Merge branch 'shri/update-SuiteSparse' into shri/external-package-KLU

Conflicts:
conf/test
config/examples/arch-linux-pkgs-dbg-ftn-interfaces.py
config/examples/arch-linux-pkgs-opt.py

Merge branch 'master' into balay/tao-to-petsc

Conflicts:
src/dm/examples/tests/ex42.c
src/dm/examples/tutorials/ex65dm.c
src/ksp/ksp/examples/tutorials/ex42.c
src/snes/examples/tutorials/cahn-hi

Merge branch 'master' into balay/tao-to-petsc

Conflicts:
src/dm/examples/tests/ex42.c
src/dm/examples/tutorials/ex65dm.c
src/ksp/ksp/examples/tutorials/ex42.c
src/snes/examples/tutorials/cahn-hilliard-schemes/ex1.c
src/snes/examples/tutorials/ex54.c
src/snes/examples/tutorials/ex55.c
src/snes/examples/tutorials/ex60.c
src/snes/examples/tutorials/ex61.c
src/snes/examples/tutorials/ex63.c
src/snes/examples/tutorials/ex633d_db.c
src/snes/examples/tutorials/ex64.c
src/snes/examples/tutorials/ex65.c
src/snes/examples/tutorials/ex653d.c
src/ts/examples/tutorials/ex23.c

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DMPlex: Added coarseMesh member to Plex
- This will be used by DMCoarsen()
- It will be set during refinement

DMPlex: Fix missing declaration

Merge branch 'knepley/feature-periodic-mesh'

* knepley/feature-periodic-mesh:
Matt moved DMDA_BOUNDARY.. to DM_BOUNDARY... but did not fix ex2f.F includes
DM Fortran examples: fix petscdm.h -> f

Merge branch 'knepley/feature-periodic-mesh'

* knepley/feature-periodic-mesh:
Matt moved DMDA_BOUNDARY.. to DM_BOUNDARY... but did not fix ex2f.F includes
DM Fortran examples: fix petscdm.h -> finclude/petscdm.h
DMPlex: Fixed markers on periodic boundary
DM examples: include petscdm.h in examples that use DM_BOUNDARY_*
DMBoundary: fix line length for Fortran
DMPlex: Now DMPlexCreateHexBox() can have a Mobius topology using DM_BOUNDARY_TWIST
DM: Moved DMDABoundaryTypes to DMBoundaryTypes - Changed the enum values as well - Changed docs and updated Changes - Updated examples
DMPlex: DMPlexCreateHexBoxMesh() now allows periodicity - Changed declaration and uses - DMPlexCreateSquareMesh() now allows periodicity - Works with refinement

Conflicts:
src/dm/impls/plex/plexcreate.c
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

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DMPlex: Documentation and declaration for creation functions

Merge branch 'master' into balay/tao-to-petsc

Conflicts:
include/makefile

Merge branch 'master' into knepley/feature-mat-zerorowscols-baij

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

Conflicts:
src/ts/examples/tutorials/advection-dif

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

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

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Merged petsc/petsc into master

DM: Moved DMDABoundaryTypes to DMBoundaryTypes
- Changed the enum values as well
- Changed docs and updated Changes
- Updated examples

DMPlex: DMPlexCreateHexBoxMesh() now allows periodicity
- Changed declaration and uses
- DMPlexCreateSquareMesh() now allows periodicity
- Works with refinement

Merge branch 'knepley/feature-dmda-section'

* knepley/feature-dmda-section: (29 commits)
DMPlex: fix stale docs about DMPlexGetCoordinateSection
DMDA: Fix compiler warnings
DMDA+DMPlex: Fixed

Merge branch 'knepley/feature-dmda-section'

* knepley/feature-dmda-section: (29 commits)
DMPlex: fix stale docs about DMPlexGetCoordinateSection
DMDA: Fix compiler warnings
DMDA+DMPlex: Fixed preallocation declarations
DMDA: c89 fix
DMDA: Forgot to add new source file
DMPlex: Fix merge from master
DMDA: Add a matrix preallocation routine that works with PetscSection
DMDA: Add transitive closure - Only working in 2D
DMDA: Add preallocation center dim for using PetscSection
DMDA: Added declaration for DMDAGetCellPoint()
DMDA: Added DMDAGetCellPoint()
DMPlex: Added documentation
DMDA: fix missing declarations and includes
DMPlex ex3: Fixed multicomponent functions - These were zero in all but the first component due to an earlier error
DMPlex: Cleaned up uses of DMPlexGet/SetCoordinateSection()
DMPlex: Cleaned up uses of DMPlexGet/SetCoordinateSection()
DMPlex ex3: Added 2D Q_1 and 3D P_2 tests - Added -simplex argument - Uses DMDA for quad tests
DMDA: Added DMDAProjectFunction() and DMDAComputeL2Diff()
DMDA: Fixed 2D geometry - Should reuse DMPlex routines
DMDA: Fix bug in 2D closure operation for cells
...

Conflicts:
src/dm/dt/interface/dtfe.c
src/dm/impls/plex/examples/tests/ex3.c
src/dm/impls/plex/examples/tests/output/ex3_2.out
src/dm/impls/plex/examples/tests/output/ex3_5.out

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Merge branch 'knepley/feature-fem-gradients'

* knepley/feature-fem-gradients:
DMPlex ex3: Fix derivative for quadratic test
DMPlex ex3: Fixed bug setting dimension (again) - Updated test output

Merge branch 'knepley/feature-fem-gradients'

* knepley/feature-fem-gradients:
DMPlex ex3: Fix derivative for quadratic test
DMPlex ex3: Fixed bug setting dimension (again) - Updated test output
DMPlex ex3: Put in gradient check - There seems to be a problem with tests 2 and 5
DMPlex: Added DMPlexComputeL2GradientDiff() - I was not sure what to do with BC
Test context passing in dm plex test ex3
Add a void *ctx argument to PetscDualSpaceApply and friends

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

* master: (319 commits)
SNESGS: Fix for uninitialized variable warning in gssecant.c
DMPlex: Fix for orientation in Gmsh files - Fixed tes

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

* master: (319 commits)
SNESGS: Fix for uninitialized variable warning in gssecant.c
DMPlex: Fix for orientation in Gmsh files - Fixed test output
do not use C99 struct initialization code in PETSc
Nightly Summary: Added time taken to each of the tests in the dashboard.
ASCII printing of floating point numbers must cast to (double) to support quad precision
configure: check fortranDatatypes only when fortran is enabled [this fixes configure crash with --with-fc=0]
don't use non-portable and also dependent on floating point precision system level math constants
picky compilers
fix a couple compiler warnings/errors (depending on compiler) for Matlab engine code
DMPlex: More fixup from bad rebase, moved to DMGet/SetCoordinateSection()
DM: Added DMGet/SetCoordinateSection()
Fuckup: Fix for merge that is still untangling bad rebase from Oct. 17th 2013 - Fixed const in declarations - Fixed merge from PetscFE - Fixed 2 mallocs
replace all echo in test/tutorial makefiles with printf since echo behaves differently on different systems
DMDA: Missing header - Damn rebase
DMPlex ex3: Added 2D Q_1 and 3D P_2 tests
DMDA: Added DMDAProjectFunction() and DMDAComputeL2Diff()
DMDA: Fixed 2D geometry - Should reuse DMPlex routines
DMDA: Fix bug in 2D closure operation for cells
DMDA: Make closure operations also return the size
DMDA: Changed DMDACreateSection() to emulate DMPlexCreateSection()
...

Conflicts:
config/builder.py
include/petscdmda.h
src/dm/dt/interface/dtfe.c
src/dm/impls/da/dageometry.c
src/dm/impls/da/dalocal.c
src/dm/impls/plex/plexgeometry.c

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Merge branch 'knepley/feature-plex-gmsh'

* knepley/feature-plex-gmsh:
DMPlex: Fix for orientation in Gmsh files - Fixed test output
DMPlex GMSH: fix MPIU_INT
DMPlex: Slience bogus compiler war

Merge branch 'knepley/feature-plex-gmsh'

* knepley/feature-plex-gmsh:
DMPlex: Fix for orientation in Gmsh files - Fixed test output
DMPlex GMSH: fix MPIU_INT
DMPlex: Slience bogus compiler warning
DMPlex Gmsh: Fixed integer size problem
DMPlex Gmsh: Fixed interface for coordinates
DMPlex ex1: Added test for Gmsh
DMPlex: Added Gmsh input

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Merge branch 'irving/dual-space-context' into knepley/feature-fem-gradients

* irving/dual-space-context:
Test context passing in dm plex test ex3
Add a void *ctx argument to PetscDualSpaceApply

Merge branch 'irving/dual-space-context' into knepley/feature-fem-gradients

* irving/dual-space-context:
Test context passing in dm plex test ex3
Add a void *ctx argument to PetscDualSpaceApply and friends

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex3.c

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DMPlex: Added DMPlexComputeL2GradientDiff()
- I was not sure what to do with BC

Add a void *ctx argument to PetscDualSpaceApply and friends

The context argument is primarily intended to get information from
outside petsc into mesh field form. We still require the field values

Add a void *ctx argument to PetscDualSpaceApply and friends

The context argument is primarily intended to get information from
outside petsc into mesh field form. We still require the field values
to be available analytically, but now the analytic function can depend
on arbitrary data.

show more ...

Merged petsc/petsc into master

Merge branch 'master' into knepley/feature-plex-gmsh

* master: (163 commits)
do not use C99 struct initialization code in PETSc
Nightly Summary: Added time taken to each of the tests in the dash

Merge branch 'master' into knepley/feature-plex-gmsh

* master: (163 commits)
do not use C99 struct initialization code in PETSc
Nightly Summary: Added time taken to each of the tests in the dashboard.
ASCII printing of floating point numbers must cast to (double) to support quad precision
configure: check fortranDatatypes only when fortran is enabled [this fixes configure crash with --with-fc=0]
don't use non-portable and also dependent on floating point precision system level math constants
picky compilers
fix a couple compiler warnings/errors (depending on compiler) for Matlab engine code
DMPlex: More fixup from bad rebase, moved to DMGet/SetCoordinateSection()
DM: Added DMGet/SetCoordinateSection()
Fuckup: Fix for merge that is still untangling bad rebase from Oct. 17th 2013 - Fixed const in declarations - Fixed merge from PetscFE - Fixed 2 mallocs
replace all echo in test/tutorial makefiles with printf since echo behaves differently on different systems
DMDA: Missing header - Damn rebase
DMPlex ex3: Added 2D Q_1 and 3D P_2 tests
DMDA: Added DMDAProjectFunction() and DMDAComputeL2Diff()
DMDA: Fixed 2D geometry - Should reuse DMPlex routines
DMDA: Fix bug in 2D closure operation for cells
DMDA: Make closure operations also return the size
DMDA: Changed DMDACreateSection() to emulate DMPlexCreateSection()
DMDA: Added functions which emulate DMPlex functionality
DMDA: Now DMDAGetNumCells() returns the cells in each direction as well
...

Conflicts:
config/builder.py

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Merge branch 'madams/gamg-destroy' into prbrune/pcgamg-classicalinterpolationstrategies

Merge branch 'master' into madams/gamg-destroy

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

Merge branch 'master' into knepley/feature-plex-refine-hex

* master: (68 commits)
DMPlex: More fixup from bad rebase, moved to DMGet/SetCoordinateSection()
DM: Added DMGet/SetCoordinateSection()

Merge branch 'master' into knepley/feature-plex-refine-hex

* master: (68 commits)
DMPlex: More fixup from bad rebase, moved to DMGet/SetCoordinateSection()
DM: Added DMGet/SetCoordinateSection()
Fuckup: Fix for merge that is still untangling bad rebase from Oct. 17th 2013 - Fixed const in declarations - Fixed merge from PetscFE - Fixed 2 mallocs
DMDA: Missing header - Damn rebase
DMPlex ex3: Added 2D Q_1 and 3D P_2 tests
DMDA: Added DMDAProjectFunction() and DMDAComputeL2Diff()
DMDA: Fixed 2D geometry - Should reuse DMPlex routines
DMDA: Fix bug in 2D closure operation for cells
DMDA: Make closure operations also return the size
DMDA: Changed DMDACreateSection() to emulate DMPlexCreateSection()
DMDA: Added functions which emulate DMPlex functionality
DMDA: Now DMDAGetNumCells() returns the cells in each direction as well
PetscFE: Added support for tensor product cells in PetscDualSpace_Lagrange
PetscFE: Added tensor product polynomial spaces
example fix /sandbox/petsc/petsc.clone-3/include/petscmath.h(260): error: identifier "PETSC_CXX_STATIC_INLINE" is undefined PETSC_STATIC_INLINE PetscReal PetscAbsScalar(PetscScalar a) {return a < 0.0 ? -a : a;} ^
remove warning in fun3d example "user.F", line 1256: warning: In-place macro substitution leaves line truncated "user.F", line 1259: warning: In-place macro substitution leaves line truncated "user.F", line 1262: warning: In-place macro substitution leaves line truncated
/Users/petsc/petsc.clone-2/src/ksp/ksp/examples/tutorials/ex56.c:59: warning: comparison between signed and unsigned integer expressions
fix examples for portability
fixed to example outputs
fix output for a few examples changed due to changes to -mat_view and not using -snes_monitor_short
...

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

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DM: Added DMGet/SetCoordinateSection()