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

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).

Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'knepley/feature-viewer-partial-read'

* knepley/feature-viewer-partial-read:
Viewer: Fixed initialization
TS: Updated example to new interface
Plex: Fix compiler warning
Viewer:

Merge branch 'knepley/feature-viewer-partial-read'

* knepley/feature-viewer-partial-read:
Viewer: Fixed initialization
TS: Updated example to new interface
Plex: Fix compiler warning
Viewer: Now ViewerRead() takes an extra argument to return the number of items read - An error is thrown for insufficient data unless the extra argument is non-NULL
Viewer: Fixes for new Read interface - Fixed example - Fixed Fortran 90 binding - Fixed type
Builder: Allow a local dictionary for run parameters
Viewer: PetscViewerRead() should return the number of items actually read - This also applies to all its implementations

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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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Fixed issues in the review: fixed TABs; C89 syntax; TSClone comm; error message; clarified implicit equations in docs

Viewer: Now ViewerRead() takes an extra argument to return the number of items read
- An error is thrown for insufficient data unless the extra argument is non-NULL

ARKIMEX implementation and TSClone notes

added some documetation/fixed some arkimex typos

Cleaned up some issues in TSClone

fixed typo in comment

Replace TSDuplicate with TSClone; all is working but there is still some concern with SNES when the clone is destroyed and a GetSNES and SetSNES is needed

TSComputeRHSJacobian: If TSComputeRHSFunctionLinear is being used, then re-computing the RHS Jacobian (when called from TSComputeRHSFunctionLinear) is necessary, because the saved Jacobian is actuall

TSComputeRHSJacobian: If TSComputeRHSFunctionLinear is being used, then re-computing the RHS Jacobian (when called from TSComputeRHSFunctionLinear) is necessary, because the saved Jacobian is actually scaled-shifted [shift*I - Jac].

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finalized TSDuplicate implementation and testing

TSDuplicate: Added an initial implementation of TSDuplicate()

added a TS statement to allow saving the last solution to a file

Merged in dalcinl/fix-ts-adapt (pull request #293)

Add TSAdaptReset()

Merge branch 'master' into knepley/feature-viewer-partial-read

* master: (48 commits)
ViennaCL: Fixes memory leak when destructing an aijviennacl matrix.
MatLoad_MPIDense() always allocated arra

Merge branch 'master' into knepley/feature-viewer-partial-read

* master: (48 commits)
ViennaCL: Fixes memory leak when destructing an aijviennacl matrix.
MatLoad_MPIDense() always allocated array space even if it was previously provided
Clarified lumping options for PCFieldSplitSchurPreType SELFP.
fixed up PetscInfo in GAMG
TSErrorWeightedNorm[2|Infinity]: API changes
MatLoad_SeqDense() always allocated new space for the data even if the user already provided it
Fixed DMCompositeGetAccessArray() to support readonly vectors
Fix obviously-wrong aspects of documentation on SNESVINEWTONRSLS and SNESVINEWTONSSLS.
fixed example to compile - demonstrates a bug
var name 'len' was F90 key word
For user provided Jacobian functions they should always assembly into the second matrix, the one from which the preconditioner is built because the first may be used as matrix-free with -snes_mf_operator
Suggest --with-64-bit-indices if users mistakenly use --with-64bit-indices
Fix configure logging of integer size.
missing underscore in #define of vecgetarrayread translation of fortran stub for VECGETARRAYREAD
updated test output files to reflect differences introduced previously in PCView output
-ksp_type preonly does not support -ksp_monitor_short so remove from test line to prevent extranious warning output
missing CHKERRQ; and ugly double declaration of ierr
Plex: Reorganized PlexPoint interface - Added DMPlexGetPointLocalField() and DMPlexGetPointGlobalField() - Now the DMPlexGetLocalOffset*_Private() functions return start and end - Uniformly use private functions
Plex: Put in explicit cast
MatSetValuesMPISBAIJ will now print correct global indices when error generated due to new nonzero location
...

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# especially if it merges an updated upstream into a topic branch.
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# Lines starting with '#' will be ignored, and an empty message aborts
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Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
thi

Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
this branch. Matt's and my fixes in DMPlex will also be relevant.

* master: (1557 commits)
MatLoad_MPIDense() always allocated array space even if it was previously provided
Clarified lumping options for PCFieldSplitSchurPreType SELFP.
fixed up PetscInfo in GAMG
TSErrorWeightedNorm[2|Infinity]: API changes
MatLoad_SeqDense() always allocated new space for the data even if the user already provided it
Fixed DMCompositeGetAccessArray() to support readonly vectors
Fix obviously-wrong aspects of documentation on SNESVINEWTONRSLS and SNESVINEWTONSSLS.
fixed example to compile - demonstrates a bug
var name 'len' was F90 key word
For user provided Jacobian functions they should always assembly into the second matrix, the one from which the preconditioner is built because the first may be used as matrix-free with -snes_mf_operator
Suggest --with-64-bit-indices if users mistakenly use --with-64bit-indices
Fix configure logging of integer size.
missing underscore in #define of vecgetarrayread translation of fortran stub for VECGETARRAYREAD
updated test output files to reflect differences introduced previously in PCView output
-ksp_type preonly does not support -ksp_monitor_short so remove from test line to prevent extranious warning output
missing CHKERRQ; and ugly double declaration of ierr
Plex ex3: For want of a semicolon, the kingdom was lost
MatSetValuesMPISBAIJ will now print correct global indices when error generated due to new nonzero location
completed basic use of MatSetValuesBlocked_SeqBAIJ_Inlined() by MatSetValuesBlocked_MPIBAIJ() to allow proper global indices being printed when error generated by new nonzero locations.
Added inline version of MatSetValuesBlocked_SeqBAIJ() to be used by MatSetValuesBlocked_MPIBAIJ() to print error message for nonzero block with global indices
...

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TSReset: Call TSAdaptReset()

Merged in dalcinl/fix-ts-errornorm (pull request #290)

TSErrorWeightedNorm[2|Infinity]: API changes

TSErrorWeightedNorm[2|Infinity]: API changes

* Accept two arguments U,Y instead of always using ts->vec_sol
* Accept argument wnormtype intead of use ts->adapt->wnormtype

Merge branch 'master' of https://bitbucket.org/petsc/petsc