[cig-commits] [commit] baagaard/dynrup-new-lagrange: Merge branch 'master' into baagaard/dynrup-new-lagrange (050017f)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Mon Nov 10 13:43:38 PST 2014
Repository : https://github.com/geodynamics/pylith
On branch : baagaard/dynrup-new-lagrange
Link : https://github.com/geodynamics/pylith/compare/ad7af47970f91fc952cbd9bf38e76f8effdf7aff...050017f6d063e02416f27641edd180a086ea74fb
>---------------------------------------------------------------
commit 050017f6d063e02416f27641edd180a086ea74fb
Merge: ad7af47 62d7066
Author: Brad Aagaard <baagaard at usgs.gov>
Date: Mon Nov 10 13:43:19 2014 -0800
Merge branch 'master' into baagaard/dynrup-new-lagrange
* master: (33 commits)
Added station names to documentation.
Add station names to examples with OutputSolnPoints.
Fix update conditions.
Added testing of OutputSolnPoints to 3-D full-scale test.
Add testing of OutputSolnPoints to full-scale test.
Use list for station names.
Added output of station name at Python level.
Added unit tests for writing point data with DataWriterHDF5Ext.
Finished C++ implementation of writing station names.
Switch to fixed length string dataset in HDF5 to allow parallel I/O.
Add station name to list of points for output.
Small improvement to unit test.
Add writePointNames() to DataWriter.
Added documentation for progress monitors.
Refactor ProgressMonitor into ProgressMonitor, ProgressMonitorTime,
and ProgressMonitorStep.
Added unit test for ProgressMonitor.
Added progress monitor to TimeDependent.
Started work on progress monitor.
Add missing files for fault interesection test to Makefile.
Small fix for getting edge nodeset in parallel.
...
Conflicts:
libsrc/pylith/faults/FaultCohesiveDyn.cc
>---------------------------------------------------------------
050017f6d063e02416f27641edd180a086ea74fb
doc/userguide/fileformats/fileformats.lyx | 29 +-
doc/userguide/runpylith/figs/hdf5layout.pdf | Bin 9007 -> 26373 bytes
doc/userguide/runpylith/figs/hdf5layout.svg | 567 ---------------------
doc/userguide/runpylith/figs/hdf5layout.tex | 60 +++
doc/userguide/runpylith/runpylith.lyx | 155 +++++-
examples/2d/greensfns/reverse/output_points.txt | 26 +-
examples/2d/greensfns/strikeslip/output_points.txt | 66 +--
examples/3d/hex8/output_points.txt | 10 +-
libsrc/pylith/bc/DirichletBC.cc | 4 +-
libsrc/pylith/bc/PointForce.cc | 6 +-
libsrc/pylith/faults/FaultCohesive.cc | 10 +-
libsrc/pylith/faults/FaultCohesiveDyn.cc | 7 +-
libsrc/pylith/faults/FaultCohesiveImpulses.cc | 2 +-
libsrc/pylith/faults/FaultCohesiveLagrange.cc | 56 +-
libsrc/pylith/materials/Material.cc | 4 +-
libsrc/pylith/meshio/DataWriter.cc | 11 +
libsrc/pylith/meshio/DataWriter.hh | 11 +
libsrc/pylith/meshio/DataWriterHDF5.cc | 36 +-
libsrc/pylith/meshio/DataWriterHDF5.hh | 15 +
libsrc/pylith/meshio/DataWriterHDF5Ext.cc | 34 +-
libsrc/pylith/meshio/DataWriterHDF5Ext.hh | 11 +
libsrc/pylith/meshio/DataWriterVTK.cc | 4 +-
libsrc/pylith/meshio/HDF5.cc | 416 +++++++++------
libsrc/pylith/meshio/HDF5.hh | 67 ++-
libsrc/pylith/meshio/OutputManager.hh | 15 +-
libsrc/pylith/meshio/OutputSolnPoints.cc | 14 +
libsrc/pylith/meshio/OutputSolnPoints.hh | 10 +
libsrc/pylith/meshio/Xdmf.cc | 9 +-
libsrc/pylith/problems/Solver.cc | 15 +-
libsrc/pylith/topology/Field.cc | 272 +++++-----
libsrc/pylith/topology/Field.hh | 49 +-
libsrc/pylith/topology/Field.icc | 39 +-
libsrc/pylith/topology/FieldBase.hh | 8 +-
libsrc/pylith/topology/VisitorMesh.hh | 2 +-
libsrc/pylith/topology/VisitorMesh.icc | 18 +-
libsrc/pylith/topology/VisitorSubMesh.icc | 4 +-
modulesrc/meshio/DataWriter.i | 11 +
modulesrc/meshio/DataWriterHDF5.i | 10 +
modulesrc/meshio/DataWriterHDF5Ext.i | 10 +
modulesrc/meshio/OutputSolnPoints.i | 12 +
modulesrc/meshio/meshio.i | 1 +
pylith/Makefile.am | 4 +
pylith/meshio/OutputSolnPoints.py | 18 +-
pylith/meshio/PointsList.py | 56 +-
pylith/problems/GreensFns.py | 13 +
pylith/problems/ProgressMonitor.py | 140 +++++
pylith/problems/ProgressMonitorStep.py | 109 ++++
pylith/problems/ProgressMonitorTime.py | 118 +++++
pylith/problems/TimeDependent.py | 25 +-
pylith/problems/__init__.py | 4 +-
pylith/tests/Fault.py | 4 +-
pylith/tests/{Solution.py => SolutionPoints.py} | 29 +-
tests_auto/2d/tri3/Makefile.am | 7 +-
...{TestSlipOneFault.py => TestFaultsIntersect.py} | 61 ++-
tests_auto/2d/tri3/TestSlipOneFault.py | 27 +
.../{sliptwofaults.cfg => faultsintersect.cfg} | 60 +--
tests_auto/2d/tri3/points.txt | 4 +
tests_auto/2d/tri3/sliponefault.cfg | 12 +-
tests_auto/2d/tri3/sliponefault_soln.py | 5 +-
tests_auto/2d/tri3/testpylith.py | 3 +
tests_auto/3d/hex8/Makefile.am | 6 +-
...{TestSlipOneFault.py => TestFaultsIntersect.py} | 71 ++-
.../{sliptwofaults.cfg => faultsintersect.cfg} | 66 +--
tests_auto/3d/hex8/testpylith.py | 3 +
tests_auto/3d/tet4/Makefile.am | 7 +-
...tSlipTwoFaultsNP2.py => TestFaultsIntersect.py} | 82 +--
tests_auto/3d/tet4/TestSlipOneFault.py | 27 +
.../{sliptwofaults.cfg => faultsintersect.cfg} | 68 +--
tests_auto/3d/tet4/points.txt | 4 +
tests_auto/3d/tet4/sliponefault.cfg | 10 +-
tests_auto/3d/tet4/sliponefault_soln.py | 5 +-
tests_auto/3d/tet4/testpylith.py | 3 +
unittests/libtests/bc/TestAbsorbingDampers.cc | 2 +-
unittests/libtests/bc/TestDirichletBC.cc | 4 +-
unittests/libtests/bc/TestDirichletBCMulti.cc | 2 +-
unittests/libtests/faults/TestFaultCohesiveDyn.cc | 4 +-
.../libtests/faults/TestFaultCohesiveImpulses.cc | 2 +-
unittests/libtests/faults/TestFaultCohesiveKin.cc | 8 +-
unittests/libtests/meshio/Makefile.am | 16 +
unittests/libtests/meshio/TestDataWriterHDF5.cc | 156 +++---
...VTKPoints.cc => TestDataWriterHDF5ExtPoints.cc} | 61 +--
...VTKPoints.hh => TestDataWriterHDF5ExtPoints.hh} | 26 +-
...ases.cc => TestDataWriterHDF5ExtPointsCases.cc} | 47 +-
...ases.hh => TestDataWriterHDF5ExtPointsCases.hh} | 60 +--
...terVTKPoints.cc => TestDataWriterHDF5Points.cc} | 59 +--
...terVTKPoints.hh => TestDataWriterHDF5Points.hh} | 26 +-
...shCases.cc => TestDataWriterHDF5PointsCases.cc} | 47 +-
...tsCases.hh => TestDataWriterHDF5PointsCases.hh} | 60 +--
.../libtests/meshio/TestDataWriterVTKPoints.cc | 2 +
unittests/libtests/meshio/TestHDF5.cc | 80 ++-
unittests/libtests/meshio/TestHDF5.hh | 13 +-
.../libtests/meshio/data/DataWriterDataPoints.cc | 3 +-
.../libtests/meshio/data/DataWriterDataPoints.hh | 1 +
...intsHex8.cc => DataWriterHDF5DataPointsHex8.cc} | 52 +-
...intsTet4.hh => DataWriterHDF5DataPointsHex8.hh} | 23 +-
...tsQuad4.cc => DataWriterHDF5DataPointsQuad4.cc} | 47 +-
...tsQuad4.hh => DataWriterHDF5DataPointsQuad4.hh} | 23 +-
...intsTet4.cc => DataWriterHDF5DataPointsTet4.cc} | 52 +-
...intsTet4.hh => DataWriterHDF5DataPointsTet4.hh} | 23 +-
...ntsQuad4.cc => DataWriterHDF5DataPointsTri3.cc} | 67 +--
...intsTet4.hh => DataWriterHDF5DataPointsTri3.hh} | 23 +-
unittests/libtests/meshio/data/Makefile.am | 11 +-
.../meshio/data/{tet4_surf.h5 => hex8_points.h5} | Bin 11016 -> 11288 bytes
.../{tri3_mat_cell.h5 => hex8_points_vertex.h5} | Bin 29088 -> 29536 bytes
.../meshio/data/{tri3_bc.h5 => quad4_points.h5} | Bin 11016 -> 11288 bytes
.../{tri3_bc_cell.h5 => quad4_points_vertex.h5} | Bin 29088 -> 29536 bytes
.../meshio/data/{tet4_surf.h5 => tet4_points.h5} | Bin 11016 -> 11288 bytes
.../{tet4_surf_cell.h5 => tet4_points_vertex.h5} | Bin 29088 -> 29536 bytes
.../meshio/data/{tri3_bc.h5 => tri3_points.h5} | Bin 11016 -> 11288 bytes
.../{tet4_bc_cell.h5 => tri3_points_vertex.h5} | Bin 29088 -> 29536 bytes
unittests/libtests/topology/TestFieldMesh.cc | 38 +-
unittests/libtests/topology/TestFieldSubMesh.cc | 12 +-
unittests/pytests/meshio/data/point.txt | 2 +-
unittests/pytests/meshio/data/points.txt | 6 +-
unittests/pytests/problems/Makefile.am | 5 +-
unittests/pytests/problems/TestProgressMonitor.py | 87 ++++
.../pytests/problems/TestProgressMonitorStep.py | 105 ++++
.../pytests/problems/TestProgressMonitorTime.py | 102 ++++
unittests/pytests/problems/data/Makefile.am | 4 +-
unittests/pytests/problems/testproblems.py | 9 +
120 files changed, 2751 insertions(+), 1776 deletions(-)
diff --cc libsrc/pylith/faults/FaultCohesiveDyn.cc
index 00b3242,22cda36..9e52331
--- a/libsrc/pylith/faults/FaultCohesiveDyn.cc
+++ b/libsrc/pylith/faults/FaultCohesiveDyn.cc
@@@ -219,12 -207,9 +219,10 @@@ pylith::faults::FaultCohesiveDyn::integ
// Get cell geometry information that doesn't depend on cell
const int spaceDim = _quadrature->spaceDim();
+ const int indexN = spaceDim - 1;
// Get sections associated with cohesive cells
- PetscDM residualDM = residual.dmMesh();assert(residualDM);
- PetscSection residualGlobalSection = NULL;
- PetscErrorCode err = DMGetDefaultGlobalSection(residualDM, &residualGlobalSection);PYLITH_CHECK_ERROR(err);assert(residualGlobalSection);
+ PetscSection residualGlobalSection = residual.globalSection();assert(residualGlobalSection);
topology::VecVisitorMesh residualVisitor(residual);
PetscScalar* residualArray = residualVisitor.localArray();
@@@ -815,12 -542,13 +814,12 @@@ pylith::faults::FaultCohesiveDyn::adjus
topology::VecVisitorMesh dispTVisitor(fields->get("disp(t)"));
const PetscScalar* dispTArray = dispTVisitor.localArray();
- scalar_array dDispTIncrVertexN(spaceDim);
- scalar_array dDispTIncrVertexP(spaceDim);
+ scalar_array dispIncrVertexN(spaceDim);
+ scalar_array dispIncrVertexP(spaceDim);
+ scalar_array lagrangeTIncrVertex(spaceDim);
topology::VecVisitorMesh dispTIncrVisitor(fields->get("dispIncr(t->t+dt)"));
- PetscScalar* dispTIncrArray = dispTIncrVisitor.localArray();
+ const PetscScalar* dispTIncrArray = dispTIncrVisitor.localArray();
- PetscSection dispTIncrGlobalSection = fields->get("dispIncr(t->t+dt)").globalSection();assert(dispTIncrGlobalSection);
-
topology::VecVisitorMesh dispTIncrAdjVisitor(fields->get("dispIncr adjust"));
PetscScalar* dispTIncrAdjArray = dispTIncrAdjVisitor.localArray();
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