petsc-3.4.2 2013-07-02

# Documentation: Changes: 2.3.0

## CHANGES in PETSc 2.3.0

#### General:

- The equivalent of building BOPT=g, BOPT=O versions for PETSC_ARCH=linux-gnu is now: config/configure.py [options] -PETSC_ARCH=linux-gnu config/configure.py [options] --with-debugging=0 -PETSC_ARCH=linux-gnu-opt
- Python bindings added to PETSc. To use, configure with: --with-python=1 ---with-shared=1 To build, use: 'make python' after building PETSc libraries. Example in src/snes/examples/tutorials/ex1.py
- Options database keys -trmalloc[_xxx] are changed to -malloc[_xxx]
- -get_resident_set_size and -trinfo are changed to -memory_info
- PetscTrValid() -> PetscMallocValidate(), PetscTrDebug() -> PetscMallocDebug()
- -trdebug -> -malloc_debug
- PetscGetResidentSetSize() -> PetscMemoryGetCurrentUsage(), added PetscMemoryGetMaximumUsage() and PetscMemorySetGetMaximumUsage()
- PetscTrSpace() -> PetscMallocGetCurrentUsage() and PetscMallocGetMaximumUsage()
- added PetscOptionsEnum() and PetscOptionsGetEnum()
- added PetscBag object for managing user created structs including initializing them and serializing them.
- removed PetscSetCommWorld(). Now you can directly assign to PETSC_COMM_WORLD before PetscInitialize().

#### Vec:

- Faster generation of VecScatter for many processes when indices are mostly sorted
- Changed BLAS-type interfaces to PETSc-style:
  - VecShift
  - VecScale
  - VecSet
  - VecSetRandom
  - VecAXPY
  - VecAXPBY
  - VecAYPX
  - VecMAXPY
  - VecWAXPY
- Changed order of arguments in pointwise routines:
  - VecPointwiseMult
  - VecPointwiseMax
  - VecPointwiseMin
  - VecPointwiseMaxAbs
  - VecPointwiseDivide

#### Mat:

- Changed MatConvert to require a reuse parameter to denote inplace converstion
- Added Cholesky and ICC support to SeqBAIJ
- Added the argument MatFactorInfo to MatLUFactorNumeric() and MatCholeskyFactorNumeric()
- Faster MatSetValues()
- Faster parallel-matrix vector products
- Changed MatCreate() to take only a communicator
- Added MatSetSize() to specify matrix sizes
- Changed BLAS-type interfaces to PETSc-style:
  - MatAXPY
  - MatAYPX
  - MatScale
  - MatShift
- Change MatZeroRows() and MatZeroRowsLocal() to use arrays, and added IS versions

#### PC:

- Added PCILUReorderForNonzeroDiagonal() and PCLUReorderForNonzeroDiagonal()
- Replace PCLUSetDamping(), PCILUSetDamping(), PCCholeskySetDamping() and PCICCSetDamping() by PCFactorSetShiftNonzero(). Change the option database keys -pc_lu_damping, -pc_ilu_damping, -pc_cholesky_damping and -pc_icc_damping to -pc_factor_shift_nonzero
- Replace PCLUSetShift(), PCILUSetShift(), PCCholeskySetShift() and PCICCSetShift() by PCFactorSetShiftPd(). Change the option database keys -pc_lu_shift, -pc_ilu_shift, -pc_cholesky_shift and -pc_icc_shift to -pc_factor_shfit_positive_definite
- PCMG: will automatically using the outer pmat operator to define the finest level operator if not user supplied
- PCMG: added MGUseGalerkin(), -pc_mg_galerkin option to have coarser grid matrices computed from the finest grid matrix
- PCMG: now does referencing counting on set vectors and restriction/interpolation matrices so user need not keep reference to free later
- PCMG: if user does not provide restriction the interpolation is used and vis versa
- PCMG: if user does not provide Vecs for each level, will automatically provide them
- All routines that began with MG now begin with PCMG
- Added PCShellSet/GetContext() and removed the context passed into PCSetApply() and PCSetApplyRichardson()

#### KSP:

- -ksp_cg_Hermitian and -ksp_cg_symmetric have been changed to -ksp_cg_type Hermitian or symmetric
- Changed options for -ksp_gmres_cgs_refinement_type from never or ifneeded or always to REFINE_NEVER or REFINE_IFNEEDED or REFINE_ALWAYS

#### config/configure.py:

#### SNES:

- Changed the name and calling sequence for SNESSetLineSearchCheck() to SNESLineSearchSetPostCheck() and added a SNESLineSearchSetPreCheck()
- Changed the names of all SNESxxxxLineSearchyyyy() to SNESLineSearchxxxxyyyy() per PETSc naming standard.
- Now allow a constant vector to be specified in SNESSolve()
- Removed the Vec argument from SNESSetUp()
- Corrected the order of function and context arguments in:
  - SNESGetFunction()
  - SNESGetJacobian()

#### TS:

#### DA:

- Added DAVecGet/RestoreArrayDOF() allowing indexing in the dimension of degrees of freedom at each point on the lattice.
- Faster DAGlobalToLocal() etc for dof > 1.

#### DMMG:

- Consolidated DMMG functionality into the new header file "petscdmmg.h".

#### SYS:

- PetscSetCommWorld() removed. [one can directly do PETSC_COMM_WORLD = comm - before PetscInitialize()]

#### Fortran:

#### ExternalPackages:

- ML support added.