[cig-commits] [commit] master: Merge branch 'master' of github.com:geodynamics/pylith (267416d)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Nov 19 20:27:35 PST 2014
Repository : https://github.com/geodynamics/pylith
On branch : master
Link : https://github.com/geodynamics/pylith/compare/1d7550d853e7269ae2c039f38f58f9436ed11d00...267416da34242c9d6d5f66fc685295b7bab12211
>---------------------------------------------------------------
commit 267416da34242c9d6d5f66fc685295b7bab12211
Merge: f061499 1d7550d
Author: Charles Williams <C.Williams at gns.cri.nz>
Date: Thu Nov 20 17:23:37 2014 +1300
Merge branch 'master' of github.com:geodynamics/pylith
* 'master' of github.com:geodynamics/pylith: (43 commits)
Fixed makefiles for 3-D plasticity test.
Cleanup of 3-D plasticity test.
Cleanup of Makefiles for creating source distribution.
Cleaned up cfg files and dir structure for 2-D plasticity test.
Updated userguide to describe feasible stress state.
Added 2D version of plasticity test and moved existing plasticity tests down a level. They probably need updating.
Added missing makefiles.
Modified Drucker-Prager for the case where there is no plastic yield and tensile yield is not allowed.
Added test for plasticity + initial stress (3d).
Some changes to plasticity section plus changed version of LyX to older version.
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.
...
Conflicts:
examples/2d/gravity/Makefile.am
examples/2d/gravity/deform_view.pvsm
tests/2d/plasticity/Makefile.am
>---------------------------------------------------------------
267416da34242c9d6d5f66fc685295b7bab12211
configure.ac | 4 +-
doc/userguide/fileformats/fileformats.lyx | 29 +-
doc/userguide/materials/materials.lyx | 104 ++--
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/gravity/Makefile.am | 6 -
examples/2d/gravity/mesh.exo | Bin 0 -> 619904 bytes
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 | 35 +-
libsrc/pylith/faults/FaultCohesiveImpulses.cc | 2 +-
libsrc/pylith/faults/FaultCohesiveLagrange.cc | 56 +-
libsrc/pylith/materials/DruckerPrager3D.cc | 50 +-
.../pylith/materials/DruckerPragerPlaneStrain.cc | 50 +-
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/SolutionPoints.py | 89 ++++
tests/2d/Makefile.am | 3 +-
.../output => tests/2d/plasticity}/Makefile.am | 6 +-
tests/2d/plasticity/{ => compare3d}/README | 0
tests/2d/plasticity/{ => compare3d}/cyclic/README | 0
.../{ => compare3d}/cyclic/cycle_cont2d.cfg | 0
.../{ => compare3d}/cyclic/cycle_cont3d.cfg | 0
.../plasticity/{ => compare3d}/cyclic/dynamic.cfg | 0
.../{ => compare3d}/cyclic/loadcycle.timedb | 0
.../{ => compare3d}/cyclic/loadcycle_sin.timedb | 0
.../{ => compare3d}/cyclic/onecell_2d.cfg | 0
.../{ => compare3d}/cyclic/onecell_3d.cfg | 0
.../plasticity/{ => compare3d}/cyclic/plot_data.py | 0
.../{ => compare3d}/cyclic/pylithapp.cfg | 0
.../{ => compare3d}/cyclic/quasistatic.cfg | 0
.../{ => compare3d}/cyclic/run-models.sh | 0
.../2d/plasticity/{ => compare3d}/cyclic/sin2d.cfg | 0
.../{ => compare3d}/cyclic/sin2d_dynamic.cfg | 0
.../{ => compare3d}/cyclic/sin2d_quasistatic.cfg | 0
.../2d/plasticity/{ => compare3d}/cyclic/sin3d.cfg | 0
.../{ => compare3d}/cyclic/sin3d_dynamic.cfg | 0
.../{ => compare3d}/cyclic/sin3d_quasistatic.cfg | 0
.../{ => compare3d}/mesh/box_hex8_0.2m.exo | Bin
.../plasticity/{ => compare3d}/mesh/geometry2d.jou | 0
.../plasticity/{ => compare3d}/mesh/geometry3d.jou | 0
.../{ => compare3d}/mesh/mesh_hex8_0.2m.jou | 0
.../{ => compare3d}/mesh/mesh_quad4_0.2m.jou | 0
.../plasticity/{ => compare3d}/mesh/onehex8.mesh | 0
.../plasticity/{ => compare3d}/mesh/onequad4.mesh | 0
.../{ => compare3d}/mesh/plane_quad4_0.2m.exo | Bin
.../plasticity/{ => compare3d}/mesh/twohex8.mesh | 0
.../plasticity/{ => compare3d}/mesh/twoquad4.mesh | 0
tests/2d/plasticity/{ => compare3d}/static/README | 0
.../{ => compare3d}/static/axialdisp_fine_2d.cfg | 0
.../{ => compare3d}/static/axialdisp_fine_3d.cfg | 0
.../static/axialdisp_twocells_2d.cfg | 0
.../static/axialdisp_twocells_3d.cfg | 0
.../{ => compare3d}/static/planestrain_fine_2d.cfg | 0
.../{ => compare3d}/static/planestrain_fine_3d.cfg | 0
.../static/planestrain_twocells_2d.cfg | 0
.../static/planestrain_twocells_3d.cfg | 0
.../{ => compare3d}/static/pylithapp.cfg | 0
.../{ => compare3d}/static/run-models.sh | 0
.../{ => compare3d}/static/sheardisp_fine_2d.cfg | 0
.../{ => compare3d}/static/sheardisp_fine_3d.cfg | 0
.../static/sheardisp_twocells_2d.cfg | 0
.../static/sheardisp_twocells_3d.cfg | 0
.../2d/plasticity/initialstress}/Makefile.am | 19 +-
tests/2d/plasticity/initialstress/README | 17 +
tests/2d/plasticity/initialstress/elastic.cfg | 18 +
.../elastic_dt01.cfg} | 20 +-
.../elastic_dt02.cfg} | 20 +-
.../elastic_dt05.cfg} | 20 +-
.../elastic_dt10.cfg} | 20 +-
tests/2d/plasticity/initialstress/mesh.jou | 52 ++
tests/2d/plasticity/initialstress/mesh_quad4.exo | Bin 0 -> 3936 bytes
tests/2d/plasticity/initialstress/plastic.cfg | 23 +
.../plastic_dt01.cfg} | 20 +-
.../plastic_dt02.cfg} | 20 +-
.../plastic_dt05.cfg} | 20 +-
.../plastic_dt10.cfg} | 20 +-
tests/2d/plasticity/initialstress/plot_invars.py | 118 +++++
tests/2d/plasticity/initialstress/pylithapp.cfg | 159 ++++++
tests/2d/plasticity/initialstress/runtests.sh | 12 +
.../initialstress/simpleshear_velbc.spatialdb | 17 +
tests/3d/plasticity/Makefile.am | 3 +-
.../3d/plasticity/initialstress}/Makefile.am | 19 +-
tests/3d/plasticity/initialstress/README | 14 +
tests/3d/plasticity/initialstress/elastic.cfg | 18 +
.../plasticity/initialstress/elastic_dt01.cfg} | 20 +-
.../plasticity/initialstress/elastic_dt02.cfg} | 20 +-
.../plasticity/initialstress/elastic_dt05.cfg} | 20 +-
.../plasticity/initialstress/elastic_dt10.cfg} | 20 +-
tests/3d/plasticity/initialstress/mesh.jou | 61 +++
tests/3d/plasticity/initialstress/mesh_hex8.exo | Bin 0 -> 15848 bytes
tests/3d/plasticity/initialstress/plastic.cfg | 17 +
.../plasticity/initialstress/plastic_dt01.cfg} | 20 +-
.../plasticity/initialstress/plastic_dt02.cfg} | 20 +-
.../plasticity/initialstress/plastic_dt05.cfg} | 20 +-
.../plasticity/initialstress/plastic_dt10.cfg} | 20 +-
tests/3d/plasticity/initialstress/plot_invars.py | 133 +++++
tests/3d/plasticity/initialstress/pylithapp.cfg | 167 ++++++
tests/3d/plasticity/initialstress/runtests.sh | 13 +
.../initialstress/simpleshear_velbc.spatialdb | 17 +
tests_auto/2d/tri3/Makefile.am | 7 +-
...{TestSlipOneFault.py => TestFaultsIntersect.py} | 61 ++-
tests_auto/2d/tri3/TestSlipOneFault.py | 27 +
.../tri3/{sliponefault.cfg => faultsintersect.cfg} | 68 ++-
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 +-
.../TestFaultsIntersect.py} | 77 ++-
.../sliponefault.cfg => hex8/faultsintersect.cfg} | 84 +--
tests_auto/3d/hex8/testpylith.py | 3 +
tests_auto/3d/tet4/Makefile.am | 7 +-
...{TestSlipOneFault.py => TestFaultsIntersect.py} | 70 ++-
tests_auto/3d/tet4/TestSlipOneFault.py | 27 +
.../tet4/{sliponefault.cfg => faultsintersect.cfg} | 74 ++-
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 +--
.../libtests/meshio/TestDataWriterHDF5ExtPoints.hh | 80 +++
.../meshio/TestDataWriterHDF5ExtPointsCases.cc | 96 ++++
.../meshio/TestDataWriterHDF5ExtPointsCases.hh | 133 +++++
...terVTKPoints.cc => TestDataWriterHDF5Points.cc} | 59 +--
.../libtests/meshio/TestDataWriterHDF5Points.hh | 80 +++
.../meshio/TestDataWriterHDF5PointsCases.cc | 96 ++++
.../meshio/TestDataWriterHDF5PointsCases.hh | 133 +++++
.../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 +
.../meshio/data/DataWriterHDF5DataPointsHex8.cc | 167 ++++++
.../meshio/data/DataWriterHDF5DataPointsHex8.hh | 77 +++
.../meshio/data/DataWriterHDF5DataPointsQuad4.cc | 119 +++++
.../meshio/data/DataWriterHDF5DataPointsQuad4.hh | 75 +++
.../meshio/data/DataWriterHDF5DataPointsTet4.cc | 135 +++++
.../meshio/data/DataWriterHDF5DataPointsTet4.hh | 77 +++
.../meshio/data/DataWriterHDF5DataPointsTri3.cc | 125 +++++
.../meshio/data/DataWriterHDF5DataPointsTri3.hh | 77 +++
unittests/libtests/meshio/data/Makefile.am | 11 +-
unittests/libtests/meshio/data/hex8_points.h5 | Bin 0 -> 11288 bytes
.../libtests/meshio/data/hex8_points_vertex.h5 | Bin 0 -> 29536 bytes
unittests/libtests/meshio/data/quad4_points.h5 | Bin 0 -> 11288 bytes
.../libtests/meshio/data/quad4_points_vertex.h5 | Bin 0 -> 29536 bytes
unittests/libtests/meshio/data/tet4_points.h5 | Bin 0 -> 11288 bytes
.../libtests/meshio/data/tet4_points_vertex.h5 | Bin 0 -> 29536 bytes
unittests/libtests/meshio/data/tri3_points.h5 | Bin 0 -> 11288 bytes
.../libtests/meshio/data/tri3_points_vertex.h5 | Bin 0 -> 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 +
209 files changed, 5222 insertions(+), 1753 deletions(-)
diff --cc examples/2d/gravity/Makefile.am
index 4354644,b0fc743..04bf2a0
--- a/examples/2d/gravity/Makefile.am
+++ b/examples/2d/gravity/Makefile.am
@@@ -18,20 -18,14 +18,18 @@@
dist_noinst_DATA = \
README \
- geometry.jou \
- mesh.jou \
grav_stress-initial.spatialdb \
grav_stress.cfg \
+ grav_stress_finite_nois.cfg \
+ grav_stress_finite_is1.cfg \
grav_stress_finite_is2.cfg \
+ grav_stress_finite_is3.cfg \
+ grav_stress_infin_nois.cfg \
grav_stress_infin_is1.cfg \
grav_stress_infin_is2.cfg \
+ grav_stress_infin_is3.cfg \
mat_elastic.spatialdb \
mat_maxwell.spatialdb \
- mesh.jou \
pylithapp.cfg \
stress2spatialdb.py
diff --cc examples/2d/gravity/mesh.exo
index 0000000,0000000..c7b7baa
new file mode 100644
Binary files differ
More information about the CIG-COMMITS
mailing list