, v, &dof);CHECK_PETSC_ERROR(err);
@@ -246,7 +246,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
// Create field with atlas to use to create new field
Field<SubMesh> fieldSrc(submesh);
@@ -326,7 +326,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<SubMesh> field(submesh);
field.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
@@ -382,7 +382,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<SubMesh> field(submesh);
field.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
@@ -440,7 +440,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<SubMesh> field(submesh);
field.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
@@ -499,7 +499,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<SubMesh> fieldSrc(submesh);
{ // Setup source field
@@ -572,7 +572,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<SubMesh> fieldSrc(submesh);
{ // Setup source field
@@ -655,7 +655,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<SubMesh> field(submesh);
field.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
@@ -715,7 +715,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<SubMesh> field(submesh);
field.newSection(Field<SubMesh>::VERTICES_FIELD, fiberDim);
@@ -754,7 +754,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<SubMesh> field(submesh);
field.newSection(FieldBase::VERTICES_FIELD, fiberDim);
@@ -812,7 +812,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<SubMesh> field(submesh);
field.newSection(FieldBase::VERTICES_FIELD, fiberDim);
@@ -870,7 +870,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<SubMesh> field(submesh);
field.newSection(FieldBase::VERTICES_FIELD, fiberDim);
@@ -912,7 +912,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<SubMesh> field(submesh);
field.newSection(FieldBase::VERTICES_FIELD, fiberDim);
@@ -971,7 +971,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
Field<SubMesh> field(submesh);
field.newSection(FieldBase::VERTICES_FIELD, fiberDim);
@@ -1051,9 +1051,9 @@
ALE::SieveBuilder<SieveMesh>::buildCoordinates(sieveMesh, spaceDim,
coordinates);
- err = DMComplexSetChart(dmMesh, 0, ncells+nvertices);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetChart(dmMesh, 0, ncells+nvertices);CHECK_PETSC_ERROR(err);
for(PetscInt c = 0; c < ncells; ++c) {
- err = DMComplexSetConeSize(dmMesh, c, ncorners);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetConeSize(dmMesh, c, ncorners);CHECK_PETSC_ERROR(err);
}
err = DMSetUp(dmMesh);CHECK_PETSC_ERROR(err);
PetscInt *cone = new PetscInt[ncorners];
@@ -1061,17 +1061,17 @@
for(PetscInt v = 0; v < ncorners; ++v) {
cone[v] = cells[c*ncorners+v]+ncells;
}
- err = DMComplexSetCone(dmMesh, c, cone);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetCone(dmMesh, c, cone);CHECK_PETSC_ERROR(err);
} // for
delete [] cone; cone = 0;
- err = DMComplexSymmetrize(dmMesh);CHECK_PETSC_ERROR(err);
- err = DMComplexStratify(dmMesh);CHECK_PETSC_ERROR(err);
+ err = DMPlexSymmetrize(dmMesh);CHECK_PETSC_ERROR(err);
+ err = DMPlexStratify(dmMesh);CHECK_PETSC_ERROR(err);
PetscSection coordSection;
Vec coordVec;
PetscScalar *coords;
PetscInt coordSize;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, ncells, ncells+nvertices);CHECK_PETSC_ERROR(err);
for(PetscInt v = ncells; v < ncells+nvertices; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
@@ -1108,7 +1108,7 @@
sieveMesh->allocate(groupField);
for(PetscInt i = 0; i < numPoints; ++i) {
- err = DMComplexSetLabelValue(dmMesh, _TestFieldSubMesh::label, ncells+_TestFieldSubMesh::groupVertices[i], 1);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(dmMesh, _TestFieldSubMesh::label, ncells+_TestFieldSubMesh::groupVertices[i], 1);CHECK_PETSC_ERROR(err);
}
spatialdata::geocoords::CSCart cs;
Modified: short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsMesh.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsMesh.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -88,7 +88,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const char* label = "field";
fields.add(label, "velocity", Field<Mesh>::VERTICES_FIELD, fiberDim);
@@ -194,7 +194,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const char* labelA = "field A";
fields.add(labelA, "displacement", Field<Mesh>::VERTICES_FIELD, fiberDim);
Modified: short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsNewMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsNewMesh.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsNewMesh.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -213,7 +213,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
fields.add("field A", "velocity", 3, FieldBase::VECTOR);
fields.add("field B", "displacement", 4, FieldBase::OTHER, 2.0, true);
@@ -270,7 +270,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
fields.add("field A", "velocity", 3, FieldBase::VECTOR);
fields.add("field B", "displacement", 4, FieldBase::OTHER, 2.0, true);
Modified: short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsSubMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsSubMesh.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/topology/TestFieldsSubMesh.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -91,7 +91,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const char* label = "field";
fields.add(label, "velocity", Field<SubMesh>::VERTICES_FIELD, fiberDim);
@@ -196,7 +196,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const char* labelA = "field A";
fields.add(labelA, "velocity", Field<SubMesh>::VERTICES_FIELD, fiberDim);
Modified: short/3D/PyLith/trunk/unittests/libtests/topology/TestSolutionFields.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/topology/TestSolutionFields.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/topology/TestSolutionFields.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -65,7 +65,7 @@
CPPUNIT_ASSERT(dmMesh);
PetscInt vStart, vEnd;
- err = DMComplexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetDepthStratum(dmMesh, 0, &vStart, &vEnd);CHECK_PETSC_ERROR(err);
const char* labels[] = { "field A", "field B", "field C" };
const int size = 3;
Modified: short/3D/PyLith/trunk/unittests/libtests/topology/TestSubMesh.cc
===================================================================
--- short/3D/PyLith/trunk/unittests/libtests/topology/TestSubMesh.cc 2012-12-30 04:06:26 UTC (rev 21206)
+++ short/3D/PyLith/trunk/unittests/libtests/topology/TestSubMesh.cc 2013-01-05 17:40:22 UTC (rev 21207)
@@ -240,9 +240,9 @@
ALE::SieveBuilder<Mesh::SieveMesh>::buildCoordinates(sieveMesh, spaceDim,
coordinates);
- err = DMComplexSetChart(dmMesh, 0, ncells+nvertices);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetChart(dmMesh, 0, ncells+nvertices);CHECK_PETSC_ERROR(err);
for(PetscInt c = 0; c < ncells; ++c) {
- err = DMComplexSetConeSize(dmMesh, c, ncorners);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetConeSize(dmMesh, c, ncorners);CHECK_PETSC_ERROR(err);
}
err = DMSetUp(dmMesh);CHECK_PETSC_ERROR(err);
PetscInt *cone = new PetscInt[ncorners];
@@ -250,17 +250,17 @@
for(PetscInt v = 0; v < ncorners; ++v) {
cone[v] = cells[c*ncorners+v]+ncells;
}
- err = DMComplexSetCone(dmMesh, c, cone);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetCone(dmMesh, c, cone);CHECK_PETSC_ERROR(err);
} // for
delete [] cone; cone = 0;
- err = DMComplexSymmetrize(dmMesh);CHECK_PETSC_ERROR(err);
- err = DMComplexStratify(dmMesh);CHECK_PETSC_ERROR(err);
+ err = DMPlexSymmetrize(dmMesh);CHECK_PETSC_ERROR(err);
+ err = DMPlexStratify(dmMesh);CHECK_PETSC_ERROR(err);
PetscSection coordSection;
Vec coordVec;
PetscScalar *coords;
PetscInt coordSize;
- err = DMComplexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
+ err = DMPlexGetCoordinateSection(dmMesh, &coordSection);CHECK_PETSC_ERROR(err);
err = PetscSectionSetChart(coordSection, ncells, ncells+nvertices);CHECK_PETSC_ERROR(err);
for(PetscInt v = ncells; v < ncells+nvertices; ++v) {
err = PetscSectionSetDof(coordSection, v, spaceDim);CHECK_PETSC_ERROR(err);
@@ -301,7 +301,7 @@
sieveMesh->allocate(groupField);
for(PetscInt i = 0; i < numPoints; ++i) {
- err = DMComplexSetLabelValue(dmMesh, _TestSubMesh::label, ncells+_TestSubMesh::groupVertices[i], 1);CHECK_PETSC_ERROR(err);
+ err = DMPlexSetLabelValue(dmMesh, _TestSubMesh::label, ncells+_TestSubMesh::groupVertices[i], 1);CHECK_PETSC_ERROR(err);
}
} // _buildMesh
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