DMPlex: Turn off Fortran stub

DMPlex: My brain did not work for several days
- I have fixed the interpolation code
- I think I can reuse that other code for something else

DMPlex: Remove MatStructure from DMPlexComputeJacobianFEM()
- Add missing declarations

DMPlex: Fixing interpolator construction
- Fixed definition of rectangular sizes
- Use PetscFERefine()
- Use special MatSet

Merge branch 'master' into prbrune/snes-fascontinuation

Conflicts:
include/petscsnesfas.h

DMPlex: Added DMBoundary struct
- This will replace the stuff in TS ex11

DMPlex: Adding support for interpolation between regularly refined meshes
- Added DMPlexComputeInterpolatorFEM()
- Added PetscFERefine()
- Added PetscFEIntegrateInterpolator_Basic()
- Not working now

DMPlex: Adding support for interpolation between regularly refined meshes
- Added DMPlexComputeInterpolatorFEM()
- Added PetscFERefine()
- Added PetscFEIntegrateInterpolator_Basic()
- Not working now since coarse meshes do not have Sections attached

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DMPlex: Fixed documentation
- FEMContext is now at the top of the user struct (hopefully remove this soon)

DT: PetscQuadrature is now a PetscObject
- Added PetscQuadratureGet/SetData()

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

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/fix-fem-opencl'

* knepley/fix-fem-opencl:
PetscFe+OpenCL: Removed N_c variable
PetscFE+OpenCL: Removed redundant numQuadraturePoints, numBasisFunctions, and numBasisCompone

Merge branch 'knepley/fix-fem-opencl'

* knepley/fix-fem-opencl:
PetscFe+OpenCL: Removed N_c variable
PetscFE+OpenCL: Removed redundant numQuadraturePoints, numBasisFunctions, and numBasisComponents
SNES ex12: Added uniform refinement
PetscFE: Fixed syntax bug
PetscFE: Removed offset members that were used once
PetscFE: Use correct flags for code inclusion for auxiliary fields in OpenCL
SNES ex12: Fix run type options
DMPlex: Fix section creation when depth == 1
DMPlex: Fixed flop calculation for OpenCL evaluator - The old version had (2+2)*dim*N_comp, but I think this should only be 2*dim, which is a 5% effect
DMPlex: Fix FEM bug with initialization of auxiliary coefficient array

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

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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.

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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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DMPlex: More fixup from bad rebase, moved to DMGet/SetCoordinateSection()