allow adjoint integration over split time intervals

Allow using -ts_save_trajectory -tstrajectory_type singlefile

One now passes the nullspace in the matrix for a linear system as the first Amat argument to KSPSetOperators, SNESSetOperators, TSSetIJacobian() not the second pmat argument

This allows nesting of K

One now passes the nullspace in the matrix for a linear system as the first Amat argument to KSPSetOperators, SNESSetOperators, TSSetIJacobian() not the second pmat argument

This allows nesting of KSP/PC where the matrix is singular but the matrix passed to construct the preconditioner (the pmat) is not singular

Reported-by: Stephan Kramer <s.kramer@imperial.ac.uk>

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Merge branch 'barry/fix-petscobjectviewfromoptions'

changed second argument of PetscObjectViewFromOptions() to PetscObject and all routines that use this routine

fix TSAdjointSetUp()

fix descriptions for TSAdjointSolve() and TSAdjointStep()

trajectory now saves current time

Merge branch 'emil/fix-ts-dae-rebased-v3'

Revert "fixed bad merge into master"

This reverts commit 781194b94830bca829637b611b5b26e16b855a34.

fixed bad merge into master

Merge branch 'emil/fix-ts-dae-rebased-v3'

Merge branch 'knepley/feature-composable-callbacks'

* knepley/feature-composable-callbacks:
TS ex28: Updated to new kernel interface
SNES ex62: Updated to new kernel interface
SNES ex12: Updat

Merge branch 'knepley/feature-composable-callbacks'

* knepley/feature-composable-callbacks:
TS ex28: Updated to new kernel interface
SNES ex62: Updated to new kernel interface
SNES ex12: Updated to new kernel interface
Plex ex3: Updated to new kernel interface
PetscDS: Added NfAux argument to FE kernels
PetscDS: Change signature of Jacobian functions to include the shift a for dF/dU_t
PetscDS: Cleanup - Removed silly consts - Removed unused vars - Fixed declarations
TS: Took extra space out of default monitor
TS ex18: Updated Riemann and pointwise interface
TS ex11: Updated Riemann interface
PetscDS: Added dimension and num fields to Riemann interface
PetscDS: Added missing declarations
SNES ex62: Updated to new pointwise interface
SNES ex12: Updated to new pointwise function interface
Plex+FEM: Update to new pointwise function interface - Basically need to also pass in field offsets
PetscDS: Change interface to pointwise functions - This is intended to make pointwise functions composable - Make function typedefs public - Store component and derivative offsets since they will be provided to the pointwise functions

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ts-isdiff: Added a note in TSSetTolerances.

Added a note on how to use TSSetTolerances if one wishes to have the local truncation error
computed only for the differential part. (same as what ts->is_

ts-isdiff: Added a note in TSSetTolerances.

Added a note on how to use TSSetTolerances if one wishes to have the local truncation error
computed only for the differential part. (same as what ts->is_diff did.)

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ts-isdiff: Removed the index set for differential variables from TS.

TS: Took extra space out of default monitor

TSClone: fix c89 syntax

TSClone: update wrt PetscHeaderCreate() change in master. [so as to work in next]

fix a bug in cost integral evaluation for explicit solvers

Merge branch 'hongzh/evaluate-cost-integral-in-fwd'

PetscHeaderCreate: Shorten argument list and optimize memory allocation

* Remove type arguments from the macro
* Use a single memory allocation call instead of three

fixed missing CHKERRQ() detected by clang's --analyze

updated PETSc directory layout to match standard packaging strategies

include/petsc finclude,private,mpiuni
lib/petsc conf
bin/petsc*

change the name for the flag costintgraldone in ts

Change names for TSAdjointSetCostXXX and TSAdjointGetCostXXX