Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with

Merge branch 'master' into knepley/fix-plex-bc-multiple

* master: (347 commits)
tests: add 'PETSC_HAVE_C99' flag - so that 'requires: c99' can be used in the test suite
PGI: fix build error with updated 17.10 compilers
Fix for test dirs that are not tutorials/tests
fix use of double in PetscAbsReal() which produces compiler warnings with single precision build
elemental: remove info on conflict of -with-cxx-dialect=C++11 on osx - it works now.
Cleanup .bib files
Fix allfortranstubs rule to rm generated files from correct directory, not outdated location
ierr set but not checked
Remove initial refine so test runs faster and does not time out on some machines
Gail's copyedits for bibtex items
Docs: manual: add further description of 3 different current testing options
DM: check for ops->localtolocalbegin/end before calling
PetscSF: fix typo in tutorial ex1
Vec+HDF5: Fix output for complex - Need to check for empty group name
SNES: SNESDestroy() can be called with snes->dm == NULL
SNES: SNESDestroy() can be called with snes->dm == NULL
Vec+HDF5: Fix output for complex - Need to check for empty group name
Docs: Manual: Update tests section
gmakegentest: also exclude .#filenames created by emacs
DMPlex: Fix output of test ex1 after changes to Gmsh reader
...

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PetscDS: Added PetscDSGetHeightSubspace()

Merge branch 'knepley/fix-plex-proj-ds' into knepley/fix-plex-multifield-eval

* knepley/fix-plex-proj-ds:
PetscDS: The x[] array should be the size of the embedding space
DM: Should do its best

Merge branch 'knepley/fix-plex-proj-ds' into knepley/fix-plex-multifield-eval

* knepley/fix-plex-proj-ds:
PetscDS: The x[] array should be the size of the embedding space
DM: Should do its best to automatically set the embedding dimension for the DS
PetscDS: Needs to know the embedding dimension

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PetscDS: The x[] array should be the size of the embedding space

PetscDS: Needs to know the embedding dimension

Merge branch 'knepley/fix-ds-memleak'

* knepley/fix-ds-memleak:
PetscDS: Fix memory leak

PetscDS: Fix memory leak

Merge branch 'maint'

Merge remote-tracking branch 'origin/balay/fix-chkerrq-after-seterrq/maint' into maint

fix: redundant CHKERRQ() call after SETERRQ()

Craycc complained about a stray CHKERRQ after SETERRQ in plextree.c
Reported-by: Patrick Sanan <patrick.sanan@gmail.com>

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 remote-tracking branch 'origin/knepley/feature-convergence-estimator'

* origin/knepley/feature-convergence-estimator:
ConvEst: Restore the SNES to the original condition after estimation
C

Merge remote-tracking branch 'origin/knepley/feature-convergence-estimator'

* origin/knepley/feature-convergence-estimator:
ConvEst: Restore the SNES to the original condition after estimation
ConvEst: Discretization can change, so move name extraction into loop
SNES ex13: Fixed test dependencies
SNES ex13: Update to new API
ConvEst: Initialize variables
Fortran: Fixed Fortran bindings - Need custom binding for all View() to handle default viewers
ConvEst: I hate Fortran
ConvEst: Damn damn damn
ConvEst: Added Fortran type
ConvEst: Fixed spelling, fixed type
ConvEst: Fixing LAPACK type
SNES ex13: Now estimate convergence using built-in test
SNES: Allow convergence estimation using -snes_convergence_estimate
PetscConvEst: Added an object which estimates the convergence rate of a discretization
PetscDT: Turn on Fortran binding
SNES ex13: Added test output
SNES ex13: Looking at automatic convergence estimation
PetscDS: Added exact solution functions - We will use these to evaluate convergence using MMS

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

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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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PetscDS: Fix print

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

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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Merge branch 'knepley/feature-fe-kernel-scalars'

* knepley/feature-fe-kernel-scalars:
SNES ex56: Update test output
Plex ex3: Update to new point function API
PetscDS: Turn off Fortran binding

Merge branch 'knepley/feature-fe-kernel-scalars'

* knepley/feature-fe-kernel-scalars:
SNES ex56: Update test output
Plex ex3: Update to new point function API
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

Conflicts:
src/dm/dt/interface/dtfe.c

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PetscDS: Added exact solution functions
- We will use these to evaluate convergence using MMS

PetscDS: Fix update fund for new API

PetscDS: Turn off Fortran bindings for Constants