Merge branch 'master' into barry/reduce-dmsetup-da-memoryusage

Conflicts:
src/dm/examples/tests/ex15.c
src/dm/examples/tutorials/ex3.c
src/dm/impls/da/da2.c
src/dm/impls/da/da3.c

Merge branch 'master' into barry/xcode

added -ts_monitor_envelope and TSMonitorEnvelope() to track extremes of solution vector
added support to extchem.c to print maximums of species
updated sample run for extchem.c for displaying only "i

added -ts_monitor_envelope and TSMonitorEnvelope() to track extremes of solution vector
added support to extchem.c to print maximums of species
updated sample run for extchem.c for displaying only "important species"

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added TSMonitorLGSetTransform() and added transform to mole fraction in extchem.c

added -ts_lg_monitor_solution_variables and TSMonitorLGSetDisplayVariables()

changed TSMonitorLGSolutionSetLegend() to TSMonitorLGSetVariableNames()

add support for providing legends for TSMonitorLGSolution()

Merge branch 'barry/minor-draw-improvements' into jed/chem

introduce XXXViewFromOptions() and use consistently when possible

Merge branch 'knepley/example-ts-friction'

* knepley/example-ts-friction:
TS ex34: Now reproducing plots from Berkeley paper - Fixed coordinate DM screwups
DMDA: Fixed bug with 1D DMDAGetRay()

Merge branch 'knepley/example-ts-friction'

* knepley/example-ts-friction:
TS ex34: Now reproducing plots from Berkeley paper - Fixed coordinate DM screwups
DMDA: Fixed bug with 1D DMDAGetRay()
TS: Allow the DMDARay viewer to operator in LG mode - Added TSMonitorLGDMDARay() activated by -ts_monitor_lg_dmda_ray - Added TSMonitorLGCtx to TSMonitorDMDARayCtx
DMDA: Allow DMDAGetRay() to work in 1D
TS: Make TSMonitorLGCtx visible to other code
TS: Added an example of DR friction

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Merge branch 'master' into knepley/feature-dmda-section

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fi

Merge branch 'master' into knepley/feature-dmda-section

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fix for TSGetRHSMats_Private() in the creation of the Arhs and Brhs matrices
protect logging of objects (which uses global variables) with PETSC_USE_LOG
error handler API had been previously changed but this example was not updated to new API.
DMPlex: Fixed bug in coordinate permutation
PetscSection: Doc fix for permutation
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bugfix of MatCreateSeqAIJFromTriple() contributed by Nicolas Marsic <nicolas.marsic@montefiore.ulg.ac.be>
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
completed removing server code that was not removed in previous commit
removed PETSc webserver and configure package files that supported it
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
fix outdated PetscOptionsList
SNESQN: only monitor real part of dot product (fails with C++ complex)
Fix for multiple definitions in mat/color/interface/ custom fortran bindings
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/da/dageometry.c
src/dm/impls/plex/examples/tests/ex4.c
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexinterpolate.c

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Merge branch 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key

Merge branch 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
SNESQN: only monitor real part of dot product (fails with C++ complex)
Corrected the #include statement in the man pages for the PetscObjectComposedDataSet/Getwhatever routines.
DMPlex: Added doc for DMPlexGetHybridBounds()
winzip: detect if winzip is used to extract petsc.tar.gz and error out.
configure: remove self.archIndependent as its not being used. [it is used to create externalpackages/package/arch dir which is unused]
configure: fix packages using package-dir/PETSC_ARCH as out-of-source-build location Perhaps this should be changed to package-dir/build?
configure: remove dead code previously used to download BuildSystem
configure: check if compilerDefines [and compilerFixes] exist in framework before using them
configure: save/restore reconfigure.py when --with-clean is used
configure: add --with-clean option to delete buildfiles/externalpackages in PETSC_DIR/PETSC_ARCH and potential externalpackages in --with-external-package-dir/PETSC_ARCH
configure: With --with-externalpackages-dir=dir store/build packages in dir/PETSC_ARCH
Add MatSeqSBAIJSetPreallocationCSR()
configure: switch to using PETSC_DIR/PETSC_ARCH/externalpackages by updating package.py to use externalpackages.py as the externalPackagesDirProvider
configure: move dead code configureExternalPackagesDir() from petscdir.py to externalpackagesdir.py Also set PETSC_DIR/PETSC_ARCH/externalpackages as the externalpackagesdir
...

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Merge branch 'master' into barry/saws

Conflicts:
src/ksp/pc/impls/gamg/gamg.c
src/sys/classes/viewer/impls/ams/ams.c
src/sys/objects/pinit.c

TS: Allow the DMDARay viewer to operator in LG mode
- Added TSMonitorLGDMDARay() activated by -ts_monitor_lg_dmda_ray
- Added TSMonitorLGCtx to TSMonitorDMDARayCtx

TS: Make TSMonitorLGCtx visible to other code

Merge branch 'emil/ts-poststage'

* emil/ts-poststage:
Added a post-stage function for time-integrators

Merge branch 'emil/ts-rk-rehab'

Renovate explicit Runge-Kutta methods to use TSAdapt and support easy
registration of additional schemes.

* emil/ts-rk-rehab:
TSRK: remove TSRKSetTolerance because

Merge branch 'emil/ts-rk-rehab'

Renovate explicit Runge-Kutta methods to use TSAdapt and support easy
registration of additional schemes.

* emil/ts-rk-rehab:
TSRK: remove TSRKSetTolerance because we now use TSAdapt
Updated the documentation for using RK schemes with variable timesteps
Changed the default RK type to be RK3BS (Bogacki-Shampine) which has an embedded method
minor edits in rk and adding petsc math types in ex31
Added comments documenting the Dormand-Prince and Bogacki-Shampine RK methods...
Added a Boolean variable to indicate of method is FSAL
Added Dormand-Prince and Bogacki-Shampine RK schemes...
Implemented the renovated RK. The first 6 commits are squashed and the text is preserved below.

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TSRK: remove TSRKSetTolerance because we now use TSAdapt

Added a post-stage function for time-integrators

Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

ts-events: Set event direction and termination flag when the event is registered.

Also, got rid of ugly long conditional for event checking.

Merge branch 'jed/fix-ts-jacobian-linear' into maint

* jed/fix-ts-jacobian-linear:
TS: fix MSVC compiler error: non-POD member of anonymous struct
TS tests/ex3: SNESFD and TSComputeIJacobianCons

Merge branch 'jed/fix-ts-jacobian-linear' into maint

* jed/fix-ts-jacobian-linear:
TS: fix MSVC compiler error: non-POD member of anonymous struct
TS tests/ex3: SNESFD and TSComputeIJacobianConstant are incompatible
TS: fix shortcut scaling; document TSComputeIJacobianConstant limitations
TS tests/ex3: fix example and inclusion in nightlies
TS tests/ex5*: re-activate test and fix monitor interval
TS: add TSRHSJacobianSetReuse, fixes TSComputeRHSJacobianConstant

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Started incorporating the event interface in TS.

Added doc for TS_CONVERGED_EVENT

Added TS_CONVERGED_EVENT.

This flag should be set when the time stepping needs to be terminated when
an event occurs.