Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Merge branch 'tisaac/feature-gamg-extensible' into barry/experiment

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

Merge branch 'knepley/feature-combined-tabulation'

* knepley/feature-combined-tabulation: (38 commits)
Plex: Fix compiler warning
Plex+SNES: Fixes for nonzero cStart
Plex: Preserve periodicity

Merge branch 'knepley/feature-combined-tabulation'

* knepley/feature-combined-tabulation: (38 commits)
Plex: Fix compiler warning
Plex+SNES: Fixes for nonzero cStart
Plex: Preserve periodicity when adding ghost cells
Plex: Fixed DMPlexGetGlobalFieldOffset_Private() in optimized mode
Plex+SNES: Offset should be into field components, not basis functions
Plex+SNES: Add guards for optional arrays
DS: Added PetscDSGetComponentOffset(), Added to petsc.h
Plex+TS: FVM RHS computation uses a global F
Plex+FV: Corrected accumulation of fluxes to cells and added time derivative term
Plex: Added DMPlexPointGlobalFieldRead/Ref()
Plex+SNES: Fixed DMPlexGetFaceFields() - It returns field values, not coefficients - FE evaluation is now done
FV: In PetscFVIntegrateRHSFunction(), the arguments are field values, not coefficients
FE: Added EvaluateFaceFields() to FE fields at face centroids
Plex: Added DMPlexPointLocalFieldRead()
FE: Have a standard tabulation at face centroids
Plex: Copy BC for hierarchical refinement
FE: Allow P0 over 1D cells
Plex+FV: Fixed BC with gradient calculation
Plex ex1: Move overlap computation after SetFromOptions
Plex: DMPlexDistribute() no longer calls DMSetFromOptions() - Fixed examples
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Merge branch 'knepley/feature-dmts-check'

* knepley/feature-dmts-check:
Plex+TS: Fixed signature of DMTSCheckFromOptions()
PetscDS: Fixed error message
Xdmf: Fix time
DMTS: Add context argum

Merge branch 'knepley/feature-dmts-check'

* knepley/feature-dmts-check:
Plex+TS: Fixed signature of DMTSCheckFromOptions()
PetscDS: Fixed error message
Xdmf: Fix time
DMTS: Add context argument to DMTSCheckFromOptions()
DMTS: DMTSCheckFromOptions() now splits the norm by field
DMTS: Added DMTSCheckFromOptions() - This executes a bunch of checks for the residual and Jacobian which are useful for verification
DM: Allow user to view default section when it is created
PetscFV: Missing destroy
SNES: Added SNESSetSolution() - This was necessary to test TS without solving

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Merge branch 'knepley/feature-dmts-check' into knepley/feature-combined-tabulation

* knepley/feature-dmts-check:
Plex+TS: Fixed signature of DMTSCheckFromOptions()

Plex+TS: Fixed signature of DMTSCheckFromOptions()

Merge branch 'knepley/feature-combined-tabulation' into knepley/feature-ts-fem+fvm-example

* knepley/feature-combined-tabulation: (41 commits)
Plex: Fix distribution of uninterpolated meshes - Doe

Merge branch 'knepley/feature-combined-tabulation' into knepley/feature-ts-fem+fvm-example

* knepley/feature-combined-tabulation: (41 commits)
Plex: Fix distribution of uninterpolated meshes - Does SF stratification by depth, not by dimension - The old code numbered cells after vertices
Plex+SNES: Fixes for nonzero cStart
cannot call PetscObjectGetName() on a subset of the MPI processes
MatView() with some matrix formats and ASCII_MATLAB did not print correct matrix name
Plex: Preserve periodicity when adding ghost cells
Plex: Fixed DMPlexGetGlobalFieldOffset_Private() in optimized mode
Plex+SNES: Offset should be into field components, not basis functions
Plex+SNES: Add guards for optional arrays
DS: Added PetscDSGetComponentOffset(), Added to petsc.h
Plex+TS: FVM RHS computation uses a global F
Plex+FV: Corrected accumulation of fluxes to cells and added time derivative term
Plex: Added DMPlexPointGlobalFieldRead/Ref()
Plex+SNES: Fixed DMPlexGetFaceFields() - It returns field values, not coefficients - FE evaluation is now done
FV: In PetscFVIntegrateRHSFunction(), the arguments are field values, not coefficients
FE: Added EvaluateFaceFields() to FE fields at face centroids
Plex: Added DMPlexPointLocalFieldRead()
FE: Have a standard tabulation at face centroids
Plex: Copy BC for hierarchical refinement
FE: Allow P0 over 1D cells
Plex+FV: Fixed BC with gradient calculation
...

Conflicts:
config/builder.py

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Plex+TS: FVM RHS computation uses a global F

Merge branch 'knepley/feature-dmts-check' into knepley/feature-combined-tabulation

* knepley/feature-dmts-check:
PetscDS: Fixed error message
Xdmf: Fix time
DMTS: Add context argument to DMTSC

Merge branch 'knepley/feature-dmts-check' into knepley/feature-combined-tabulation

* knepley/feature-dmts-check:
PetscDS: Fixed error message
Xdmf: Fix time
DMTS: Add context argument to DMTSCheckFromOptions()
DMTS: DMTSCheckFromOptions() now splits the norm by field
DMTS: Added DMTSCheckFromOptions() - This executes a bunch of checks for the residual and Jacobian which are useful for verification
DM: Allow user to view default section when it is created
PetscFV: Missing destroy
SNES: Added SNESSetSolution() - This was necessary to test TS without solving

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Merge branch 'knepley/feature-dmts-check' into knepley/feature-ts-fem+fvm-example

* knepley/feature-dmts-check:
PetscDS: Fixed error message
Xdmf: Fix time
DMTS: Add context argument to DMTSCh

Merge branch 'knepley/feature-dmts-check' into knepley/feature-ts-fem+fvm-example

* knepley/feature-dmts-check:
PetscDS: Fixed error message
Xdmf: Fix time
DMTS: Add context argument to DMTSCheckFromOptions()
DMTS: DMTSCheckFromOptions() now splits the norm by field
DMTS: Added DMTSCheckFromOptions() - This executes a bunch of checks for the residual and Jacobian which are useful for verification
DM: Allow user to view default section when it is created
PetscFV: Missing destroy
SNES: Added SNESSetSolution() - This was necessary to test TS without solving

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DMTS: Add context argument to DMTSCheckFromOptions()

DMTS: DMTSCheckFromOptions() now splits the norm by field

DMTS: Added DMTSCheckFromOptions()
- This executes a bunch of checks for the residual and Jacobian which are useful for verification

Merge branch 'master' into knepley/fix-configure-petsc-dep

* master: (210 commits)
error out on special cases where DMLocalToGlobal_DA won't work
remove unneed uses of local DM vectors and DMLoc

Merge branch 'master' into knepley/fix-configure-petsc-dep

* master: (210 commits)
error out on special cases where DMLocalToGlobal_DA won't work
remove unneed uses of local DM vectors and DMLocalToGlobalBegin/End in examples removed to prevent cut and paste repeats of their use
openmpi: update to version 1.8.3
added more movies and pubs
more movies
MatGetDiagonalBlock() can be called before matrix is assembled
added a couple more movies/images
PetscLogEventGetId() was missing public prototype
simply output from make streams benchmark test
c2html: fixup so that C2HTML make variable is set [similar to cmake.py]
chaco: current blas test does'nt work with Cray CC [which automatically links with blas] and linux - where -lm needs to be listed explicitly. Switch the test to check if we are using PETSc modifled chaco
builddist: always install c2html/sowing
argonne logo for users manual cover
Remove PETSC_HAVE_CUSP_SMOOTHED_AGGREGATION, use PETSC_HAVE_CUSP instead.
mpich: use older tarball with cygwin/gnu compilers
updated information about packages PETSc can use in users manual
Updated users manual to latest ANL Report format requirements
mpich: update to mpich-3.1.3.tar.gz - remove -download-mpich-mpe [mpich no longer packages mpe] - remove -download-mpich-shared. It was added as a split from --with-mpi-shared to --known-mpi-shared and --download-mpich-shared in 50237a55163f90ac7341b723c6422dfa1dbce792 removing this gives back the control of shared=0/1 to package.py - remove download_solaris as the new tarball works with both gcov and on solaris - remove MPICHInstall() [and use GNUPackage.Install()] as the new tarball fixes 'make clean' requiring sudo
added more images and PETSc pubs
Doc: More refs
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Merge branch 'tisaac/feature-fe-geom-dim' into tisaac/plex-flexible-projection

Use the new PetscFECellGeom

Conflicts:
include/petscdmplex.h
include/petscfe.h
src/dm/impls/plex/plexfem.c

Merge branch 'knepley/feature-fe-fv-hybrid'

* knepley/feature-fe-fv-hybrid: (43 commits)
PetscFE: Small fixes
Plex+SNES: Volumes are PetscReal
Plex+SNES: Missing declaration
TS ex11: Remove

Merge branch 'knepley/feature-fe-fv-hybrid'

* knepley/feature-fe-fv-hybrid: (43 commits)
PetscFE: Small fixes
Plex+SNES: Volumes are PetscReal
Plex+SNES: Missing declaration
TS ex11: Remove unused var
Plex+SNES+TS: Complete reorganization of residual evaluation - Now both FE and FV examples use the same method, but there are a bunch of switches which should be eliminated - There is a confusion about IFunction and RHS, but I think they can both be in one function - Added DMPlexSNESGetGeometryFVM() and DMPlexSNESGetGradientFVM() - Added DMPlexGet/RestoreCellFields() and DMPlexGet/RestoreFaceFields() and DMPlexGet/RestoreFaceGeometry() - I think that FV geometry caching needs to be redone - Added DMPlexReconstructGradients_Internal() - Added DMPlexComputeBdResidual_Internal() which does not work for FV - Replaced DMPlexComputeResidualFEM_Internal() with DMPlexComputeResidual_Internal()
Plex: Added DMPlexInsertBoundaryValues() - Unified FE and FV boundary values
Plex: DMPlexProjectFunctionLableLocal() gets discretizations from the DM now
Plex: Added DMPlexComputeGradientFVM()
PetscDS: Fix up some functions to work for both FV and FE
PetscFV: Change PetscFVIntegrateRHSFunction() to get info from PetscDS
TS ex11: There is only one field in our current paradigm - We would need to split Riemann solvers for multiple fields right now
Plex+TS: Remove use of computeGradients in favor of check for dmGrad
TS ex11: Updated interface calls
Plex+TS: Change DMPlexTSGetGradientDM() to automatically construct the gradient info, DMPlexTSSetRHSFunctionLocal() can now be replaced by the DMTS version - Remove unnecessary declarations
Plex+SNES: Add missing declaration
Plex+FE: Removed all use of PetscCellGeometry, Changed FE integration to use PetscFECellGeom
DMSNES+Plex: Added DMPlexSNESGetGeometryFEM() to cache geometry
PetscDualSpace: Remove use of PetscCellGeometry in PetscDualSpaceApply() - Fixed up calls to it for projection into spaces
DMDA: Remove use of PetscCellGeometry in DMDAProjectFunctionLocal()
Plex: Added DMPlexComputeGeometryFEM() and PetscFECellGeom structure
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Plex+SNES+TS: Complete reorganization of residual evaluation
- Now both FE and FV examples use the same method, but there are a bunch of switches which should be eliminated
- There is a confusion abo

Plex+SNES+TS: Complete reorganization of residual evaluation
- Now both FE and FV examples use the same method, but there are a bunch of switches which should be eliminated
- There is a confusion about IFunction and RHS, but I think they can both be in one function
- Added DMPlexSNESGetGeometryFVM() and DMPlexSNESGetGradientFVM()
- Added DMPlexGet/RestoreCellFields() and DMPlexGet/RestoreFaceFields() and DMPlexGet/RestoreFaceGeometry()
- I think that FV geometry caching needs to be redone
- Added DMPlexReconstructGradients_Internal()
- Added DMPlexComputeBdResidual_Internal() which does not work for FV
- Replaced DMPlexComputeResidualFEM_Internal() with DMPlexComputeResidual_Internal()

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Plex+TS: Remove use of computeGradients in favor of check for dmGrad

Plex+TS: Change DMPlexTSGetGradientDM() to automatically construct the gradient info, DMPlexTSSetRHSFunctionLocal() can now be replaced by the DMTS version
- Remove unnecessary declarations

PetscFV+TS: Removed use of PetscCellGeometry from PetscFVIntegrateRHSFunction()
- Moving toward cached geometry with arrays of structs
- Changed DMPlexTSGetGeometry() to DMPlexTSGetGeometryFVM()

Plex+SNES+TS: Moved residual computation to solver utilities

PetscFV+Plex+TS: Reorganized computation of FV geometry
- Now DMPlexTSGetGeometry() computes and stashed FV geometry automatically
- Moved WaxpyD, DotD, DotRealD, and NormD inside Plex
- Changed Cell

PetscFV+Plex+TS: Reorganized computation of FV geometry
- Now DMPlexTSGetGeometry() computes and stashed FV geometry automatically
- Moved WaxpyD, DotD, DotRealD, and NormD inside Plex
- Changed CellGeom to PetscFVCellGeom
- Changed FaceGeom to PetscFVFaceGeom
- Moved DMPlexTSSetupGeometry() to DMPlexComputeGeometryFVM()
- Verified using TS ex11

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