Plex: Reorganized Latex output

Plex: Fix deadlock in DMPlexCreatePointNumbering

Use dim instead of depth for unstratified meshes.

Merge branch 'knepley/fix-plex-orient'

* knepley/fix-plex-orient:
Plex: Fix serial orientation
TetGen: Syntax fix
Plex: Fix MPI type for orientation
Plex: Small orientation fix
Plex ex13:

Merge branch 'knepley/fix-plex-orient'

* knepley/fix-plex-orient:
Plex: Fix serial orientation
TetGen: Syntax fix
Plex: Fix MPI type for orientation
Plex: Small orientation fix
Plex ex13: Orientation now working for flipped connected components
Plex: Reworked orientation to respect connected components on each process
Plex ex13: Check in initial output
Plex: Now mark initial cell as seen - Changes the outcome slightly
Plex: Added DMPlexCheckFace_Internal() - This checks a face in the mesh for orientation consistency
Plex: Fix orientation diagnostics
Plex: Added declaration for DMPlexReverseCell()
Plex ex13: Tests orientation - Only 2D triangle tests now - Last test shows problem for disconnected domains
Plex: Small example fixes
PetscBT: Do not overwrite a viewer passed to PetscBTView()
Plex: Remove unneeded headers
Plex: Added a file for orientation calculations - Moved DMPlexOrient()

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

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Merge branch 'barry/remove-unneeded-paren-petscmalloc'

Conflicts:
src/mat/impls/baij/seq/baij.c

Plex: Remove unneeded headers

Plex: Added a file for orientation calculations
- Moved DMPlexOrient()

convert some PetscMalloc() to PetscMalloc1()
remove unneeded () in first argument to PetscMalloc/Calloc1()
fixes for MATLAB examples

Merge branch 'master' into knepley/fix-plex-examples-refinement

* master: (62 commits)
Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would mean a ton of

Merge branch 'master' into knepley/fix-plex-examples-refinement

* master: (62 commits)
Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would mean a ton of infrastructure I think
Plex ex12: Fix output after label distribution fix
Plex: Only call SetFromOptions() after Distribute, since we cannot avoid it
TS ex11: Since DMPlexDistribute() calls SetFromOptions(), do not call it again, and cleaned up tests
Plex+FV: If using FVM adjacency, do not create ghost cells for faces in the overlap, or set BC on them
Plex: If using FVM adjacency, we must include the closure in the overlap
Plex+Label: All processes with a valid label should participate in label distribution - Formerly it was just proc 0
Plex: Add check that parallel renumbering fully covers the cone points
Plex: For one level adjacency, include the point itself since this makes sense when looking in parallel from the overlap
Plex: Cannot Malloc2() the arrays passed to PetscSFSetGraph()
Plex: Preallocation fixes for indegree > 1 - Again this should be rewritten
SNES ex62: Changes to output for fixes with quads
Plex+Label: Set default output flag to PETSC_TRUE
Plex ex1: Fixed LaTeX output
Plex ex12: Fixed overlap test
Plex: Fixed incorrect usage of PetscSFGatherBegin/End() in preallocation - This should be rewritten using new style
PetscSF: Incorrect check for computed degrees
Builder: Fix bad search and replace
Configure: Fix for Barry's change to organization - I do not know what happened here
Builder: Fix for Barry's change
...

Conflicts:
src/snes/examples/tutorials/ex12.c

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Merge branch 'mlange/feature-parallel-distribute'

* mlange/feature-parallel-distribute: (33 commits)
Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would

Merge branch 'mlange/feature-parallel-distribute'

* mlange/feature-parallel-distribute: (33 commits)
Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would mean a ton of infrastructure I think
Plex ex12: Fix output after label distribution fix
Plex: Only call SetFromOptions() after Distribute, since we cannot avoid it
TS ex11: Since DMPlexDistribute() calls SetFromOptions(), do not call it again, and cleaned up tests
Plex+FV: If using FVM adjacency, do not create ghost cells for faces in the overlap, or set BC on them
Plex: If using FVM adjacency, we must include the closure in the overlap
Plex+Label: All processes with a valid label should participate in label distribution - Formerly it was just proc 0
Plex: Add check that parallel renumbering fully covers the cone points
Plex: For one level adjacency, include the point itself since this makes sense when looking in parallel from the overlap
Plex: Cannot Malloc2() the arrays passed to PetscSFSetGraph()
Plex: Preallocation fixes for indegree > 1 - Again this should be rewritten
SNES ex62: Changes to output for fixes with quads
Plex ex1: Fixed LaTeX output
Plex ex12: Fixed overlap test
Plex: Fixed incorrect usage of PetscSFGatherBegin/End() in preallocation - This should be rewritten using new style
PetscSF: Incorrect check for computed degrees
Builder: Fix for Barry's change
PetscSF: Fixes for sparse leaves - When sf->mine exists, the leaves can be numbered non-sequentially. This causes allocation based upon sf->nleaves to underallocate. Replacing sf->nleaves with the maximum leaf number is sufficient in this case.
Plex: Fix leaks
Configure: How did this break?
...

Conflicts:
config/builder.py

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Merge branch 'knepley/feature-plex-partitioner-shell'

* knepley/feature-plex-partitioner-shell:
Plex: Cleanup of examples to use new interfaces
Plex: Added DMPlexCreateFromFile() - Dispatches to

Merge branch 'knepley/feature-plex-partitioner-shell'

* knepley/feature-plex-partitioner-shell:
Plex: Cleanup of examples to use new interfaces
Plex: Added DMPlexCreateFromFile() - Dispatches to the right constructor based on extension
Plex ex1: Added test partitioner
Plex: Added DMPlexGetPartitioner() and PetscPartitionerShellSetPartition()
PetscSection: Added PetscSectionCopy()
Plex ex1: Cleaned up mesh creation - Now use -dm_refine for uniform refinement
Plex: Remove superfluous argument from DMPlexDisitrbute()
Plex: Fixed Fortran stub
PetscFV: Lots of small naming fixes
Partitioner+Plex: Added PetscPartitioner class - Plex holds a PetscPartitioner - Changed args so that PetscSections are modified, not created (also of DMPlexEnlargePartition) - Now partition routine takes a number of partitions instead of assuming commSize - Added a shell partitioner intended to be used for regression testing

Conflicts:
src/dm/impls/plex/examples/tests/ex1.c

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Merge branch 'knepley/feature-plex-label-output'

* knepley/feature-plex-label-output:
Plex+Label: Set default output flag to PETSC_TRUE
Plex+Label: Added output flag for labels - Meant storing l

Merge branch 'knepley/feature-plex-label-output'

* knepley/feature-plex-label-output:
Plex+Label: Set default output flag to PETSC_TRUE
Plex+Label: Added output flag for labels - Meant storing labels in a struct inside Plex - Added DMPlexGetLabelByNum() - Added DMPlexGet/SetLabelOutput() - Got rid of most of the mucking with the internal label storage

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Merge branch 'knepley/feature-parallel-partition'

* knepley/feature-parallel-partition:
Plex: Silence compiler warning
Plex: Needs custom Fortran binding
Plex: Fix distribution for meshes with

Merge branch 'knepley/feature-parallel-partition'

* knepley/feature-parallel-partition:
Plex: Silence compiler warning
Plex: Needs custom Fortran binding
Plex: Fix distribution for meshes without coordinates
Plex ex12: Added test from Michael
Plex: Added methods to support distributed overlap calculation - Added DMPlexCreateTwoSidedProcessSF() - Added DMPlexDistributeOwnership() - Added DMPlexCreateOverlap()
PetscSF: Fix ComputeDegree and GetMultiSF for sparse SFs
Plex: Added DMPlexDistributeFieldIS() - Small doc fix
Plex: DMPlexCreateProcessSF() is now documented and the outputs are optional - The root space is also correct
PetscSF: The declaration of PetscSFNode should be in the types header
Plex ex12: Add overlap
Plex ex12: Added test for parallel partitioning
SNES ex12: Misspelling
Plex ex1: Typo
Plex: Fix LaTeX mesh output

Conflicts:
include/petscdmplex.h

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Merge branch 'master' into knepley/fix-configure-petsc-dep

* master: (210 commits)
error out on special cases where DMLocalToGlobal_DA won't work
remove unneed uses of local DM vectors and DMLoc

Merge branch 'master' into knepley/fix-configure-petsc-dep

* master: (210 commits)
error out on special cases where DMLocalToGlobal_DA won't work
remove unneed uses of local DM vectors and DMLocalToGlobalBegin/End in examples removed to prevent cut and paste repeats of their use
openmpi: update to version 1.8.3
added more movies and pubs
more movies
MatGetDiagonalBlock() can be called before matrix is assembled
added a couple more movies/images
PetscLogEventGetId() was missing public prototype
simply output from make streams benchmark test
c2html: fixup so that C2HTML make variable is set [similar to cmake.py]
chaco: current blas test does'nt work with Cray CC [which automatically links with blas] and linux - where -lm needs to be listed explicitly. Switch the test to check if we are using PETSc modifled chaco
builddist: always install c2html/sowing
argonne logo for users manual cover
Remove PETSC_HAVE_CUSP_SMOOTHED_AGGREGATION, use PETSC_HAVE_CUSP instead.
mpich: use older tarball with cygwin/gnu compilers
updated information about packages PETSc can use in users manual
Updated users manual to latest ANL Report format requirements
mpich: update to mpich-3.1.3.tar.gz - remove -download-mpich-mpe [mpich no longer packages mpe] - remove -download-mpich-shared. It was added as a split from --with-mpi-shared to --known-mpi-shared and --download-mpich-shared in 50237a55163f90ac7341b723c6422dfa1dbce792 removing this gives back the control of shared=0/1 to package.py - remove download_solaris as the new tarball works with both gcov and on solaris - remove MPICHInstall() [and use GNUPackage.Install()] as the new tarball fixes 'make clean' requiring sudo
added more images and PETSc pubs
Doc: More refs
...

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Merge branch 'knepley/feature-plex-label-output' into mlange/feature-parallel-distribute

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

Plex: Add performance and debug logging

Merge branch 'knepley/feature-plex-partitioner-shell' into mlange/feature-parallel-distribute

Merge branch 'knepley/feature-parallel-partition' into mlange/feature-parallel-distribute

Conflicts:
include/petscdmplex.h

Partitioner+Plex: Added PetscPartitioner class
- Plex holds a PetscPartitioner
- Changed args so that PetscSections are modified, not created (also of DMPlexEnlargePartition)
- Now partition routine

Partitioner+Plex: Added PetscPartitioner class
- Plex holds a PetscPartitioner
- Changed args so that PetscSections are modified, not created (also of DMPlexEnlargePartition)
- Now partition routine takes a number of partitions instead of assuming commSize
- Added a shell partitioner intended to be used for regression testing

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Plex+Label: Added output flag for labels
- Meant storing labels in a struct inside Plex
- Added DMPlexGetLabelByNum()
- Added DMPlexGet/SetLabelOutput()
- Got rid of most of the mucking with the inte

Plex+Label: Added output flag for labels
- Meant storing labels in a struct inside Plex
- Added DMPlexGetLabelByNum()
- Added DMPlexGet/SetLabelOutput()
- Got rid of most of the mucking with the internal label storage

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Merge branch 'knepley/feature-plex-generator-args'

* knepley/feature-plex-generator-args:
Plex: Small fix
Plex: Fixed misspelling
Plex: Move generation to a separate source file, Can now speci

Merge branch 'knepley/feature-plex-generator-args'

* knepley/feature-plex-generator-args:
Plex: Small fix
Plex: Fixed misspelling
Plex: Move generation to a separate source file, Can now specify operator for mesh generators - Added DMPlexTriangleSetOptions() and DMPlexTetgenSetOptions()

Conflicts:
src/dm/impls/plex/makefile

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Merge branch 'tisaac/feature-fe-geom-dim' into tisaac/plex-flexible-projection

Use the new PetscFECellGeom

Conflicts:
include/petscdmplex.h
include/petscfe.h
src/dm/impls/plex/plexfem.c

Merge branch 'tisaac/thplex'

This merge brings in related work in the following areas:
- Added a local constraint matrix to DM (see DMSetDefaultConstraints())
- Added point-to-anchor-point constrain

Merge branch 'tisaac/thplex'

This merge brings in related work in the following areas:
- Added a local constraint matrix to DM (see DMSetDefaultConstraints())
- Added point-to-anchor-point constraints in DMPlex (see
DMPlexSetAnchors()), which build on the DM constraints
- Added hierarchically-constrained points to DMPlex (see
DMPlexSetReferenceTree(), DMPlexSetTree()), which builds on the anchor
constraints
- Tests for these constraints in src/dm/impls/plex/examples/ex3.c (try
runex3_* examples in that directory)
- Added quadrature order (see PetscQuadratureGet/SetOrder()) (work by
Matt Knepley)
- Added default return values for DMGetCoordinateDim() (defaults to
DMGetDimension())

Conflicts:
include/petscdmplex.h
src/dm/dt/interface/dt.c
src/dm/impls/plex/examples/tests/ex3.c
src/dm/impls/plex/makefile
src/dm/impls/plex/plexfem.c

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Merge branch 'knepley/feature-fe-fv-hybrid'

* knepley/feature-fe-fv-hybrid: (43 commits)
PetscFE: Small fixes
Plex+SNES: Volumes are PetscReal
Plex+SNES: Missing declaration
TS ex11: Remove

Merge branch 'knepley/feature-fe-fv-hybrid'

* knepley/feature-fe-fv-hybrid: (43 commits)
PetscFE: Small fixes
Plex+SNES: Volumes are PetscReal
Plex+SNES: Missing declaration
TS ex11: Remove unused var
Plex+SNES+TS: Complete reorganization of residual evaluation - Now both FE and FV examples use the same method, but there are a bunch of switches which should be eliminated - There is a confusion about IFunction and RHS, but I think they can both be in one function - Added DMPlexSNESGetGeometryFVM() and DMPlexSNESGetGradientFVM() - Added DMPlexGet/RestoreCellFields() and DMPlexGet/RestoreFaceFields() and DMPlexGet/RestoreFaceGeometry() - I think that FV geometry caching needs to be redone - Added DMPlexReconstructGradients_Internal() - Added DMPlexComputeBdResidual_Internal() which does not work for FV - Replaced DMPlexComputeResidualFEM_Internal() with DMPlexComputeResidual_Internal()
Plex: Added DMPlexInsertBoundaryValues() - Unified FE and FV boundary values
Plex: DMPlexProjectFunctionLableLocal() gets discretizations from the DM now
Plex: Added DMPlexComputeGradientFVM()
PetscDS: Fix up some functions to work for both FV and FE
PetscFV: Change PetscFVIntegrateRHSFunction() to get info from PetscDS
TS ex11: There is only one field in our current paradigm - We would need to split Riemann solvers for multiple fields right now
Plex+TS: Remove use of computeGradients in favor of check for dmGrad
TS ex11: Updated interface calls
Plex+TS: Change DMPlexTSGetGradientDM() to automatically construct the gradient info, DMPlexTSSetRHSFunctionLocal() can now be replaced by the DMTS version - Remove unnecessary declarations
Plex+SNES: Add missing declaration
Plex+FE: Removed all use of PetscCellGeometry, Changed FE integration to use PetscFECellGeom
DMSNES+Plex: Added DMPlexSNESGetGeometryFEM() to cache geometry
PetscDualSpace: Remove use of PetscCellGeometry in PetscDualSpaceApply() - Fixed up calls to it for projection into spaces
DMDA: Remove use of PetscCellGeometry in DMDAProjectFunctionLocal()
Plex: Added DMPlexComputeGeometryFEM() and PetscFECellGeom structure
...

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Plex: Move generation to a separate source file, Can now specify operator for mesh generators
- Added DMPlexTriangleSetOptions() and DMPlexTetgenSetOptions()

Plex: Fix LaTeX mesh output