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

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

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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Merge remote-tracking branch 'origin/jed/dmsneslocal-fortran' into knepley/plex

* origin/jed/dmsneslocal-fortran:
SNES: add Fortran bindings to DMSNESSet{Function,Jacobian}
SNES: remove superflu

Merge remote-tracking branch 'origin/jed/dmsneslocal-fortran' into knepley/plex

* origin/jed/dmsneslocal-fortran:
SNES: add Fortran bindings to DMSNESSet{Function,Jacobian}
SNES: remove superfluous casting in DM local Fortran bindings
SNES: compile zdmlocalsnesf.c

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SNES: add Fortran bindings to DMSNESSet{Function,Jacobian}

SNES: compile zdmlocalsnesf.c

Merge branch 'master' into jed/ts-eimex

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

Conflicts:
src/ts/interface/tsregall.c

commit after merge

Hg-commit: 76831309032f5585424cb3e5e4c7f8f754699d5d

cleanup zda2f.c and move dmdasnessetjacobianlocal_(),
dmdasnessetfunctionlocal_(), dmdagetownershipranges_(),
dmdagetneighbors_() to corresponding ftn-custom source files.

Hg-commit: 32eee7b00cf9569

cleanup zda2f.c and move dmdasnessetjacobianlocal_(),
dmdasnessetfunctionlocal_(), dmdagetownershipranges_(),
dmdagetneighbors_() to corresponding ftn-custom source files.

Hg-commit: 32eee7b00cf956995e91d3252754892e1acc2c71

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commit after merge

Hg-commit: d540875a63b3c979c82b6a7fa7f062571e906d10

Mass revert file modes that were made executable in f6e61ee9c329

Hg-commit: 116d90d0b66125cee0db3e7351047057e756baf5

Merge

Hg-commit: ee8d91ae0580d1d4fa92be38a18d40c838b9a257

changed MatMatMult to MatTranposeMatMult.

Hg-commit: f6e61ee9c329774cd5343eea1ee6b7432be17c3f

Now requirepackage is only used for proper packages, functions use requiresfunction, and the rest use requiresdefine

Hg-commit: dd65fd3461c02753386917514e6ebe12d345a30e

Merge

Hg-commit: 9c9e2b0243eedf0151e3676f8f4ccde9f7b93898

merge TrMalloc/MEMALIGN updates

Hg-commit: e66e6e0b392d0e3456a0c4fdee411b9bff8fd74a

removed PETSC_ARCH/conf/base and
added support for not setting PETSC_ARCH and PETSC_DIR with --prefix option

Hg-commit: e478f4df238e5763b64567336d7cf94ca5d89d58

commit aFTERmerge

Hg-commit: 45a698803bd457bdc2ba32be5035e710250a5320

Merge

Hg-commit: 89a88a4570a641b3af1b53853d576da3947e5ca7

changed bmake/common everywhere to conf
fixed a little more for new install system

Hg-commit: 1aa781ff09e652ebafd6f016d84e88c15ea650f1

bk-changeset-1.3349.1.3
kaushik@manu.mcs.anl.gov|ChangeSet|20050620221736|50543
ChangeSet
1.3349.1.3 05/06/20 17:17:36 kaushik@manu.mcs.anl.gov +0 -0
Merge bk://petsc@petsc.bkbits.net/petsc-dev

bk-changeset-1.3349.1.3
kaushik@manu.mcs.anl.gov|ChangeSet|20050620221736|50543
ChangeSet
1.3349.1.3 05/06/20 17:17:36 kaushik@manu.mcs.anl.gov +0 -0
Merge bk://petsc@petsc.bkbits.net/petsc-dev
into manu.mcs.anl.gov:/home/kaushik/petsc


Hg-commit: e28f09e984c4b10dc1c40090e54df9bfb9cd3802

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bk-changeset-1.3352
bsmith@harley.mcs.anl.gov|ChangeSet|20050620195348|49723
ChangeSet
1.3352 05/06/20 14:53:48 bsmith@harley.mcs.anl.gov +0 -0
Merge bk://petsc.bkbits.net/petsc-dev
into harley

bk-changeset-1.3352
bsmith@harley.mcs.anl.gov|ChangeSet|20050620195348|49723
ChangeSet
1.3352 05/06/20 14:53:48 bsmith@harley.mcs.anl.gov +0 -0
Merge bk://petsc.bkbits.net/petsc-dev
into harley.mcs.anl.gov:/sandbox/bsmith/petsc-dev


Hg-commit: 9d0f44d4bded27b8f28504d10500c18b9650c939

show more ...

bk-changeset-1.3349.19.1
balay@asterix.mcs.anl.gov|ChangeSet|20050616200636|58139
ChangeSet
1.3349.19.1 05/06/16 15:06:36 balay@asterix.mcs.anl.gov +0 -0
Merge bk://petsc@petsc.bkbits.net/petsc-d

bk-changeset-1.3349.19.1
balay@asterix.mcs.anl.gov|ChangeSet|20050616200636|58139
ChangeSet
1.3349.19.1 05/06/16 15:06:36 balay@asterix.mcs.anl.gov +0 -0
Merge bk://petsc@petsc.bkbits.net/petsc-dev
into asterix.mcs.anl.gov:/home/balay/bk-rep/petsc-dev


Hg-commit: 4600480e4617258844053d6c5e0df99ff0839980

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bk-changeset-1.3349.18.1
balay@asterix.mcs.anl.gov|ChangeSet|20050616200622|58125
ChangeSet
1.3349.18.1 05/06/16 15:06:22 balay@asterix.mcs.anl.gov +3 -0
splitup zdmmg.c [ftn-custom]

src/snes/

bk-changeset-1.3349.18.1
balay@asterix.mcs.anl.gov|ChangeSet|20050616200622|58125
ChangeSet
1.3349.18.1 05/06/16 15:06:22 balay@asterix.mcs.anl.gov +3 -0
splitup zdmmg.c [ftn-custom]

src/snes/utils/ftn-custom/zdamgf.c
1.1 05/06/16 15:06:20 balay@asterix.mcs.anl.gov +120 -0

src/snes/utils/ftn-custom/zdamgf.c
1.0 05/06/16 15:06:20 balay@asterix.mcs.anl.gov +0 -0
BitKeeper file /home/balay/bk-rep/petsc-dev/src/snes/utils/ftn-custom/zdamgf.c

src/snes/utils/ftn-custom/makefile
1.2 05/06/16 15:06:20 balay@asterix.mcs.anl.gov +1 -1
splitup zdmmg.c

src/snes/ftn-custom/zdmmg.c
1.23 05/06/16 15:06:20 balay@asterix.mcs.anl.gov +0 -111
splitup zdmmg.c


Hg-commit: 668a3b0a53687bbc86afd6b17f235e6dc5a2dd59

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bk-changeset-1.3351
bsmith@harley.mcs.anl.gov|ChangeSet|20050616185417|41391
ChangeSet
1.3351 05/06/16 13:54:17 bsmith@harley.mcs.anl.gov +1 -0
Merge bk://petsc.bkbits.net/petsc-dev
into harley

bk-changeset-1.3351
bsmith@harley.mcs.anl.gov|ChangeSet|20050616185417|41391
ChangeSet
1.3351 05/06/16 13:54:17 bsmith@harley.mcs.anl.gov +1 -0
Merge bk://petsc.bkbits.net/petsc-dev
into harley.mcs.anl.gov:/sandbox/bsmith/petsc-dev

bmake/common/rules
1.162 05/06/16 13:54:16 bsmith@harley.mcs.anl.gov +0 -2
Auto merged


Hg-commit: 11aa0449394a382a20394ec945c8939ed3e4760a

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