DMPlex_GMSH: revert to not inverting triangles

Reported by: T. Isaac <tisaac@uchicago.edu>

Merge branch 'stefano_zampini/fix-gmsh-inverted-triangles'

Merge branch 'knepley/feature-mantle-example' into stefano_zampini/feature-fetidp-ex69

DMPlex_GMSH: triangles are inverted

DMPlex_GMSH: Mark slave and master in periodicV

Localization is done on every cell that has either a master or a slave node

DMPlex_GMSH: localize just on periodic cells

DMPlex_GMSH: finish support for reading periodic meshes

DMPlex: consistently with creating the BoxMesh, create a "marker" label

DMPlex_GMSH: fix memory leak

DMPlex: allow uniform refinement for periodic meshes without maxCell/L

Needed an API change for DMSet/GetPeriodicity

DMPlex: fix gmsh reader for periodic meshes

Still some problems with the GMSH format

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-plex-pragmatic-parallel

* knepley/feature-plex-tests-new: (105 commits)
SNES ex62: Make test 31 less sensitive
Plex: Remove ext

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-plex-pragmatic-parallel

* knepley/feature-plex-tests-new: (105 commits)
SNES ex62: Make test 31 less sensitive
Plex: Remove extra semicolons
Test: Reverted cherry pick
Plex: Damn Absoft, Trying to get under the 132 character line limit for Absoft
Testing: Cherry picked a fix
Plex: Trying to get under the 132 character line limit for Absoft
Plex: Fix small compiler warnings
Plex ex2f90: Removed comment line Absoft does not like
Plex: Turn off some tests for quad
Plex ex6: Fix printing for quad
Plex: Removed extra semicolon
SNES ex12: Moved restart test to subtests
Plex ex15: Switched to simple partitioning
SNES ex12: Switched to simple partitioning
SNES ex62: Updated output for small numerical diffs
SNES ex62: Switched to simple partitioning
Tests: Turned off some tests that do not very in single precision
all requires need to go on the same line in test definition otherwise they are skipped
TS ex47: Added test output
replace numProcs with standard size
...

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Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

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fix field dof

DMPLEX: added initial implementation for handling periodicity with gmsh

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-mantle-example

* knepley/feature-plex-tests-new: (103 commits)
Test: Reverted cherry pick
Plex: Damn Absoft, Trying to get unde

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-mantle-example

* knepley/feature-plex-tests-new: (103 commits)
Test: Reverted cherry pick
Plex: Damn Absoft, Trying to get under the 132 character line limit for Absoft
Testing: Cherry picked a fix
Plex: Trying to get under the 132 character line limit for Absoft
Plex: Fix small compiler warnings
Plex ex2f90: Removed comment line Absoft does not like
Plex: Turn off some tests for quad
Plex ex6: Fix printing for quad
Plex: Removed extra semicolon
SNES ex12: Moved restart test to subtests
Plex ex15: Switched to simple partitioning
SNES ex12: Switched to simple partitioning
SNES ex62: Updated output for small numerical diffs
SNES ex62: Switched to simple partitioning
Tests: Turned off some tests that do not very in single precision
all requires need to go on the same line in test definition otherwise they are skipped
TS ex47: Added test output
replace numProcs with standard size
Plex+Gmsh: Fix for complex
fix accidently changed code
...

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Merge remote-tracking branch 'origin/knepley/feature-plex-tests-new' into tisaac/fix-pipeline-tests

* origin/knepley/feature-plex-tests-new: (101 commits)
Plex: Fix small compiler warnings
Plex

Merge remote-tracking branch 'origin/knepley/feature-plex-tests-new' into tisaac/fix-pipeline-tests

* origin/knepley/feature-plex-tests-new: (101 commits)
Plex: Fix small compiler warnings
Plex ex2f90: Removed comment line Absoft does not like
Plex: Turn off some tests for quad
Plex ex6: Fix printing for quad
Plex: Removed extra semicolon
SNES ex12: Moved restart test to subtests
Plex ex15: Switched to simple partitioning
SNES ex12: Switched to simple partitioning
SNES ex62: Updated output for small numerical diffs
SNES ex62: Switched to simple partitioning
Tests: Turned off some tests that do not very in single precision
all requires need to go on the same line in test definition otherwise they are skipped
TS ex47: Added test output
replace numProcs with standard size
Plex+Gmsh: Fix for complex
fix accidently changed code
another fix for Plex for complex numbers
fix for example that did not handle complex numbers correctly
mark example tests that do not work with complex, fix warning about use of possibly uninitialized values
Fix MPI type to match PetscReal
...

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DMPlexRefine_CTetgen() mimics DMPlexRefine_Tetgen()

Merge remote-tracking branch 'origin/knepley/feature-fe-dual-apply' into tisaac/feature-fe-dual-apply

* origin/knepley/feature-fe-dual-apply: (75 commits)
Plex: Screwed up last fix
Plex: Fix ove

Merge remote-tracking branch 'origin/knepley/feature-fe-dual-apply' into tisaac/feature-fe-dual-apply

* origin/knepley/feature-fe-dual-apply: (75 commits)
Plex: Screwed up last fix
Plex: Fix overeager protection of function
PetscFE: Fixed declaration
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newer macOS image
clarify damping and other issues related to SNESLINESEARCHBASIC
change example in new harness to use simple partitioner so gets consistent output on all systems
remove unused function from test file
cleanup formatting in example, plus myrank not rank
all requires need to go on the same line in test definition otherwise they are skipped
missing - makes the manual page formatting wrong
The developer manual clearly states that MPI_Comm_size() returns size it doesn't return numProcs or other nonsense. Pretty soon you'll start using mype instead of rank?
fix typo and cut and paste error in docs
bugfix for !HYPRE
fix warning for ';;'
may switch to scalable only when B->cmap->N > 100000
MatLRC: store in the context the parallel matrices rather than the sequential ones
Bib: Add ref
set default algorithm based on B->cmap->N for MatMatMult_MPIAIJ_MPIAIJ()
Error in VecScatterView_MPI() had the meaning of from and to backwards
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Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new: (73 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to s

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new: (73 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newer macOS image
clarify damping and other issues related to SNESLINESEARCHBASIC
change example in new harness to use simple partitioner so gets consistent output on all systems
remove unused function from test file
cleanup formatting in example, plus myrank not rank
all requires need to go on the same line in test definition otherwise they are skipped
missing - makes the manual page formatting wrong
The developer manual clearly states that MPI_Comm_size() returns size it doesn't return numProcs or other nonsense. Pretty soon you'll start using mype instead of rank?
fix typo and cut and paste error in docs
bugfix for !HYPRE
fix warning for ';;'
may switch to scalable only when B->cmap->N > 100000
MatLRC: store in the context the parallel matrices rather than the sequential ones
Bib: Add ref
set default algorithm based on B->cmap->N for MatMatMult_MPIAIJ_MPIAIJ()
Error in VecScatterView_MPI() had the meaning of from and to backwards
fix build warning as reported by the nightly tests
Update alquimia.py to use Glenn's branch that updates alquimia for pflotran xsdk
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Merge branch 'master' into knepley/feature-plex-tests-new

* master: (94 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newe

Merge branch 'master' into knepley/feature-plex-tests-new

* master: (94 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newer macOS image
clarify damping and other issues related to SNESLINESEARCHBASIC
change example in new harness to use simple partitioner so gets consistent output on all systems
remove unused function from test file
cleanup formatting in example, plus myrank not rank
missing - makes the manual page formatting wrong
The developer manual clearly states that MPI_Comm_size() returns size it doesn't return numProcs or other nonsense. Pretty soon you'll start using mype instead of rank?
fix typo and cut and paste error in docs
bugfix for !HYPRE
fix warning for ';;'
may switch to scalable only when B->cmap->N > 100000
MatLRC: store in the context the parallel matrices rather than the sequential ones
Bib: Add ref
set default algorithm based on B->cmap->N for MatMatMult_MPIAIJ_MPIAIJ()
Error in VecScatterView_MPI() had the meaning of from and to backwards
fix build warning as reported by the nightly tests
Update alquimia.py to use Glenn's branch that updates alquimia for pflotran xsdk
fix divide by zero exposed by 8534686b5096cd4c91a8f3895408b386c0628431 - and produced by petsc4py testsuite
...

Conflicts:
src/dm/impls/plex/examples/tests/ex13.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tests/ex2.c
src/snes/examples/tests/output/ex2_3.out
src/snes/examples/tests/output/ex2_4.out
src/snes/examples/tests/output/ex2_5.out

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Merge branch 'knepley/feature-plex-gmsh-nodes'

* knepley/feature-plex-gmsh-nodes:
Plex+Gmsh: Read higher order cells and ignore extra nodes

Conflicts:
src/dm/impls/plex/plexgmsh.c

Merge branch 'knepley/fix-plex-docs'

* knepley/fix-plex-docs:
Plex: Fix the fix
fix -Wmaybe-uninitialized
Doc+Plex: Add PetscUnit to Fortran
Doc+Plex: Fix function name
Plex: Fix declarati

Merge branch 'knepley/fix-plex-docs'

* knepley/fix-plex-docs:
Plex: Fix the fix
fix -Wmaybe-uninitialized
Doc+Plex: Add PetscUnit to Fortran
Doc+Plex: Fix function name
Plex: Fix declaration
Doc+Plex: Added function docs
Doc+Plex: More function docs - Make functions static - Move internal declarations
Doc+Plex: More function docs
Doc+Plex: Document DMPlexGetOrientedFace() and DMPlexSetSubpointMap() - Make functions static
Doc+Plex: Document DMPlexCreateOverlapMigrationSF() - Make functions static
Plex: Make functions static - Move internal declarations to private header
Plex: Make functions internal
Plex+HDF5: Make functions internal
Plex: Make functions static
Plex: Make functions static
Doc+Plex: Document DMPlexCreateNeighborCSR() - Make functions static
Doc+Plex: Document DMPlexPreallocateOperator() - Make functions static
Plex: Make function static
Plex+VTK: Make functions static
Plex+VTK: Make DMPlexVTKGetCellType() internal

Conflicts:
src/dm/impls/plex/plexvtk.c

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Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new:
Plex+Gmsh: Fix for complex

Plex+Gmsh: Fix for complex