knepley/pylith

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knepley/pylith
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94 commits behind master.
Matthew Knepley
Merge branch 'knepley/feature-plex-elasticity-test' into knepley/pylith * knepley/feature-plex-elasticity-test: SNES ex17: Updated test output SNES ex17: Linear elastic test case - Somehow it got deleted from this branch earlier, so this is a recreation Plex+SNES: If no exact solutions are provided to Check, get them from DS
Matthew Knepley
SNES ex17: Updated test output
Matthew Knepley
SNES ex17: Linear elastic test case - Somehow it got deleted from this branch earlier, so this is a recreation
Matthew Knepley
Plex+SNES: If no exact solutions are provided to Check, get them from DS
Matthew Knepley
Merge branch 'knepley/fix-plex-bd-int' into knepley/pylith * knepley/fix-plex-bd-int: DMField: Added cast Plex: Fixed call
Matthew Knepley
DMField: Added cast
Matthew Knepley
Plex: Fixed call
Matthew Knepley
Merge branch 'knepley/fix-plex-bd-int' into knepley/pylith * knepley/fix-plex-bd-int: (22 commits) Added DMPlexComputeBdResidualSingle() Dev manual: assignment/comparison spaces section copyedit zlib: add backup download url Suggested changes/additions to DMPlex manual pages and users manual to clarify DMPlex migrate warning fix from next-tmp Revert "Remove dead code." clarifying comment in the code Remove dead code. Need PetscLogSetThre…
Matthew Knepley
Added DMPlexComputeBdResidualSingle()
Matthew Knepley
Merge branch 'knepley/fix-plex-residual-loop' into knepley/pylith * knepley/fix-plex-residual-loop: (107 commits) Add more protection to intrinsics MPI: protect arguments in MPI macros Add the missing conditionals for 64-bit build Plex: Updated test output - I am now hating this shit SNES ex12: Updated test output SNES ex62: Set name of solution vector - Update test output move output file to the correct location. i.e fix 305862f9cd0dc399542ae11dd7…
Matthew Knepley
Merge branch 'knepley/fix-plex-pointfunc-dim' into knepley/fix-plex-residual-loop * knepley/fix-plex-pointfunc-dim: Sys: Added a check for gnome-terminal, which never uses -display - Added some docs Plex: Made a public interface for ComputeBdResidualSingle() Plex: The first argument to a pointfunc should be the coordinate dimension Conflicts: src/dm/impls/plex/plexproject.c src/snes/utils/dmplexsnes.c
Matthew Knepley
Merge branch 'master' into knepley/fix-plex-residual-loop Warning: This merge includes real changes * master: (188 commits) Add JuMP citation Copyedits and updates to developers manual Add more protection to intrinsics MPI: protect arguments in MPI macros Add the missing conditionals for 64-bit build Plex+VTK: Fix field type determination Fix bug in name cleanup Bib: Added ref Plex+VTK: Fix field type determination Plex: Updated test output - I am now hating this shit forgo…
Matthew Knepley
Merge branch 'knepley/fix-section-clone' into knepley/pylith * knepley/fix-section-clone: Section: Must also copy field symmetries when cloning
Matthew Knepley
Merge branch 'knepley/fix-section-clone' into knepley/pylith * knepley/fix-section-clone: Section: Allow NULL argument to PetscSectionSetSym()
Matthew Knepley
Merge branch 'knepley/fix-section-clone' into knepley/pylith * knepley/fix-section-clone: (79 commits) Plex ex3: Added tests for Q3 Plex: Added picture for 3D hex interpolation Section: Copy symmetries when cloning Add JuMP citation Copyedits and updates to developers manual Plex+VTK: Fix field type determination Fix bug in name cleanup Bib: Added ref Plex+VTK: Fix field type determination forgot to save file after moving prototypes to p…
Matthew Knepley
Merge branch 'knepley/feature-plex-elasticity-test' into knepley/pylith * knepley/feature-plex-elasticity-test: SNES ex17: Added test output SNES ex17: Added test for vector Laplacian and linear elasticity Doc+Configure: Spelling error SNES ex17: Added dsymutil - This should always happen DM+SNES: Changed signature for internal check function Doc+Options: Fix doc for -options_view
Matthew Knepley
Merge branch 'knepley/fix-plex-residual-loop' into knepley/pylith * knepley/fix-plex-residual-loop: Plex+SNES/TS: Moved zeroing of Jacobian out of DMPlexComputeJacobian_Internal() - Should probably go in DMLocal versions, but now its in the top-level Plex FEM versions
Matthew Knepley
Plex+SNES/TS: Moved zeroing of Jacobian out of DMPlexComputeJacobian_Internal() - Should probably go in DMLocal versions, but now its in the top-level Plex FEM versions
Matthew Knepley
Merge branch 'knepley/fix-plex-residual-loop' into knepley/pylith * knepley/fix-plex-residual-loop: (390 commits) SNES+Plex: Needed cell offset, not cell number DM tests ex26: Fixed incorrect use of PetscMalloc() instead of PetscMalloc1() fix unused variable warnings Added DMSet/GetISColoringType() and cleaned up related manual pages slightly add more alt files due to KNL for biharmonic examples configure: remove debuging printf petsc4py: update to…
Matthew Knepley
SNES+Plex: Needed cell offset, not cell number
Matthew Knepley
SNES ex17: Added test output
Matthew Knepley
SNES ex17: Added test for vector Laplacian and linear elasticity
Matthew Knepley
Doc+Configure: Spelling error
Matthew Knepley
SNES ex17: Added dsymutil - This should always happen
Matthew Knepley
DM+SNES: Changed signature for internal check function
Matthew Knepley
Doc+Options: Fix doc for -options_view
Matthew Knepley
Merge branch 'knepley/fix-fe-bd-integral' into knepley/pylith * knepley/fix-fe-bd-integral: Plex+SNES: Fix BdResidual - Use DMPlexGetSubpoint() for aux closure, in case it is a boundary mesh - Be careful about Plex conversion FE: Fixed boundary integration - Allow auxiliary dm to be a different dimension, need dimAux and different tabulation FE: Small confusion about topological vs coordinate dimension PetscDS: The u_x array must have size dimEmbed b…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (278 commits) Website: Added news entry for PETSc User Meeting 2018 on main page. CUDA: Further test output fixes for mat_tests-ex2 Turn off elemental test for parmetis running since this does not work on batch systems. CUDA: Fixed most test errors due to MatMultTranspose* website: update urls website: fix Jason's name to match pic. Also add Todd's pic Dev manual: copyedit …
Matthew Knepley
Merge branch 'knepley/fix-plex-pointfunc-dim' into knepley/pylith * knepley/fix-plex-pointfunc-dim: Sys: Added a check for gnome-terminal, which never uses -display - Added some docs
Matthew Knepley
Sys: Added a check for gnome-terminal, which never uses -display - Added some docs
Matthew Knepley
Merge branch 'knepley/fix-plex-pointfunc-dim' into knepley/pylith * knepley/fix-plex-pointfunc-dim: Plex: Made a public interface for ComputeBdResidualSingle()
Matthew Knepley
Plex: Made a public interface for ComputeBdResidualSingle()
Matthew Knepley
Merge branch 'knepley/fix-plex-pointfunc-dim' into knepley/pylith * knepley/fix-plex-pointfunc-dim: (876 commits) Plex: The first argument to a pointfunc should be the coordinate dimension MatIS: fix MatShift_IS tests: print the list of 5 longest running tests [within 'make alltests'] Adding timing feature to test harness and report More (void*) to prevent compiler warnings regarding const More minor fixes for spectral burgers examples need custom…
Matthew Knepley
Plex: The first argument to a pointfunc should be the coordinate dimension
Matthew Knepley
Merge branch 'knepley/feature-plex-bd-integration' into knepley/pylith * knepley/feature-plex-bd-integration: Plex+SNES: Split boundary integration into a separate function Missing CHKERRQ() revert change from 5aa18e1fedd8a30a61875ae8fea36ac48058e4ca and add back -mP2OPT_hpo_vec_remainder=F
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (189 commits) Reduce -dm_refine of test so that it won't take too much time in gcov testing tao_manual: use preinstalled sty files [and avoid the cp and gitignore for sty files] TAO manual: add .gitignore petsc4py: update to use latest 3.8 snapshot petsc4py: update to snapshot that syncs with 276c550 fix warning Plex ex26: Protect ExodusII stuff DM: DMCreateSubDM() field …
Matthew Knepley
Merge branch 'knepley/fix-plex-multifield-eval' into knepley/pylith * knepley/fix-plex-multifield-eval: TS ex46: Newlines and some numerical jitter TS ex45: Newlines and some numerical jitter TS ex11: Fixed indentation and time step numbering SNES ex12: Update for DM view changes Plex tests: Update to new DM output Plex ex23: Use Nc not dim for vector fields Plex: Default section now ignores cells hanging off boundary meshes Plex: Viewer now report…
Matthew Knepley
Merge branch 'knepley/fix-plex-geometry-3d-init' into knepley/pylith * knepley/fix-plex-geometry-3d-init: (50 commits) Plex: Fixed array initialization Bib: More refs test: remove runex13f90 as its now converted to new test suite fix win32 crash. This test was previously run with '-n 4' - so restoring it builds: attempt to do maint/master/next test builds in separate clones ex62: it turned out that CHACO partioning is not deterministic. Use a prescribed…
Matthew Knepley
Merge branch 'knepley/feature-plex-parallel-submesh' into knepley/pylith * knepley/feature-plex-parallel-submesh: Vec: Small doc fix Plex: Remove check on submesh faces since in parallel the other cell can be absent IS: Allow ISExpand() to have optional arguments Plex ex5: Added parallel test case Plex ex5: Reorder tests Plex: DMPlexCreateHybridMesh() now takes a boundary label and returns the submesh - Added check that no cell has all vertices on the subme…
Matthew Knepley
Merge branch 'knepley/fix-l2-projection-submesh' into knepley/pylith * knepley/fix-l2-projection-submesh: Plex+FEM: Now L2 Diff applies boundary values, instead of projecting the input function Plex: Added DMPlexComputeL2DiffLocal() - Fix docs to say that DM version uses global vectors Plex: Now the L2 diff can work on sub meshes
Matthew Knepley
Merge branch 'knepley/fix-plex-multifield-eval' into knepley/pylith * knepley/fix-plex-multifield-eval: Plex ex23: Added all types of projection iterations Plex: Fixed projection routines when we iterate over a surface with volume field and surface aux fields - If we are iterating over a surface with volume input, then the effective DS is the height=1 subspace - Made DS an argument for projection functions - Only allow iteration over a surface with volume inpu…
Matthew Knepley
Merge branch 'knepley/fix-plex-proj-ds' into knepley/pylith * knepley/fix-plex-proj-ds: PetscDS: The x[] array should be the size of the embedding space DM: Should do its best to automatically set the embedding dimension for the DS PetscDS: Needs to know the embedding dimension
Matthew Knepley
Vec: Small doc fix
Matthew Knepley
Plex: Remove check on submesh faces since in parallel the other cell can be absent
Matthew Knepley
IS: Allow ISExpand() to have optional arguments
Matthew Knepley
Plex ex5: Added parallel test case
Matthew Knepley
Plex ex5: Reorder tests
Matthew Knepley
Plex: DMPlexCreateHybridMesh() now takes a boundary label and returns the submesh - Added check that no cell has all vertices on the submesh
Matthew Knepley
Plex ex5: Renamed tests