Merge branch 'master' into madams/gamg-destroy

Conflicts:
src/ksp/pc/impls/gamg/gamg.c

Merge branch 'master' into barry/reduce-dmsetup-da-memoryusage

Conflicts:
src/dm/examples/tests/ex15.c
src/dm/examples/tutorials/ex3.c
src/dm/impls/da/da2.c
src/dm/impls/da/da3.c

Merge branch 'master' into barry/xcode

DMPlex: Added Gmsh input

Merge branch 'master' into knepley/feature-dmda-section

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fi

Merge branch 'master' into knepley/feature-dmda-section

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fix for TSGetRHSMats_Private() in the creation of the Arhs and Brhs matrices
protect logging of objects (which uses global variables) with PETSC_USE_LOG
error handler API had been previously changed but this example was not updated to new API.
DMPlex: Fixed bug in coordinate permutation
PetscSection: Doc fix for permutation
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bugfix of MatCreateSeqAIJFromTriple() contributed by Nicolas Marsic <nicolas.marsic@montefiore.ulg.ac.be>
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
completed removing server code that was not removed in previous commit
removed PETSc webserver and configure package files that supported it
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
fix outdated PetscOptionsList
SNESQN: only monitor real part of dot product (fails with C++ complex)
Fix for multiple definitions in mat/color/interface/ custom fortran bindings
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/da/dageometry.c
src/dm/impls/plex/examples/tests/ex4.c
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexinterpolate.c

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Merge branch 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key

Merge branch 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
SNESQN: only monitor real part of dot product (fails with C++ complex)
Corrected the #include statement in the man pages for the PetscObjectComposedDataSet/Getwhatever routines.
DMPlex: Added doc for DMPlexGetHybridBounds()
winzip: detect if winzip is used to extract petsc.tar.gz and error out.
configure: remove self.archIndependent as its not being used. [it is used to create externalpackages/package/arch dir which is unused]
configure: fix packages using package-dir/PETSC_ARCH as out-of-source-build location Perhaps this should be changed to package-dir/build?
configure: remove dead code previously used to download BuildSystem
configure: check if compilerDefines [and compilerFixes] exist in framework before using them
configure: save/restore reconfigure.py when --with-clean is used
configure: add --with-clean option to delete buildfiles/externalpackages in PETSC_DIR/PETSC_ARCH and potential externalpackages in --with-external-package-dir/PETSC_ARCH
configure: With --with-externalpackages-dir=dir store/build packages in dir/PETSC_ARCH
Add MatSeqSBAIJSetPreallocationCSR()
configure: switch to using PETSC_DIR/PETSC_ARCH/externalpackages by updating package.py to use externalpackages.py as the externalPackagesDirProvider
configure: move dead code configureExternalPackagesDir() from petscdir.py to externalpackagesdir.py Also set PETSC_DIR/PETSC_ARCH/externalpackages as the externalpackagesdir
...

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Merge branch 'master' into barry/saws

Conflicts:
src/ksp/pc/impls/gamg/gamg.c
src/sys/classes/viewer/impls/ams/ams.c
src/sys/objects/pinit.c

Merge branch 'knepley/feature-plex-refine-3d'

* knepley/feature-plex-refine-3d: (96 commits)
DMPlex: Fix label creation for 3D simplicial refinement
DMPlex ex4: Added another 2D simplex hybrid t

Merge branch 'knepley/feature-plex-refine-3d'

* knepley/feature-plex-refine-3d: (96 commits)
DMPlex: Fix label creation for 3D simplicial refinement
DMPlex ex4: Added another 2D simplex hybrid test
DMPlex ex4: Reworked 2D simplex hybrid test
DMPlex: Fixed bug for label creation in hex refinement
DMPlex: Fixed compiler warnings
DMPlex: Fix uniform refinement for empty mesh
DMPlex: Fixed creation of hybrid submesh - No more Lagrange flag, just check for proper prism hybrid cells
DMPlex ex5: Added test output for 2D quad test with fault ending in the domain
DMPlex: Major fix for hybrid cell creation - Faults that ended in the domain created inconsistent meshes - I now add a cohesive cell at the edge of a fault which may have some pieces "unsplit" - Unsplit points are connected by hybrid points, but are not replicated - This has only been tested in 2D
DMPlex: Fix bug with multiple point labels for cohesive completion
DMPlex: Allow an increase in support size for split points in hybrid construction
DMPlex: Fixed compiler warning
DMPlex ex5: Added a new quad test - Its broken for a good reason, need to deal with fault boundaries
DMPlex ex5: Added test output
DMPlex ex4 and ex5: Added new hexahedral test
DMPlex: Streamlined marking of points along a fault - Changed iteration strategy - Added comments
DMPlex ex4: Added hybrid hex tests
DMPlex ex4: Added test with 6 tets
DMPlex ex4: Now check initial mesh for consistency
DMPlex: Fix bug with DMPlexLabelCohesiveComplete() - Must mark point with correct dimension
...

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/makefile
src/dm/impls/plex/plexinterpolate.c

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Merge branch 'knepley/feature-plex-reordering'

* knepley/feature-plex-reordering:
doc: update makefile with order.h -> ../../../include/petsc-private/matorderimpl.h rename
DMPlex: Fixed bug with

Merge branch 'knepley/feature-plex-reordering'

* knepley/feature-plex-reordering:
doc: update makefile with order.h -> ../../../include/petsc-private/matorderimpl.h rename
DMPlex: Fixed bug with DMPlexPermute - Fixed label permutation
DMPlex: Check whether default section exists to be reordered
DMPlex: Fixed compiler warning
DMPlex ex10: Fixed test output
DMPlex: Added missing declarations
DMPlex: Fixed misuse of PetscObjectSetName()
MatComputeBandwidth: use PetscInt instead of PetscMPIInt
Mat: Fixed declaration
Mat: Changed MatCalcBandwidth() to MatComputeBandwidth() - Added Fortran interface
DMPlex ex10: This tests reordering of meshes
DMPlex: Added DMPlexGetOrdering() and DMPlexPermute()
PetscSection: Added PetscSectionPermute()
DMLabel: Added DMLabelPermute()
DMPlex: Added DMPlexCreateDoublet()
DMPlex: Added DMPlexCopyLabels()
Mat: Added MatCalcBandwidth()
MatOrdering: Moved private header into petsc-private - Fix to pointer checks in sorder.c

Conflicts:
include/petscdmplex.h

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DMPlex: Added DMPlexGetOrdering() and DMPlexPermute()

Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

DMPlex: Add plexrefine.c to makefile

Merged petsc/petsc into rmills/petsc master.

Merge branch 'knepley/plex'

Improved support for discretizing PDEs. Cell geometry and FVM. Little to
no topology.

* knepley/plex:
SNES ex12: Fix leak
TS ex11: error if dim != DIM because memory

Merge branch 'knepley/plex'

Improved support for discretizing PDEs. Cell geometry and FVM. Little to
no topology.

* knepley/plex:
SNES ex12: Fix leak
TS ex11: error if dim != DIM because memory corruption occurs otherwise
DMPlex: All quadrilateral geometry tests working
DMPlex: remove unused variable
DMPlex: Hexahedron geometry tests now pass
DMPlex: More geometry work
DMPlex: use PETSC_HAVE_TGAMMA to get the build working on windows
configure: add test for tgamma() [this is missing on windows]
DMPlex: Added random transform tests for tets - Fixed memory leak
DMPlex: Fixed 3D geometry
DMPlex: FVM geometry tests now work for triangles
DMPlex: one more win32/complex fix
DMPlex: Enhanced geometry tests - Added random transforms of the reference triangle in 2D
DMPlex: Fixed complex problems in geometry calculation
DMPlex: Fixed Fortran test output
DMDT: M_PI --> PETSC_PI
DMPlex: Reorganized geometry testing
TS ex11: Put in 3D inflow and outflow ids from the command line
DMPlex: Added DMPlexRestoreCone/Support() to F90 interface definition header - Also added to test ex1f90
TS ex11: Need to make these ids input from the command line
DMPlex: Add Fortran bindings
DMPlex: Reorder tet output since I order tets differently
Builder: Link Fortran examples with Fortran linker
DMPlex: Fixed leak in example
DMPlex: Tutorial now shows how to output VTK
PetscViewer: Added VTK type for Fortran
DMPlex: Remove parameter names from prototype
DMPlex: Geometry fixes for C++ complex
DMAKKT: Remove from build
DMPlex: Now DMPlexCreateSection() only has an F90 interface
SNES: add Fortran bindings to DMSNESSet{Function,Jacobian}
SNES: remove superfluous casting in DM local Fortran bindings
SNES: compile zdmlocalsnesf.c
DMDT: Fix Fortran wrapper
DMPlex: Added Fortran interface for DMPlexMatSetClosure()
PetscSection: Added docs, enabled Fortran wrappers
DM: Added Fortran bindings for DMSNESSetFunction/JacobianLocal()
SNES ex12: Looks like 3D Neumann conditions are working
DMPlex: Fix volume determination for 2D in 3D
DMPlex: Better error reporting
SNES ex12: Boundary integration seems to work in 2D
DMPlex+FEM: Fix for boundary integration
TS ex11: Better error reporting
DMPlex ex8: Added FVM geometry tests
DMPlex: Fixed FVM geometry for 2D in 3D
SNES ex62: Now using PetscDT quadrature
DMDT: Translated FIAT's Gauss-Jacobi quadrature
DMPlex: Fix geometry tests - Fix tests for 2D projection
DMPlex: Geometry fixes
DMPlex: Small fixes for geometry
DMPlex: Fixed damn prototype
PetscSection: Added VecSetValuesSectionF90() - Fixed bug in Vec Fortran header
DMPlex: Added Fortran defines for additional insert modes
DMPlex: Silence warning in DMPlexInvertCells_Internal()
DMPlex: Functions passed to evaluation routines now return void and pass results in arguments
DMPlex: Now we give an explicit embedding dimension to the FVM geometry methods
DMPlex: Fixed complication with complex - Started to add 3D geometry stuff
TS ex11: Replace edge geometry with call to DMPlexComputeCellGeometryFVM()
DMPlex: Added normal argument to DMPlexComputeCellGeometryFVM() - This is only calculated for faces - Added calculation for faces in 2D
DMPlex: Damn makefiles
DMPlex: Added declaration for DMPlexCreateCGNS()
TS ex11: Reorganized computation of geometry in preparation for 3D
Builder: Now individual tests can have requirements - The key is 'requires', and it takes a list of package names - Also fixed up showSingleRun()
TS ex11: Use new DMPlexComputeCellGeometryFVM()
DMPlex: Added DMPlexComputeCellGeometryFVM() - Added internal volume methods
DMPlex: fix const and int vs. PetscInt
DMPlex: Better error reporting
DMPlex+ExodusII: Fixed reading of quads - Was broken by 2e1b13c25062c3c40593ce7412c5cd227259ade7
DMPlex: Hex cell geometry was broken - I don't see how this test passed before
DMPlex: Regression cleanup
DMPlex: Regression cleanup
SNES ex12: Fixed sign for Neumann BC
DMPlex+FEM: The dimension does not change for boundary elements
DMPlex: Geometry now works for boundary elements
DMPlex+FEM: Fixed quadrature coordinate handling for boundary integrals
SNES ex12: Reorganized tests, still working on Neumann conditions - Fixed boundary face label
DMPlex: Turn off CGNS by default
DMPlex: Added 1D cell geometry
DMPlex: DMPlexCreateCGNS()
DMPlex: Updated test ex1 output
DMPlex: Fixed compiler problems with complex
SNES ex12: Now does boundary integration - Still not verifying exact solution for Neumann conditions
DMPlex: Fix DMPlexComputeCellGeometry() to handle lower dimensional cells
DMPlex: Fixed error in projection from 3D to 2D - Need to check for case where normal is already z
DMPlex: Adding boundary integration
DMPlex: Fixed cell inversion for TetGen to commute with mesh interpolation
SNES ex12: Cleaning up ex12 testing
DMPlex: Added integration over boundary to DMPlexComputeResidualFEM() - Added quadBd, f0/1BdFuncs to PetscFEM struct - Needs to be tested
FEM Generation: We now allow a *_bd.h header that holds boundary discreization
Builder: Fixed regression requirements
Builder: Fixed specification of multiple tests to run
DMPlex ex7: Orientations now working properly
DMPlex: Changed orientation convention and fixed many bugs
SNEX ex12: Ignore generated headers
SNEX ex12 and ex52: Remove CTetGen warnings from test output - Fixed this in CTetGen repository
DMPlex: Fix default |J| for DMPlexComputeCellGeometry()
DMPlex: Fix for cell geometry (unbelievable screwup)
DMPlex ex7: Check that |J| is nonzero for each cell in interpolated mesh
DMPlex: Allow DMPlexComputeCellGeometry() to work with interpolated meshes
DMPlex: Added prototype for DMPlexCopyCoordinates(), and docs for that and DMPlexInterpolate()
DMPlex: Added F90 interface for DMPlexComputeCellGeometry()

Conflicts:
include/petscdmplex.h

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DMPlex: Damn makefiles

Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

Merge branch 'master' into tautges/dmmoab

* master: (24 commits)
testexamples: support *.cxx
...

DMPlex: Moved out Preallocation and FEM support to other files

Hg-commit: b2561291e574ff9a0f8a073426e136d4a44a4dde

commit after merge

Hg-commit: 22b02cb090aac02c6dc216e44019c448d4ec4cfa

DMPlex: Moved point location and cell geometry to another file

Hg-commit: 25a74dae76510764633f1fe53279f557673f39fb

DMPlex: Moved mesh interpolation routines to a separate source file

Hg-commit: 54e9f2d9a76a30973b86463d1b42a59184d81f03

commit after merge

Hg-commit: 03fb15d4af310051f85168e52abca3062e87dfd6

commit after merge.

Hg-commit: e15fd985275e9e6c40407ae90b2d69ed97fbf48d

DMPlex: Added DMPlexCreateSubpointIS(), fixed bug in DMPlexMatSetClosure(), moved submesh ops to a file
- Use subpointIS where we used old subpointMap which is now a DMLabel
- Bug was a failure to up

DMPlex: Added DMPlexCreateSubpointIS(), fixed bug in DMPlexMatSetClosure(), moved submesh ops to a file
- Use subpointIS where we used old subpointMap which is now a DMLabel
- Bug was a failure to update the index offset correctly in the case with no fields in the section
- Moved all submesh operations to plexsubmesh.c

Hg-commit: 8163c5abcc24b59cbb866a576cd085c13542a9b1

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Rename DMComplex -> DMPlex

Hg-commit: f768b4255f3d1c199623a7a4aeb9be630bec7076