Merge remote-tracking branch 'origin/maint'

Merged in dalcinl/fix-dm-localize-coordinates (pull request #591)

DMLocalizeCoordinates: Use PETSC_COMM_SELF for local coordinate vector

DMLocalizeCoordinates: Use PETSC_COMM_SELF for local coordinate vector

Merge branch 'tisaac/dmplex-fix-hex-box-periodicity'

* tisaac/dmplex-fix-hex-box-periodicity:
DMPlexCreateHexBoxMesh(): again, fix initialization for c89
DMPlexCreateHexBoxMesh: c86-compatible i

Merge branch 'tisaac/dmplex-fix-hex-box-periodicity'

* tisaac/dmplex-fix-hex-box-periodicity:
DMPlexCreateHexBoxMesh(): again, fix initialization for c89
DMPlexCreateHexBoxMesh: c86-compatible initializiation
DMPlexView_HDF5: use DMGetCoordinatesLocalized() instead of bad test
DMGetCoordinatesLocalized(): fix for change to localization strategy
DMPlex: set periodicity automatically in DMPlexCreateHexBoxMesh

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Merge branch 'tisaac/dmplex-feature-real-to-ref'

This branch introduces DMPlexReferenceToCoordinates() and
DMPlexCoordinatesToReference() and push finite element reference element
points forward int

Merge branch 'tisaac/dmplex-feature-real-to-ref'

This branch introduces DMPlexReferenceToCoordinates() and
DMPlexCoordinatesToReference() and push finite element reference element
points forward into the mesh and inverting to pull them back.

DMPlexCoordinatesToReference() is currently implemented with a simple
Newton iteration. When the reference maps extend outside the element in
a non-unique way, a Newton iteration doesn't always do what we want.

What we really want are two properties:

- If there is a solution inside the reference element domain, converge
preferentially to that one.
- If there is no solution inside the reference element domain, diverge
outside of the domain.

Newton has no guarantee of which solution will be found, so
DMPlexCoordinatesToReference() can fail for very nonlinearly deformed
elements. Fixing this is a project for another time.

* tisaac/dmplex-feature-real-to-ref:
DMPlex tests ex22: larger tolerance, so that single precision passes
DMPlex tests ex22: use petsc portable implementation of snprintf
DMPlexComputeProject3Dto2D(): precision-aware bounds for orthogonalization success
DMPlex: fix bad declaration order in point location routine
DMPlex: complex and C++ fixes to recent point location routines
DMPlex: added point location to regression tests
DMPlex: reduce max iterations for point location.
DMPlex: indexing and work array size corrections for point location routines
DMPlex: add debugging info in point location routines
DMPlex tests ex22: fix memory leak
DMPlex: fix work array declarations in reference/coordinate transformations
DMPlex test ex22: added iso parametric test
DM: fix reference/reference order in DMSetCoordinateDM()
DMPlex tests: move my ex21 to ex22 to prepare for merge
DMPlex: implement point inversion for multilinear maps.
CoordinatesRealToRef(): correct stride
DMPlex: propose DMPlexCoordinatesToReference() interface

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Fix typo in manual page

Funded-by: Hierarchical solvers
Time: 0 hours
Reported-by: Peter J. Puchyr <pjpuchyr@gmail.com>

DMGetCoordinatesLocalized(): fix for change to localization strategy

We used to localize all cells: now we only localize cells on periodic boundaries.
Because of this difference, we need to check al

DMGetCoordinatesLocalized(): fix for change to localization strategy

We used to localize all cells: now we only localize cells on periodic boundaries.
Because of this difference, we need to check all cells for signs of localization.

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DM: fix reference/reference order in DMSetCoordinateDM()

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_A

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_ATTRIBUTEALIGNED flag to makefile
PCSetUp_SVD() used incorrect matrix for matrix size in parallel, also need to skip LAPACK call if matrix size is zero
strumpack: update to latest version 1.0.4
Remove valgrind warning about MPI_Allreduce() with uninitialized data
sed for test output that has atol convergence with quad precision
updated ex1_nest tests
fixed incorrect key value
fix: bad merge a69d34a
test: move runex78 to TESTEXAMPLES_C_NOTSINGLE
build: fix warnings
sys: update test to produce same result - irrespective of debug/opt build - and presence of ~/.petscrc
sys: src/sys/examples/tests/ex30.c -> src/sys/examples/tests/ex32.c to avoid conflict in master
Sed output, since quad precision reduces below atol on these tests
remove automatically generated matrix names from test output files since can be different
Fixes for MatMPIXXXSetPreallocation(), they were not reentrant, since they kept the information used for matrix-vector products
GAMG: fix PCView_GAMG() format - and update output/ex56_0.out
superlu_dist: 64-bit-indices fix https://github.com/xiaoyeli/superlu_dist/issues/4
Add SNESSetDivergenceTolerance / -snes_divergence_tolerance.
fixed unit read in Plex
...

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Merge branch 'knepley/feature-plex-bdfunc'

* knepley/feature-plex-bdfunc: (56 commits)
updated snes/ex56
updated snes/ex56
Plex: Goddamn it! Shadowing a variable name
PetscDS: Must be setup

Merge branch 'knepley/feature-plex-bdfunc'

* knepley/feature-plex-bdfunc: (56 commits)
updated snes/ex56
updated snes/ex56
Plex: Goddamn it! Shadowing a variable name
PetscDS: Must be setup in order to access field sizes and components
fix bad merge 44ac993612e1ca111ab14eba1c22039e0ba32a12 wrt src/snes/examples/tutorials/ex56.c [by attempting to redo the merge with kdiff3 - and then comparing the final result with the result in the above merge]
fixed snes/ex56 for PetscDSAddBoundary change
dmplexsnes: Remove more unused variables
Remove unused variables
SNES ex77: Must also set face quadrature
SNES ex12: No longer need boundary discretization orders
SNES ex62: Numerical flutter
SNES ex12: Numerical flutter
Plex: In projection, get Nc from DS instead of calculating it again
PetscFE: Added missing destroy
SNEX ex77: Update boundary args and FE creation
Plex: Update boundary integrals to new API
SNES ex12: Tests of bc from fields
SNES ex12: Added the ability to use finite element fields as boundary conditions
Plex: Need invJ for field projection
Plex: Fix bug with field projection - We must tabulate the FE on the dual basis quadrature points
...

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Merge branch 'knepley/feature-plex-interpolation-perf'

* knepley/feature-plex-interpolation-perf:
DM: Forgot in last commit
DM: Added timing of DMRefine()
Plex ex21: Test for interpolation per

Merge branch 'knepley/feature-plex-interpolation-perf'

* knepley/feature-plex-interpolation-perf:
DM: Forgot in last commit
DM: Added timing of DMRefine()
Plex ex21: Test for interpolation performance
Plex: Added event for SF interpolation

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Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/featu

Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/feature-pcbddc-saddlepoint
that prevents me to smoothly merge stefano_zampini/feature-convert-matnest-matis into next.

This will also facilitate merging stefano_zampini/feature-pcbddc-saddlepoint into master

Conflicts:
src/docs/website/documentation/changes/dev.html

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DM: Added timing of DMRefine()

Merge branch 'knepley/fix-dm-ltog-bs'

* knepley/fix-dm-ltog-bs:
Plex: Fix L2G map for MatIS
DM: The L2G mapping is incorrect for bs > 1 - We should not give absolute indices, but block indices

DM+KSP: Changed projection functions to accept multiple BC function types
- DMProjectField() now takes the time

DM+DS: Allow different kinds of BC functions
- Added DMBoundaryConditionType
- Changed DMGetBoudnary() and DMAddBoundary() and the DS versions

Fix outdate function reference in manual page, clarify manual pages

Reported-by: Victor Eijkhout <eijkhout@tacc.utexas.edu>

Merge branch 'maint'

Merged in psanan/petsc/psanan/dm-domaindecomposition-null (pull request #568)

DMCreateDomainDecomposition: allow for *dmlist=NUL

DM: The L2G mapping is incorrect for bs > 1
- We should not give absolute indices, but block indices

DM: allow for NULL dmlist with DMCreateDomainDecomposition

now compiler had an issue with this bug for six months until now, that is amazing!

Time: 0 hours
Reported-by: nightly tests

Merge branch 'barry/add-matfdcoloring-ghosted-example'

Hoist management of DM usage for MatFDColoringApply() for IS_COLORING_LOCAL up to dm

This is because the DM calls cannot be made in the Mat library when not using --with-single-library

Time: 1.6 ho

Hoist management of DM usage for MatFDColoringApply() for IS_COLORING_LOCAL up to dm

This is because the DM calls cannot be made in the Mat library when not using --with-single-library

Time: 1.6 hours
Reported-by: nightly tests

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Merged in psanan/petsc/psanan/dm-subdomain-fixes (pull request #533)

DMCreateDomainDecomposition: only copy ctx if it exists