fix a bug in cost integral evaluation for explicit solvers

add costintegral to rk

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*

Updated TSFunctionDomainError signature

Instead of getting all stages and the stage index, the function gets
directly the current state (e.g. the one to check).

Added domain error checks at each stage

This patch adds two functions:
1 - TSSetFunctionDomainError
2 - TSFunctionDomainError

The first one to set a user function, the second one to call it.
It als

Added domain error checks at each stage

This patch adds two functions:
1 - TSSetFunctionDomainError
2 - TSFunctionDomainError

The first one to set a user function, the second one to call it.
It also adds the calls to TSFunctionDomainError in all implementations calling TSPostStage.

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updates to TSAdjoint users manual documentation and related manual pages
to make things more consistently and clearer

removed unused variables in bus adjoint examples
fix uninitialized variables issues for adjoint solver

fix TSTrajectory for Fortran
remove illegal declaration of variable within code

drop the P from TSAdjointSetRHSJacobian() remove C++ commments from adjoint examples

fix naming of TSAdjoint function pointers

more merges in rebase

Fixed major memory leak in rk adjoint solver because ts->setup was reset to zero when entering reverse mode which caused all basic TS work objects to be created a second time.

Fixed by adding a TSAd

Fixed major memory leak in rk adjoint solver because ts->setup was reset to zero when entering reverse mode which caused all basic TS work objects to be created a second time.

Fixed by adding a TSAdjointSetUp() for its own work objects and not calling the original setup multiple times.

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add output files for make tests for TSAdjoint examples
include power-system and stability-bus directories to automatic testing!
Rename basic functions of discrete adjoint integrators as first step of

add output files for make tests for TSAdjoint examples
include power-system and stability-bus directories to automatic testing!
Rename basic functions of discrete adjoint integrators as first step of refactorization

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Sensitivity w.r.t. parameters is optional now

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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stage values can be checkpointed now

simplify option object names

moved PetscOptionsObject from global variable to local variable in functions