Merge branch 'pr1353/jpusztay/feature-swarm-symplectic-example/master' [PR #1353]

* pr1353/jpusztay/feature-swarm-symplectic-example/master:
This pull request contains example usage of a DMSwarm wit

Merge branch 'pr1353/jpusztay/feature-swarm-symplectic-example/master' [PR #1353]

* pr1353/jpusztay/feature-swarm-symplectic-example/master:
This pull request contains example usage of a DMSwarm with symplectic (basic) integrators in TS.
ex4 demonstrates a spring as seen with the hamiltonian example in TS, but with two particles.
ex5 demonstrates particles orbiting a central point, and the energy conservation of tsbsi type 2 in comparison to tsbsi type 1, and Euler.
Swarm visualization was also implemented in ts as a monitor option, which is contained in this PR as well because ex5 demonstrates its functionality.

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PetscStackCallStandard: use local error code

Fix PETSc for unused/set-but-not-used variables

ts: changed sp plot inputs to PetscReal from PetscScalar

Fixed memory cleanup

ex5: reduce max steps for shorter test time. ts: doc changes for spswarm

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

ts.c: added documentation to swarm monitor

ex4: cleaned up and formatted outputs

Merged petsc/petsc into master

Merged jpusztay/feature-ts-swarm-visualization into jpusztay/feature-swarm-symplectic-example

Fixes to ex5

Merge branch 'master' into knepley/feature-snes-patch

Added SP context to TS and implemented swarm monitor

Merged petsc/petsc into master

Merged petsc/petsc into master

Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patc

Merge branch 'master' into knepley/fix-plex-partition-parallel

* master: (414 commits)
very small updates to users manual
syntax is define(XXX) in examples tests not defined(XXX)
Increase patchlevel to 3.10.3
petsc4py: updat to latest maint snapshot with SNESTEST updates
Fix link for CUDA example in PETSc from GPUs.html page Minor fixes to installation instructions
Mat: Fixed types in Pardiso interface
Converted example comment to latex
This example crashes (for unknown reasons, probably related to the handling of extended derived types passed as arguments) with the PGI Fortran compiler
Remove outdated requires: from top of several examples
remove outdated test requires: command from top of source file
Fix the documentation for -ksp_gmres_cgs_refinement_type
Commit f20c2d659b168217cb455989f28afe052d71a64c broke lex.py so the users manual was no longer being built. There reverted the changes to lex.py
Plex: Add PetscPartitioner to fort list Suggested-by: Jiaoyan Li <Jiaoyan.Li@inl.gov>
Doc: Fix spelling Suggested-by: Manuel Colera Rico <m.colera@upm.es>
Mat ex88: check in double or quad precision only
Fix error with PetscComplex when PETSc is compiled with C and used in C++
configure: fix typo endwith -> endswith
Sys ex23: Migrated to ts_max_time in yaml file as well.
AO ex5: Fixed missing CHKERRQ();
Mat test ex88: add tests for MatMultAdd and MatMultTranposeAdd
...

Conflicts:
src/dm/impls/plex/examples/tests/ex12.c

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Merge branch 'barry/deprecate-ts-final-time'

Merge branch 'master' into knepley/feature-snes-patch

Not sure if this has done the right thing because there are no tests
yet. Also, the fortran stubs break (it doesn't know what to do with
SNESCo

Merge branch 'master' into knepley/feature-snes-patch

Not sure if this has done the right thing because there are no tests
yet. Also, the fortran stubs break (it doesn't know what to do with
SNESCompositeType), and I don't know how to fix it.

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Merged petsc/petsc into master

Mark -ts_final_time as deprecated for -ts_max_time

Commit-type: documentation
Reported-by: Sophie Blondel <sblondel@utk.edu>
Thanks-to: Emil Constantinescu <emconsta@mcs.anl.gov>

Merged petsc/petsc into master

Merge branch 'stefano_zampini/cherrypick-from-continuous-adjoint' [PR #1250]

* stefano_zampini/cherrypick-from-continuous-adjoint:
Few improvements from the continuous adjoint branch
This branch ext

Merge branch 'stefano_zampini/cherrypick-from-continuous-adjoint' [PR #1250]

* stefano_zampini/cherrypick-from-continuous-adjoint:
Few improvements from the continuous adjoint branch
This branch extracts few things that are in the continuous adjoint branch that should go into PETSc

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TS: added interface function to reset the internal trajectory object

this calls TSTrajectoryDestroy since TSTrajectoryReset may not free diskspace

Update examples

TS: fix few cases for improper scaling of matrices in Jacobian computations

Make TSGetRHSMats_Private PETSC_INTERN

TSGetStages: make each return argument optional