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Fix allfortranstubs rule to rm generated files from correct directory, not outdated location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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Merge commit 'd47bf9aaf1e5266cc3f0ff499f934c85788965a9' into jed/fix-matcreatempibaij/maint

Obtain changed (v3.5) handling of MatMPIBAIJSetPreallocationCSR to match
documentation.

typo
Reported-by: Jaroslaw Piwonski (CAU) <jpi@informatik.uni-kiel.de>

Merge remote-tracking branch 'origin/balay/fix-quad-complex-from-cxx'

fix quad/cxx compile warnings/errors [with gcc-7.1/fedora]
Also add PetscRoundReal()

fix arch-linux-opt-cxx-quad build errors

quad: fix for using a quad/c/complex build from c++ user code

Reported-by: Michael Gegg <michael.gegg@tu-berlin.de>

Merge branch 'tisaac/fix-cmplx'

* tisaac/fix-cmplx:
PetscCMPLX(): remove use of CMPLX and CMPLXH

Merged in dalcinl/math-isinf-isnan (pull request #733)

Math: Refactor and fix Inf/NaN test routines

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

PetscCMPLX(): remove use of CMPLX and CMPLXH

You'd think that a compiler that alread makes the mistake of defining
CMPLX when compiling in c89 mode would at least let you use CMPLX in c89
mode. But

PetscCMPLX(): remove use of CMPLX and CMPLXH

You'd think that a compiler that alread makes the mistake of defining
CMPLX when compiling in c89 mode would at least let you use CMPLX in c89
mode. But clang for osx has other ideas.

Reported-by: Barry Smith <bsmith@mcs.anl.gov>

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Math: Refactor IsInf/IsNan checker routines

* Add PetscIsInfReal() checker with `a && a/2 == a` as fallback.
A separate checker for infinity is useful elsewhere to distinguish
between infinitiy

Math: Refactor IsInf/IsNan checker routines

* Add PetscIsInfReal() checker with `a && a/2 == a` as fallback.
A separate checker for infinity is useful elsewhere to distinguish
between infinitiy and not-a-number floating point values.
* Reimplement PetscIsInfOrNanReal() using IsInf and IsNan checkers.

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Math: Fix PetscIsXXX{Real|Scalar}() to return PetscBool

Also fix IsNan fallback to use `a != a`, otherwise it gives the wrong result
for infinity floating point input values.

Merged in dalcinl/collective-check (pull request #732)

Prevent -Wfloat-equal warnings in error-checking macros

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

Math: Add PetscEqualReal() and PetscEqualScalar()

These are both equivalent to `a == b`. Should be used to prevent
compilers from emitting floating point comparison warnings
(e.g. GCC's `-Wfloat-equ

Math: Add PetscEqualReal() and PetscEqualScalar()

These are both equivalent to `a == b`. Should be used to prevent
compilers from emitting floating point comparison warnings
(e.g. GCC's `-Wfloat-equal` flag) in PETSc header files or user code.

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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/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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protect '-' in macros

Thanks-to: Lisandro Dalcin <dalcinl@gmail.com>

fix compile error with --download-petsc4py

Thanks-to: Lisandro Dalcin <dalcinl@gmail.com>

src/petsc4py.PETSc.c: In function ‘PyObject* __pyx_pf_8petsc4py_5PETSc_3TAO_60computeVariableBounds(PyPetsc

fix compile error with --download-petsc4py

Thanks-to: Lisandro Dalcin <dalcinl@gmail.com>

src/petsc4py.PETSc.c: In function ‘PyObject* __pyx_pf_8petsc4py_5PETSc_3TAO_60computeVariableBounds(PyPetscTAOObject*, PyPetscVecObject*, PyPetscVecObject*)’:
/home/balay/petsc/include/petscmath.h:637:53: error: no match for ‘operator/’ (operand types are ‘PetscScalar {aka std::complex<double>}’ and ‘int’)
#define PETSC_INFINITY PETSC_MAX_REAL/4
/home/balay/petsc/include/petscmath.h:638:39: note: in expansion of macro ‘PETSC_INFINITY’
#define PETSC_NINFINITY -PETSC_INFINITY
^~~~~~~~~~~~~~
src/petsc4py.PETSc.c:198294:89: note: in expansion of macro ‘PETSC_NINFINITY’
__pyx_t_1 = __pyx_f_8petsc4py_5PETSc_CHKERR(VecSet(__pyx_v_xl->vec, ((PetscScalar)PETSC_NINFINITY))); if (unlikely(__pyx_t_1 == -1)) __PYX_ERR(38, 315, __pyx_L1_error)

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Merged in dalcinl/macro-real-constant (pull request #689)

Add macro PetscRealConstant

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

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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Add macro PetscRealConstant() for floating point literals