TS: Add TSGetExactFinalTime()

Merged in dalcinl/ts-solve (pull request #722)

Proper support for successive TSSolve() calls

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

TS: Add TSGetStepNumber() and TSSetStepNumber()

* Remove TSGetTotalSteps()
* Remove TSGetTimeStepNumber()

TS: Add TS{Set|Get}MaxSteps() and TS{Set|Get}MaxTime()

Merge remote-tracking branch 'origin/hongzh/ts-direct-sa'

Refactor forward SA

Renamed a TS public function (TSAdjointComputeCostIntegrand->TSComputeCostIntegrand); implementations have been simplifed.

add the forward SA capability for Theta methods

-Support the calculation of the gradients of integrals.
-The integrals are treated as additional differential equations.
-Trajectory sensitivities

add the forward SA capability for Theta methods

-Support the calculation of the gradients of integrals.
-The integrals are treated as additional differential equations.
-Trajectory sensitivities to parameters and initial values are handled separatedly.
-Two examples are included: van der Pol and a power grid problem.
-The forward SA modle is implemented in a separate file because ts.c is already a monster and it is still growing.
-TSAdjointComputeDRDYFunction is always required.

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Merge branch 'master' into knepley/fix-fe-default

* master: (297 commits)
Bib: Added refs and fixed one
Doc: Fixed formatting problems for MatCreateAIJ() manual page.
Add to PCSOR manual page

Merge branch 'master' into knepley/fix-fe-default

* master: (297 commits)
Bib: Added refs and fixed one
Doc: Fixed formatting problems for MatCreateAIJ() manual page.
Add to PCSOR manual page information about convergence testing when using KSPRICHARDSON
SNES ex5: Restore old output since this breaks an example I have
Noted that some Cray XC systems will use 'aprun' instead of 'srun'. Thanks to Herr Doktor Hong Zhang for this suggestion.
Added example configure script for Cray XC40 with KNL processors (e.g., NERSC Cori).
Fix possible sprintf -Wformat-overflow
PetscMalloc2-7: fix -Wint-in-bool-context for GCC 7
SNES ex5: make boundary condition handling consistent for symmetry
SNES ex5: use L2 norm and *_monitor_short for output
SNES ex5: the L^2 norm scales with the l^2 norm over sqrt(N)
SNES ex5: refactor MMS capability to avoid extreme code duplication
Documentation fix: typo in PetscLogStageRegister manual page.
nodes -> vertices
rename DMNetworkGetComponentTypeOffset -> DMNetworkGetComponentKeyOffset
rename DMNetworkGetConnectedNodes() -> DMNetworkGetConnectedVertices()
Jacobians for adjoints for explicit methods and constant Jacobians never got initialized
fix complex build error
fix build failure with fortran interface
fix compile error with cdc753b64c658d532d7813e942002e67025667a6
...

Conflicts:
src/snes/examples/tutorials/ex13.c
src/snes/examples/tutorials/ex62.c
src/snes/examples/tutorials/ex69.c

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Merge branch 'master' into knepley/feature-rigid-bodies

* master: (204 commits)
windows fixes
revert this change as a relavent fix is already in origin/knepley/fix-ex-types
regenerate output l

Merge branch 'master' into knepley/feature-rigid-bodies

* master: (204 commits)
windows fixes
revert this change as a relavent fix is already in origin/knepley/fix-ex-types
regenerate output log for snes_tutorials-ex62_fetidp_3d_tet that got corrupted in 188e10d6f1cffa866ec0197053a0e55fa4e7da41
fix opensolaris build error with --with-log=0 Undefined first referenced symbol in file PetscLogEventGetPerfInfo arch-opensolaris-misc/tests/src/dm/impls/plex/examples/tests/ex9.o
fix warnings on windows C:\cygwin64\home\petsc\PETSC~1.CLO\src\tao\examples\TUTORI~1\ex1.c(217): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)'
disable example with absoft (due to fixed/free form limit)
c89 fixes
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
Plex ex19: Remove unneeded code
Plex: Fix projection when we have a dmAux which is a domain boundary - If we are projecting on a lower dimension thing (effectiveHeight > 0), then we need to get the space and dual space on this subcell - The tabulation needs to be in the right dimension for both dm and dmAux
PetscFE: Added height subspaces to PetscFE - Added PetscFEGetHeightSubspace() - Added array in struct
PetscDualSpace: Small cleanup of parameter name
PetscSpace: Added height subspaces for PetscSpace - Added PetscSapceGetHeightSubspace() and member function - Added subspaces array
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 some minor style issues
Extend AMS/ADS to support high-order element.
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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 remote-tracking branch 'origin/hongzh/adjoint-parallel'

Merge branch 'scott/test-datafiles-fix' of https://bitbucket.org/petsc/petsc into scott/test-datafiles-fix

Change TSSetCostIntegrand interface

Originally PETSc creates a sequential vec to hold the integral values for users. This is ok for common senarios where there is just one integral to calculate. Whe

Change TSSetCostIntegrand interface

Originally PETSc creates a sequential vec to hold the integral values for users. This is ok for common senarios where there is just one integral to calculate. When there are multiple integrals (e.g. coming from multiple cost functions), one might want to do it in parallel. The new interface allows users to provide their own vec to support parallelization. If the users do not provide one, a sequential vec will be created.

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Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
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
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

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Merge branch 'master' into stefano_zampini/feature-fetidp-ex69

Merge branch 'master' into knepley/feature-plex-boundary-values

* master: (487 commits)
Bib: More refs
Fixed errors in the manuals and ts_glee source code doc
fix bug to enable '-xxx_via [alg]

Merge branch 'master' into knepley/feature-plex-boundary-values

* master: (487 commits)
Bib: More refs
Fixed errors in the manuals and ts_glee source code doc
fix bug to enable '-xxx_via [alg]' to showup in '-help' Reported-by: Mark Adams <mfadams@lbl.gov>
Plex: Remove dead code
TS tutorials ex11: remove unused functions
TSAdapt: Set TSADAPTNONE as default adapt type
DMPlex: missed viewer change in synchronized output
Revert "Merge branch 'hzhang/ts-ex9busdmnetwork'"
TSAdapt: Update changes/dev.html
TSAdapt: Set default type for TSGLEE
TS tutorials ex11: make work with complex scalars
Bib: Added ref
TS ex18: Fix initializer
TS ex11: Fix M_PI
Plex ex1f90: FUCK FORTRAN
f2cblaslapack: remove duplicate xerbla.o and xerbla_array.o from lapack [they are already in blas]
TSAdapt: Refactor handling of default adapt type
TSAdapt: Update changes/dev.html
TSAdapt: Update manual
TSAdapt: Refactor interface and implementations
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Merged in dalcinl/ts-adapt-default-type (pull request #674)

TSAdapt: Refactor handling of default adapt type

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

TSAdapt: Refactor handling of default adapt type

* Let TS subtypes state its preference for adaptivity
* Methods without embedded error estimators prefer TSADAPTNONE
* If not set, use TS_EXACTFINALT

TSAdapt: Refactor handling of default adapt type

* Let TS subtypes state its preference for adaptivity
* Methods without embedded error estimators prefer TSADAPTNONE
* If not set, use TS_EXACTFINALTIME_MATCHSTEP when using adaptivity

* Remove command line option -ts_theta_adapt
* Use `-ts_adapt_type basic` to turn on adaptivity in TSTHETA

* Remove command line option -ts_alpha_adapt
* Remove routine TSAlphaUseAdapt() and TSAlpha2UseAdapt()
* Use `-ts_adapt_type basic` to turn on adaptivity in TSALPHA/TSALPHA2

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Merged in dalcinl/refactor-ts-adapt (pull request #669)

TSAdapt: Refactor interface and implementations

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

TSAdapt: Refactor interface and implementations

* Move the handling of step limits, clipping factors, and safety factors
to the base TSAdapt type to simplify implementation of subtypes.
* Add TSAd

TSAdapt: Refactor interface and implementations

* Move the handling of step limits, clipping factors, and safety factors
to the base TSAdapt type to simplify implementation of subtypes.
* Add TSAdapt{Set|Get}Clip() and remove TSAdaptBasic{Set|Get}Clip().
* Add TSAdapt{Set|Get}Safety() to set safety factors.
* Add TSAdaptGetStepLimits().

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TSAdapt: Add TSAdaptGetType() and add/fix Fortran bindings

Merge branch 'master' into knepley/feature-plex-torus

* master: (174 commits)
Bib: Another ref
Increase patchlevel to 3.7.6
Explicitly listing the LTO library causes difficulties on MacOS so a

Merge branch 'master' into knepley/feature-plex-torus

* master: (174 commits)
Bib: Another ref
Increase patchlevel to 3.7.6
Explicitly listing the LTO library causes difficulties on MacOS so avoid it
TSBDF: Update changes/dev.html
Added Fortran TaoType and TaoLineSearchType definitions
Add Fortran TaoType and TaoLineSearchType definitions
setblocksize for iscol_sub
TSBDF: Use standard TS API and options to control adaptivity
Bib: More refs and a correction
SNESTest: Bug-fix in SNESTest when threshold printing option is turned on.
fix warning and valgrind complains reported by the nightly tests
Section+Doc: Small doc fix
pflotran: switch to using the new upstream git repo
DMPlex: Error if attempt to partition a distributed graph with Chaco
fix complex build error
fix complex build
PetscError() did not properly copy over the specific error message when error type was PETSC_ERROR_INITIAL
TSAdapt: Refactor handling of the always_accept flag
Additional clarification for MatMeshToCellGraph() manual page
optimize MatCreateSubMatrix_MPIAIJ() by merging check of sameXXXDist() into one MPI_AllReduce
...

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

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Merged in dalcinl/fix-bdf-adapt (pull request #667)

TSBDF: Use standard TS API and options to control adaptivity

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

Merge branch 'dalcinl/fix-bdf-adapt' into barry/update-petscfileretrieve