Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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PCIS: added flag to PCIS to control for reusage of local submatrices

when using change of basis with PCBDDC, local submatrices should be destroyed because the nonzero pattern is not the same of the

PCIS: added flag to PCIS to control for reusage of local submatrices

when using change of basis with PCBDDC, local submatrices should be destroyed because the nonzero pattern is not the same of the original one

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Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

PCBDDC: forgot to add bddc.c in the previous commit

PCBDDC; add flag to invert or not Stildas

small fixes

PCBDDC: fixes bugs

- dirichlet dofs should be computed since the PCBDDCGraph code allows to specify nonn-consistent sets among neighbours
- add dirichlet dofs to the list of simpli scalied dofs in d

PCBDDC: fixes bugs

- dirichlet dofs should be computed since the PCBDDCGraph code allows to specify nonn-consistent sets among neighbours
- add dirichlet dofs to the list of simpli scalied dofs in deluxe
- fix number of constraints computed during adaptive selection

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PCBDDC; prepare for upcoming VecLockPush/Pop

Merge branch 'barry/experiment'

PCBDDC: added initial implementation for adaptive selection of constraints

positive definite case covered only
untested for complex

generalized eigenvalue problem is inv(sum(inv(S_F))) = lambda inv

PCBDDC: added initial implementation for adaptive selection of constraints

positive definite case covered only
untested for complex

generalized eigenvalue problem is inv(sum(inv(S_F))) = lambda inv(sum(inv(St_F)))
this is the right one for 2D problems and for faces in 3D; it is an heuristic for edges in 3D

tested with H(div) and H(curl) (3D) and works like a charm

cholesky support for matrix inversion should still be added

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PCBDDC; added slot for threshold when adaptively computing constraints

PCBDDC; clean up of sub_schurs/deluxe code

* options database are now part of sub_schurs setup
* eliminated unneeded field from sub_schurs structure
* added 2 interface functions to init and setup s

PCBDDC; clean up of sub_schurs/deluxe code

* options database are now part of sub_schurs setup
* eliminated unneeded field from sub_schurs structure
* added 2 interface functions to init and setup sub_schurs when setupping the preconditioner
* if a change of basis is requested, releveant matrices are projected
* still need to be tested when the BDDC is reused

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simplify option object names

PCBDDC: add function to extract sequential matrices from parallel or sequential matrices using unordered index sets

This is just to allow code reuse inside PCBDDC

moved PetscOptionsObject from global variable to local variable in functions

PCBDDC: added a second sub_schurs structure to pcbddc data structure

Begin reorganization of SubSchurs code for code reuse for adaptive selection of constraints

PCBDDC; split computation of local solvers

PCIS: added reusability of PCISSetUp

PCBDDC: make sub_schurs a member of PC_BDDC data structure

Merge branch 'barry/remove-unneeded-paren-petscmalloc'

Conflicts:
src/mat/impls/baij/seq/baij.c

Merge branch 'master' into mlange/refactor-plex-distribute

Conflicts:
src/dm/impls/plex/examples/tests/output/ex12_1.out
src/dm/impls/plex/examples/tests/output/ex12_2.out

FETIDP: bug fix. Rhs vector passed wasn't properly restored if change of basis or dirichlet dofs were not present.

Merge branch 'stefano_zampini/fixes-for-raviart-thomas'

PCBDDC: QR decomposition for change of basis can now be also used for connected components with only 1 constraint

This partially solves the following issue with Raviart Thomas elements
Using standar

PCBDDC: QR decomposition for change of basis can now be also used for connected components with only 1 constraint

This partially solves the following issue with Raviart Thomas elements
Using standard change of basis, the coarse matrix produced is singular and CG doesn't converge to the exact solution (even if the eigenvalues of the preconditioned operator are the same of the unchanged basis case)
On the other hand, using QR, CG converges to the exact solution but the eigenvalues of the preconditioned operator are very different from not using the change of basis.
Still needs to be investigated...

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PCBDDC: for raviart thomas elements, the nearnullspace contains face orientations and should not be modified internally by PCBDDC

convert some PetscMalloc() to PetscMalloc1()
remove unneeded () in first argument to PetscMalloc/Calloc1()
fixes for MATLAB examples