Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \(

Man pages: add newlines after "Notes:"

This allows for proper formatting from sowing.

On OS X (using gsed, not the default BSD sed), from the PETSc root directory:

find src include -type f \( -name "*.c" -or -name "*.h" -or -name "*.cxx" \) | xargs gsed -i 's/Notes\s*:\s*\(\w.*\)/Notes:\n \1/'

This adds a newline and 4 spaces whenever "Notes:" is followed by any "word" character, in any .c, .h, or .cxx file in src/ or include/

show more ...

Suggested changes/additions to DMPlex manual pages and users manual to clarify DMPlex

Commit-type: documentation

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead code.
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
...

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

show more ...

Merge branch 'master' into knepley/fix-plex-residual-loop
Warning: This merge includes real changes

* master: (188 commits)
Add JuMP citation
Copyedits and updates to developers manual
Add mor

Merge branch 'master' into knepley/fix-plex-residual-loop
Warning: This merge includes real changes

* master: (188 commits)
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
SNES ex62: Set name of solution vector - Update test output
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
move output file to the correct location. i.e fix 305862f9cd0dc399542ae11dd744508e4b6ad2e3
...

Conflicts:
src/snes/utils/dmplexsnes.c
src/ts/utils/dmplexts.c

show more ...

Merge remote-tracking branch 'origin/tisaac/feature-dmfield'

* origin/tisaac/feature-dmfield: (56 commits)
Plex: Updated test output for DMLabel change
DMLabel: make empty ISs strides
DMSwarm:

Merge remote-tracking branch 'origin/tisaac/feature-dmfield'

* origin/tisaac/feature-dmfield: (56 commits)
Plex: Updated test output for DMLabel change
DMLabel: make empty ISs strides
DMSwarm: silence static analyzer warning
PetscFECreateDefault: fix custom Fortran interface to use MPI_Comm
SNES ex69: Updated test output
SNES ex69: Removed all mantle stuff and change fields to constants - Also use dsymutil for executables
SNES ex69: Removed special partition
SNES ex69: Fixed null space creation - Null space locks its vectors
PetscFE: PetscFECreateDefault() now takes MPI_Comm instead of DM
DMField: default initialization of variable
PetscFE: fix integration for openCL
PetscFEGeomComplete(): correct normal vector in 2D.
DMField: c++/complex fixes
DMField: empty processor protections
DMField regression test fixes
DMLabel: try to keep stride IS as stride IS as much as possible
DMPlexRefine(): create depth before hybrid-bounded label
DMField: documentation of interface
DMField: implement shell
DMPlex: rename newly created label
...

Conflicts:
src/dm/dt/interface/dtfe.c
src/snes/examples/tutorials/ex69.c
src/snes/utils/dmplexsnes.c

show more ...

Merge remote-tracking branch 'origin/knepley/fix-fe-vector-spaces'

* origin/knepley/fix-fe-vector-spaces: (21 commits)
SNES ex12: Updated test output
Plex ex8: Updated test output
Plex ex7: Up

Merge remote-tracking branch 'origin/knepley/fix-fe-vector-spaces'

* origin/knepley/fix-fe-vector-spaces: (21 commits)
SNES ex12: Updated test output
Plex ex8: Updated test output
Plex ex7: Updated test output
Plex ex5: Updated test output
Plex ex4: Updated test output
Plex ex3: Updated test output
Plex ex20: Updated test output
Plex ex19: Updated test output
Plex ex18: Updated test output
Plex ex17: Updated test output
Plex ex16: Updated test output
Plex ex13: Updated test output
Plex ex12: Updated test output
Plex ex1: Updated test output
DualSpace: Interaction of branches
FAS: Added viewing during coarse correction
Plex+FEM: Fixes for reorg of vector spaces which I missed - Fixed DMPlexComputeInterpolatorNested() field offsets - Fixed DMPlexComputeInjector()
PetscFE: Fixed viewers - Added PetscDualSpace viewer - Can view FE without quadrature
PC: Added some options and documentation for BJacobi, ASM, Richardson
Plex: Fixes for ASCII viewer
...

show more ...

Plex+VTK: Fix field type determination

Plex+VTK: Fix field type determination

Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep us

Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep usage on solaris [use egrep]
opensolaris: fix errors
Update timer reporting and minor reporting fix
Remove redundant if statement. Found by @jedbrown
Fixed problem with order of developer photos on website.
superlu_dist: use correct flag in example [PETSC_HAVE_SUPERLU -> PETSC_HAVE_SUPERLU_DIST]
Bib: PERMON ref
fix for osx
doc: more author fixes
doc: more author fixes
Italicized "orderings" in MPI process placement discussion.
Added Richard to the user manual author list.
Added Richard to the list of active developers on the website.
add string check for MS-MPI and IMPI timeout errors
opensolaris does not have multiple grep utils - but default one does not support -F. So use fgrep instead
Standardizing timeout checks
Report wall clock time of total tests
Use time instead of date %s
...

Conflicts:
include/petscpc.h
src/ksp/ksp/interface/itfunc.c

show more ...

Deprecate DMSet/GetDefaultSection() for DMSet/GetSection()

Revert manual page change per Matt's preference

Commit-type: style-fix
Thanks-to: Matthew Knepley

Merge branch 'bourdin/fix-dm-ex26-memleaks'

fix crash in snes_tutorials-ex62_bddc_quad due to c40e949533

==15095== Invalid read of size 8
==15095== at 0x5BB7305: DMCreateSubDM_Plex (plex.c:2155)
==15095== by 0x59B3579: DMCreateSubDM (dm

fix crash in snes_tutorials-ex62_bddc_quad due to c40e949533

==15095== Invalid read of size 8
==15095== at 0x5BB7305: DMCreateSubDM_Plex (plex.c:2155)
==15095== by 0x59B3579: DMCreateSubDM (dm.c:1624)
==15095== by 0x59B2D3C: DMCreateFieldDecomposition (dm.c:1578)
==15095== by 0x5E87AFC: PCBDDCComputeLocalTopologyInfo (bddcprivate.c:1690)
==15095== by 0x5E6055E: PCSetUp_BDDC (bddc.c:1508)
==15095== by 0x60BBCE3: PCSetUp (precon.c:924)
==15095== by 0x6208BDB: KSPSetUp (itfunc.c:381)
==15095== by 0x620A8BA: KSPSolve (itfunc.c:612)
==15095== by 0x63721C2: SNESSolve_NEWTONLS (ls.c:224)
==15095== by 0x62E9E4E: SNESSolve (snes.c:4312)
==15095== by 0x407121: main (ex62.c:515)
==15095== Address 0x0 is not stack'd, malloc'd or (recently) free'd

show more ...

DMPlex: fix all memory leaks in src/dm/impls/plex/examples/tests/ex26.c

Suggested changes/additions to DMPlex manual pages and users manual to clarify DMPlex

Commit-type: documentation

Plex: Now have MatSetClosure() that allows non-contiguous global offsets for fields

Plex: Better LaTeX viewing

Plex: Get rid of compiler warning

Merge branch 'pr872/bourdin/dmplex-GlobalToNatural/master'

* pr872/bourdin/dmplex-GlobalToNatural/master:
Makes a subDM inherit the NaturalToGlobal SF from their parent upon creation.

Revert "Bug in viewing multiple vectors with VecView_Plex_Local_Draw() each overwrote the previous"

This reverts commit 29c95491dc1710544f73d25ac98dc64225f2d7e1.

Merge branch 'master' into knepley/feature-pc-patch

* master: (33 commits)
cleanup very ugly PCGAMG manual page
minor clarifications for VecScatterCreate() manual page
gcov: PETSC_ARCH is requ

Merge branch 'master' into knepley/feature-pc-patch

* master: (33 commits)
cleanup very ugly PCGAMG manual page
minor clarifications for VecScatterCreate() manual page
gcov: PETSC_ARCH is required onlyfor -run_gcov - and not for -merge_gcov [where it doesn't exist]
make clearer in help statements what --with-external-packages-dir is for.
Website: Added news entry for PETSc User Meeting 2018 on main page.
KSPGUESSPOD: exclude negative of zero eigenvalues from the energy computation
KSPGUESSFISCHER: use PetscInfo for KSP class
CUDA: Further test output fixes for mat_tests-ex2
Turn off elemental test for parmetis running since this does not work on batch systems.
3.8 Changes: KSPCHEBYSHEV
CUDA: Fixed most test errors due to MatMultTranspose*
KSPFGMRES: add KSP_NORM_NONE / PC_RIGHT as supported
KSPSetSupportedNorm man page: remove old note about default support for KSP_NORM_NONE
Dev manual: copyedit
DMPlexDistributeLabels: Propagate the output flag
cuda/cusp: update minimum supported versions of cuda to 7.5 and cusp to 0.5.0
cuda: remove configure option -with-cuda-arch. [use CUDAFLAGS instead]
projected gradient code fixed to obey recent convergence test changed
Merge conflicts resolved after rebase
norm update bug fixed in GPGC, test output reverted
...

show more ...

Merge remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_

Merge remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_Comm
SNES ex69: Updated test output
SNES ex69: Removed all mantle stuff and change fields to constants - Also use dsymutil for executables
SNES ex69: Removed special partition
SNES ex69: Fixed null space creation - Null space locks its vectors
PetscFE: PetscFECreateDefault() now takes MPI_Comm instead of DM
cleanup very ugly PCGAMG manual page
minor clarifications for VecScatterCreate() manual page
gcov: PETSC_ARCH is required onlyfor -run_gcov - and not for -merge_gcov [where it doesn't exist]
make clearer in help statements what --with-external-packages-dir is for.
Website: Added news entry for PETSc User Meeting 2018 on main page.
CUDA: Further test output fixes for mat_tests-ex2
Turn off elemental test for parmetis running since this does not work on batch systems.
3.8 Changes: KSPCHEBYSHEV
CUDA: Fixed most test errors due to MatMultTranspose*
website: update urls
website: fix Jason's name to match pic. Also add Todd's pic
Dev manual: copyedit
DMPlexDistributeLabels: Propagate the output flag
cuda/cusp: update minimum supported versions of cuda to 7.5 and cusp to 0.5.0
...

show more ...

PetscFE: PetscFECreateDefault() now takes MPI_Comm instead of DM

dmplex: construct sfNaturalToGlobal in DMCreateSuperDM_Plex if any of the input DM has useNatural set

DM: only create sfMigration if useNatural is true
Add reference counting on sfMigration so that it can be shared between subDMs

Merge branch 'master' of bitbucket.org:petsc/petsc