[cig-commits] [commit] master's head updated: Added more notes to release checklist. (1b3d6d3)

[cig_noreply at geodynamics.org]

Repository : ssh://geoshell/pylith

Branch 'master' now includes:

     b10003a Topology: Updated to new DMCreateMatrix() interface
     f1007d5 Topology: Updated to new DMPlexDistribute() interface
     6b5ddb4 Topology+Fault: Updated to new DMPlexCreateSubmesh() interface
     0f1f7b7 Mesh: Hardwire mesh interpolation
     9f8e24d BC: Only allow vertices in BC points
     aba87a2 Update ReverseCuthillMcKee for DMPlex [unit tests not passing].
     8e347a9 Enable unit tests for refinement with faults (all but hex).
     3a351f6 Turn off some debugging
     000fc3e Faults: Turn off Line2 test for cohesive fault right now
     3a1c2fe Merge branch 'knepley/upgrade-petsc-interface' of github.com:geodynamics/pylith into knepley/upgrade-petsc-interface
     750d1ef Merge branch 'knepley/upgrade-petsc-interface' of github.com:geodynamics/pylith into knepley/upgrade-petsc-interface
     90bb0cd More work on reordering unit tests.
     885a302 Add some output to indicate forced failure of test.
     1a9e203 Finish implementation of unit tests for reordering.
     cccfaaa Remove debugging output from reordering tests.
     ddb7dc0 Added edge identifier to Fault for marking buried fault edges.
     45c4093 Merge branch 'knepley/upgrade-petsc-interface' of github.com:geodynamics/pylith into knepley/upgrade-petsc-interface
     1151666 Updated refinement test (non-identity).
     67be97c MeshIO: Fixed label creation - Add in all points with marked vertices in cone
     ddec17c Refinement: Fixed test data
     2ae1c47 Merge branch 'master' into knepley/upgrade-petsc-interface
     bdcd276 Fault: Fixed construction of cohesive cells - I think that whole 'flip' argument is broken
     249ab15 MeshRefine: Remove diagnostic print
     98b94cb TopologyTests: Fixed data for tet4 fault test
     4d86128 TopologyTests: Fixed data for tri3 fault test
     9559ab4 TopologyTests: Only need to disable tensor product fault mesh tests
     fa51e99 TopologyTests: Fixed label check
     2588b6b Updated fault unit tests for interpolated meshes.
     9a3a8bc Switch to non-identity tests.
     7bbdc39 Added topology consistency checks to adjustTopology() test.
     ab98cb7 Faults: Changing from Lagrange vertices to hybrid edges
     0c6f872 Added notes on what needs updating.
     0e5e1c1 Merge branch 'knepley/upgrade-petsc-interface' of github.com:geodynamics/pylith into knepley/upgrade-petsc-interface
     4966842 MeshIO: Change check for groups to only use original points
     89e29fa MeshIO: Updated VTK Mesh tests - Note that data on the hybrid edges is now not tested
     d2e775b Cleanup of some names of Field methods.
     d4a29d6 Turn off some debugging output.
     4aaefd3 Update method name.
     c9f03f2 Worked on updating fault unit tests for interpolated meshes.
     52536fa Merge branch 'knepley/upgrade-petsc-interface' of github.com:geodynamics/pylith into knepley/upgrade-petsc-interface
     4fd816f Updated fault test data for interpolated meshes.
     086b7b9 Cleanup of names for Lagrange edges.
     4563c9e Faults: Better consistency testing
     433d7a7 Remove unnecessary header include.
     38a7730 Updated fault impulse tests for interpolated meshes.
     f29f8c0 Added consistency check of fault mesh for FaultCohesiveKin.
     84adc7d Merge branch 'knepley/upgrade-petsc-interface' of github.com:geodynamics/pylith into knepley/upgrade-petsc-interface
     aadf883 Improved comments.
     eb2a274 Updated FaultCohesiveDyn test data for interpolated meshes. Some data may be wrong.
     e5afe93 Removed some old debugging stuff.
     1162fc6 Added simple checksum for coordinates of cell vertices to reordering test.
     d80fbaf Removed unnecessary condition on skeleton consistency check for boundary meshes.
     34069d0 Merge branch 'master' into knepley/upgrade-petsc-interface
     d60fd06 Removed flip fault flag in creating fault mesh.
     f4fc4fb Update meshio test data for interpolated meshes.
     98eaaef Store alternate test data with flipped fault for future reference.
     6be2a62 Update meshio test data for interpolated meshes.
     3a389e4 Merge branch 'master' into knepley/upgrade-petsc-interface
     292dcca Merge branch 'master' into knepley/upgrade-petsc-interface
     e8880aa Remove obsolete function splitField().
     286ea25 Update PETSc settings to generate error if solver fails to converge.
     859a3b3 Merge branch 'master' into knepley/upgrade-petsc-interface
     0939f41 Remove splitField() from modules (removed from C++).
     7dc1717 Update to Python unit tests for C++ interface changes.
     6d86867 Update to Python unit tests for C++ interface changes.
     ae1c78e Merge branch 'knepley/upgrade-petsc-interface' of github.com:geodynamics/pylith into knepley/upgrade-petsc-interface
     f706511 Updated Python unit tests for interpolated meshes.
     02d6f9c Merge branch 'master' into knepley/upgrade-petsc-interface
     7dc94c6 Fixed typo in error message.
     c1b02f5 Added missing methods to module interface.
     7b13d2f Updated Python fault unit tests for interpolated meshes.
     44dc346 Fixed name of Lagrange multiplier field (consistency with C++).
     1f1ab42 Trivial code cleanup.
     38bd321 Added MeshOps::checkTopology().
     99cb2e2 VTK: Did not clear label before writing
     3cb90b6 MeshIO Tests: Changed what seem to be clearly wrong test data
     44a899a Merge branch 'knepley/upgrade-petsc-interface' of github.com:geodynamics/pylith into knepley/upgrade-petsc-interface
     dcfe4fb Updated fault C++ unit tests.
     1cae3da Updated meshio C++ test data for acceptable permutations.
     c7807de Faults: Added a check for hybrid edges in verifyConfiguration()
     e2c0b27 Remove reordering after adjusting topology and refinement.
     258af47 Updated hex8 fault meshio C++ test data for allowable perturbation.
     5812103 Integrator: Material-Id label has more than cells in it after refinement
     4829f3c Turn on DMPlexCheckSkeleton for any cellDim (not just cellDim > 1).
     70e98ee Setup topology::StratumIS interface to take arg to filter to cells only. New functionality NOT IMPLEMENTED.
     1955c80 Implemented StratumIS filtering to cells only.
     056b660 Throw exception with error message instead of assert.
     fd50ef8 Mesh: Fix DMPlexCheckSkeleton() for submeshes
     f1c4e75 Update creating solution field in Formulation.py.
     04bbef4 Merge branch 'knepley/upgrade-petsc-interface' of github.com:geodynamics/pylith into knepley/upgrade-petsc-interface
     b7e83fd Update to SNESGetLineSearch() from SNESGetSNESLineSearch().
     522e87e Faults: Orient cohesive submesh
     38af70f Added Field::copySubfield() to permit extracting subfields for output.
     e85362d Copy field and subfield metadata when cloning fields.
     cc6d236 Always create lagrange_multiplier subfield.
     e07734d Added C++ unit test for Field::copySubfield(). Fix bugs exposed.
     79acad1 Fix memory leak in extracting subfield.
     87dfaf0 Fix clearning of metadata when extracting subfield.
     bda5253 Extract displacement/velocity subfield from solution for output.
     391968f Cleanup adding subfields to field (include metadata).
     03bb552 Really fixed copying the metadata when extracting subfields.
     469a389 Fixed setting up Jacobian field for interpolated meshes.
     8f854fa Fixed C++ tet4 feassemble stuff for outward order.
     b685ee0 Add missing timedb file for examples/bar_shearwave/quad4.
     83238c2 Use more efficient Field::zeroAll() rather than Field::zero().
     9880964 Create local index set for cells associated with material.
     06c0bcc Topology+Faults: When using ‘depth’ to check for an interpolated mesh in parallel, need to account for −1 on empty meshes
     94a0fc3 Topology: Took groupField out of createInterpolate() interface
     14e3c72 Topology: Check for empty material-id label
     6886b45 Topology: Reordering now works in parallel
     ecf2a17 Faults: Fixed unittests for new interface
     f0259ae Fixed one case of handling NULL PetscIS after DMLabelGetStratumIS().
     f0a3d32 Fixed some parallel issues.
     7f05bb7 More ignores
     0de634f Clean up of refinement (fix memory leak).
     ed24816 Fixed another potential use of NULL index set in parallel runs.
     fc9bae9 Add number of levels refinement setting.
     9c58e45 Create path (if necessary) for output files.
     8328801 Improvement to creating output directory if it doesn't exist.
     f4faf94 Corrected coordinates in spatial data file.
     0b72e51 Fault Test: Fault meshes now have correct coordinates
     0b9b0aa Visitor: Now create an index for closure of coordinates and fields
     a9a1eb4 Topology: Added optimizeClosure() to visitors - Creates a closure index associated with the DM only if one does not already exist
     5b37d1e Optimization: Call optimizeClosure() for every visitor that calls getClosure() except the VisitorSubmesh
     a0bd2c3 Minor cleanup of optimizeClosure().
     6fe83b0 Converted shell script for running examples to Python script.
     361dd21 Flush stdout in script running examples.
     e028746 Update PetscMalloc3() call for interface changes. Updated test data.
     483d179 Enabled C++ unit test for hex8 refinement w/fault.
     176b7be Begin improvement of full-scale tests (quad4).
     a2cf235 General: Changes DMPlexGetCoordinateSection() to DMGetCoordinateSection()
     7ca6198 General: Changes DMPlexGetCoordinateSection() to DMGetCoordinateSection()
     993cc75 Fault tests: corrected group sizes - face 2 has one duplicated edge, so 3 vertices and 2 edges extra - fault just duplicates the whole face, so 4+12+9 extra
     8c284b9 Updated test data for C++ refinement test for quad4 w/fault.
     94aa2ec Made some of the needed changes to the manual. Not yet complete.
     780dd63 Added a couple of sentences about nondimsionalization, and added some more on stable time step size.
     3f1dca7 Fixed stable time step for power-law.
     7a219df Added missing file for full-scale automated parallel test.
     166d20d Fixed const correctness for getting field metadata.
     9d55cac Add ability to use subfield section in VecVisitor via argument to constructor.
     53ca3eb Update elasticity integrators to use subfield in visitors for optimization.
     dff5362 Use zeroAll() (more efficient than zero()).
     a289b5b Work on removing use of newSection(). Code commented out.
     c0cc1d5 Faults: After cohesive cell creation, only label NEW cohesive cells with material id
     4968170 Switch a bunch of newSection() calls in reassemble unit tests to new approach.
     fa8f90c Fields.cc missing PYLITH_METHOD_BEGIN/END.
     edfb2b6 Fix memory leak in visitor for subfield.
     9a0a280 Fixed some subfield setup errors in Python unit tests.
     4293872 Add openmpi valgrind suppression file.
     f00b38b HDF5: Must use local IS size when accessing indices
     881bf58 Fix parallel bug in DataWriterHDF5Ext (ISGetSize -> ISGetLocalSize).
     6557fff Merge branch 'knepley/upgrade-petsc-interface' of github.com:geodynamics/pylith into knepley/upgrade-petsc-interface
     900b50f Fix bug in MeshOps SWIG interface (missing return).
     ce57346 Fixed bug in SWIG interface (missing return).
     c43037a Added tests for out-of-plane initial stress.
     ff1bbb5 Added info on how to use stress-zz-initial for plane strain problems.
     8ad5845 Fixed typo in PETSc parameter.
     7b36c05 Improve some comments and improve error message.
     9eb83e5 Field: Better viewing in parallel
     22a549b Fixed typo in manual.
     4440eb5 Updated manual for Github issue tracking.
     eca576d Updated for v2.0 capabilities.
     f532fcf Renamed bash script to update .cfg files for v2.0.
     97b2503 Added release notes.
     304e4be More work on description of v2.0 changes.
     5ecc1e4 Moved .cfg files in share folder to settings directory.
     7cafe87 Updated information.
     f322c74 Small fixes for v2.0.
     9180dc2 Improved a few glossary terms.
     d65d136 Moved share .cfg file to share/settings.
     5528e2a Updated copyright script.
     13b43af Updated date in copyright.
     c8dceaf Updated date in copyright.
     437d52c Merge branch 'knepley/upgrade-petsc-interface' of github.com:geodynamics/pylith into knepley/upgrade-petsc-interface
     654d9ac More updates to v2.0 info.
     1cdc9e8 Improved parameter specification.
     ab65d94 Fixed discussion of initial state variables.
     b8f09f2 More work on release notes.
     6577078 Updated place to report bugs in NEWS.
     6b95d7a Remove obsolete tests.
     5253432 Improve solution test for full-scale testing.
     53a49dc Fix clean for full-scale test.
     5712dd2 Add some full-scale tet4 tests.
     ff8c198 Move tests_auto/3dnew to tests_auto/3d.
     24efc9f Add script to remove output generated by examples.
     40ec07c Upgrade to latest petsc - KSPSetOperators() changed
     f40b3d3 Debugging: Allow Brad to check example
     6f6cd6e Remove Matt's temporary code. Add try/catch/throw for proper memory cleanup.
     896a7cf Started adding some 3d/hex8 full-scale tests.
     0f9aecd Added some adjusting topology unit tests for embedded faults in 2-D.
     21f83b2 Updated adjust topology test data for removal of halo cells from material-id label.
     69d1381 Setup some prescribed slip unit tests with embedded faults (currently disabled).
     53819bd Faults: Exclude cohesive cells with unsplit edges/vertices from the calculation
     d5cd09c Fault test quad4h: Fixed material id data
     37e2098 Faults: We were smarter than we thought - Cohesive cell closures determine the edges used, so we don't need to do anything
     c652d13 Remove autogenerated file.
     3661713 Skip fault halo cells in checking material ids (not assigned label).
     8203543 Updated point labels.
     a3bb9ff Enable tri3g FaultCohesiveKin unit tests.
     deb61c5 Enabled prescribed slip quad4 embedded fault unit tests.
     687c383 Update embedded fault full-scale tests with fault info.
     f47c6e3 Fixed Mesh::view() with view option. Updated unit tests.
     138f727 Update calls to Mesh::view() for change in interface.
     b82388a Added label for material properties spatialdb
     0e1bd7c Modified static plasticity examples to run without errors.
     dc85186 Fixed material label.
     8c9ba89 Created subdirectory for output.
     97f2a9c Removed __requires__ statement, which is no longer needed.
     59a6c78 Enable 3-D fault full-scale test.
     1330564 Added C++ unit test for viewing mesh with VTK viewer.
     8cb1561 Small update to changelog.
     096d4cb Added embedded fault + refinement full-scale tet4 test.
     1c6555b Added full-scale test for embedded fault + refinement.
     a2ce49c Improved tri3 full-scale unit tests.
     ab12415 Updated checklist for releases.
     dae2d6e Minor cleanup of 3-D tet4 full-scale tests.
     fb662cc Updated tet4 full-scale tests to use smaller mesh.
     c55f238 More work on hex8 full-scale tests. Two fault analytical soln not yet correct.
     a5ef048 Updated README for initial stress case.
     d1785f1 Added script to run tests.
     bd7c2e5 Merge branch 'knepley/upgrade-petsc-interface' of github.com:geodynamics/pylith into knepley/upgrade-petsc-interface Trying to add a script to run tests.
     1e3ea1f Added output directory and script to run models.
     9af1ef7 Updated old fieldsplit settings.
     a447594 Added mention of fieldsplit solver settings in share directory.
     7bf5901 Merge branch 'knepley/upgrade-petsc-interface'
     d4a9a18 Fix filename in Makefile.am for full-scale 3d/tet4 test.
     aa1c4e1 Fixed solution so that it matches mesh.
     560463e Added one and two fault hex8 full scale tests.
     952e221 Merge branch 'baagaard/fix-fullscale-3d-tests'
     8fa3b45 Updated packaging scripts for cygwin.
     289f7d6 Merge branch 'baagaard/fix-packaging'
     151a658 Small fix to manual.
     c6b0af0 Small fix to table caption (move to body text).
     f46bff6 Update sizing function calls to work on all volumes.
     9535cd1 Merge branch 'baagaard/fix-cubit-cellsize'
     6c1d8c8 Cleanup. Mesh surfaces and then volumes.
     5eb07b9 Merge branch 'baagaard/fix-cubit-cellsize'
     e80acbb Use one block for cleaning sizing operations.
     f4c8ba3 Merge branch 'baagaard/fix-cubit-cellsize'
     51c6784 Updated PETSc version.
     61e0b28 Merge branch 'knepley/upgrade-petsc-interface'
     67897f5 Merge branch 'master' into baagaard/fix-fullscale-3d-tests
     169bd63 Reduced size of problem (coarser mesh). Updated mesh info.
     99fa210 Merge branch 'baagaard/fix-fullscale-3d-tests'
     0630870 Added comments to READMEs and release notes on improvements to using CUBIT cell sizing.
     15ffa6f Merge branch 'baagaard/fix-cubit-cellsize'
     34dc24b Small fix to PETSc solver setting to permit convergence (nearly converged anyway).
     346ff23 Merge branch 'knepley/upgrade-petsc-interface'
     e5caf46 Fixed bug in setting up fields for output of stable time step.
     c44102d Merge branch 'knepley/upgrade-petsc-interface'
     f04210a Setup example for 2 proc test with 2 faults.
     9e687af MeshIO: Broadcast the space dimension so that block size gets set correctly
     a68f689 HDF5: Short circuit new Plex code - We will eventually switch over to it
     f3f8abf Switch to HDF5Ext output in test to expose bug.
     a213c30 Fix bug related to HDF5Ext data writer coordinate output.
     76f389f Merge branch 'knepley/fix-parallel-mult-faults'
     80029c3 Spell check release notes.
     1b3d6d3 Added more notes to release checklist.