clang-5 fixes

fix compiler error with gcc-4.8 & complex

/sandbox/balay/petsc/include/petscmath.h:35:37: error: cannot convert ‘PetscScalar {aka std::complex<float>}’ to ‘float’ for argument ‘1’ to ‘float log10f(f

fix compiler error with gcc-4.8 & complex

/sandbox/balay/petsc/include/petscmath.h:35:37: error: cannot convert ‘PetscScalar {aka std::complex<float>}’ to ‘float’ for argument ‘1’ to ‘float log10f(float)’
#define PetscLog10Real(a) log10f(a)
^
/sandbox/balay/petsc/src/ts/utils/dmnetworkts.c:141:31: note: in expansion of macro ‘PetscLog10Real’
else yv[j] = PetscLog10Real(yv[j]);
^

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fix doc format

Publication update and minor edit. A new simple graphical monitor for DMNetwork

Add support for doing a line graph plot of TS solutions on Networks.

Each vertex and edge gets its own window that plots all the solutions for the point

Commit-type: feature
Funded-by: ECP
Project:

Add support for doing a line graph plot of TS solutions on Networks.

Each vertex and edge gets its own window that plots all the solutions for the point

Commit-type: feature
Funded-by: ECP
Project: Epidemic
/spend 4h

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Fix typos, otherwise they fail or warn in compilation with complex

doc fixes

Merge branch 'stefanozampini/feature-vecgetsubcector-cuda' into 'master'

Stefanozampini/feature vecgetsubcector cuda

See merge request petsc/petsc!3170

Merge branch 'barry/2020-09-01/fix-with-log-zero' into 'master'

Clean up examples so they run correctly without warnings configured using...

See merge request petsc/petsc!3193

fixing hardwired constants that did not work for single precision

Clean up examples so they run correctly without warnings configured using --with-log=0 and --with-info=0

Make CI pipeline linux job build with these options

Commit-type: testing-fix, style-fix, mai

Clean up examples so they run correctly without warnings configured using --with-log=0 and --with-info=0

Make CI pipeline linux job build with these options

Commit-type: testing-fix, style-fix, maintainability
/spend 1h

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DMPLEXLANDAU: fix compiler warning

/home/zampins/Devel/petsc/src/ts/utils/dmplexlandau/plexland.c: In function ‘LandauFormJacobian_Internal’:
/home/zampins/Devel/petsc/src/ts/utils/dmplexlandau/plex

DMPLEXLANDAU: fix compiler warning

/home/zampins/Devel/petsc/src/ts/utils/dmplexlandau/plexland.c: In function ‘LandauFormJacobian_Internal’:
/home/zampins/Devel/petsc/src/ts/utils/dmplexlandau/plexland.c:149:34: warning: ‘refSpaceDer[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
u_x[fOffset*dim+d] += invJ[qj * dim * dim + e*dim+d]*refSpaceDer[e];
^
/home/zampins/Devel/petsc/src/ts/utils/dmplexlandau/plexland.c:149:34: warning: ‘refSpaceDer[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized]

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PETSC_VIEWER_ASCII_VTK: deprecate, encourage use of XML

Add a Landau collision operator, based on DMPlex and PetscFE, that uses p4est. It uses the new Kokkos interface and has a separate Cuda implementation. This could be deployed as 3rd party library, bu

Add a Landau collision operator, based on DMPlex and PetscFE, that uses p4est. It uses the new Kokkos interface and has a separate Cuda implementation. This could be deployed as 3rd party library, but this is easier to deploy to ECP, among other apps.

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Turn on checkbadSource test to generate an error when found; fix all source code that causes errors

Commit-type: portability-fix, testing-fix, style-fix, feature, maintainability
/spend 1.5h

DM: Nullspace constructor should report old and new field numbers

Add calling sequence for function provided to TSSetTransientVariable
Fix other TS manual pages

Commit-type: documentation
/spend 10m
Reported-by: Kyle B. Thompson <kyle.b.thompson@nasa.gov>

ConvEst: Now use -ts_convergence_temporal 0 to check spatial convergence of a TS model
- Added argument to PetscConvEstUseTS()

Plex: Need to add BC for the solution time derivative in TS problems
- Added DMPlexInsertTimeDerivativeBoundaryValues()
- Added time derivative of the solution argument to DMAddBoundary(),
DMGetBou

Plex: Need to add BC for the solution time derivative in TS problems
- Added DMPlexInsertTimeDerivativeBoundaryValues()
- Added time derivative of the solution argument to DMAddBoundary(),
DMGetBoundary(), PetscDSAddBoundary(), PetscDSUpdateBoundary(),
PetscDSGetBoundary()

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Plex: Allow us to specify that an output vector has 0 boundary conditions
- This is for residuals

TS+Plex: Convergence estimation now working of time dependent PDEs
- Add exact solution time derivative to DS
- Put monitor in ConvEst for TS
- Fixed error determination in ConvEst for TS

Co-Authore

TS+Plex: Convergence estimation now working of time dependent PDEs
- Add exact solution time derivative to DS
- Put monitor in ConvEst for TS
- Fixed error determination in ConvEst for TS

Co-Authored-By: Brad Aagaard <baagaard@usgs.gov>

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Plex: Move FEM assembly from dmplexsnes.c to plexfem.c, and fix DMCreateMassMatrix()
- Create regular mass matrix if we pass in the same DM to DMCreateMassMatrix()
- Changed DMPlexSNESGetGeometryFVM(

Plex: Move FEM assembly from dmplexsnes.c to plexfem.c, and fix DMCreateMassMatrix()
- Create regular mass matrix if we pass in the same DM to DMCreateMassMatrix()
- Changed DMPlexSNESGetGeometryFVM() to DMPlexGetGeometryFVM()
- Changed DMPlexSNESGetGradientDM() to DMPlexGetGradientDM()

Co-authored-by: Mark Adams <mfadams@lbl.gov>

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DM: Now DS stores exact solution functions for everything
- Added DMComputeExactSolution()
- DMSNES/TSCheck*() now use DS for functions