Merge branch 'pr874/mapdes/pcmg-inject/master'

* pr874/mapdes/pcmg-inject/master:
This hooks everything up so that if the DM provides an injection we remember it in PCMG.
* Add DMHasCreateInjection

Merge branch 'pr874/mapdes/pcmg-inject/master'

* pr874/mapdes/pcmg-inject/master:
This hooks everything up so that if the DM provides an injection we remember it in PCMG.
* Add DMHasCreateInjection: Will be needed in PCMG.
* FAS: guard DMCreateInjection with DMHasCreateInjection
* PCMG: Use injection if the DM provides it

The mass-lumped scaling of the restriction is complete nonsense for most discretisations.
If the DM provides an injection, use it.
This injection is now used by DMRestrictHook_SNESVecSol for transferring the current state to the coarse grid.

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Make DMHasCreateInjection overrideable by subclasses

Default to PETSC_FALSE. It's only provided by Plex, Pforest, and DA
in (if using DMDA_Q1 as interpolation type).

Fix some minor/semantic bugs identified by clang analyzer

Merge branch 'knepley/feature-plex-cv-input'

Added DMGetCoordinateField()

Merge branch 'stefano_zampini/feature-glvis-homesh-periodic'

Plex: Added a reader for cell-vertex meshes

DMPlex: Copy over localized coordinates in DMPlexCopyCoordinates

Add a couple of missing checks in DMPlex{Un}Interpolate
Fix documentation for coordinates
ex4: fix output with coordinates
ex1: added

DMPlex: Copy over localized coordinates in DMPlexCopyCoordinates

Add a couple of missing checks in DMPlex{Un}Interpolate
Fix documentation for coordinates
ex4: fix output with coordinates
ex1: added test for periodic case with uninterpolation

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Merge branch 'barry/tao-to-new-test-harness' into barry/all-new-test-harness-branches

Merge branch 'barry/move-to-new-test-harness' into barry/all-new-test-harness-branches

Merge branch 'barry/vec-to-test-harness' into barry/all-new-test-harness-branches

Merge branch 'jed/tests-cxx-linker' into barry/more-to-new-test-harness

Merge branch 'master' into knepley/feature-ts-plasma-example

* master: (22 commits)
Section: Fix CreateSupersection - Missing call to GetNumFields() for subsection
SNES ex13: Update test output

Merge branch 'master' into knepley/feature-ts-plasma-example

* master: (22 commits)
Section: Fix CreateSupersection - Missing call to GetNumFields() for subsection
SNES ex13: Update test output
PetscFE: Complex fixes for PetscFEIntegrate()
SNE ex13: Got adjoint solution and almost have a good error estimate
Section: Fix init in PetscSectionCreateSupersection()
DM: Remove debugging view
SNES ex13: Updated output after fix
Section: If global section allocates bc indices, must copy them
Section: Cleaned up PetscSectionCreateGlobalSection() - Used local variable and added input checks
Bib: Added pages
Section: Fix leaks in DMCreateSuperDM()
SNES ex13: Adding adjoint capability
DM: Use new PetscGlobalMinMaxInt()
DM: Added DMCreateSuperDM()
Plex: Refactor computation of integrals over the domain - Added DMPlexComputeCellwiseIntegral()
PetscFE: Fix PetscFEIntegrate() for multicomponent integrals
Adaptor: Use new PetscGlobalMinMaxInt()
Section: Added PetscSectionCreateSupersection() - This merges several sections together
Vec+Doc: Fix docs for VecISAXPY()
Vec: Added VecISCopy() - Use ScatterMode to determine direction of copying
...

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Merge branch 'knepley/feature-plex-adjoint-prelim'

* knepley/feature-plex-adjoint-prelim: (22 commits)
Section: Fix CreateSupersection - Missing call to GetNumFields() for subsection
SNES ex13:

Merge branch 'knepley/feature-plex-adjoint-prelim'

* knepley/feature-plex-adjoint-prelim: (22 commits)
Section: Fix CreateSupersection - Missing call to GetNumFields() for subsection
SNES ex13: Update test output
PetscFE: Complex fixes for PetscFEIntegrate()
SNE ex13: Got adjoint solution and almost have a good error estimate
Section: Fix init in PetscSectionCreateSupersection()
DM: Remove debugging view
SNES ex13: Updated output after fix
Section: If global section allocates bc indices, must copy them
Section: Cleaned up PetscSectionCreateGlobalSection() - Used local variable and added input checks
Bib: Added pages
Section: Fix leaks in DMCreateSuperDM()
SNES ex13: Adding adjoint capability
DM: Use new PetscGlobalMinMaxInt()
DM: Added DMCreateSuperDM()
Plex: Refactor computation of integrals over the domain - Added DMPlexComputeCellwiseIntegral()
PetscFE: Fix PetscFEIntegrate() for multicomponent integrals
Adaptor: Use new PetscGlobalMinMaxInt()
Section: Added PetscSectionCreateSupersection() - This merges several sections together
Vec+Doc: Fix docs for VecISAXPY()
Vec: Added VecISCopy() - Use ScatterMode to determine direction of copying
...

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Merge branch 'knepley/feature-plex-adjoint-prelim' into knepley/feature-plex-exodus-update

* knepley/feature-plex-adjoint-prelim:
SNE ex13: Got adjoint solution and almost have a good error estima

Merge branch 'knepley/feature-plex-adjoint-prelim' into knepley/feature-plex-exodus-update

* knepley/feature-plex-adjoint-prelim:
SNE ex13: Got adjoint solution and almost have a good error estimate
Section: Fix init in PetscSectionCreateSupersection()
DM: Remove debugging view
SNES ex13: Updated output after fix
Section: If global section allocates bc indices, must copy them
Section: Cleaned up PetscSectionCreateGlobalSection() - Used local variable and added input checks
Bib: Added pages
Section: Fix leaks in DMCreateSuperDM()
SNES ex13: Adding adjoint capability
DM: Use new PetscGlobalMinMaxInt()
DM: Added DMCreateSuperDM()
Plex: Refactor computation of integrals over the domain - Added DMPlexComputeCellwiseIntegral()
PetscFE: Fix PetscFEIntegrate() for multicomponent integrals
Adaptor: Use new PetscGlobalMinMaxInt()
Section: Added PetscSectionCreateSupersection() - This merges several sections together
Vec+Doc: Fix docs for VecISAXPY()
Vec: Added VecISCopy() - Use ScatterMode to determine direction of copying
Sys: Added PetscGlobalMinMaxReal/Int()
Plex: Make preallocation debugging work in serial

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Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (60 commits)
petsc4py: update to use latest 3.8 snapshot
petsc4py: update to snapshot that syncs with 276c550
fix warni

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (60 commits)
petsc4py: update to use latest 3.8 snapshot
petsc4py: update to snapshot that syncs with 276c550
fix warning
Plex ex26: Protect ExodusII stuff
DM: DMCreateSubDM() field argument should be const
TS ex46: Newlines and some numerical jitter
TS ex45: Newlines and some numerical jitter
TS ex11: Fixed indentation and time step numbering
SNES ex12: Update for DM view changes
Plex tests: Update to new DM output
Plex ex23: Use Nc not dim for vector fields
Plex: Default section now ignores cells hanging off boundary meshes
Plex: Viewer now reports the cell Height
Increase patchlevel to 3.8.3
Plex: Fixed DMPlexInterpolate() bugs - Do not copy associated data if we are not interpolating - Do not interpolate if we already have full depth
fix valgrind errors with using PetscObjectGetName()/SetName() with the same object - resulting in a free() before copy.
ex4: fix compile warning and update makefile
Minor fixes
Improving report_tests
PetscDS: Must initialize the default adjacency
...

Conflicts:
include/petsc/private/dmimpl.h
include/petscdm.h
include/petscis.h
src/dm/impls/plex/plexcreate.c

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Merge branch 'master' into knepley/feature-plex-exodus-update

* master:
petsc4py: update to use latest 3.8 snapshot
petsc4py: update to snapshot that syncs with 276c550
fix warning
Plex ex26

Merge branch 'master' into knepley/feature-plex-exodus-update

* master:
petsc4py: update to use latest 3.8 snapshot
petsc4py: update to snapshot that syncs with 276c550
fix warning
Plex ex26: Protect ExodusII stuff
DM: DMCreateSubDM() field argument should be const
TS ex46: Newlines and some numerical jitter
TS ex45: Newlines and some numerical jitter
TS ex11: Fixed indentation and time step numbering
SNES ex12: Update for DM view changes
Plex tests: Update to new DM output
Plex ex23: Use Nc not dim for vector fields
Plex: Default section now ignores cells hanging off boundary meshes
Plex: Viewer now reports the cell Height
DM: Check IS block size in DMCreateSubDM()
DM: DMCreateSubDM() should take a const array
Plex ex26: Test for FEM dof layout and DMCreateSubDM() Contributed-by: Blaise A Bourdin <bourdin@lsu.edu>

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Merge remote-tracking branch 'origin/knepley/feature-subdm-test'

DM: DMCreateSubDM() field argument should be const

Merge remote-tracking branch 'origin/knepley/fix-plex-interpolation-consistency'

Merge remote-tracking branch 'origin/knepley/fix-plex-fvm-adjacency'

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (251 commits)
yaml: add a backup download URL
Fix documentation of MatSetRandom function
Ignore -malloc-hbw option if m

Merge branch 'master' into knepley/feature-plex-adjoint-prelim

* master: (251 commits)
yaml: add a backup download URL
Fix documentation of MatSetRandom function
Ignore -malloc-hbw option if malloc is already set
Plex: Fixed array initialization
pgi: compile fix
knl: update test to use memkind and remove option that worked arround a bug with intel 17
Check the return value for memkind_posix_memalign
Change the default behavour for -malloc_hbw
Bib: More refs
test: remove runex13f90 as its now converted to new test suite
fix win32 crash. This test was previously run with '-n 4' - so restoring it
Fix petscsfgetgraph_ to work for all Fortran compilers by directly using array of PetscSFNodes
bugfix for MatDuplicate_MPIAIJ_PtAP Reported-by: Samuel Lanthaler <s.lanthaler@gmail.com>
strip out dead sundials usage code; change sundials test to only run 5 timesteps to prevent different number of steps on different systems.
Remove extra lines of output file
Example uses C99 constructs so must mark with requires: c99
fix const missmatch for DMDAVecRestoreArrayRead()
remove conflict between function name in example and new PETSc TS function
builds: attempt to do maint/master/next test builds in separate clones
ex62: it turned out that CHACO partioning is not deterministic. Use a prescribed partition instead
...

Conflicts:
src/dm/interface/dm.c
src/snes/examples/tutorials/ex13.c

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Plex: Update to new Interpolate interface

Plex+DS: Moved adjacency information completely to DS
- The Plex versions now just delegate to DS
- Defaults in DS are clearer
- Input to GetAdjacency are optional

Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with

Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with updated 17.10 compilers
Fix for test dirs that are not tutorials/tests
fix use of double in PetscAbsReal() which produces compiler warnings with single precision build
elemental: remove info on conflict of -with-cxx-dialect=C++11 on osx - it works now.
Cleanup .bib files
Fix allfortranstubs rule to rm generated files from correct directory, not outdated location
ierr set but not checked
Remove initial refine so test runs faster and does not time out on some machines
Gail's copyedits for bibtex items
Docs: manual: add further description of 3 different current testing options
DM: check for ops->localtolocalbegin/end before calling
PetscSF: fix typo in tutorial ex1
Vec+HDF5: Fix output for complex - Need to check for empty group name
SNES: SNESDestroy() can be called with snes->dm == NULL
SNES: SNESDestroy() can be called with snes->dm == NULL
Vec+HDF5: Fix output for complex - Need to check for empty group name
Docs: Manual: Update tests section
gmakegentest: also exclude .#filenames created by emacs
DMPlex: Fix output of test ex1 after changes to Gmsh reader
...

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