PetscFE: Complex fixes for PetscFEIntegrate()
Merge branch 'master' into knepley/feature-plex-adjoint-prelim* master: (60 commits) petsc4py: update to use latest 3.8 snapshot petsc4py: update to snapshot that syncs with 276c550 fix warni
Merge branch 'master' into knepley/feature-plex-adjoint-prelim* master: (60 commits) 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 argument should be const 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 reports the cell Height Increase patchlevel to 3.8.3 Plex: Fixed DMPlexInterpolate() bugs - Do not copy associated data if we are not interpolating - Do not interpolate if we already have full depth fix valgrind errors with using PetscObjectGetName()/SetName() with the same object - resulting in a free() before copy. ex4: fix compile warning and update makefile Minor fixes Improving report_tests PetscDS: Must initialize the default adjacency ...Conflicts: include/petsc/private/dmimpl.h include/petscdm.h include/petscis.h src/dm/impls/plex/plexcreate.c
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Merge remote-tracking branch 'origin/knepley/fix-plex-multifield-eval'
Merge remote-tracking branch 'origin/knepley/fix-plex-fvm-adjacency'
Merge branch 'master' into knepley/feature-plex-adjoint-prelim* master: (251 commits) yaml: add a backup download URL Fix documentation of MatSetRandom function Ignore -malloc-hbw option if m
Merge branch 'master' into knepley/feature-plex-adjoint-prelim* master: (251 commits) yaml: add a backup download URL Fix documentation of MatSetRandom function Ignore -malloc-hbw option if malloc is already set Plex: Fixed array initialization pgi: compile fix knl: update test to use memkind and remove option that worked arround a bug with intel 17 Check the return value for memkind_posix_memalign Change the default behavour for -malloc_hbw 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 Fix petscsfgetgraph_ to work for all Fortran compilers by directly using array of PetscSFNodes bugfix for MatDuplicate_MPIAIJ_PtAP Reported-by: Samuel Lanthaler <s.lanthaler@gmail.com> strip out dead sundials usage code; change sundials test to only run 5 timesteps to prevent different number of steps on different systems. Remove extra lines of output file Example uses C99 constructs so must mark with requires: c99 fix const missmatch for DMDAVecRestoreArrayRead() remove conflict between function name in example and new PETSc TS function 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 partition instead ...Conflicts: src/dm/interface/dm.c src/snes/examples/tutorials/ex13.c
PetscDS: Must initialize the default adjacency
PetscDS: Can now store default adjacency when it has no fields- Get it with PETSC_DEFAULT for field
PetscDS: Now allow a hierarchy of subspaces
Plex+DS: Moved adjacency information completely to DS- The Plex versions now just delegate to DS- Defaults in DS are clearer- Input to GetAdjacency are optional
PetscDS: Added PetscDSGetHeightSubspace()
PetscFE: Allow face tabulation to return NULL if no face quadrature is present
PetscFE: Fix PetscFEIntegrate() for multicomponent integrals
PetscDS: The x[] array should be the size of the embedding space
PetscDS: Needs to know the embedding dimension
Merge branch 'knepley/fix-ds-memleak'* knepley/fix-ds-memleak: PetscDS: Fix memory leak
Remove use of PetscDataType from DMGetWorkArray() and one absurd usagePart of process of removing PetscDataType from PETSc since it duplicates MPI_DatatypeCommit-type: style-fixThanks-to: Jed Bro
Remove use of PetscDataType from DMGetWorkArray() and one absurd usagePart of process of removing PetscDataType from PETSc since it duplicates MPI_DatatypeCommit-type: style-fixThanks-to: Jed Brown <jed@jedbrown.org>
PetscDS: Fix memory leak
F90Array routines now take a MPI_Datatype argument instead of PetscDataTypeThis is part of the refactorization to limit and maybe eventually eliminate PetscDataType sinceit duplicates MPI_Datatype
F90Array routines now take a MPI_Datatype argument instead of PetscDataTypeThis is part of the refactorization to limit and maybe eventually eliminate PetscDataType sinceit duplicates MPI_Datatype functionality (poorly).Commit-type: style-fixThanks-to: Jed Brown <jed@jedbrown.org>
Merge branch 'maint'
PetscDualSpaceApplyFVM(): Fix for change in dual space semanticsEvery dual space functional is a scalar now; this function was treatinga functional for FVM like a pointwise evaluation, which is no
PetscDualSpaceApplyFVM(): Fix for change in dual space semanticsEvery dual space functional is a scalar now; this function was treatinga functional for FVM like a pointwise evaluation, which is not scalar ifthe field is vector.
fix: redundant CHKERRQ() call after SETERRQ()Craycc complained about a stray CHKERRQ after SETERRQ in plextree.cReported-by: Patrick Sanan <patrick.sanan@gmail.com>
configure: add option --with-fortran-bindingsNow one can use --with-fc=gfortran --with-fortran-bindings=0 to detect fortran compiler properly[for externalpacakge use - for eg: scalapack] but avoid
configure: add option --with-fortran-bindingsNow one can use --with-fc=gfortran --with-fortran-bindings=0 to detect fortran compiler properly[for externalpacakge use - for eg: scalapack] but avoid building PETSc fortran bindings in library and modules.Also disable sowing when with-fortran-bindings is disabledFix makefiles (corresponding to fortran bindings) to consistantly use PETSC_HAVE_FORTRANAlso remove unused PETSC_USE_FORTRAN_DATATYPES flagReported-by: Patrick Farrell <patrick.farrell@maths.ox.ac.uk>
Merge branch 'master' into knepley/fix-fe-default* master: (297 commits) Bib: Added refs and fixed one Doc: Fixed formatting problems for MatCreateAIJ() manual page. Add to PCSOR manual page
Merge branch 'master' into knepley/fix-fe-default* master: (297 commits) Bib: Added refs and fixed one Doc: Fixed formatting problems for MatCreateAIJ() manual page. Add to PCSOR manual page information about convergence testing when using KSPRICHARDSON SNES ex5: Restore old output since this breaks an example I have Noted that some Cray XC systems will use 'aprun' instead of 'srun'. Thanks to Herr Doktor Hong Zhang for this suggestion. Added example configure script for Cray XC40 with KNL processors (e.g., NERSC Cori). Fix possible sprintf -Wformat-overflow PetscMalloc2-7: fix -Wint-in-bool-context for GCC 7 SNES ex5: make boundary condition handling consistent for symmetry SNES ex5: use L2 norm and *_monitor_short for output SNES ex5: the L^2 norm scales with the l^2 norm over sqrt(N) SNES ex5: refactor MMS capability to avoid extreme code duplication Documentation fix: typo in PetscLogStageRegister manual page. nodes -> vertices rename DMNetworkGetComponentTypeOffset -> DMNetworkGetComponentKeyOffset rename DMNetworkGetConnectedNodes() -> DMNetworkGetConnectedVertices() Jacobians for adjoints for explicit methods and constant Jacobians never got initialized fix complex build error fix build failure with fortran interface fix compile error with cdc753b64c658d532d7813e942002e67025667a6 ...Conflicts: src/snes/examples/tutorials/ex13.c src/snes/examples/tutorials/ex62.c src/snes/examples/tutorials/ex69.c
PetscFE: Set default PetscSpace to polynomial. This allows us to set the tensor property automatically
PetscFE: Added height subspaces to PetscFE- Added PetscFEGetHeightSubspace()- Added array in struct
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