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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Plex+Fluent: Finally got warning working for me

Plex+Fluent: numFaces should not have been unsigned

fix sign-compare warning in arch-linux-pkgs-cxx-mlib_el6

/sandbox/petsc/petsc.clone-3/src/dm/impls/plex/plexfluent.c:295:38: warning: comparison between signed and unsigned integer expressions [-Wsi

fix sign-compare warning in arch-linux-pkgs-cxx-mlib_el6

/sandbox/petsc/petsc.clone-3/src/dm/impls/plex/plexfluent.c:295:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]

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plex+MED: fix -Wunused-variable

Merged in michael_afanasiev/petscfork-dmplex-read-exodusii-mod/afanasiev/side-set-labels-plex-exodusii (pull request #545)

Added exodus side set names to DMLabel [plex].

Plex+MED: Fix variable protection

Plex+MED: Fix unsigned ints in the Fluent format

Merge branch 'knepley/fix-plex-mat-dm'

* knepley/fix-plex-mat-dm:
Plex: Attach DM to Mat

Remove the needed def extension from Fortran include files

Time: .3 hours
Thanks-to: Satish Balay <balay@mcs.anl.gov>

Plex: Attach DM to Mat

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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hdf5: add a seprate test category for TRIANGLE_HDF5
rename runex15_0 to ex15
and add "-petscpartitioner_type simple" output to output/ex15_alt_2.out

Add support for Chaco from the Trilinos distribution

It includes a chaco.h file and has a small API change

Funded-by: IDEAS
Project: IDEAS/xSDK
Time: .4 hours
Reported-by: Satish Balay <balay@mcs.

Add support for Chaco from the Trilinos distribution

It includes a chaco.h file and has a small API change

Funded-by: IDEAS
Project: IDEAS/xSDK
Time: .4 hours
Reported-by: Satish Balay <balay@mcs.anl.gov>

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Merge branch 'pr575/knepley/fix-labels-coordinatedm/master'

* pr575/knepley/fix-labels-coordinatedm/master:
Plex: swap DMPlexDistributeCoordinates() and DMPlexDistributeLabels()

DMPlex: use new geometry in L2 calculations

DMPlex: fixes to recent geometry calculation changes

DMPlexComputeCellGeometryFEM(): change interface to take quadrature points

The choice of points at which to evaluate the geometry shouldn't depend
on the discretization of the coordinates.

DMPlexCo

DMPlexComputeCellGeometryFEM(): change interface to take quadrature points

The choice of points at which to evaluate the geometry shouldn't depend
on the discretization of the coordinates.

DMPlexComputeCellGeometryFEM(): fix assumed presence of PetscDS fields

DMPlexComputeCellGeometryFEM(): more fixes for implicit discretizations

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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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DMPlexCreateHexBoxMesh(): again, fix initialization for c89

DMPlexCreateHexBoxMesh: c86-compatible initializiation

DMPlex tests ex22: larger tolerance, so that single precision passes

Merge branch 'maint'

* maint:
PetscPartitioner: fix documentation of PetscPartitionerShellSetPartition

DMPlexView_HDF5: use DMGetCoordinatesLocalized() instead of bad test