DMPlexOrient(): add flag for synchronized output

Merge remote-tracking branch 'origin/knepley/feature-plex-tests-new' into tisaac/feature-plex-tests-new

* origin/knepley/feature-plex-tests-new:
SNES ex12: Allow more exotic periodicity
SNES ex6

Merge remote-tracking branch 'origin/knepley/feature-plex-tests-new' into tisaac/feature-plex-tests-new

* origin/knepley/feature-plex-tests-new:
SNES ex12: Allow more exotic periodicity
SNES ex69: Added to makefile
SNES ex69: Fix for parallelism
Plex+HDF5: Output mapping for torus
Plex ex1: Fixed periodic cylinder test
Plex: Fixed periodic cylinder - Needed to use 3 layers of cells - Fixed periodic length - Fixed cell orientation
DM: Should not be localizing coordinates in non-periodic directions
Plex ex1: Test cell shape in cylinder meshes
Plex: Flip orientation of hexes in cylinder mesh - Periodic is still broken
Plex: Fixed cylinder tests
Plex: Fixes creation of hex box meshes and added tests

show more ...

Plex+HDF5: Output mapping for torus

DMPlex geometry: make constants work for quad precision

DMSwarmPIC:
* Code fixes for complex builds

Merge branch 'tisaac/feature-plex-deterministic-viewing' into tisaac/feature-plex-tests-new

* tisaac/feature-plex-deterministic-viewing:
DMPlexinterpolatePointSF(): deterministic leaf order

DMPlexinterpolatePointSF(): deterministic leaf order

DMLocatePoints_Plex:
* Added early abort case for points outside the domain bounding box
* Added reporting of the method used to locate each point
* Added hack option flag to allow the number of boxe

DMLocatePoints_Plex:
* Added early abort case for points outside the domain bounding box
* Added reporting of the method used to locate each point
* Added hack option flag to allow the number of boxes to be set when using the grid hash method

show more ...

DMPlex: Error if attempt to partition a distributed graph with Chaco

DMLocatePoints_Plex:
* Add info logging points/sec processed
* Added method PetscGridHashGetEnclosingBoxQuery() to get box and return true/false if point was located (or not). It is completely valid

DMLocatePoints_Plex:
* Add info logging points/sec processed
* Added method PetscGridHashGetEnclosingBoxQuery() to get box and return true/false if point was located (or not). It is completely valid that we are given a point to locate which is outside of all boxes.
* Added logic to re-use a star forest node list

show more ...

plex tests ex11: update output for sorted distributed labels

Merge branch 'tisaac/feature-plex-deterministic-viewing' into tisaac/feature-plex-tests-new

* tisaac/feature-plex-deterministic-viewing:
DMLabel: sort strata after distributing
PetscError() did

Merge branch 'tisaac/feature-plex-deterministic-viewing' into tisaac/feature-plex-tests-new

* tisaac/feature-plex-deterministic-viewing:
DMLabel: sort strata after distributing
PetscError() did not properly copy over the specific error message when error type was PETSC_ERROR_INITIAL
Additional clarification for MatMeshToCellGraph() manual page
med: --with-hdf5, not --with-hdf5-dir
DMPlex_GMSH: revert to not inverting triangles
sys tests ex13f: fix type mismatch in composition test
PCBDDC: use a sparse rhs when the solver is MUMPS
Sys ex13: Added test for object composition in Fortran
Sys: Added Fortran binding for object composition
MatMUMPS: added support for sparse right-hand sides in sequential

show more ...

tests: remove 'quad' requirement, replace with '__float128'

DMPlexCreateGmsh(): fix types when reading from binary

Plex tests ex8: precision-agnostic estimate of one third

So tests can run correctly in different precisions

PetscViewerSetFromOptions(): protect tests from misparsing

Some platforms apparently have problems with parsing option keys that start
with colons, so e.g. isn't processed correctly.
We should fix

PetscViewerSetFromOptions(): protect tests from misparsing

Some platforms apparently have problems with parsing option keys that start
with colons, so e.g. isn't processed correctly.
We should fix that, but I'm just going to make the viewer types explicit in
regression tests to avoid the issue

show more ...

test harness 'requires' lists are not comma delimited

Plex tests ex1: not for mpiuni because of custom data type

Plex tests ex1: fix cylinder mesh output

DMPlex: partitioner must be set from options explicitly

Yes, it's not nice to have to call this before every DMPlexDistribute(),
but it's better than hidden implicit SetFromOptions calls.

Merge branch 'tisaac/fix-dm-tests' into tisaac/feature-plex-tests-new

* tisaac/fix-dm-tests:
dmplex tests ex1: update output for ISLocalToGlobalMapping changes
DMNetwork: Use the default section

Merge branch 'tisaac/fix-dm-tests' into tisaac/feature-plex-tests-new

* tisaac/fix-dm-tests:
dmplex tests ex1: update output for ISLocalToGlobalMapping changes
DMNetwork: Use the default sections with plex when getting offset.
Add another extchem test case
Fix for extchem.c when envelop monitor is on, but graphical monitoring is off
TSAdapt ascii view should show dt_min and dt_max
Forgot to include example file
Change extchem.c to accept mole values for initial conditions instead of mole fractions
Update extchem.c example to 1) use pressure, 2) use options file, 3) read initial conditions from file
DMNetwork: API to return the underlying DMPlex.
deprecate MatGetSubMatXXX Requested-by: Jed Brown <jed@jedbrown.org>
Work around for Apple Xcode bug with rpath
DMPlex_GMSH: triangles are inverted
bib: fix URL for StarForest note
rm MatLUFactorNumeric_SeqBAIJ_11_NaturalOrdering() because it does not improve performance add MatSolve_SeqBAIJ_bs_NaturalOrdering(), bs=12,...,14 add test runex50_2
experiment PetscKernel_A_gets_A_minus_B_times_C_11
add timer to MatLUFactorNumeric_SeqBAIJ_11_NaturalOrdering()
test new A = A*B
implement MatSolve_SeqBAIJ_11_NaturalOrdering
Merge two line TSAdapt monitor to a single line, shorten line, reorder presented values
implement PetscKernel_A_gets_A_times_B_11()

show more ...

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

There has unfortunately been a lot of interplay between our work to
change the petscspace/dualspace to accept vector co

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

There has unfortunately been a lot of interplay between our work to
change the petscspace/dualspace to accept vector components, and the
work to transfer the tests in config/builder.py to the new test harness.
I'm merging them together to get them to play nice with each other, and
so that I only have one feature branch to handler when merging into
master/next.

* tisaac/feature-fe-dual-apply: (64 commits)
snes tutorials ex12: fix restart test arguments
nightly build fixes for arch-viennacl
fix run command to match the command in master/makefile. [the diff will be correct in master/next]
PetscFE: fix typo in for loop declaration
PetscPartitioner: use simple partitioning for regression tests
DT tests ex1: fix test arguments to match regression output
DT ex1: fix options
DMPlexCreateHexBoxMesh: no cells in z direction for 2D
PCBDDC: use %D for PetscInt printfs
Plex: helper function used in all cases now
Plex tests ex7: make partitions portable for testing
Plex: use MPIU_2INT instead of MPI_2INT
MatAIJ KLU: remove redefinition of SuiteSparse_long
DMPlexRefine_CTetgen() mimics DMPlexRefine_Tetgen()
DMPlexGenerate_Tetgen(): mimic ctetgen so it can be used equivalently
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
...

show more ...

Fix compiler warnings

Added simplex2tensor to the testsuite

Move hash.h to include/petsc/private/.