Plex: Fixed name for internal function

Plex: Moved projection code to a new file

remove example from single precision tests since result is computed to rull precision

Reported-by: nightly tests

Merge branch 'barry/use-fortran-kind-consistently' into barry/fix-dmdacreate

Need to resolve conflicts with .F90 code reformating

Plex: Fix L2G map for MatIS

Removed DMSetFromOptions() and DMSetUp() from DMDACreateNd()

Time: 4 hours

Fortran updates

Updated all F90 examples to use free form with full error checking
Update all Fortran examples to check error code for PetscInitialize() call

Time: 2 hours

Fixes for f90

1) insure all Fortran examples with f90 in their name end with .F90
2) insure that all .F90 examples are only tested in F90 tests, some were tested in Fortran tests
3) only turn on isF

Fixes for f90

1) insure all Fortran examples with f90 in their name end with .F90
2) insure that all .F90 examples are only tested in F90 tests, some were tested in Fortran tests
3) only turn on isF90 and isF2003 and hence testing of F90 examples if compiler supports long fortran lines
(Satish won't like this).

This now allows our .F90 examples to have error checking and still be readable without endless continuations

Time: 2 hours

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clang: more -Wcomma fixes [use (void)() notation]

Merge branch 'knepley/fix-plex-cgns'

* knepley/fix-plex-cgns:
Plex: Fix comment Reported-by: The Jed
Plex: Fix for non-compliant use of 'I' by CGNS which fails for complex Reported-by: Dave Love

Merge branch 'knepley/fix-plex-cgns'

* knepley/fix-plex-cgns:
Plex: Fix comment Reported-by: The Jed
Plex: Fix for non-compliant use of 'I' by CGNS which fails for complex Reported-by: Dave Love <d.love@liverpool.ac.uk>

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Merge branch 'tisaac/petscfe-matching-quadrature-order'

* tisaac/petscfe-matching-quadrature-order:
Share quadrature instead of sharing quadrature order
SNES tutorials ex12: update regression te

Merge branch 'tisaac/petscfe-matching-quadrature-order'

* tisaac/petscfe-matching-quadrature-order:
Share quadrature instead of sharing quadrature order
SNES tutorials ex12: update regression tests for new quadrature
DMPlex tests ex3: finish updating tests for more quadrature
DMPlex tests ex3: update regression test for discontinuous elements
DMPlex: silence compiler warning for uninitialized variable.
DMPlex tests ex3: update interpolation/convergence tests for higher-order quadrature
DMPlex: use temporary detJ everywhere
fixing Toby's fix
DMPlexComputeGeometryFEM(): clarify what is expected if fe != NULL and correct computations accordingly
PetscFECreateDefault(): increase default quadrature order, make configurable

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Added exodus side set names to DMLabel [plex].

By default, the exodusii reader in DMPlex stores all exodus side sets
under the DMLabel 'Face Sets'. This PR adds the side set names from the
exodusii

Added exodus side set names to DMLabel [plex].

By default, the exodusii reader in DMPlex stores all exodus side sets
under the DMLabel 'Face Sets'. This PR adds the side set names from the
exodusii file to the set of DMLabels associated with the DM. The facets
lying on a specific side set can now be queried later by passing their
label.

Previous functionality is also retained: the 'Face Sets' label is still
constructed as before. Additionally, if no labelled side sets are
present in the exodus file, then no extra labels are added to the DM.

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Removed crumbs from previous support of Netcdf. Support was removed in 2010

Time: .2 hours

Plex: Fix comment
Reported-by: The Jed

Plex: Fix for non-compliant use of 'I' by CGNS which fails for complex
Reported-by: Dave Love <d.love@liverpool.ac.uk>

Merge remote-tracking branch 'origin/maint'

DMPlex: Fixes to builtin hex box mesh generator

* Fix bad handling of twist boundary type in Z-direction
* Fix bad X-edge loop count for building Y-faces
* Reduce local array size for cell cones and

DMPlex: Fixes to builtin hex box mesh generator

* Fix bad handling of twist boundary type in Z-direction
* Fix bad X-edge loop count for building Y-faces
* Reduce local array size for cell cones and orientations
* Remove whitespace

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DMPlex: Fix arg number in error check macro

Merge branch 'pr529/sanderarens/plex_gmsh_vertex_sets/master'

* pr529/sanderarens/plex_gmsh_vertex_sets/master:
Plex ex1: Fixed Gmsh output for gmsh_5
Plex: add test for Gmsh reader for binary f

Merge branch 'pr529/sanderarens/plex_gmsh_vertex_sets/master'

* pr529/sanderarens/plex_gmsh_vertex_sets/master:
Plex ex1: Fixed Gmsh output for gmsh_5
Plex: add test for Gmsh reader for binary files with physical names
Plex: fix bug that occurs when reading a binary gmsh file with a PhysicalNames section
Plex: add Vertex Sets to Gmsh reader

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Merge branch 'tisaac/sys-fix-realloc' into tisaac/petscfe-matching-quadrature-order

* tisaac/sys-fix-realloc: (71 commits)
Sys: fix PetscTrReallocDefault() and PetscReallocAlign()
clearify when

Merge branch 'tisaac/sys-fix-realloc' into tisaac/petscfe-matching-quadrature-order

* tisaac/sys-fix-realloc: (71 commits)
Sys: fix PetscTrReallocDefault() and PetscReallocAlign()
clearify when MatMkl_CPardisoSetCntl() can be used in the manual pages
Fixed manual page for -snes_anderson_beta
Update zfftf.c
remove Hermitian information from output since it is only produced in complex case and thus produces different test output
fixes for 64 bit integers in test example, fix uninitialized variable in test example
tests: move runex49 to TESTEXAMPLES_C_NOTSINGLE
add a PCView_SVD to show parameters
-petscpartitioner_type simple was not being picked up by options thus generating test error
missing CHKERRQ(ierr) on PetscPrintf() statements in newly added test example
PetscViewerVTK: Move DM reference increment into the VTK viewer and out of the DM implementation, as suggested by Jed Brown
missing crosslinks between manual pages
Updated 3.7 release notes to clearly indicate how to update usage of KSP/SNES/TS/SetMonitor(xxx,XXXMonitorDefault,NULL,NULL);
Fix for commit b6480e041dd2293a65f96222772d68cdb4ed6306 that broke this example
Example of factorization of a singular matrix may actually work due to round off
removed unused variables
matshell: clean up and add some new MATOPs to Fortran.
Remove unneeded checks for use of the compressed row for diagonal block of matrices in GAMG
ptscotch: update to version 6.0.4
ptscotch: fix buggy pthread detection code on Mac/Linux
...

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Merge branch 'pr520/psanan/psanan/vtk-viewer-leak-fix/master'

Plex ex1: Fixed Gmsh output for gmsh_5

Plex: add test for Gmsh reader for binary files with physical names

Plex: fix bug that occurs when reading a binary gmsh file with a PhysicalNames section

Plex: add Vertex Sets to Gmsh reader