TSBDF: Use standard TS API and options to control adaptivity

* Adaptivity is enabled by default
* Use "-ts_adapt_type none" to turn off adaptivity
* Remove the TSBDFUseAdapt() routine
* Remove the -

TSBDF: Use standard TS API and options to control adaptivity

* Adaptivity is enabled by default
* Use "-ts_adapt_type none" to turn off adaptivity
* Remove the TSBDFUseAdapt() routine
* Remove the -ts_bdf_adapt option

show more ...

Merged in dalcinl/refactor-ts-adapt (pull request #665)

TSAdapt: Refactor handling of the always_accept flag

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Jed Brown <jed@59a2.org>

TSAdapt: Refactor handling of the always_accept flag

* Add TSAdaptSetAlwaysAccept()
* Store the always_accept flag in the base TSAdapt type
* Fix/refactor bad printf args in TSAdaptView()
* Fix TSAd

TSAdapt: Refactor handling of the always_accept flag

* Add TSAdaptSetAlwaysAccept()
* Store the always_accept flag in the base TSAdapt type
* Fix/refactor bad printf args in TSAdaptView()
* Fix TSAdaptSetFromOptions() to use TSAdaptSetXXX()

show more ...

Merge branch 'master' into knepley/feature-plex-tests-new

* master: (108 commits)
Bib: Added ref
Bib: Updated reference
Bib: Updated reference
Work around problems with Apple Xcode 8.3 and h

Merge branch 'master' into knepley/feature-plex-tests-new

* master: (108 commits)
Bib: Added ref
Bib: Updated reference
Bib: Updated reference
Work around problems with Apple Xcode 8.3 and handling of rpath argument with gfortran
help menu update for MatCreateSubMatrices() Reported-by: Brad Aagaard <baagaard@usgs.gov>
fix flops for PCApply_PBJacobi_1 and PCApply_PBJacobi_7 Reported-by: Pierre Jolivet <pierre.jolivet@enseeiht.fr>
TSRK: Fix FSAL optimization to not skip update and check or stages.
Travis-CI: Workaround too long TMPDIR in macOS with Open MPI
test: Fix type mismatch in KSP test.
test: Fix warnings from gfortran -Wconversion (OS X, Homebrew build)
MPIUNI: Silence GCC -Wconversion warnings
Fortran: Add error checking for incorrect PETSC_NULL_XXX argument when expecting function
fix test output per changes in 517c9301b2e9239931bfd644803fd6bb859387ea
MUMPS: update to version 5.1.1 with opensolaris compile fixes
TSRK: Mention 5BS in the changelog.
TSRK: Mention the new 5BS scheme in the manual.
fix 'unused variable' warning
Remove unused code
added hbw_realloc
fixed undefined ptr
...

Conflicts:
config/BuildSystem/config/packages/med.py

show more ...

Merged in dalcinl/feature-ts-rk (pull request #653)

TSRK: Enhancements and new BS(4,5) scheme

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

Merge remote-tracking branch 'origin/barry/improve-ts-trajectory-viz'

TSRK: Add the Bogacki-Shampine (4,5) RK scheme.

Add TSTrajectorySetTransform() to allow transforming the solutions before saving

Updates extchem.c to is TSTrajectorySetTransform() to save the trajectory in mole fraction

Funded-by: IMEX
Project:

Add TSTrajectorySetTransform() to allow transforming the solutions before saving

Updates extchem.c to is TSTrajectorySetTransform() to save the trajectory in mole fraction

Funded-by: IMEX
Project: IMEX
Thanks-to: Shashikant M. Aithal <aithal@cels.anl.gov>

show more ...

A variety of improvements/fixes for saving and accessing trajectories.

Fixed bugs in PetscReadBinaryTrajectory.m
Added PetscBinaryIOTrajectory.py to read in trajectories in Python
Fixed bug in all t

A variety of improvements/fixes for saving and accessing trajectories.

Fixed bugs in PetscReadBinaryTrajectory.m
Added PetscBinaryIOTrajectory.py to read in trajectories in Python
Fixed bug in all the trajectory file saving routines that used PETSC_COMM_WORLD instead of the MPI_Comm associated with the TS object.

Funded-by: IMEX
Project: adjoints
Time: 2 hours
Reported-by: Shashikant M. Aithal <aithal@cels.anl.gov>

show more ...

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_A

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_ATTRIBUTEALIGNED flag to makefile
PCSetUp_SVD() used incorrect matrix for matrix size in parallel, also need to skip LAPACK call if matrix size is zero
strumpack: update to latest version 1.0.4
Remove valgrind warning about MPI_Allreduce() with uninitialized data
sed for test output that has atol convergence with quad precision
updated ex1_nest tests
fixed incorrect key value
fix: bad merge a69d34a
test: move runex78 to TESTEXAMPLES_C_NOTSINGLE
build: fix warnings
sys: update test to produce same result - irrespective of debug/opt build - and presence of ~/.petscrc
sys: src/sys/examples/tests/ex30.c -> src/sys/examples/tests/ex32.c to avoid conflict in master
Sed output, since quad precision reduces below atol on these tests
remove automatically generated matrix names from test output files since can be different
Fixes for MatMPIXXXSetPreallocation(), they were not reentrant, since they kept the information used for matrix-vector products
GAMG: fix PCView_GAMG() format - and update output/ex56_0.out
superlu_dist: 64-bit-indices fix https://github.com/xiaoyeli/superlu_dist/issues/4
Add SNESSetDivergenceTolerance / -snes_divergence_tolerance.
fixed unit read in Plex
...

show more ...

Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/featu

Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/feature-pcbddc-saddlepoint
that prevents me to smoothly merge stefano_zampini/feature-convert-matnest-matis into next.

This will also facilitate merging stefano_zampini/feature-pcbddc-saddlepoint into master

Conflicts:
src/docs/website/documentation/changes/dev.html

show more ...

Merge branch 'emil/ts-glee'

Added new TS eror norms that use the error directly, added new example ODE in ex31, fixed interface comments/doc. Fixed TSAdapt glee.

modified TSGetTime error to include an index that indicates when to estimate the error.

fixed warning and added citation for glee

extended the TS weighted error norm to compute the norms relative to absolute and relative tolerances separatelly

rebasing TS/GLEE to current master

Setting up TSAdaptGlee

TS: Created an interface to initialize the time integrator error to a specific value (for restarts)
TSGLEE: Implemented the initialization of the error/auxiliary solution

TS: created interfaces for TSGetAuxSolution, and TSGetTimeError
TSGLEE: Implemented TSGetAuxSolution, and TSGetTimeError, also TSGetSolutionComponents return all r components, not r-1

TSGLEE, TS: Renamed TSGetAuxSolution to TSGetSolutionComponents

TSGLEE: fixed the computing of solution with embedded methods, needed by TSAdapt.

Adding the first implicit GLEE method based on extrapolated backward Euler

TS,TSGLEE: declared the TSGetAuxSolution in header file, and fixed its implementation for TSGLEE

TSGLEE: Implemented the General Linear methods with Error Estimation