petsc-3.6.2 2015-10-02
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# Documentation: Changes: 3.1

## CHANGES in PETSc 3.1

#### General:

- PetscOptionsHasName() and PetscOptionsName() now return PETSC_TRUE if the options are set to any value, include false or 0. You may need to change some of your PetscOptionsXXName() to PetscOptionsXXTruth()
- Added configure option --with-single-library that causes all PETSc code to be compiled into the single library libpetsc.XXX
- PetscMap changed to PetscLayout and PetscMapInitialize() changed to PetscLayoutCreate() and it now allocates the space of the object.
- In makefiles include ${PETSC_DIR}/conf/base is replaced with two lines include ${PETSC_DIR}/conf/variables and include ${PETSC_DIR}/conf/rules
- BlockSolve95 interface is removed
- petsc.h and petscdef.h are replaced with petscsys.h and petscsysdef.h; while petsc.h now includes ALL PETSc include files.
- win32fe [used for MS/Intel compiler builds on windows] now defaults to 'noautodetect' mode. However the previous behavior can be restored by using the option '--autodetect'. For eg: '--withcc=win32fe cl --autodetect'. This works primarily with old VC6/VC7/Intel8 etc compilers anyway.

#### Logging:

- PetscLogFlops(int) ->PetscLogFlops(PetscLogDouble). [check fortran usage]

#### config/configure.py:

- All ./configure options that state known values, so that ./configure doesn't try to test for them. Often used with the --with-batch option now begin with --known-

#### IS:

#### Vec:

#### VecScatter:

#### Mat:

- MatGetSubMatrix:
  - Now takes a parallel IS for the columns, the csize argument has been dropped. The local part of this IS corresponds to the local columns of the new submatrix.
- MatGetSubMatrixRaw
  - Removed, use MatGetSubMatrix
- Changed name of option MAT_KEEP_ZEROED_ROWS to MAT_KEEP_NONZERO_PATTERN to more clearly indicate what it does.
- Added MAT_SHARE_NONZERO_PATTERN as option for MatDuplicate() this allows several matrices to share the same data structures for the nonzeros and thus save memory.
- The function provided to MatNullSpaceSetFunction() now takes a MatNullSpace() as the first argument. Added Fortran interface for this function as well.
- Removed MatPBRelax() merged its functionality into MatRelax()
- Changed MatRelax() to MatSOR() to match MatSORType() and PCSOR
- Removed requirement that rows be sorted in MatCreateMPIAIJWithArrays() and MatMPIAIJSetPreallocationCSR().
- Changed MATOP_DIAGONAL_SHIFT to MATOP_DIAGONAL_SET to match function name MatDiagonalSet().
- MATMPIROWBS i.e BlockSolve95 interface is now removed.

#### PC:

- PCShell All user-provided functions now have PC as first argument instead of the application context. Users should obtain the context with PCShellGetContext, similar to MatShell.
- Removed -pc_asm_in_place and PCASMSetUseInPlace() since the option made no sense
- PCApplyRichardson() has an additional argument indicating if the initial guess being passed in is nonzero. SOR will save some work if it is zero.
- MatSetBlockSize() is no longer an error for BAIJ matrices, but the argument must be the same as when the matrix was preallocated.
- PCFactorSetPivoting() renamed to PCFactorSetColumnPivot()
- Replaced PCFactorSetShiftNonzero(), PCFactorSetShiftPd() and PCFactorSetShiftInBlocks() with PCFactorSetShiftType() and PCFactorSetShiftAmount(). Replaced -pc_factor_shift_nonzero, -pc_factor_shift_positive_definite and -pc_factor_shift_in_blocks with -pc_factor_shift_type <shifttype> and -pc_factor_shift_amount <shiftamount>.
- Added PCREDISTRIBUTE for load balancing and removal of Dirichlet degrees of freedom.

#### KSP:

- Added KSPCGUseSingleReduction() -ksp_cg_single_reduction; recommended for use with many processors when VecDot() starts to take a large amount of time, Requires 2 extra work vectors.
- Added KSPGCR (Generalized Conjugate Residuals), a flexible method (like FGMRES) providing inexpensive residuals.

#### SNES:

#### TS:

- Rename TS_EULER, TS_BEULER, etc like TSEULER for consistency with other packages.
- Add Theta and General Linear time integrators (TSTHETA, TSGL). These can be used for solving differential algebraic equations (DAE) using the new TSSetIFunction() and TSSetIJacobian().
- Add TSSSP which implements optimal strong stability preserving time integrators of order 2, 3, and 4 using a low-storage explicit Runge-Kutta scheme.
- Change TSSetPreStep() and TSSetPostStep() to run before and after each step instead of before and after each solve.

#### DA:

- DAGetColoring() now takes a MatType as an additional argument, should be MATAIJ or MATBAIJ
- Added DARefineHierarchy(), DMMG now always uses DMRefineHierarchy to generate refined grids. Added options -da_refine_hierarchy_[xyz] to allow semi-coarsening at some levels of the hierarchy.
- DASetCoordinates() now references the vector, so the user should release their reference by calling VecDestroy().

#### DMMG:

#### PetscViewer:

#### SYS:

- PetscSleep(), PetscDrawGetPause(), and PetscDrawSetPause() now take PetscReal instead of int. Also, -draw_pause takes a real value.
- PetscRandomGetValueImaginary() is removed. To get a complex number with only a random imaginary part first call PetscRandomSetInterval() with the same low and high real part. Similarly one can obtain a complex number with only a random real part by setting the low and high imaginary part to be the same.

#### AO:

#### Sieve:

#### Fortran:

- Removed the old compiler dependent implementation of f90 interface sources in favor of the new compiler independent implementation. Consequently the configure option --with-f90-interface is removed. And the f90 interface is automatically built - if an f90 compiler is detected. [this is the default behavior before this change aswell]
- use petsc and use petscdef are now use petscsys and use petscsysdef

#### ExternalPackages:

- Added MATORDERING_AMD for Tim Davis' Approximate Minimum Degree package.