Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bdd

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddcprivate.c

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Merge branch 'knepley/feature-fe-dg-space'

* knepley/feature-fe-dg-space: (38 commits)
DMPlex: Added coordinate field info for generated mesh
DMPlex: Update to new DMPlexGetBoundary() interface

Merge branch 'knepley/feature-fe-dg-space'

* knepley/feature-fe-dg-space: (38 commits)
DMPlex: Added coordinate field info for generated mesh
DMPlex: Update to new DMPlexGetBoundary() interface
PetscFE: Fix complex casting
DMPlex: Fixup type mismatch in PetscFEIntegrate()
DMPlex ex62: Fixed test output
SNES ex62: Added test output
SNES ex62: Added tests for Q2-Q1 and Q2-P1disc - Added -show_error - Removed spurious refinement of quads - Fixed cast - CreatePressureNullspace() now uses DMPlexProjectFunction() - Replace SetupElement() with PetscFECreateDefault()
DMPlex ex3: Added tests for P1disc
SNES ex12: Updated to new PetscFECreateDefault()
PetscFE: Fixes for discontinuous elements
PetscSpace: Fixed polynomial space view
PetscFE: Changed PetscFECreateDefault() - Now continuity and reference cell shape are set from the command line
PetscFE: Added domain integration - Added PetscFEIntegrate(), only implemented for Basic - Added DMPlexComputeIntegralFEM() and DMPlexComputeL2FieldDiff() - This should replace the L2Diff functions
Mat+Doc: Fixed MatNullSpaceRemove()
SNES ex62: Updated to new PetscFECreateDefault()
SNES ex12: Updated to new PetscFECreateDefault() - 3D simplex moves the P_0 point from the centroid
DMPlex ex3: Updated for corrected cell dof
PetscFE: I think I finally fixed the cell dof
DMPlex ex3: Added test case for P1disc on a quad
DMPlex ex3: Added P1 discontinuous test - Something looks wrong with interpolation
...

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DMPlex: Added DMPlexCopyBoundary()
- Copy boundary conditions after DMRefine() and DMPlexConstructGhostCells()

DMPlex+DMLabel: Added DMLabelStratumHasPoint() and DMPlexIsBoundaryPoint()

DMPlex: Removed DMPlexInsertBoundaryValuesFVM()

DMPlex: Added labelname to the DMBoundary structure

PetscFV: Initial checkin
- Added an Upwind implementation

Merge remote-tracking branch 'origin/master' into feature-dmmoab

Merged petsc/petsc into master

PetscFE: Added domain integration
- Added PetscFEIntegrate(), only implemented for Basic
- Added DMPlexComputeIntegralFEM() and DMPlexComputeL2FieldDiff()
- This should replace the L2Diff functions

Merge branch 'knepley/feature-optcontrol-mg' into knepley/feature-fe-dg-space

* knepley/feature-optcontrol-mg:
TAO ex1: documentation
TAO ex1: Now we have a full optimal control problem - The da

Merge branch 'knepley/feature-optcontrol-mg' into knepley/feature-fe-dg-space

* knepley/feature-optcontrol-mg:
TAO ex1: documentation
TAO ex1: Now we have a full optimal control problem - The data for the state is perfect (Q is I) - The regularization is perfect (L is I and a_ref is the exact control)
TAO ex1: Constructed saddle point problem, but control is given exactly
PetscFE: Fix array initialization bug
TAO ex1: Starting an IPM example
DMPlex: When creating a section, we should only complete a label once
DMPlex: Now DMPlexProjectFieldLocal() correctly masks out fields with no function
DMPlex: Added DMPlexVecSetFieldClosure_Internal() - Allows fields to be masked
SNES ex62: Updates for printing changes
DMPlex: Fixes preallocation checks
SNES ex12: Updates for printing changes

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DMPlex: Now DMPlexProjectFieldLocal() correctly masks out fields with no function

Merge branch 'knepley/feature-plex-neumann-bc'

* knepley/feature-plex-neumann-bc:
SNES ex12: Added support for boundary Jacobian
DMPlex: Added boundary Jacobian to DMPlexComputeJacobianFEM()
D

Merge branch 'knepley/feature-plex-neumann-bc'

* knepley/feature-plex-neumann-bc:
SNES ex12: Added support for boundary Jacobian
DMPlex: Added boundary Jacobian to DMPlexComputeJacobianFEM()
DMPlex: Removed defunct interpolator function
PetscFE: Added PetscFEIntegrateBdJacobian() - Added pointwise functions to PetscFEM - Added an implementation for Basic
DMPlex: Correct boundary iteration for Neumann conditions in residual assembly

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Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this wa

Merge branch 'master' into knepley/feature-plex-hdf5-parallel-load

* master: (125 commits)
since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this was really bad)
outdated example that doesn't match coding style removed and buggy
petscversion.h: workaround ifort -cpp lack of referential transparency
configure: ignore AR, MAKEFLAGS [if set in env]
incorrect first entry in array being zeroed in example
sizeof.c: remove dependence on petsc [and fix syntax error]
nightlybuilds: use consistant PETSC_ARCH, machine names
TS: Allow viewing of TS solutions
DMPlex: Fix comparison for complex
change MPIVersion streams to use MPI_Wtime() to be portable to Windows do not use scalar square root on real number; it upsets Microsoft
cannot use I in PETSc code because in complex it sometimes represents imaginary number cannot pass PetscScalar * to VecNorm()
in dashboard don't warn about SSL and BOI deprecated
TS ex11: Fixed output formatting
Doc+DMPlex: Added function documentation for some refinement functions
streams: translate code from 'bash' to 'sh' [fix freebsd]
barry is an idiot who doesn't have a clue as to what he is doing (and git's unfriendlyness doesn't help matters)
don't list examples under C that don't work with complex!
forgotten output file
removed valgrind warning about sending uninitialized data
nightly builds ignore unrecognized pragma and .c file as C++ code
...

Conflicts:
include/petsc-private/dmpleximpl.h

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Merge branch 'master' of bitbucket.org:petsc/petsc
Fuck if git tells me to git pull then I pull, if you want me to do something else than have git tell what to do

Merge branch 'knepley/fix-plex-bc'

* knepley/fix-plex-bc:
TS ex11: Fixed output formatting
Doc+DMPlex: Added function documentation for some refinement functions
TS ex11: Must separate reconst

Merge branch 'knepley/fix-plex-bc'

* knepley/fix-plex-bc:
TS ex11: Fixed output formatting
Doc+DMPlex: Added function documentation for some refinement functions
TS ex11: Must separate reconstruction setup from geometry setup
DMPlex: DMPlexConstructGhostCells() should not be calling DMSetFromOptions()
DMPlex: FVM BC should only be applied to faces - Refinement adds in vertices/edges on refined faces
DMPlex: Must decide what kind of BC to apply for output

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DMPlex: Added boundary Jacobian to DMPlexComputeJacobianFEM()

DMPlex: Removed defunct interpolator function

DMPlex: FVM BC should only be applied to faces
- Refinement adds in vertices/edges on refined faces

DMPlex: Correct boundary iteration for Neumann conditions in residual assembly

Merge branch 'knepley/feature-plex-bc'

* knepley/feature-plex-bc:
DMPlex: Cells in the boundary marker should not be interpreted as constraints
DMPlex: Fix declaration
TS ex11: Replace ApplyBC

Merge branch 'knepley/feature-plex-bc'

* knepley/feature-plex-bc:
DMPlex: Cells in the boundary marker should not be interpreted as constraints
DMPlex: Fix declaration
TS ex11: Replace ApplyBC() with DMPlexInsertBoundaryValuesFVM()
DMPlex: Fixed DMPlexInsertBoundaryValuesFVM() - Remove redundant variable - Handle absence of id
TS ex11: Reorganization so that physics creation functions can take the DM - This required splitting the options block
DMPlex: DMPlexInsertBoundaryValues() --> DMPlexInsertBoundaryValuesFEM(), and added an FVM version - The FVM version depends on precalculated geometry which needs to be pulled into the library
TS ex11: Remove unused RHSFunction()
TS ex11: Remove Model from BC func - We do not want opaque objects outside of the context so we can pull this in the library
TS ex11: Now use TS infrastructure for local functions
DMPlex: Fix signature for IFunction - Note that the time is still not being passed down to the pointwise function
TS: Added local versions of assembly to DMTS - I was not sure whether everything was necessary
SNES ex62: Updated output
SNES ex12: Removed outdated BC handling - Removed unnecessary label completion - Updated output
DMPlex: Switched FEM assembly routines to use DMPlexInsertBoundaryValues()
DMPlex: Now DMPlexInsertBoundaryValue() only sets values for the given label - Added DMPlexProjectFunctionLabelLocal()
DMPlex: Now DMCreateSection() calls DMPlexLabelAddCells() - This is necessary for FEM boundary conditions, but we do not want it for FVM so we need some control divergence here soon
DMPlex: Added DMPlexLabelAddCells() - Needed this for FEM BC
DMPlex: Fix Gmsh test

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Merge branch 'knepley/feature-plex-bc' into knepley/feature-plex-periodic

* knepley/feature-plex-bc:
DMPlex: Cells in the boundary marker should not be interpreted as constraints
DMPlex: Fix dec

Merge branch 'knepley/feature-plex-bc' into knepley/feature-plex-periodic

* knepley/feature-plex-bc:
DMPlex: Cells in the boundary marker should not be interpreted as constraints
DMPlex: Fix declaration
TS ex11: Replace ApplyBC() with DMPlexInsertBoundaryValuesFVM()
DMPlex: Fixed DMPlexInsertBoundaryValuesFVM() - Remove redundant variable - Handle absence of id
TS ex11: Reorganization so that physics creation functions can take the DM - This required splitting the options block
DMPlex: DMPlexInsertBoundaryValues() --> DMPlexInsertBoundaryValuesFEM(), and added an FVM version - The FVM version depends on precalculated geometry which needs to be pulled into the library
TS ex11: Remove unused RHSFunction()
TS ex11: Remove Model from BC func - We do not want opaque objects outside of the context so we can pull this in the library
TS ex11: Now use TS infrastructure for local functions
DMPlex: Fix signature for IFunction - Note that the time is still not being passed down to the pointwise function
TS: Added local versions of assembly to DMTS - I was not sure whether everything was necessary
SNES ex62: Updated output
SNES ex12: Removed outdated BC handling - Removed unnecessary label completion - Updated output
DMPlex: Switched FEM assembly routines to use DMPlexInsertBoundaryValues()
DMPlex: Now DMPlexInsertBoundaryValue() only sets values for the given label - Added DMPlexProjectFunctionLabelLocal()
DMPlex: Now DMCreateSection() calls DMPlexLabelAddCells() - This is necessary for FEM boundary conditions, but we do not want it for FVM so we need some control divergence here soon
DMPlex: Added DMPlexLabelAddCells() - Needed this for FEM BC
DMPlex: Fix Gmsh test

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DMPlex: Fix declaration

DMPlex: Fixed DMPlexInsertBoundaryValuesFVM()
- Remove redundant variable
- Handle absence of id

DMPlex: DMPlexInsertBoundaryValues() --> DMPlexInsertBoundaryValuesFEM(), and added an FVM version
- The FVM version depends on precalculated geometry which needs to be pulled into the library