change names for the quadrature term in the cost function

working on the quadrature function

add support for sensitivity w.r.t. parameters (mu)

lambda as an array evolve simultaneously

TSStepAdj_RK added. Now users only need to provide RHSJacobian
New Features:
1. Checkpointed data go to TS->vec_sol, RK->Y directly, a forward run can be easily performed at any time, leaving room fo

TSStepAdj_RK added. Now users only need to provide RHSJacobian
New Features:
1. Checkpointed data go to TS->vec_sol, RK->Y directly, a forward run can be easily performed at any time, leaving room for the switch between forward run and reverse run;
2. Adjoint sensivitiy analysis use a new state TS->vec-sensi, which can be intialized by TSSetSensitivity() and fetched by TSGetSensitivity();
3. Variables storing stages and temprary vectors of reverse run are defined in the TSRK context, e.g. VecDeltaLam and VecSensiTemp.

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New features:

1. Use one TS object for both forward run and backward run
2. Adjoint coefficients are computed based on the forward method without registering new schemes
3. Take advantage of the for

New features:

1. Use one TS object for both forward run and backward run
2. Adjoint coefficients are computed based on the forward method without registering new schemes
3. Take advantage of the formal adjoint for TSRK methods with nonzero b or that only the last element of b is 0.
4. Users need to call TSSolve() twice with the second one preceded by a function swithcing TS to reverse mode.

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SA for van der Pol

stage values can be checkpointed now

Merge branch 'barry/experiment'

Merge branch 'tisaac/feature-gamg-extensible' into barry/experiment

Conflicts:
src/ksp/pc/impls/gamg/gamg.h

Merge branch 'knepley/feature-dmts-check'

* knepley/feature-dmts-check:
Plex+TS: Fixed signature of DMTSCheckFromOptions()
PetscDS: Fixed error message
Xdmf: Fix time
DMTS: Add context argum

Merge branch 'knepley/feature-dmts-check'

* knepley/feature-dmts-check:
Plex+TS: Fixed signature of DMTSCheckFromOptions()
PetscDS: Fixed error message
Xdmf: Fix time
DMTS: Add context argument to DMTSCheckFromOptions()
DMTS: DMTSCheckFromOptions() now splits the norm by field
DMTS: Added DMTSCheckFromOptions() - This executes a bunch of checks for the residual and Jacobian which are useful for verification
DM: Allow user to view default section when it is created
PetscFV: Missing destroy
SNES: Added SNESSetSolution() - This was necessary to test TS without solving

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Merge branch 'knepley/feature-dmts-check' into knepley/feature-combined-tabulation

* knepley/feature-dmts-check:
Plex+TS: Fixed signature of DMTSCheckFromOptions()

Plex+TS: Fixed signature of DMTSCheckFromOptions()

simplify option object names

Merge branch 'knepley/feature-dmts-check' into knepley/feature-combined-tabulation

* knepley/feature-dmts-check:
PetscDS: Fixed error message
Xdmf: Fix time
DMTS: Add context argument to DMTSC

Merge branch 'knepley/feature-dmts-check' into knepley/feature-combined-tabulation

* knepley/feature-dmts-check:
PetscDS: Fixed error message
Xdmf: Fix time
DMTS: Add context argument to DMTSCheckFromOptions()
DMTS: DMTSCheckFromOptions() now splits the norm by field
DMTS: Added DMTSCheckFromOptions() - This executes a bunch of checks for the residual and Jacobian which are useful for verification
DM: Allow user to view default section when it is created
PetscFV: Missing destroy
SNES: Added SNESSetSolution() - This was necessary to test TS without solving

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Merge branch 'knepley/feature-dmts-check' into knepley/feature-ts-fem+fvm-example

* knepley/feature-dmts-check:
PetscDS: Fixed error message
Xdmf: Fix time
DMTS: Add context argument to DMTSCh

Merge branch 'knepley/feature-dmts-check' into knepley/feature-ts-fem+fvm-example

* knepley/feature-dmts-check:
PetscDS: Fixed error message
Xdmf: Fix time
DMTS: Add context argument to DMTSCheckFromOptions()
DMTS: DMTSCheckFromOptions() now splits the norm by field
DMTS: Added DMTSCheckFromOptions() - This executes a bunch of checks for the residual and Jacobian which are useful for verification
DM: Allow user to view default section when it is created
PetscFV: Missing destroy
SNES: Added SNESSetSolution() - This was necessary to test TS without solving

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DMTS: Add context argument to DMTSCheckFromOptions()

DMTS: Added DMTSCheckFromOptions()
- This executes a bunch of checks for the residual and Jacobian which are useful for verification

Merge branch 'master' of bitbucket.org:petsc/petsc into mark/gamg-crs-ksp2

moved PetscOptionsObject from global variable to local variable in functions

mv include/finclude to include/petsc-finclude for namespacing in installs

mv include/finclude to include/petsc-finclude for namespacing in installs

Remove XXXRegisterAll() from public interface

This means we are relying on packages to be well behaved, to set
themselves up properly. Passes testexamples in my builds (haven't tried
complex).

Remove XXXRegisterAllCalled from public interface.

All XXXRegisterAll() methods are now idempotent, so a boolean indicating
whether they can be called or not is no longer necessary.

Merge branch 'master' into knepley/fix-configure-petsc-dep

* master: (210 commits)
error out on special cases where DMLocalToGlobal_DA won't work
remove unneed uses of local DM vectors and DMLoc

Merge branch 'master' into knepley/fix-configure-petsc-dep

* master: (210 commits)
error out on special cases where DMLocalToGlobal_DA won't work
remove unneed uses of local DM vectors and DMLocalToGlobalBegin/End in examples removed to prevent cut and paste repeats of their use
openmpi: update to version 1.8.3
added more movies and pubs
more movies
MatGetDiagonalBlock() can be called before matrix is assembled
added a couple more movies/images
PetscLogEventGetId() was missing public prototype
simply output from make streams benchmark test
c2html: fixup so that C2HTML make variable is set [similar to cmake.py]
chaco: current blas test does'nt work with Cray CC [which automatically links with blas] and linux - where -lm needs to be listed explicitly. Switch the test to check if we are using PETSc modifled chaco
builddist: always install c2html/sowing
argonne logo for users manual cover
Remove PETSC_HAVE_CUSP_SMOOTHED_AGGREGATION, use PETSC_HAVE_CUSP instead.
mpich: use older tarball with cygwin/gnu compilers
updated information about packages PETSc can use in users manual
Updated users manual to latest ANL Report format requirements
mpich: update to mpich-3.1.3.tar.gz - remove -download-mpich-mpe [mpich no longer packages mpe] - remove -download-mpich-shared. It was added as a split from --with-mpi-shared to --known-mpi-shared and --download-mpich-shared in 50237a55163f90ac7341b723c6422dfa1dbce792 removing this gives back the control of shared=0/1 to package.py - remove download_solaris as the new tarball works with both gcov and on solaris - remove MPICHInstall() [and use GNUPackage.Install()] as the new tarball fixes 'make clean' requiring sudo
added more images and PETSc pubs
Doc: More refs
...

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