Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into jpustay/feature-swarm-example

Merged petsc/petsc into master

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an already factored matrix
Mat: Small fix for checking and docs
Mat: Added MatSetFactorType() - Needed it when making a shell matrix look factored
PetscDS: Added PetscDSUpdateBoundary() - Lets the user change the boundary condition
single precision produces different convergence history
p4est: has a dependency on zlib - so handle it correctly
Add -mat_mffd_complex to use the Lyness complex number trick to compute J_u * v instead of differencing.
Replace VecWAXPY by VecAXPY if needed
Revert "Replace VecWAXPY by VecAXPY if needed"
Replace VecWAXPY by VecAXPY if needed
MatHermitianTransposeGetMat and MatCreateVecs
ex19: Updated test filter to avoid false positives.
DM: Improved Global-To-Natural docs Suggested-by: Josh L <ysjosh.lo@gmail.com>
Do not build shared openblas when doing static build
Upgrade OpenBLAS to 0.3.3
test: add alt output file for changes in OSX-10.14 and Xcode-10.0 [perhaps related to ML]
...

Conflicts:
src/vec/is/utils/vsectionis.c

show more ...

Merged petsc/petsc into master

Merge remote-tracking branch 'origin/psanan/dm-l2g-singlecall'

DM: add DMLocalToGlobal() and DMGlobalToLocal()

These functions simply capture the common pattern of calling the
corresponding "Begin" and "End" functions subsequently with identical
arguments.

The

DM: add DMLocalToGlobal() and DMGlobalToLocal()

These functions simply capture the common pattern of calling the
corresponding "Begin" and "End" functions subsequently with identical
arguments.

The new man pages note the availability of split usage.

show more ...

DM: add DMLocalToGlobal() and DMGlobalToLocal()

These functions simply capture the common pattern of calling the
corresponding "Begin" and "End" functions subsequently with identical
arguments.

The

DM: add DMLocalToGlobal() and DMGlobalToLocal()

These functions simply capture the common pattern of calling the
corresponding "Begin" and "End" functions subsequently with identical
arguments.

The new man pages note the availability of split usage.

show more ...

Merge branch 'knepley/fix-dminterpolation-docs' [PR #1167]

DM: Added documentation for DMInterpolation

DMGetCoordinatesLocalTuple() impl.

DMGetCoordinatesLocalSetUp() and DMGetCoordinatesLocalNoncollective() added

Merge branch 'psanan/dmstag' [PR #1146]

* psanan/dmstag:
DMStag basic implementation
Basic implementations of DMStag and DMProduct, with some accompanying documentation and tests.

DM: Added DMSetCoarsenLevel()

DM: Add DMStag

Features include:
- 1d, 2d, 3d grids
- ghosted, periodic and "none" boundary conditions
- box and star communication patterns
- stencil-based setting of Vec and Mat entries
- direct a

DM: Add DMStag

Features include:
- 1d, 2d, 3d grids
- ghosted, periodic and "none" boundary conditions
- box and star communication patterns
- stencil-based setting of Vec and Mat entries
- direct array-based access to local vectors
- product coordinates
- helper functions for product coordinate arrays
- helper to split DMStag+Vec to a DMDA+Vec
- 4 tutorial examples
- 152+ test cases for the test suite (make -f gmakefile test globsearch="*stag*" to run them)

show more ...

DM: Add DMProduct

Merge branch 'knepley/feature-dm-nearnullspace' [PR #1128]

* knepley/feature-dm-nearnullspace:
DM: Added interface for (near) nullspace constructors
DM: Now DMCreateMatrix() adds a (near) nullspace

Merge branch 'knepley/feature-dm-nearnullspace' [PR #1128]

* knepley/feature-dm-nearnullspace:
DM: Added interface for (near) nullspace constructors
DM: Now DMCreateMatrix() adds a (near) nullspace if we have only 1 field and the constructor set
Plex+FEM: Fix corner case where space is smaller than the proposed number of null modes
Plex+FEM: Fix another corner case in CreateRigidBody
SNES ex17: Now use rigid body modes as the near null space

show more ...

Merged petsc/petsc into master

Merge from master

Merge branch 'master' into knepley/feature-dm-nearnullspace

* master: (219 commits)
petsc4py: update with VecScatter API changes
remove duplicate code
petsc4py: update to version 3.10.0
fixe

Merge branch 'master' into knepley/feature-dm-nearnullspace

* master: (219 commits)
petsc4py: update with VecScatter API changes
remove duplicate code
petsc4py: update to version 3.10.0
fixed typos in documentation
fixed typos in documentation
Fix some remaining Register()s to call InitializePackage()
Remove memory leaks of XXXRegister() is called but XXX object is never used
Add to PCTFS manual page that it does not work for complex numbers
Stray , in manual page that should be .
Only register MPI3 VecScatter if they are built
clarification of KSPSetComputeInitialGuess()
Add missing makefiles for VecScatter implementations
Changed VecScatterCreate() to take a communicator and return scatter as other first class PETSc objects do. Changed old VecScatterCreate() to VecScatterCreateWithData()
Added VecScatterSetUp() and converted implementations to use it to compute scatter information
Pull "MPI1" and "MPI3" specific code out of common VecScatter impls code This allows future implementations to use the common code also without changing the common code
Seperate VecScatter implementation code into three subdirectories seq, mpi1, and mpi3
doc: fix author list in manual wrt 6402aee
doc: fix LOCDIR wrt broken URL from MatHYPRESetPreallocation.html
ifort: ifx compile error with --with-mpi=0
changes/310.html: merged two TAO sections
...

Conflicts:
src/dm/interface/dm.c

show more ...

Merge branch 'master' into knepley/feature-ksp-ex10-transpose

* master: (219 commits)
petsc4py: update with VecScatter API changes
remove duplicate code
petsc4py: update to version 3.10.0
fi

Merge branch 'master' into knepley/feature-ksp-ex10-transpose

* master: (219 commits)
petsc4py: update with VecScatter API changes
remove duplicate code
petsc4py: update to version 3.10.0
fixed typos in documentation
fixed typos in documentation
Fix some remaining Register()s to call InitializePackage()
Remove memory leaks of XXXRegister() is called but XXX object is never used
Add to PCTFS manual page that it does not work for complex numbers
Stray , in manual page that should be .
Only register MPI3 VecScatter if they are built
clarification of KSPSetComputeInitialGuess()
Add missing makefiles for VecScatter implementations
Changed VecScatterCreate() to take a communicator and return scatter as other first class PETSc objects do. Changed old VecScatterCreate() to VecScatterCreateWithData()
Added VecScatterSetUp() and converted implementations to use it to compute scatter information
Pull "MPI1" and "MPI3" specific code out of common VecScatter impls code This allows future implementations to use the common code also without changing the common code
Seperate VecScatter implementation code into three subdirectories seq, mpi1, and mpi3
doc: fix author list in manual wrt 6402aee
doc: fix LOCDIR wrt broken URL from MatHYPRESetPreallocation.html
ifort: ifx compile error with --with-mpi=0
changes/310.html: merged two TAO sections
...

Conflicts:
src/ksp/ksp/interface/itfunc.c

show more ...

Merged petsc/petsc into master

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (345 commits)
Update dev notes for the coming release
Increase patchlevel to 3.9.4
doc fixes
Added some AIJSELL tests t

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (345 commits)
Update dev notes for the coming release
Increase patchlevel to 3.9.4
doc fixes
Added some AIJSELL tests that mirror the SELL tests.
Bib: More refs
Removed use of hardwired -1 to represent PETSC_NULL_XXX object, since the null value is now 0.
fix memleaks flagged by valgrind
ex62: disable long running test and workaround differences in iteration counts on various builds.
Add FAQ we can point to when users get error messages such as: "PETSc was configured with one OpenMPI mpi.h version but now appears to be compiling using a different OpenMPI mpi.h version"
swith test from mpich to openmpi as mpich ch3:sock is unuserable per PetscShmCommGet()
DM: Forgot to move include statement
fix nightlybuild issues - disable hypre [for openmp] and fix uninitialized variables
tests: enable openmp and hwloc with one of the mumps tests
Default BoomerAMG smoothers
Configure: Revert changes from debb90c, so that we are back to the original Libmesh
Configure: Reverted change for Libmesh from 83cd5d7
Split vecimpl.h into vecimpl.h and vecscatterimpl.h
SNES ex62: Turned off some tests for other precisions and shortened output of sensitive tests
Use mmap to allocate the shared pthread barrier if available
Add configure test for functional mmap
...

Conflicts:
include/petscconvest.h
src/snes/examples/tutorials/ex13.c
src/snes/interface/snes.c
src/snes/utils/convest.c

show more ...

Merge branch 'knepley/feature-pc-patch'

DM: Added interface for (near) nullspace constructors