Merge remote-tracking branch 'origin/knepley/feature-plex-torus' into tisaac/feature-fe-dual-apply

* origin/knepley/feature-plex-torus:
Plex: Cylinder fixes for complex
Plex ex1: Test for period

Merge remote-tracking branch 'origin/knepley/feature-plex-torus' into tisaac/feature-fe-dual-apply

* origin/knepley/feature-plex-torus:
Plex: Cylinder fixes for complex
Plex ex1: Test for periodic cylinder
Plex: I think periodic cylinder is working
Plex ex1: Updated torus test
Plex: Torus can now be arbitrarily refined
Plex ex1: Added a cylinder test
Plex: Added cylinder mesh
Plex: Some cleanup with mesh generation

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Plex: Torus can now be arbitrarily refined

Plex: Added cylinder mesh

Plex: Some cleanup with mesh generation

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new:
fix accidently changed code
another fix for Plex for complex numbers
fix for

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new:
fix accidently changed code
another fix for Plex for complex numbers
fix for example that did not handle complex numbers correctly
mark example tests that do not work with complex, fix warning about use of possibly uninitialized values
Fix MPI type to match PetscReal
No Matt triangle is not by default installed on every machine in the world
Matt forgot to require triangle in many tests
fix incorrect requires, fix incorrect name for __float128
since hdf5 doesn't allow PETSc to be built with 16 or 128 bit floating point then say it
fix requires
removed unneeded change to test harness since already supports requires: double
bunch of fixes in plex tests and code for single precision
Many missing requires ctetgen
Certain test examples require ctetgen but it is not listed in test rules

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bunch of fixes in plex tests and code for single precision

Reported-by: nightly tests

Merge branch 'tisaac/dmplex-feature-quadrature-in-geom'

* tisaac/dmplex-feature-quadrature-in-geom:
DMPlex: use new geometry in L2 calculations
DMPlex: fixes to recent geometry calculation chang

Merge branch 'tisaac/dmplex-feature-quadrature-in-geom'

* tisaac/dmplex-feature-quadrature-in-geom:
DMPlex: use new geometry in L2 calculations
DMPlex: fixes to recent geometry calculation changes
DMPlexComputeCellGeometryFEM(): change interface to take quadrature points

Conflicts:
src/dm/impls/plex/plexgeometry.c

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

Merge branch 'mlange/feature-plex-med'

* mlange/feature-plex-med:
Plex+Fluent: Finally got warning working for me
Plex+Fluent: numFaces should not have been unsigned
fix sign-compare warning i

Merge branch 'mlange/feature-plex-med'

* mlange/feature-plex-med:
Plex+Fluent: Finally got warning working for me
Plex+Fluent: numFaces should not have been unsigned
fix sign-compare warning in arch-linux-pkgs-cxx-mlib_el6
plex+MED: fix -Wunused-variable
Plex+MED: Fix variable protection
Plex+MED: Fix unsigned ints in the Fluent format
Plex-MED: Adding test output
Plex-MED: Updating the MED version to download
Configure: Make MED configure with given HDF5 path
Plex-Med: Read, communicate and identify facets in parallel
Plex: Optionally return vertex SF from DMPlexCreateFromCellListParallel
Plex-Med: Switch to parallel facet reads from file
Plex: Cannot assume hash keys are sorted
Plex-Med: Adding partitioned reads of coordinates and cell-connectivity
Plex-Med: Apply facet IDs via vertex joins
Plex-Med: Build DM from cells and coordinated in the .med file
Plex-Med: Add skeleton reader for .med mesh files with simple tests
Plex-Med: Add .med mesh library to build system

Conflicts:
src/dm/impls/plex/makefile

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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

This is needed to deal with some changes in MatNullSpace from commit 9d2471e

DMPlexComputeCellGeometryFEM(): change interface to take quadrature points

The choice of points at which to evaluate the geometry shouldn't depend
on the discretization of the coordinates.

DMPlexCo

DMPlexComputeCellGeometryFEM(): change interface to take quadrature points

The choice of points at which to evaluate the geometry shouldn't depend
on the discretization of the coordinates.

DMPlexComputeCellGeometryFEM(): fix assumed presence of PetscDS fields

DMPlexComputeCellGeometryFEM(): more fixes for implicit discretizations

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Merge branch 'tisaac/dmplex-feature-real-to-ref'

This branch introduces DMPlexReferenceToCoordinates() and
DMPlexCoordinatesToReference() and push finite element reference element
points forward int

Merge branch 'tisaac/dmplex-feature-real-to-ref'

This branch introduces DMPlexReferenceToCoordinates() and
DMPlexCoordinatesToReference() and push finite element reference element
points forward into the mesh and inverting to pull them back.

DMPlexCoordinatesToReference() is currently implemented with a simple
Newton iteration. When the reference maps extend outside the element in
a non-unique way, a Newton iteration doesn't always do what we want.

What we really want are two properties:

- If there is a solution inside the reference element domain, converge
preferentially to that one.
- If there is no solution inside the reference element domain, diverge
outside of the domain.

Newton has no guarantee of which solution will be found, so
DMPlexCoordinatesToReference() can fail for very nonlinearly deformed
elements. Fixing this is a project for another time.

* tisaac/dmplex-feature-real-to-ref:
DMPlex tests ex22: larger tolerance, so that single precision passes
DMPlex tests ex22: use petsc portable implementation of snprintf
DMPlexComputeProject3Dto2D(): precision-aware bounds for orthogonalization success
DMPlex: fix bad declaration order in point location routine
DMPlex: complex and C++ fixes to recent point location routines
DMPlex: added point location to regression tests
DMPlex: reduce max iterations for point location.
DMPlex: indexing and work array size corrections for point location routines
DMPlex: add debugging info in point location routines
DMPlex tests ex22: fix memory leak
DMPlex: fix work array declarations in reference/coordinate transformations
DMPlex test ex22: added iso parametric test
DM: fix reference/reference order in DMSetCoordinateDM()
DMPlex tests: move my ex21 to ex22 to prepare for merge
DMPlex: implement point inversion for multilinear maps.
CoordinatesRealToRef(): correct stride
DMPlex: propose DMPlexCoordinatesToReference() interface

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Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_A

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_ATTRIBUTEALIGNED flag to makefile
PCSetUp_SVD() used incorrect matrix for matrix size in parallel, also need to skip LAPACK call if matrix size is zero
strumpack: update to latest version 1.0.4
Remove valgrind warning about MPI_Allreduce() with uninitialized data
sed for test output that has atol convergence with quad precision
updated ex1_nest tests
fixed incorrect key value
fix: bad merge a69d34a
test: move runex78 to TESTEXAMPLES_C_NOTSINGLE
build: fix warnings
sys: update test to produce same result - irrespective of debug/opt build - and presence of ~/.petscrc
sys: src/sys/examples/tests/ex30.c -> src/sys/examples/tests/ex32.c to avoid conflict in master
Sed output, since quad precision reduces below atol on these tests
remove automatically generated matrix names from test output files since can be different
Fixes for MatMPIXXXSetPreallocation(), they were not reentrant, since they kept the information used for matrix-vector products
GAMG: fix PCView_GAMG() format - and update output/ex56_0.out
superlu_dist: 64-bit-indices fix https://github.com/xiaoyeli/superlu_dist/issues/4
Add SNESSetDivergenceTolerance / -snes_divergence_tolerance.
fixed unit read in Plex
...

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DMPlex: implement point inversion for multilinear maps.

This is implemented by a fixed number of Newton iterations. In 2D, I
know that this is a contraction map for a non-degenerate element, and
wi

DMPlex: implement point inversion for multilinear maps.

This is implemented by a fixed number of Newton iterations. In 2D, I
know that this is a contraction map for a non-degenerate element, and
will always converge to the right solution. The same cannot be said in
3D. There are non-degenerate trilinearly mapped hexahedra for which any
Newton iteration, damped or undamped, can converge to a spurious
solution outside of the element, even if there is a solution inside the
element. One could go about a costly procedure of trying to determine
if the target coordinate is inside of the region defined by the mapped
boundary of the reference cell, but this is an expensive procedure. For
now, I am relying on the elements not being so deformed that Newton
doesn't converge. I spent much longer than I should have trying to come
up with a better solution to this problem. I should write the whole
thing up.

WIP: implementation of all point location routines

DMPlex: added complementary DMPlexReferenceToCoordinates() methods

For affine, this just wraps CoordinatesRefToReal.
For tensor, it uses the tensor structure.
In general, the basis space of the PetscDS is used to map points.

WIP: DMPlex: test point inversion.

It seems to work, but the test is flawed for simplicial elements

DMPlex: point location is working for implicit discretizations

Now to do the work for non-implicit (e.g. isoparametric) meshes

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Merge branch 'knepley/feature-partition-random'

* knepley/feature-partition-random:
Plex: Forgot declarations
Plex: Fix for complex numbers
Partition: Added -petscpartitioner_shell_random for

Merge branch 'knepley/feature-partition-random'

* knepley/feature-partition-random:
Plex: Forgot declarations
Plex: Fix for complex numbers
Partition: Added -petscpartitioner_shell_random for a random partition - Also fixed SetFromOptions

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Plex: Forgot declarations

Plex: Optionally return vertex SF from DMPlexCreateFromCellListParallel

This is needed by file readers to use the created vertex partitioning.

Plex-Med: Add skeleton reader for .med mesh files with simple tests

DMPlex: propose DMPlexCoordinatesToReference() interface

Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in m

Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in master (the introduction of MatFactorGetError()) therefor need
to merge in master and use the new construct before merging to next

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Merge branch 'master' into psanan/pc-telescope-nearnullspace

Merge branch 'master' into mark/snes-ex56

* master: (93 commits)
Web: Added a tutorial
typo
rename X -> U
sowing: update to version that creates manpage URLs for 'enum' types/values
Increa

Merge branch 'master' into mark/snes-ex56

* master: (93 commits)
Web: Added a tutorial
typo
rename X -> U
sowing: update to version that creates manpage URLs for 'enum' types/values
Increase patchlevel to 3.7.3
move runex3_3 to NOTSINGLE [ partial backport 9ed0bd76d5c329eb91401ebabfbd851446214e20 ]
DMPlex: local coordinate vector should be a sequential vector
DM: Name coordinate vectors in subdomain and restrict hooks
tests: disable a couple of TS examples from single precision tests
reduce TS ex12_2 output
fix PetscFormatRealArray() to cast PetscReal in print statement to double so works for __float128 precision
Vec: enable Fortran interfaces for VecGetLocalVectorRead and VecRestoreLocalVectorRead
Bib: Added refs
PCShell: man page fixes
update handling of latex in example code to use https
fix typo in isltog comment
test: Avoid conversion of object <-> function pointer type [-Wpedantic]
fortran: enable interface for VecGetLocalVector(), VecRestoreLocalVector()
update citation for cmz2016
PCBDDC: silent compilation warnings from nightlybuilds
...

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

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Plex: Added DMPlexCreateQuadSphereMesh()
- Creates a spherical surface with 6 quads

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcfetidp.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c
src/mat/impls/is/matis.h

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Merge branch 'tisaac/plex-tree-transfer-vec-doc'

* tisaac/plex-tree-transfer-vec-doc:
DMPlex: move DMPlexTransferVecTree() to public interface
DMPlexTree: write doc for DMPlexTransferVecTree()