Merge branch 'knepley/feature-plex-boxmesh-create'

* knepley/feature-plex-boxmesh-create:
testing
Plex: Change initializers for C89
Plex: All tests now passing after DMPlexCreateBoxMesh() upda

Merge branch 'knepley/feature-plex-boxmesh-create'

* knepley/feature-plex-boxmesh-create:
testing
Plex: Change initializers for C89
Plex: All tests now passing after DMPlexCreateBoxMesh() update
Plex: Small fix for box meshing
Plex: Unified box mesh creation to DMPlexCreateBoxMesh() - Makes simplices and tensor cells - Does not work for all combinations, but gives correct error
Plex: Added bounds and faces in each dim to DMPlexCreateBoxMesh()
Plex: Added domain bounds to HexBoxMesh()

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Plex: Unified box mesh creation to DMPlexCreateBoxMesh()
- Makes simplices and tensor cells
- Does not work for all combinations, but gives correct error

Plex: Added bounds and faces in each dim to DMPlexCreateBoxMesh()

Plex: Added domain bounds to HexBoxMesh()

Plex: Added DMPlexComputeGradientClementInterpolant()

Merge remote-tracking branch 'origin/pr690/mapdes/feature-plex-user-adjacency/master'

plex: Support user-defined adjacencies via callback

Plex: Added declaration

Merge branch 'master' into knepley/fix-fe-default

* master: (297 commits)
Bib: Added refs and fixed one
Doc: Fixed formatting problems for MatCreateAIJ() manual page.
Add to PCSOR manual page

Merge branch 'master' into knepley/fix-fe-default

* master: (297 commits)
Bib: Added refs and fixed one
Doc: Fixed formatting problems for MatCreateAIJ() manual page.
Add to PCSOR manual page information about convergence testing when using KSPRICHARDSON
SNES ex5: Restore old output since this breaks an example I have
Noted that some Cray XC systems will use 'aprun' instead of 'srun'. Thanks to Herr Doktor Hong Zhang for this suggestion.
Added example configure script for Cray XC40 with KNL processors (e.g., NERSC Cori).
Fix possible sprintf -Wformat-overflow
PetscMalloc2-7: fix -Wint-in-bool-context for GCC 7
SNES ex5: make boundary condition handling consistent for symmetry
SNES ex5: use L2 norm and *_monitor_short for output
SNES ex5: the L^2 norm scales with the l^2 norm over sqrt(N)
SNES ex5: refactor MMS capability to avoid extreme code duplication
Documentation fix: typo in PetscLogStageRegister manual page.
nodes -> vertices
rename DMNetworkGetComponentTypeOffset -> DMNetworkGetComponentKeyOffset
rename DMNetworkGetConnectedNodes() -> DMNetworkGetConnectedVertices()
Jacobians for adjoints for explicit methods and constant Jacobians never got initialized
fix complex build error
fix build failure with fortran interface
fix compile error with cdc753b64c658d532d7813e942002e67025667a6
...

Conflicts:
src/snes/examples/tutorials/ex13.c
src/snes/examples/tutorials/ex62.c
src/snes/examples/tutorials/ex69.c

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Merge branch 'master' into knepley/feature-rigid-bodies

* master: (204 commits)
windows fixes
revert this change as a relavent fix is already in origin/knepley/fix-ex-types
regenerate output l

Merge branch 'master' into knepley/feature-rigid-bodies

* master: (204 commits)
windows fixes
revert this change as a relavent fix is already in origin/knepley/fix-ex-types
regenerate output log for snes_tutorials-ex62_fetidp_3d_tet that got corrupted in 188e10d6f1cffa866ec0197053a0e55fa4e7da41
fix opensolaris build error with --with-log=0 Undefined first referenced symbol in file PetscLogEventGetPerfInfo arch-opensolaris-misc/tests/src/dm/impls/plex/examples/tests/ex9.o
fix warnings on windows C:\cygwin64\home\petsc\PETSC~1.CLO\src\tao\examples\TUTORI~1\ex1.c(217): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)'
disable example with absoft (due to fixed/free form limit)
c89 fixes
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
Plex ex19: Remove unneeded code
Plex: Fix projection when we have a dmAux which is a domain boundary - If we are projecting on a lower dimension thing (effectiveHeight > 0), then we need to get the space and dual space on this subcell - The tabulation needs to be in the right dimension for both dm and dmAux
PetscFE: Added height subspaces to PetscFE - Added PetscFEGetHeightSubspace() - Added array in struct
PetscDualSpace: Small cleanup of parameter name
PetscSpace: Added height subspaces for PetscSpace - Added PetscSapceGetHeightSubspace() and member function - Added subspaces array
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix some minor style issues
Extend AMS/ADS to support high-order element.
...

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Merge remote-tracking branch 'origin/knepley/fix-plex-parallel-load'

Merge remote-tracking branch 'origin/knepley/feature-dm-bc-components'

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warni

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix output file - corresponding to code changes in efd4aadf157bf1ba2d80c2be092fcf4247860003
disable test on windows
update log from opensolaris so that the diff is clean on linux aswell
update grep in sync with change in efd4aadf157bf1ba2d80c2be092fcf4247860003
Fixed code that did not correctly set current color for block insertion
Update output files that did not get fixed after previous merges
Change MPIUni to not immediately abort on operations it cannot perform, instead return error code
Add filter for example that can produce 1 different iteration count
Example add system calloc, bad formating of %d in print, commented out code
Always use (void) for functions that take no arguments, never ()
always need to caste PetscReal variables to (double) in print statements
updates to manual page for clarity
update help menu for MatRARt() -- MatRARt_mpiaij_mpiaij is supported now, but not efficient.
fix nightlybuild error with c1cbb1def3f8ddca04c3998b9c06618fd1ffef35 on arch-linux-IPL64 src/ksp/pc/examples/tests ex5_1
...

Conflicts:
include/petscdm.h
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/dm/impls/plex/plexhdf5.c

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Merge branch 'master' into knepley/feature-dm-bc-components

* master: (320 commits)
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ m

Merge branch 'master' into knepley/feature-dm-bc-components

* master: (320 commits)
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix output file - corresponding to code changes in efd4aadf157bf1ba2d80c2be092fcf4247860003
disable test on windows
update log from opensolaris so that the diff is clean on linux aswell
update grep in sync with change in efd4aadf157bf1ba2d80c2be092fcf4247860003
Fixed code that did not correctly set current color for block insertion
Update output files that did not get fixed after previous merges
Change MPIUni to not immediately abort on operations it cannot perform, instead return error code
Add filter for example that can produce 1 different iteration count
Example add system calloc, bad formating of %d in print, commented out code
Always use (void) for functions that take no arguments, never ()
always need to caste PetscReal variables to (double) in print statements
updates to manual page for clarity
update help menu for MatRARt() -- MatRARt_mpiaij_mpiaij is supported now, but not efficient.
fix nightlybuild error with c1cbb1def3f8ddca04c3998b9c06618fd1ffef35 on arch-linux-IPL64 src/ksp/pc/examples/tests ex5_1
output has changed with e6d0a238963c2a97dd04845ea512b529992c7cdb so update the output file
...

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Merge branch 'knepley/feature-dm-bc-components' into knepley/feature-rigid-bodies

* knepley/feature-dm-bc-components:
DM: Fixed problem with setting boundary conditions for selected components - T

Merge branch 'knepley/feature-dm-bc-components' into knepley/feature-rigid-bodies

* knepley/feature-dm-bc-components:
DM: Fixed problem with setting boundary conditions for selected components - The problem was that projection always set every component of a field, even when the BC was only for a certain component. Now you can pass in masking components. - Added masking components to projections over labels - Changed interface to boundary value insertion

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Plex: Added DMPlexCreateRankField()

Merge branch 'knepley/test-process-arg' into knepley/feature-adapt-interface

* knepley/test-process-arg: (49 commits)
Test: Can now use make test NP=<num procs>
Testing: Fix error reporting
I

Merge branch 'knepley/test-process-arg' into knepley/feature-adapt-interface

* knepley/test-process-arg: (49 commits)
Test: Can now use make test NP=<num procs>
Testing: Fix error reporting
I didn't realize there was a hacky special case for dense B matrix
Fix example to support -snes_mf_operator
cleanup src/ksp/ksp/examples/tutorials/network/makefile
add missing input in the help menu of PetscOptionsView() Reported-by: Richard Katz <richard.katz@earth.ox.ac.uk>
Fix docs for MatMatMult() that C matrix can only be created by user for sequential case.
protect '-' in macros
fix compile error with --download-petsc4py
Plex: Removed useless CHKERRQ
Configure: Replace use of PETSc modules
Plex ex7: Damn, quad precision is named __float128
TSSetFromOptions: Give subtypes a chance to set the default adapt type
TS ex11.c: fix corrupt filename initialization
small fix
Plex ex1: Update output
DT: Fixed Fortran module - Add DT module to DM and Petsc modules - Fix makefile to generate DT F90 module - Fix PetscQuadratureGet/Restore/SetData() F90 defs
Plex ex19: Updated output
Plex ex7: Update output
p4est: Update to new API
...

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Merge branch 'knepley/feature-plex-wedge'

* knepley/feature-plex-wedge:
Plex ex1: Update output
Plex ex1: Added a wedge test
Plex: Added DMPlexCreateWedgeCylinderMesh()
Xdmf: Also handle wed

Merge branch 'knepley/feature-plex-wedge'

* knepley/feature-plex-wedge:
Plex ex1: Update output
Plex ex1: Added a wedge test
Plex: Added DMPlexCreateWedgeCylinderMesh()
Xdmf: Also handle wedge elements

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DM: Fixed problem with setting boundary conditions for selected components
- The problem was that projection always set every component of a field, even when the BC was only for a certain component.

DM: Fixed problem with setting boundary conditions for selected components
- The problem was that projection always set every component of a field, even when the BC was only for a certain component. Now you can pass in masking components.
- Added masking components to projections over labels
- Changed interface to boundary value insertion

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Merge branch 'master' into knepley/feature-plex-wedge

* master: (61 commits)
Added ignore
Plex ex7: Fixed mesh name
Plex ex1/ex2: Fixed requirements
PCGAMG: fix spelling in option docs
Pet

Merge branch 'master' into knepley/feature-plex-wedge

* master: (61 commits)
Added ignore
Plex ex7: Fixed mesh name
Plex ex1/ex2: Fixed requirements
PCGAMG: fix spelling in option docs
PetscDS: Fix print
Plex ex19: Output fixes for proper destruction
TSMonitorDrawSolutionPhase: Add missing draw pause
fix warning with gcc-7.1
Docs+PetscFE: Evaluate() operates in reference space
Plex ex7: Added 600 cell test
Plex: Added 600-cell for S^3
Math: Add the golden ratio
Plex: Handle unused variable
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
Mat: Added example for MatIS
PetscSpace: Handle 0 point case for evaluation
PetscSpacePoint: Fix memory handling
PetscDS: Fix update fund for new API
...

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

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Merge branch 'master' into knepley/fix-fe-fortran

* master: (56 commits)
PCGAMG: fix spelling in option docs
PetscDS: Fix print
Plex ex19: Output fixes for proper destruction
TSMonitorDrawSo

Merge branch 'master' into knepley/fix-fe-fortran

* master: (56 commits)
PCGAMG: fix spelling in option docs
PetscDS: Fix print
Plex ex19: Output fixes for proper destruction
TSMonitorDrawSolutionPhase: Add missing draw pause
fix warning with gcc-7.1
Plex ex7: Added 600 cell test
Plex: Added 600-cell for S^3
Math: Add the golden ratio
Plex: Handle unused variable
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
PetscSpace: Handle 0 point case for evaluation
PetscSpacePoint: Fix memory handling
PetscDS: Fix update fund for new API
Plex: Fixing insertion of boundary values - If we have a dmAux that is a boundary, we need minHeight = 1, since faces can be mapped from submesh to mesh, but not cells (since they have incomplete cones) - However, in this case the effectiveHeight should be h, whereas when using a boundary as the mesh as well, the effectiveHeight should be h - minHeight - Obviously, we need more thinking here to make the iteration make sense in general
PetscFE: Derivatives for Point class are all zero
Small fixes
TS ex46: Fix sin and cos
TS ex18: Fix sin and cos
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Merge branch 'master' into knepley/feature-ex11-simplex

* master: (63 commits)
TSMonitorDrawSolutionPhase: Add missing draw pause
fix warning with gcc-7.1
Docs+PetscFE: Evaluate() operates in

Merge branch 'master' into knepley/feature-ex11-simplex

* master: (63 commits)
TSMonitorDrawSolutionPhase: Add missing draw pause
fix warning with gcc-7.1
Docs+PetscFE: Evaluate() operates in reference space
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
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
Mat: Added example for MatIS
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
PetscSpace: Handle 0 point case for evaluation
PetscSpacePoint: Fix memory handling
update tests
...

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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()