[cig-commits] [commit] baagaard/feature-output-station-names, baagaard/feature-progress-monitor, baagaard/fix-faults-intersect, master: Merge branch 'master' into baagaard/fix-faults-intersect (73e9867)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Nov 5 15:47:27 PST 2014
Repository : https://github.com/geodynamics/pylith
On branches: baagaard/feature-output-station-names,baagaard/feature-progress-monitor,baagaard/fix-faults-intersect,master
Link : https://github.com/geodynamics/pylith/compare/f33c75b19fd60eedb2a3405db76a1fee333bb1d7...5b6d812b1612809fea3bd331c4e5af98c25a536a
>---------------------------------------------------------------
commit 73e98674057018c1fc39a80722d1d2d463fe0db8
Merge: a606bd8 f339645
Author: Brad Aagaard <baagaard at usgs.gov>
Date: Tue Oct 28 10:17:47 2014 -0700
Merge branch 'master' into baagaard/fix-faults-intersect
* master: (39 commits)
Cleanup by using Field::globalSection().
Fix bug. Remove superfluous DMDestroy().
Add DM for subfields in Field. Refactor Field metadata.
Fix small compile bug.
Create Lagrange DM to get global section for fault preconditioner.
More updates for partitioner setting to PETSc.
Use PETSc partitioner setting.
Fixed partitioner settings.
Update Distributor for moving partitioner to PETSc setting.
Updated Distributor Python object for removal of partitioner
parameter.
Fixes to comments.
Distribution: Fixed interface to DMPlexDistribute()
Minor fix in Drucker-Prager equations (does not affect results).
Modified manual, code, and unit tests for error in Drucker-Prager
elastoplasticity. We were missing the initial pressure term. I haven't
tested yet.
Small fix for running tests with latest automake.
Configure: Upgrade to PETSc 3.5.2
Another update for PETSc 3.5.1 in libtests.
Update PETSc version check
Change DMPlexGet/SetDImension() to DMGet/SetDimension()
Small fixes to release announcement.
...
Conflicts:
libsrc/pylith/topology/Jacobian.cc
tests_auto/2d/tri3/Makefile.am
tests_auto/3d/hex8/testpylith.py
tests_auto/3d/tet4/Makefile.am
>---------------------------------------------------------------
73e98674057018c1fc39a80722d1d2d463fe0db8
CHANGES | 2 +-
README | 12 +-
.../meshing/surface_nurbs/Makefile.am => check.am | 10 +-
configure.ac | 9 +-
.../{announce_v2.0.1.txt => announce_v2.0.3.txt} | 44 +++-
doc/userguide/materials/materials.lyx | 95 +++----
doc/userguide/runpylith/runpylith.lyx | 45 ++--
libsrc/pylith/Makefile.am | 6 +-
libsrc/pylith/bc/DirichletBC.cc | 4 +-
libsrc/pylith/bc/PointForce.cc | 6 +-
libsrc/pylith/faults/CohesiveTopology.cc | 14 +-
libsrc/pylith/faults/FaultCohesive.cc | 5 +-
libsrc/pylith/faults/FaultCohesiveDyn.cc | 35 +--
libsrc/pylith/faults/FaultCohesiveImpulses.cc | 13 +-
libsrc/pylith/faults/FaultCohesiveLagrange.cc | 132 ++++------
libsrc/pylith/faults/TimeHistorySlipFn.cc | 4 +-
libsrc/pylith/faults/TopologyOps.cc | 2 +-
libsrc/pylith/faults/TractPerturbation.cc | 6 +-
libsrc/pylith/feassemble/CellGeometry.cc | 3 +-
libsrc/pylith/friction/FrictionModel.cc | 22 +-
libsrc/pylith/materials/DruckerPrager3D.cc | 24 +-
.../pylith/materials/DruckerPragerPlaneStrain.cc | 24 +-
libsrc/pylith/materials/ElasticMaterial.cc | 10 +-
libsrc/pylith/materials/Material.cc | 18 +-
libsrc/pylith/meshio/DataWriterHDF5.cc | 6 +-
libsrc/pylith/meshio/DataWriterHDF5Ext.cc | 8 +-
libsrc/pylith/meshio/DataWriterVTK.cc | 4 +-
libsrc/pylith/meshio/MeshBuilder.cc | 3 +-
libsrc/pylith/meshio/MeshIOCubit.cc | 3 +-
libsrc/pylith/problems/Solver.cc | 15 +-
libsrc/pylith/topology/Distributor.cc | 5 +-
libsrc/pylith/topology/Distributor.hh | 4 +-
libsrc/pylith/topology/Field.cc | 285 +++++++++++----------
libsrc/pylith/topology/Field.hh | 49 ++--
libsrc/pylith/topology/Field.icc | 39 +--
libsrc/pylith/topology/FieldBase.hh | 8 +-
libsrc/pylith/topology/Fields.cc | 18 +-
libsrc/pylith/topology/Jacobian.cc | 4 +-
libsrc/pylith/topology/Mesh.cc | 8 +-
libsrc/pylith/topology/Mesh.icc | 2 +-
libsrc/pylith/topology/MeshOps.cc | 5 +-
libsrc/pylith/topology/SolutionFields.cc | 3 +-
libsrc/pylith/topology/VisitorMesh.hh | 2 +-
libsrc/pylith/topology/VisitorMesh.icc | 18 +-
libsrc/pylith/topology/VisitorSubMesh.icc | 4 +-
modulesrc/bc/Makefile.am | 3 +-
modulesrc/faults/Makefile.am | 3 +-
modulesrc/feassemble/Makefile.am | 3 +-
modulesrc/friction/Makefile.am | 3 +-
modulesrc/materials/Makefile.am | 3 +-
modulesrc/meshio/Makefile.am | 3 +-
examples/2d/Makefile.am => modulesrc/module.am | 11 +-
modulesrc/mpi/Makefile.am | 3 +-
modulesrc/problems/Makefile.am | 3 +-
modulesrc/topology/Distributor.i | 5 +-
modulesrc/topology/Makefile.am | 3 +-
modulesrc/utils/Makefile.am | 4 +-
pylith/topology/Distributor.py | 9 +-
pylith/topology/MeshImporter.py | 2 +-
subpackage.am | 17 --
templates/friction/Makefile.am | 6 +-
templates/materials/Makefile.am | 6 +-
tests/3d/refine/pylithapp.cfg | 2 +-
tests/distribute/mesherapp.cfg | 4 +-
tests/topology/Makefile.am | 4 +-
tests_auto/2d/quad4/Makefile.am | 10 +-
tests_auto/2d/quad4/testpylith.py | 2 +-
tests_auto/2d/tri3/Makefile.am | 10 +-
tests_auto/2d/tri3/sheardispfriction.cfg | 2 +
tests_auto/2d/tri3/testpylith.py | 2 +-
tests_auto/3d/hex8/Makefile.am | 13 +-
...estShearDispNoSlip.py => TestFrictionNoSlip.py} | 37 +--
...hearDispNoSlip.py => TestFrictionNoSlipHalo.py} | 50 ++--
.../frictionnoslip.cfg} | 148 +++++++----
.../frictionnoslip_halo.cfg} | 152 ++++++-----
tests_auto/3d/hex8/testpylith.py | 8 +-
tests_auto/3d/tet4/Makefile.am | 9 +-
tests_auto/3d/tet4/testpylith.py | 2 +-
tests_auto/eqinfo/Makefile.am | 5 +-
tests_auto/eqinfo/test_eqinfo.py | 0
tests_auto/petsc/Makefile.am | 4 +-
tests_auto/petsc/testpetsc.py | 2 +-
unittests/libtests/bc/Makefile.am | 5 +-
unittests/libtests/bc/TestAbsorbingDampers.cc | 2 +-
unittests/libtests/bc/TestDirichletBC.cc | 4 +-
unittests/libtests/bc/TestDirichletBCMulti.cc | 2 +-
unittests/libtests/faults/Makefile.am | 3 +-
unittests/libtests/faults/TestFaultCohesiveDyn.cc | 4 +-
.../libtests/faults/TestFaultCohesiveImpulses.cc | 2 +-
unittests/libtests/faults/TestFaultCohesiveKin.cc | 8 +-
unittests/libtests/feassemble/Makefile.am | 3 +-
unittests/libtests/friction/Makefile.am | 3 +-
unittests/libtests/materials/Makefile.am | 3 +-
.../materials/data/DruckerPrager3DTimeDep.py | 2 +-
.../materials/data/DruckerPrager3DTimeDepData.cc | 96 +++----
.../data/DruckerPragerPlaneStrainTimeDep.py | 2 +-
.../data/DruckerPragerPlaneStrainTimeDepData.cc | 32 +--
unittests/libtests/meshio/Makefile.am | 3 +-
unittests/libtests/topology/Makefile.am | 3 +-
unittests/libtests/topology/TestFieldMesh.cc | 38 ++-
unittests/libtests/topology/TestFieldSubMesh.cc | 12 +-
unittests/libtests/topology/TestMesh.cc | 2 +-
unittests/libtests/utils/Makefile.am | 3 +-
unittests/pytests/bc/Makefile.am | 5 +-
unittests/pytests/bc/testbc.py | 2 +-
unittests/pytests/faults/Makefile.am | 5 +-
unittests/pytests/faults/testfaults.py | 2 +-
unittests/pytests/feassemble/Makefile.am | 5 +-
unittests/pytests/feassemble/testfeassemble.py | 2 +-
unittests/pytests/friction/Makefile.am | 5 +-
unittests/pytests/friction/testfriction.py | 2 +-
unittests/pytests/materials/Makefile.am | 5 +-
unittests/pytests/materials/testmaterials.py | 2 +-
unittests/pytests/meshio/Makefile.am | 5 +-
unittests/pytests/meshio/testcubit.py | 2 +-
unittests/pytests/meshio/testhdf5.py | 2 +-
unittests/pytests/meshio/testmeshio.py | 2 +-
unittests/pytests/mpi/Makefile.am | 5 +-
unittests/pytests/mpi/testmpi.py | 2 +-
unittests/pytests/problems/Makefile.am | 5 +-
unittests/pytests/problems/testproblems.py | 2 +-
unittests/pytests/topology/Makefile.am | 12 +-
unittests/pytests/topology/TestMeshGenSimple.py | 82 ------
unittests/pytests/topology/testgensimple.py | 75 ------
unittests/pytests/topology/testtopology.py | 2 +-
unittests/pytests/utils/Makefile.am | 5 +-
unittests/pytests/utils/testmanager.py | 2 +-
unittests/pytests/utils/testutils.py | 2 +-
128 files changed, 945 insertions(+), 1118 deletions(-)
diff --cc tests_auto/2d/tri3/Makefile.am
index c480638,18a7b87..b5443ec
--- a/tests_auto/2d/tri3/Makefile.am
+++ b/tests_auto/2d/tri3/Makefile.am
@@@ -34,9 -36,7 +36,8 @@@ dist_noinst_PYTHON =
TestSlipOneFault.py \
sliponefault_soln.py \
TestSlipTwoFaults.py \
- sliptwofaults_soln.py
+ sliptwofaults_soln.py \
- TestFaultsIntersect.py \
- testpylith.py
++ TestFaultsIntersect.py
dist_noinst_DATA = \
geometry.jou \
diff --cc tests_auto/2d/tri3/testpylith.py
index 69a3b77,8c3d90d..39227eb
mode 100644,100755..100755
--- a/tests_auto/2d/tri3/testpylith.py
+++ b/tests_auto/2d/tri3/testpylith.py
diff --cc tests_auto/3d/hex8/testpylith.py
index 983ae9e,4c5c3ed..207ab31
mode 100644,100755..100755
--- a/tests_auto/3d/hex8/testpylith.py
+++ b/tests_auto/3d/hex8/testpylith.py
@@@ -42,9 -42,12 +42,15 @@@ def suite()
from TestSlipTwoFaults import TestSlipTwoFaults
suite.addTest(unittest.makeSuite(TestSlipTwoFaults))
+ from TestFaultsIntersect import TestFaultsIntersect
+ suite.addTest(unittest.makeSuite(TestFaultsIntersect))
+
+ from TestFrictionNoSlip import TestFrictionNoSlip
+ suite.addTest(unittest.makeSuite(TestFrictionNoSlip))
+
+ from TestFrictionNoSlipHalo import TestFrictionNoSlipHalo
+ suite.addTest(unittest.makeSuite(TestFrictionNoSlipHalo))
+
return suite
diff --cc tests_auto/3d/tet4/Makefile.am
index b59df47,52b0a15..1d132e3
--- a/tests_auto/3d/tet4/Makefile.am
+++ b/tests_auto/3d/tet4/Makefile.am
@@@ -33,9 -35,7 +35,8 @@@ dist_noinst_PYTHON =
TestSlipOneFault.py \
sliponefault_soln.py \
TestSlipTwoFaults.py \
- sliptwofaults_soln.py
+ sliptwofaults_soln.py \
- TestFaultsIntersect.py \
- testpylith.py
++ TestFaultsIntersect.py
dist_noinst_DATA = \
diff --cc tests_auto/3d/tet4/testpylith.py
index 983ae9e,e293cb6..0e402f9
mode 100644,100755..100755
--- a/tests_auto/3d/tet4/testpylith.py
+++ b/tests_auto/3d/tet4/testpylith.py
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