Merge branch 'master' into pr358/buptphyphy/addmatcreatenormalhermitian/master

Merge branch 'tisaac/plex-feature-tree-fv'

Make the PetscFV gradient reconstruction method work for the
non-conforming meshes introduced by the Tree extension to DMPlex.

* tisaac/plex-feature-tree-

Merge branch 'tisaac/plex-feature-tree-fv'

Make the PetscFV gradient reconstruction method work for the
non-conforming meshes introduced by the Tree extension to DMPlex.

* tisaac/plex-feature-tree-fv: (52 commits)
Plex ex3: make test that works for single precision
PlexSNES: address compiler warning
DMPlex ex3: make test output PASS/FAIL rather than precision specific
Plex: fix type punning problem stuffing (PetscFECellGeom *) in a Vec
Plex: allow ex3 testFVgrad examples in complex
PetscFV: allow SVD pseudoinverse least squares gradient calculation for complex.
Plex ex3: put fv tensor examples in C_NoComplex tests
Plex ex3: update regression output for nonconforming examples
Plex ex3: make separate fe and fv tests
Plex ex3: use MPIU_MAX, not MPI_MAX
DMPlex: added DMPlexReconstructGradientsFVM()
Plex: fix typo in change to cohesive cell creation
Plex: add ex4 and ex5 to makefile so they can be used for regression tests
DMPlex: remove overzealous error condition from FV gradient reconstruction
DMPlex: correct pointSF size in new point shift approach
DMPlexMigrate(): use correct global indices when migrating tree
DMPlexMigrate(): Don't invalidate old DM by overwriting cones
Plex ex3: use DMPlexDistributeOverlap()
DMPlexPartitionLabelClosure: traverse the tree up and down
PetscPartitionerSimple: work in parallel
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Merge branch 'tisaac/dt-fix-geom-punning' into tisaac/plex-feature-tree-fv

Pull in a fix to FE geometry that affects the complex,64bit case

* tisaac/dt-fix-geom-punning: (240 commits)
Plex: fix t

Merge branch 'tisaac/dt-fix-geom-punning' into tisaac/plex-feature-tree-fv

Pull in a fix to FE geometry that affects the complex,64bit case

* tisaac/dt-fix-geom-punning: (240 commits)
Plex: fix type punning problem stuffing (PetscFECellGeom *) in a Vec
PGI compiler cannot handle [restrict] usage therefor disable restrict for PGI compiler Fix ex48.c to use PETSc standard way of marking restrict
PETSC_UNUSED must occur before the typename. With PGI compilers they error if it is after the type name
on solaris in TSAdaptChoose_Basic() negative root for zero could produce -infinity thus causing time step to be decreased even though the error estimate was zero
MatGetSchurComplement: revert test from LUMP back to DIAG and update output
there are no tests for opencl or viennacl so prevent warning message: make[2]: *** No rule to make target `testexamples_OPENCL', needed by `tree'. Stop. make[2]: *** No rule to make target `testexamples_VIENNACL', needed by `tree'. Stop.
incorrect initial conditions function that could produce floating point exception value (and does on windows) due to squareroot of non-negative number
forgot to fix rule for building ex194
move ex193.c to ex194 because someone else created a 193
remove outdate manual page comment
add missing VecRestoreArray()
add missing VecRestoreArray()
missing restore array in example
formating for print statements of test example with __float128 precision
fix example for __float128 precision by using PETSc math macros and casting PetscReal in print statements
remove Tao example custom monitor that produced different results for __float128 precision
all PETSc built in monitors require a valid PetscViewer, NULL is not acceptable
PETSc built in monitors always require viewers to be passed in, no longer support a NULL viewer
use tigher haptol for minres for quad precision because otherwise false positive of indefinite matrix appeared in example
check for PetscMPIInt overflow in ISAllGather()
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Merge branch 'master' into jed/process-options-handler

Merge branch 'tisaac/dmplex-stable-tet-refinement' into tisaac/plex-feature-tree-fv

This feature branch also changed the topology of nonconforming examples:
I am merging so that I can make the regre

Merge branch 'tisaac/dmplex-stable-tet-refinement' into tisaac/plex-feature-tree-fv

This feature branch also changed the topology of nonconforming examples:
I am merging so that I can make the regression output that should be
correct in master and next

* tisaac/dmplex-stable-tet-refinement: (594 commits)
plex: added tet shape regression test
plexrefine: remove replaced code
plex: update test output for new tet refinement order
plex: fix tet refinement for stable element shape
DMPlex: added test of shape quality to ex1
Better to use the proper error handling version of PetscViewerASCIIGetStdout() instead of PETSC_VIEWER_STDOUT_()
Generate a very useful error message if PetscLogView(), PetscLogEventGetPerfInfo() or PetscLogEventGetFlops() is called with a preceeding call to PetscLogBegin() and friends (also -log_summary which triggers a PetscLogBegin())
fix compile warnings
Plex: Fix bug with bcComps initialization
Turn off elemental shared libraries if --with-shared-libraries=0 is used
Bib: Added refs
Bib: Fixed a bunch of errors
add warning/error flag for '-mat_superlu_dist_parsymbfact' when MatInputMode=GLOBAL
makefile: fix format
tests: add back ex6f, runex6f targets - that got removed in 2f1d3d565a6a43067e6df75b043e6343b05fcd1d
accessing option that may never have been set
typo in DMNetworkSetNumVariables() reported by Sean Shahkarami
superlu_dist: update to using latest 4.1 version
fix compile warnings
Generate an error message when trying to overwrite default options of CN and BEULER
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DMPlex: remove overzealous error condition from FV gradient reconstruction

We only care about whether there are enough faces to reconstruct a
gradient if a cell is local: ghost cell gradients are br

DMPlex: remove overzealous error condition from FV gradient reconstruction

We only care about whether there are enough faces to reconstruct a
gradient if a cell is local: ghost cell gradients are broadcast from
their owners anyway, right?

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Plex Tree: small fixes (bounds, frees) for Tree+FVM

Merge branch 'master' into barry/fix-petscviewer-attempt-2

Merge branch 'master' into knepley/fix-plex-examples

* master: (75 commits)
increase the size of the ex25.c multigrid example so that the eigenestimator does not produce numbers that depend on mac

Merge branch 'master' into knepley/fix-plex-examples

* master: (75 commits)
increase the size of the ex25.c multigrid example so that the eigenestimator does not produce numbers that depend on machine roundoff and thus are different on different OS/hardware and produce different test restults. Previously the GMRES converged to 16 digits in 4 iterations and spent the next 6 churning but that churning produced different eigenvalues which produced different convergence for the multigrid method
Bib: More references
example used int and double !
added long forgotten test output file
removed tao test example run that uses random numbers since not reproducable on different systems
Jason changed a default TAO tolerance but did not update example test output that viewer the tolerance
Plex: Correct complex problem
Plex ex12: Now PCMG monitor creates its own coarse solutions
Plex ex12: Put in working setting for PCMG coarsening test
XDMF: Now take a bunch of files as input
SNES ex12: Use monitors instead of brute force to monitor errors
SNES ex12: Renumber meshes to match MG numbering
PC+SNES: Attach a level id to subsolvers in a multilevel solve - We should have done this years ago
Plex: Added epsilon to point location check
Plex ex12: Added error output on each level
Plex: Added DMPlexComputeL2DiffVec() - This puts cellwise error integrals in a Vec
Plex: Fix complex conversion
Plex: Fix variable init
Add an option to ex12 to dump the coarsened hierarchy to disk.
Plex: Fixed unused variables
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Merge remote-tracking branch 'origin/knepley/feature-plex-point-location'

* origin/knepley/feature-plex-point-location:
Plex: Added epsilon to point location check
Plex: Fix complex conversion

Merge remote-tracking branch 'origin/knepley/feature-plex-point-location'

* origin/knepley/feature-plex-point-location:
Plex: Added epsilon to point location check
Plex: Fix complex conversion
Plex: Now check whether a cell edge intersects a box edge as well - Added DMPlexGetLineIntersection_2D_Internal()
Plex: Fix marking of boxes enclosing cell vertices
Plex: Added error if point is not found - Might remove this later
Plex: Fixed initialization in point location
Plex: Removed unused vars, Initialized vars
Plex: Fixed signature for PetscGridHashGetEnclosingBox()
Plex ex17: Tests point location - One test which locates cell centroids right now
Plex: Replaced brute force search with grid hashing for point location
Plex: Now every Plex has a PetscGridHash
PetscGridHash: Added a simple regular point location data structure
DMLabel: Added DMLabelConvertToSection() - This routine converts a label to a Section+IS
Doc+Plex: Fixed function name

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Merge branch 'barry/add-concurrencykit'

Merging with Barry's refactor of PetscViewerGetSubComm

Merge branch 'barry/fix-petscviewer-attempt-2' into dmay/pcsemiredundant

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of git. I think it is not justified to ever have anything in next for more than a few weeks at most.
Either take it out of next if it is broken or put it in master if it is not broken. Hanging around in next but
not master for ever is not a good policy.

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Merge branch 'barry/add-concurrencykit' into barry/fix-petscviewer-attempt-2

fixes for missing ierr = around PetscLogFlops()

Merge branch 'knepley/feature-plex-point-location' into knepley/feature-snes-deflation

* knepley/feature-plex-point-location:
Plex: Added epsilon to point location check

Plex: Added epsilon to point location check

Merge branch 'knepley/feature-plex-point-location' into knepley/feature-snes-deflation

* knepley/feature-plex-point-location:
Plex: Fix complex conversion

Plex: Fix complex conversion

Merge branch 'knepley/feature-plex-point-location' into knepley/feature-snes-deflation

* knepley/feature-plex-point-location:
Plex: Now check whether a cell edge intersects a box edge as well - Ad

Merge branch 'knepley/feature-plex-point-location' into knepley/feature-snes-deflation

* knepley/feature-plex-point-location:
Plex: Now check whether a cell edge intersects a box edge as well - Added DMPlexGetLineIntersection_2D_Internal()
Plex: Fix marking of boxes enclosing cell vertices
Plex: Added error if point is not found - Might remove this later
Plex: Fixed initialization in point location

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Plex: Now check whether a cell edge intersects a box edge as well
- Added DMPlexGetLineIntersection_2D_Internal()

Plex: Fix marking of boxes enclosing cell vertices

Plex: Added error if point is not found
- Might remove this later

Plex: Fixed initialization in point location

Merge branch 'knepley/feature-plex-point-location' into knepley/feature-snes-deflation

* knepley/feature-plex-point-location:
Plex: Removed unused vars, Initialized vars
Plex: Fixed signature fo

Merge branch 'knepley/feature-plex-point-location' into knepley/feature-snes-deflation

* knepley/feature-plex-point-location:
Plex: Removed unused vars, Initialized vars
Plex: Fixed signature for PetscGridHashGetEnclosingBox()
Plex ex17: Tests point location - One test which locates cell centroids right now
Plex: Replaced brute force search with grid hashing for point location
Plex: Now every Plex has a PetscGridHash
PetscGridHash: Added a simple regular point location data structure
DMLabel: Added DMLabelConvertToSection() - This routine converts a label to a Section+IS
Doc+Plex: Fixed function name

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