Plex: Fix coordinates for submesh projection

Merge remote-tracking branch 'origin/barry/remove-petscdatatype-dmgetworkarray'

Remove use of PetscDataType from DMGetWorkArray() and one absurd usage

Part of process of removing PetscDataType from PETSc since it duplicates MPI_Datatype
Commit-type: style-fix
Thanks-to: Jed Bro

Remove use of PetscDataType from DMGetWorkArray() and one absurd usage

Part of process of removing PetscDataType from PETSc since it duplicates MPI_Datatype
Commit-type: style-fix
Thanks-to: Jed Brown <jed@jedbrown.org>

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Plex: Now pass affected components through DMPlexVecSetFieldClosure_Internal()
- I only changed the BC update function

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/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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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 subc

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

show more ...

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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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-project-submesh'

* knepley/feature-plex-project-submesh:
Plex: Fixing insertion of boundary values - If we have a dmAux that is a boundary, we need minHeight = 1

Merge branch 'knepley/feature-plex-project-submesh'

* knepley/feature-plex-project-submesh:
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
Plex: Submeshes should set the embedding dimension
DM: DMClone() should propagate the embedding dimension
Plex: Point projection functions should be passed the effective height - This makes projection over a boundary mesh work
DMProject: If dmAux is a sub mesh, get correct mapped point corresponding to p
Plex: Choose correct dual space for sub meshes
Plex: Allow projection to work for submeshes of lower dimension

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

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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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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

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

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 con

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

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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: Point projection functions should be passed the effective height
- This makes projection over a boundary mesh work