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 '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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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?

Using consistent names for va

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?

Using consistent names for variables makes code simpler to maintain

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PetscFE+FV: Now discretization can be vector spaces
- Space and DualSpace have a number of components
- Now the dimension of a space incorporates the components, so all size determinations changed
-

PetscFE+FV: Now discretization can be vector spaces
- Space and DualSpace have a number of components
- Now the dimension of a space incorporates the components, so all size determinations changed
- The default is to form direct sums of scalar spaces, e.g. for constants (1, 0) and (0, 1) so every
basis vector is a vector with only one component nonzero
- DualSpaceApply() is now handled by the implementation
- FE now uses numDof directly from the DualSpace
- Changed SpaceDG --> SpacePoint
- Updated ex3 tests (DA and p4est is still broken)

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Plex+HDF5: Make functions internal

DM: Fixed Fortran for DMGetStratumIS and

Minor cleanup, remove some outdated code, remove unneeded constructs, improve manual pages slightly, add missing test case

Time: 2.5 hours

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-t

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-to: Andreas Mang <andreas@ices.utexas.edu>

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Updated and simplified Fortran interface

Reduced from 4 distinct approaches to using PETSc from Fortran to 1
No more .h90 files (Fortran 90 functionality is now always available)
Parameters and func

Updated and simplified Fortran interface

Reduced from 4 distinct approaches to using PETSc from Fortran to 1
No more .h90 files (Fortran 90 functionality is now always available)
Parameters and function prototypes are now provide through Fortran modules, not includes;
only #define are provided in the petscXXXdef.h files
PETSc objects can be declared as either type(tXXX) or XXX. For example type(tVec) or Vec
Moved now private Fortran include files out of public include directory since uses don't use them;
they are only used to generate the Fortran modules
Easier to support and test; we can now easily add more function prototypes
Also had to rework generation of manual pages to consistently use MANSEC and SUBMANSEC
since these variables also handle how the Fortran modules are generated.

Time: 57 hours

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Improve ex65 for -pc_type mg -pc_mg_galerkin

Time: .2 hours
Reported-by: Anton Popov <popov@uni-mainz.de>

Merge remote-tracking branch 'origin/maint'

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 '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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DM: Added timing of DMRefine()