Merge branch 'jolivet/typos' into 'master'

Some typos.

See merge request petsc/petsc!2010

fixed spelling error in plex.c

Some typos.

Merge branch 'barry/2019-09-01/rm-default-language-from-dm' into 'master'

Update public API, and internal naming conventions for DM to eliminate use of...

See merge request petsc/petsc!1998

Update public API, and internal naming conventions for DM to eliminate use of "default" (previously refered to default sections)

Commit-type: style-fix, documentation

plex tests/ex36: fix FV cell geometry for complex

Four real values are packed into two complex, so we can't access it as
the real parts of four complex values. Use PetscFVCellGeom for clarity.

Com

plex tests/ex36: fix FV cell geometry for complex

Four real values are packed into two complex, so we can't access it as
the real parts of four complex values. Use PetscFVCellGeom for clarity.

Commit-type: bug-fix
Reported-by: Barry Smith <bsmith@mcs.anl.gov>

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Merge branch 'haplav/fix-hdf5-include' [PR #1967]

* haplav/fix-hdf5-include:
redo Pull Request #1943 in master
This is intended to unify master with maint after Pull Request #1943 to avoid confusion

Merge branch 'haplav/fix-hdf5-include' [PR #1967]

* haplav/fix-hdf5-include:
redo Pull Request #1943 in master
This is intended to unify master with maint after Pull Request #1943 to avoid confusions.

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Merge branch 'stefano_zampini/fix-plex-matis-bs' [PR #1971]

* stefano_zampini/fix-plex-matis-bs:
Fix MATIS construction for DMPLEX when bs > 1

DMPLEX: fix bug for bs > 1 introduced in 4fa2624631c

Typos.

DMGetSection: replace all internal usage with DMGetLocalSection

Same for DMSetSection -> DMSetLocalSection. We retain the interface
for DMGetSection/DMSetSection without deprecation warnings (for n

DMGetSection: replace all internal usage with DMGetLocalSection

Same for DMSetSection -> DMSetLocalSection. We retain the interface
for DMGetSection/DMSetSection without deprecation warnings (for now).

Suggested-by: Barry Smith <bsmith@mcs.anl.gov>

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DMGetDefaultSection et al: add PETSC_DEPRECATED_FUNCTION

These functions were deprecated in v3.9, but no
PETSC_DEPRECATED_FUNCTION was added at that time so many uses crept
back into the source code

DMGetDefaultSection et al: add PETSC_DEPRECATED_FUNCTION

These functions were deprecated in v3.9, but no
PETSC_DEPRECATED_FUNCTION was added at that time so many uses crept
back into the source code. Here we mark it deprecated and fix all
existing uses in PETSc.

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Merged in balay/updated-med-4.0.0/master (pull request #1662)

Balay/updated med 4.0.0/master

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

Move higher level (IS level) hdf5 function prototypes to new file petsclayouthdf5.h

This is a fix for PETSc v3.11.3 which cannot compile code that does not include the -I search path for HDF5 even t

Move higher level (IS level) hdf5 function prototypes to new file petsclayouthdf5.h

This is a fix for PETSc v3.11.3 which cannot compile code that does not include the -I search path for HDF5 even though
the code do not use HDF5 since the #if defined(PETSC_HAVE_HDF5) #include <H5Ipublic.h> is directly in petscis.h

This prevents polluting the public IS level include files with HDF5 material

This hopefully can be ported directly also to the master branch and cleanup the pollution there as well.

Note that the code in question does not use IS but does use PetscLayout hence the name of the new include file

Commit-type: bug-fix, portability-fix
Reported-by: Drew Parson
Thanks-to: Lisandro Dalcin <dalcinl@gmail.com>
(cherry picked from commit 51e210a943a96e6acf92eea785f1e143d67148d9)

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MED: temporarily disable failing tests

Merge branch 'barry/2019-08-04/fix-maint-hdf5-include/maint' into maint [PR #1943]

* barry/2019-08-04/fix-maint-hdf5-include/maint:
Move higher level (IS level) hdf5 function prototypes to new file

Merge branch 'barry/2019-08-04/fix-maint-hdf5-include/maint' into maint [PR #1943]

* barry/2019-08-04/fix-maint-hdf5-include/maint:
Move higher level (IS level) hdf5 function prototypes to new file petsclayouthdf5.h
This is a fix for PETSc v3.11.3 which cannot compile code that does not include the -I search path for HDF5 even though the code do not use HDF5 since the #if defined(PETSC_HAVE_HDF5) #include <H5Ipublic.h> is directly in petscis.h
This prevents polluting the public IS level include files with HDF5 material

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Merge branch 'haplav/fix-petscviewerhdf5pushgroup-empty-string' [PR #1950]

* haplav/fix-petscviewerhdf5pushgroup-empty-string:
fix/generalize PetscViewerHDF5PushGroup for empty string

- add dm_impl

Merge branch 'haplav/fix-petscviewerhdf5pushgroup-empty-string' [PR #1950]

* haplav/fix-petscviewerhdf5pushgroup-empty-string:
fix/generalize PetscViewerHDF5PushGroup for empty string

- add dm_impls_plex_{tests-ex18_9%,tutorials-ex5_9%} loading an HDF5/XDMF file with custom naming
- PetscViewerHDF5{Push,Get}Group: *name -> name[] to unify with the rest of header file
- PetscViewerHDF5PushGroup: Allow to push NULL, "", or all slashes.

In all cases, store NULL, interpret as "/".
This also fixes the problem in DMPlexLoad_HDF5_Xdmf_Internal() when the specified datasets locations are in / (like e.g. -dm_plex_hdf5_topology_path /cells in the new examples).

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Merge branch 'jczhang/fix-unused-variable' [PR #1955]

* jczhang/fix-unused-variable:
Remove an unused variable

Remove an unused variable

examples: use DMBoundaryTypes instead of manually replicating it

add dm_impls_plex_{tests-ex18_9%,tutorials-ex5_9%} loading an HDF5/XDMF file with custom naming

Move higher level (IS level) hdf5 function prototypes to new file petsclayouthdf5.h

This is a fix for PETSc v3.11.3 which cannot compile code that does not include the -I search path for HDF5 even t

Move higher level (IS level) hdf5 function prototypes to new file petsclayouthdf5.h

This is a fix for PETSc v3.11.3 which cannot compile code that does not include the -I search path for HDF5 even though
the code do not use HDF5 since the #if defined(PETSC_HAVE_HDF5) #include <H5Ipublic.h> is directly in petscis.h

This prevents polluting the public IS level include files with HDF5 material

This hopefully can be ported directly also to the master branch and cleanup the pollution there as well.

Note that the code in question does not use IS but does use PetscLayout hence the name of the new include file

Commit-type: bug-fix, portability-fix
Reported-by: Drew Parson
Thanks-to: Lisandro Dalcin <dalcinl@gmail.com>

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ex18: Fixed incorrect merge from maint in parent commit. [PR #1921]

Merge should have used theirs-strategy instead of ours-strategy.

ex18: 7_exo_metis made temporarily TODO

ex18: 7_hdf5_repart_ppu made TODO.

Parallel partitioning of uninterpolated meshes not supported.