Merge branch 'prbrune/mat-matcolor' into barry/saws

Conflicts:
src/docs/website/documentation/changes/dev.html

Merge branch 'master' into barry/saws

Conflicts:
src/ksp/pc/impls/gamg/gamg.c
src/sys/classes/viewer/impls/ams/ams.c
src/sys/objects/pinit.c

Merge branch 'hzhang/snes-jacobiancoloropt'

Added event logging for function evaluations in GSSecant

Merge branch 'master' into prbrune/fas-gscolorsecant

There was a build error in master when I last merged.

Banished all mention of the old MatGetColoring() and use in examples

Merge branch 'prbrune/mat-matcolor' into prbrune/fas-gscolorsecant

SNES: Fix missing include

SNES: Now work vectors come from the DM

SNES: Move setup involving snes->vec_sol from SNESSetUp() to SNESolve()

Merge branch 'master' into prbrune/mat-matcolor

Conflicts:
src/snes/interface/snesj2.c

add MatFDColoringSetUp(); rename MatFDColoringCreate_xxx -> MatFDColoringSetUp_xxx

Wrapped math.h and quadmath.h functions used in petsc source exempting examples

Added a missing makefile; added option -snes_fd_color_use_mat

rename ams -> saws

Added MatColoring object to replace MatGetColor()

Merge branch 'barry/dmvecmattypes'

The MatType argument is removed from DMCreateMatrix(), you can use
DMSetMatType() to indicate the type you want used with a DM, defaults to
MATAIJ.

* barry/dmvecm

Merge branch 'barry/dmvecmattypes'

The MatType argument is removed from DMCreateMatrix(), you can use
DMSetMatType() to indicate the type you want used with a DM, defaults to
MATAIJ.

* barry/dmvecmattypes:
DMPlex ExodusII: fix dm->vectype pointer syntax
removed use of VecSetFromOptions() all over the placed, instead use MatGetVecs() or use dm->vectype to determine type added DMGetVecType() and DMGetMatTYpe()
removed MatType argument from DMCreateMatrix() and DMCreateColoring() since information is obtained from DM

Conflicts:
src/dm/impls/da/fdda.c
src/dm/impls/plex/plex.c

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Merge branch 'jed/remove-dynamic-loading-option'

Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.

* jed/remove-d

Merge branch 'jed/remove-dynamic-loading-option'

Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.

* jed/remove-dynamic-loading-option:
Sys: PetscContainerCreate must call PetscSysInitializePackage
Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

Conflicts:
src/dm/impls/mesh/mesh.c
src/dm/interface/dlregisdmdm.c
src/docs/website/documentation/changes/dev.html

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add -snes_monitor_saws

Merge branch 'maint'

* maint:
Revert "MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values"
MatMPIBAIJSetPreallocationCSR() hand

Merge branch 'maint'

* maint:
Revert "MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values"
MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values was provided ordered by row within the block rows instead of by block as it was originally designed to be. Also added more discussion to the manual pages on the expected order of the values
PCGAMG: add man page for PCGAMGType
Add a test example for TS + MG + MatFDColoring
Fixed SNESComputeJacobianDefaultColor() in the case of multilevel PC

Conflicts:
src/ts/examples/tutorials/makefile

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Merge branch 'jed/converged-default-and-skip'

fortran: fix snesconvergedskip_() kspconvergedskip_() kspconvergeddefault*_()

Merge branch 'jed/converged-default-and-skip'

This process started with SNESDefaultConverged -> SNESConvergedDefault
in v3.4, but the other parts have been added piecemeal. Deprecation
support in C

Merge branch 'jed/converged-default-and-skip'

This process started with SNESDefaultConverged -> SNESConvergedDefault
in v3.4, but the other parts have been added piecemeal. Deprecation
support in C interface.

* jed/converged-default-and-skip:
SNES and KSP: add deprecation for *DefaultConverged and *SkipConverged
KSP: rename KSPDefaultConverged* to KSPConvergedDefault*
KSP: rename KSPSkipConverged -> KSPConvergedSkip
SNES: document SNESSkipConverged -> SNESConvergedSkip
snes->ttol to be used only in convergence tests.
Renamed SNESKSPEW_Pre/PostSolve --> KSPPre/PostSolve_SNESEW.
Renamed SNESSkipConverged --> SNESConvergedSkip.

Conflicts:
include/petscsnes.h
src/docs/website/documentation/changes/dev.html

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fix name for PetscOptionsFList() and get FList() and EList() working properly with SAWs legal values

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
s

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
src/snes/impls/composite/snescomposite.c
src/snes/impls/gs/snesgs.c
src/snes/impls/nasm/nasm.c
src/snes/impls/ngmres/snesngmres.c

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