Merge branch 'knepley/feature-plex-boundary-values'

* knepley/feature-plex-boundary-values:
PetscSpace: Handle 0 point case for evaluation
PetscSpacePoint: Fix memory handling
PetscDS: Fix upd

Merge branch 'knepley/feature-plex-boundary-values'

* knepley/feature-plex-boundary-values:
PetscSpace: Handle 0 point case for evaluation
PetscSpacePoint: Fix memory handling
PetscDS: Fix update fund for new API
PetscFE: Derivatives for Point class are all zero
Small fixes
TS ex46: Fix sin and cos
TS ex18: Fix sin and cos
PetscFE: Fixing Point subclass
Plex: Fixed bug with refinement, fixed composed functions for Plex - When we refine, we were calling DMDestroy_Plex(), which wiped out the composed funds, but not calling DMInitialize_Plex() to reinsert them in to the refined mesh
PetscSpacePoint: Fix handling of points
PetscDS: Added update() function for fields - This is intended to directly update the values at points
Plex: DMPlexInsertBoundaryValues() can now be overridden by the user

Conflicts:
include/petsc/private/petscdsimpl.h
include/petscds.h

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Merge branch 'knepley/feature-plex-sphere-mesh'

* knepley/feature-plex-sphere-mesh:
Plex ex7: Added 600 cell test
Plex: Added 600-cell for S^3
Math: Add the golden ratio
Plex ex7: Meshing a

Merge branch 'knepley/feature-plex-sphere-mesh'

* knepley/feature-plex-sphere-mesh:
Plex ex7: Added 600 cell test
Plex: Added 600-cell for S^3
Math: Add the golden ratio
Plex ex7: Meshing a sphere
Plex: Changed to DMPlexCreateSphereMesh() - Now can do quads or triangles
Share: Added large 3D mesh file - Its the only one I have gotten to work
Plex ex1: Added cow mesh - Not sure why TetGen is puking
CTetGen: Updated to newest commit
Plex ex7: Mesh a sphere
SNES ex63: Fixed help message
Plex: Added DMPlexCreateQuadSphereMesh() - Creates a spherical surface with 6 quads
Plex: Simple corrections
Plex ex1: Allow a mesh boundary to be loaded and meshed
Plex: Allow Gmsh loads that are zero-based and embedded meshes - I know this is non-standard, but its an easy format to manipulate

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Merge branch 'scott/test-datafiles-fix' of https://bitbucket.org/petsc/petsc into scott/test-datafiles-fix

Plex: Added DMPlexCreateWedgeCylinderMesh()

Plex: Added 600-cell for S^3

Plex: Changed to DMPlexCreateSphereMesh()
- Now can do quads or triangles

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

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Merge branch 'master' into knepley/feature-convergence-estimator

* master: (27 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables

Merge branch 'master' into knepley/feature-convergence-estimator

* master: (27 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
PetscDS: Allow point functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
dmda matstructure_only
add 'structure_only' to seqbaij matrices -- MatView() does not work yet
PetscFE: Initialize temp array before calling f1
...

Conflicts:
include/petsc/private/petscdsimpl.h
include/petscds.h
src/dm/dt/interface/dtds.c

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Plex: CreateSquareBoundary() now also sets FaceSets label

Merge branch 'knepley/feature-plex-ply'

* knepley/feature-plex-ply:
Plex: Added PLY to file support
Plex: Adding PLY support

Merge branch 'knepley/feature-plex-ply' into knepley/feature-ex11-simplex

* knepley/feature-plex-ply:
Plex: Added PLY to file support
Plex: Adding PLY support

Plex: Added PLY to file support

Merge branch 'master' into stefano_zampini/feature-fetidp-ex69

Merge branch 'knepley/feature-plex-torus'

* knepley/feature-plex-torus:
Plex: Fix initialization
DM: Fixed floor
TS ex18: Updated localization call
Plex: Fix for periodic cut
Plex: Forgot

Merge branch 'knepley/feature-plex-torus'

* knepley/feature-plex-torus:
Plex: Fix initialization
DM: Fixed floor
TS ex18: Updated localization call
Plex: Fix for periodic cut
Plex: Forgot guard when making periodic cut label
DM: Damn forgot to checkin declaration change
Plex+HDF5: Use label to decide which periodic cells need vertex replacement
Plex: Mark cells on one side of periodic cut - Also use label object in routine
Plex+HDF5: Force coordinates onto same sheet when cutting periodic surfaces
DM: Allow localization with an endpoint
Plex+HDF5: Fix vertex field output for periodic cuts
Plex: Fix periodic cut label - Fix option spelling - Add edges into cut label
Plex+HDF5: If periodic_cut label is defined, create extra vertices in periodic meshes for embedding in coordinate dimension
Plex: Now -dm_plex_periodic_cut creates a label with the cut necessary to embed a periodic domain - Label is names "periodic_cut" and only has vertices right now

Conflicts:
src/dm/impls/plex/plexhdf5.c
src/dm/interface/dm.c

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Plex: Fixed bug with refinement, fixed composed functions for Plex
- When we refine, we were calling DMDestroy_Plex(), which wiped out the composed funds, but not calling DMInitialize_Plex() to reins

Plex: Fixed bug with refinement, fixed composed functions for Plex
- When we refine, we were calling DMDestroy_Plex(), which wiped out the composed funds, but not calling DMInitialize_Plex() to reinsert them in to the refined mesh

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Plex: Fix initialization

Merge branch 'master' into knepley/feature-plex-boundary-values

* master: (487 commits)
Bib: More refs
Fixed errors in the manuals and ts_glee source code doc
fix bug to enable '-xxx_via [alg]

Merge branch 'master' into knepley/feature-plex-boundary-values

* master: (487 commits)
Bib: More refs
Fixed errors in the manuals and ts_glee source code doc
fix bug to enable '-xxx_via [alg]' to showup in '-help' Reported-by: Mark Adams <mfadams@lbl.gov>
Plex: Remove dead code
TS tutorials ex11: remove unused functions
TSAdapt: Set TSADAPTNONE as default adapt type
DMPlex: missed viewer change in synchronized output
Revert "Merge branch 'hzhang/ts-ex9busdmnetwork'"
TSAdapt: Update changes/dev.html
TSAdapt: Set default type for TSGLEE
TS tutorials ex11: make work with complex scalars
Bib: Added ref
TS ex18: Fix initializer
TS ex11: Fix M_PI
Plex ex1f90: FUCK FORTRAN
f2cblaslapack: remove duplicate xerbla.o and xerbla_array.o from lapack [they are already in blas]
TSAdapt: Refactor handling of default adapt type
TSAdapt: Update changes/dev.html
TSAdapt: Update manual
TSAdapt: Refactor interface and implementations
...

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Merge branch 'tisaac/feature-plex-tests-new'

This merge changes PetscSpace and PetscQuadrature to have a number of
components, so that vector-valued functionals can be defined for
non-Lagrange finit

Merge branch 'tisaac/feature-plex-tests-new'

This merge changes PetscSpace and PetscQuadrature to have a number of
components, so that vector-valued functionals can be defined for
non-Lagrange finite elements. Along the way, this branch also converts
the regression tests related to DMPlex that were in config/builder.py to
the new test harness, and makes lots of changes necessary for them to
be portable tests.

* tisaac/feature-plex-tests-new: (263 commits)
TS tutorials ex11: remove unused functions
DMPlex: missed viewer change in synchronized output
TS tutorials ex11: make work with complex scalars
TS ex18: Fix initializer
TS ex11: Fix M_PI
Plex ex1f90: FUCK FORTRAN
TS tutorials ex11: use a union when punning
silence compiler warnings
SNES tutorials ex56: set partitioner from options
Plex: once again, MPI_Barrier() can't be used to synch output
windows compile fixes balay@ps4 ~/petsc/src/ts/examples/tutorials $ make PETSC_DIR=$HOME/petsc ex11 /home/balay/petsc/bin/win32fe/win32fe cl -o ex11.o -c -MD -wd4996 -Z7 -I/home/balay/petsc/include -I/home/balay/petsc/arch-mswin-uni/include -I/home/balay/petsc/include/petsc/mpiuni `pwd`/ex11.c ex11.c C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(300): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(301): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(370): error C2229: struct '<unnamed-tag>' has an illegal zero-sized array C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(463): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(505): error C2229: struct '<unnamed-tag>' has an illegal zero-sized array C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(724): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(728): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1179): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1184): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1191): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1194): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1383): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1521): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1522): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1523): warning C4090: 'function': different 'const' qualifiers
PetscMath: check for math functions by function pointer resolvability
another windows fix for log2() C:\cygwin64\home\petsc\PETSC~1.CLO\include\petscmath.h(28): warning C4273: 'log2': inconsistent dll linkage C:\Program Files (x86)\Windows Kits\10\include\10.0.10240.0\ucrt\../ucrt/math.h(506): note: see previous definition of 'log2'
fix log2() compile error on windows /home/petsc/petsc.clone-4/include/petscmath.h:28:8: error: expected ‘)’ before ‘/’ token double log2(double); ^
SNES tutorials ex12: turn off complex for restart test
Add empty file to silence warnings
TS tutorials ex46: make output match floating point filter
TS tutorials ex18: remove unused flags
SNES tutorials ex69: use end of line anchor instead of word boundary
SNES tutorials ex69: portable word boundary regex
...

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Plex: Forgot guard when making periodic cut label

Plex: Mark cells on one side of periodic cut
- Also use label object in routine

Plex: Fix periodic cut label
- Fix option spelling
- Add edges into cut label

Plex: Now -dm_plex_periodic_cut creates a label with the cut necessary to embed a periodic domain
- Label is names "periodic_cut" and only has vertices right now

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-plex-torus

* knepley/feature-plex-tests-new: (40 commits)
SNES ex12: Allow more exotic periodicity
SNES ex69: Added to makefile

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-plex-torus

* knepley/feature-plex-tests-new: (40 commits)
SNES ex12: Allow more exotic periodicity
SNES ex69: Added to makefile
SNES ex69: Fix for parallelism
Plex+HDF5: Output mapping for torus
TS ex18: Shut off all these tests until we can figure out why you get NaNs on some builds
TS ex11: More fixes to the horrible Riemann code
Plex: Fix section creating for random partitioning
Plex-ex12: Fix LogStage scope for load balancing
TS ex11: Mark, this code is disgusting
TS ex18: Shut off all these tests until we can figure out why you get NaNs on some builds
TS ex11: Silence IDIOT FUCKING COMPILER that has no idea what it is talking about
Plex: I think I fixed random partitioning
Plex: Awful fix for partitioner options - I cannot see a better way to solve this right now
Plex: Bug fixes for shell partitioning
Plex ex12: Fix partitioning - Now give load balancing DM prefix "lb_" so I can change partitioners - Do not force test partition in load balancing
Plex: Now set partitioner type from options in GetPartitioner() instead of on creation - Also set it from options with DM, but this is probably useless because most DM are partitioned before SetFromOptions
Plex: Add DMPlexSetOptionsPrefix() - This gives the prefix to the partitioner
TS ex18: Indicate broken tests
TS ex11: Indicate broken test
SNES ex62: Added SIMPLE tests
...

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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

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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
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