Remove unused variables

DMPlexSNES: fix type of depth label

Use DMField / PetscFEGeom in integration

Merge branch 'pr1/haplav/fix-DMPlexGetCellFields/master'

* pr1/haplav/fix-DMPlexGetCellFields/master:
Plex ex25: Fix leaks
small ex25 fixes based on PR review
fix DMPlexRestoreCellFields for c

Merge branch 'pr1/haplav/fix-DMPlexGetCellFields/master'

* pr1/haplav/fix-DMPlexGetCellFields/master:
Plex ex25: Fix leaks
small ex25 fixes based on PR review
fix DMPlexRestoreCellFields for cStart=cEnd
fix DMCreateDefaultSection_Plex for 0 fields
DMPlex test 25 created

show more ...

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

* knepley/feature-ts-plasma-example:
TS ex48: Turn off plotting by default since it fails for complex
TS ex48: c89 fixes
TS ex48: Protect HDF5

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

* knepley/feature-ts-plasma-example:
TS ex48: Turn off plotting by default since it fails for complex
TS ex48: c89 fixes
TS ex48: Protect HDF5
TS ex48: More complex fixes
TS ex48: Update to latest API
Plex: Fix return type of DMPlexComputeIntegralFEM()
TS ex48: Plasma physics example

show more ...

Merge branch 'knepley/feature-plex-bd-integration'

* knepley/feature-plex-bd-integration:
Plex+SNES: Split boundary integration into a separate function

Plex: Fix return type of DMPlexComputeIntegralFEM()

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
...

show more ...

Plex+SNES: Split boundary integration into a separate function

fix DMPlexRestoreCellFields for cStart=cEnd

Missing CHKERRQ()

Commit-type: testing-fix,style-fix
Reported-by: clang static analyzer

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

show more ...

Merge remote-tracking branch 'origin/knepley/feature-adaptor-plex' into next-tmp

Adaptor: Silly casts for MS

Adaptor: Use new PetscGlobalMinMaxInt()

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

* knepley/feature-adaptor-plex: (38 commits)
SNES ex12: Fixed AMR tests - Cleaned up use of r Vec - Updated out

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

* knepley/feature-adaptor-plex: (38 commits)
SNES ex12: Fixed AMR tests - Cleaned up use of r Vec - Updated output
DMAdaptor: Fixes handling of original Vec and DM - Fix handling of input vector x - Only LABEL needs a Plex conversion
fixed uninitialized var
SNES ex12: Added adaptation test for p4est
DMAdaptor: Error indicator working for p4est on SNES ex12 - Changed DMAdaptor to a DM class - Added DMAdaptorComputeErrorIndicator_Private() - Added DMAdaptorSimpleErrorIndicator_Private() - Name projected solution vector
PetscFE: Added PetscFEInterpolateFieldAndGradient_Internal()
DMPlexComputeGradientClementInterpolant: fix debug statement for complex
SMAdaptor: Fix for complex ev decamp
compile fixes
DMAdaptor: Correct warnings and complex problems
Plex: Added versions of the Det functions that take Scalar data
DMAdaptor: Declare DMAdaptorSet/GetSequenceLength()
SNES+ex12: Added support for ascii_info_detail in -snes_converged_reason - It prints the L_2 error using the DS information - SNES ex12 output updated
DMAdaptor: Added options - Added options for N_adapt, refinement factor, h_min and h_max
SNES ex12: I finally think test output is correct
DMAdaptor: Refine viewing
SNES ex12: Updated adaptation tests - Added sequential adaptation
SNES: Added -snes_adapt_sequence - Eventually remove snes_grid_sequence
DMAdaptor: - Added sequential adaptation - Added DMAdaptorGet/SetSequenceLength() - Use AdaptationCriterion now - Added untested unstructured interpolation
DMAdaptor: Now I have AdaptationStrategy and AdaptationCriterion - Fixed some docs
...

show more ...

DMAdaptor: Fixes handling of original Vec and DM
- Fix handling of input vector x
- Only LABEL needs a Plex conversion

fixed uninitialized var

Remove use of PetscDataType from DMGetWorkArray() and one absurd usage

Part of process of removing PetscDataType from PETSc since it duplicates MPI_Datatype
Commit-type: style-fix
Thanks-to: Jed Bro

Remove use of PetscDataType from DMGetWorkArray() and one absurd usage

Part of process of removing PetscDataType from PETSc since it duplicates MPI_Datatype
Commit-type: style-fix
Thanks-to: Jed Brown <jed@jedbrown.org>

show more ...

DMAdaptor: Error indicator working for p4est on SNES ex12
- Changed DMAdaptor to a DM class
- Added DMAdaptorComputeErrorIndicator_Private()
- Added DMAdaptorSimpleErrorIndicator_Private()
- Name pro

DMAdaptor: Error indicator working for p4est on SNES ex12
- Changed DMAdaptor to a DM class
- Added DMAdaptorComputeErrorIndicator_Private()
- Added DMAdaptorSimpleErrorIndicator_Private()
- Name projected solution vector

show more ...

F90Array routines now take a MPI_Datatype argument instead of PetscDataType

This is part of the refactorization to limit and maybe eventually eliminate PetscDataType since
it duplicates MPI_Datatype

F90Array routines now take a MPI_Datatype argument instead of PetscDataType

This is part of the refactorization to limit and maybe eventually eliminate PetscDataType since
it duplicates MPI_Datatype functionality (poorly).

Commit-type: style-fix
Thanks-to: Jed Brown <jed@jedbrown.org>

show more ...