Docs: Changes: 2.0.28

CHANGES in PETSc 2.0.28 (see new features)

General:

• No longer support PETSC_ARCH=sun4
• The macros in petscconf.h now begin with PETSC_
• PetsReal() and PetscImaginary() are now PetscRealPart() PetscImaginaryPart()
• -optionstable -> -options_table -optionsleft -> -options_left but old left for compatibility

AO (Application Orderings):

TS (Timestepping Solvers):

• TSSetMonitor() now takes an additional final optional argument that will destroy the
  monitor context.

SNES (Nonlinear Solvers):

• SNES_EQ_LS etc changed to drop _, for example SNESEQLS
• nged calling sequence of SNES monitoring routines to add an additional output parameter indicating
  why it converged or diverged.
• Added additional final argument to SNESSetMonitor() an optional destroy routine for the
  monitor context.
• Changed calling sequence of MatSNESMFAddNullSpace() to take PCNullSpace object rather than
  array of vectors.

• Added final ctx argument to SNESGetFunction(), SNESGetGradient() and SNESGetMinimizationFunction()
  

SLES (Linear Solvers):

• See PC and KSP
• SLESSolveTrans() is now SLESSolveTranspose()
• SLESSolve() now ALWAYS returns a 0 or positive iteration count. Call KSPGetConvergedReason()
  to see if converged or diverged and why.

KSP (Krylov Subspace Methods):

• Added additional final argument to KSPSetMonitor() an optional destroy routine for the
  monitor context.
• KSPSolvetrans() is now KSPSolveTranspose()
• Added flexible gmres (use fgmres or KSPFGMRES as the type) see KSPFGMRESSetModifyPC() for
  one way to change PC at each iteration.

PC (Preconditioners):

• MGSetRestriction() and MGSetInterpolation() now accept either the appropriate matrix or its transpose;
  PETSc figures out which one it is based on the number of rows and columns. Now you don't need to use
  the Shell matrices if you computed it "the other way then PETSc use to expect".
• PCApplyTrans() is now PCApplyTranspose()
• options -pc_ilu_mat_ordering_type <nd,...> and -pc_lu_mat_ordering_type <nd,...> now set
  the ordering type.
  

MAT (Matrices):

• Added two additional arguments to MatCreate(MPI_Comm comm,int m,int n,int M,int N,Mat *)
  where m and n are the local ownership sizes. To get the effect of the old MatCreate()
  use m and n equal to PETSC_DECIDE
• Changed MatSetLocalToGlobalMappingBlocked() to MatSetLocalToGlobalMappingBlock() so that it would be less then 32 characters long.
• MatSolveTrans() and MatSolveTransAdd() are now MatSolveTransposeXXX()
  MatMultTrans() and MatMultTransAdd() are now MatMultTransposeXXX()
• MatCreateMPIAdj() changed to MatCreateMPICSR(); MatCreateSeqAdj() dropped.
• Another MatSetOption(), MAT_IGNORE_ZERO_ENTRIES for AIJ matrices with ADD_VALUES.
• added matrix option MAT_KEEP_ZEROED_ROWS causes MatZeroRows() to keep the original nonzero data structure and just put 0.0 into the elements that are to be zeroed. Without this option it removes the locations from the nonzero structure.

DA (Distributed Arrays):

VEC (Vectors):

• Added VecGetArray2d() and VecRestoreArray2d() 
  

IS (Index Sets):

• Added second argument to ISInvertPermutation() that indicates how many indices are to be stored on that processor; ignored for one processor code. If you use ISInvertPermutation() simply add a second argument of PETSC_DECIDE.

Draw (Graphics):

• DrawHistxxx changed to DrawHGxxx

Viewers:

System:

• Routines XXXRegister() are now XXXRegisterDynamic() used for registering new object types
  in dynamic libraries and XXXRegister_Private() is now XXXRegister() used to register new object
  types whose definitions are in the exectuable.
• The final argument to OptionsHasName() and OptionsGetXXX() is a PetscTruth * instead
  of an int*
• PETSc functions and objects that began with Table now begin with PetscTable
• Changed these routines to return an error code.
  extern int PetscStrchr(const char[],char,char **);
  extern int PetscStrrchr(const char[],char,char **);
  extern int PetscStrstr(const char[],const char[],char **);
  extern int PetscStrtok(const char[],const char[],char **);
  extern int PetscStrlen(const char[],int *);
  added PetscStrallocpy(const char[],char **);
  PetscStrncmp() and PetscStrcasecmp() now return PETSC_TRUE as a final argument
  if the strings match else PETSC_FALSE. Note this means removing ! from your current
  tests and adding it where you don't have it.
• PetscMemcmp() now has a final argument of true for matching memories.
• The Fortran versions of the PetscStrxxx() and PetscMemxxx() routines also now
  have the error flag as the final argument

• PetscFree() now always returns an error code that may be checked with CHKERRQ().
  On systems where free() returns a void (and the user has no access to an error
  condition in free(), PetscFree() returns 0 i.e. no error; on other systems it
  returns the error number from free.
• The BT bitarray macros are now prefixed with PetscBT

Error Handling:

Event Logging:

Fortran Interface:

New Features in PETSc 2.0.28 (see changes above)

General:

• When doing string substitutions in library directory paths etc one must use ${PETSC_DIR} ${BOPT} etc now instead of $PETSC_DIR etc. Also you can put anything in {anything} as long as it is an environmental variable or passed in the options database with -anything
• Added PetscEmacsclientErrorHandler() -on_error_emacs [machinename] to allow emacs to jump to error; can be used
  with any other error handler.
• So long as you have defined the macro __FUNC__ "main" before your main C/C++ subroutine you can
  use SETERRQ() and CHKERRQ() instead of SETERRA(), CHKERRA().

AO (Application Orderings):

TS (Timestepping Solvers):

SNES (Nonlinear Solvers):

• Added SNESSetLineSearchParams() and SNESGetLineSearchParams(), contributed by Matt Knepley.
• Added SNESGetConvergedReason() to find out if a SNESSolve() has converged/diverged and why
• Added SNESVecViewMonitorUpdate() and -snes_vecmonitor_update to display the Newton update at each iteration.

SLES (Linear Solvers):

• See PC and KSP

KSP (Krylov Subspace Methods):

• Added -ksp_gmres_krylov_monitor and KSPGMRESKrylovMonitor() to allow one to view the vectors
  in the Krylov space.

PC (Preconditioners):

• We now provide a drop tolerance based ILU for SeqAIJ matrix format via Yousef Saad's SPARSEKIT2
  software. Use -pc_ilu_use_drop_tolerance <dt,dtcol,rowmax> or
  PCILUSetUseDropTolerance(pc,dt,dtcol,rowmax).

MAT (Matrices):

DA (Distributed Arrays):

VEC (Vectors):

IS (Index Sets):

Draw (Graphics):

• DrawCreate() and DrawOpenX() now can take DRAW_FULL_SIZE, DRAW_HALF_SIZE, DRAW_THIRD_SIZE ... as arguments for w and or h.

Viewers:

• Added ViewerASCIIUseTabs() to allow turning off tabbing during certain viewer operations.
• Added ViewerGetSingleton(), ViewerRestoreSingleton() to allow managing the calling a a sequential viewer from within a parallel viewer.
• Added ViewerASCIISynchronizedPrintf(viewer,....)
• Binary and ASCII viewers can create compressed files by simply appending a .gz on the
  filename.
• PETSc now has a new viewer that generates rudimentary Postscript.
  Improvements, additions may be added as needed.
  DrawOpenPS(), or DrawSetType(,DRAW_PS); or -draw_type ps
  
  

System:

• using -trdump with PETSC_USE_STACK compile option (default for BOPT=g*) will print the entire
  stack for each malloc, allow one to more easily track down where mallocs where made that where not
  freed.
• Added PetscSum_Op to replace MPI_SUM for reductions with MPIU_SCALAR
• Added PetscMaxSum_Op to do max on first half of entries and sum on second half.
• Added CHKMEMQ and CHKMEMA macros to help track down memory corruption.
  

Error Handling:

Event Logging:

Fortran Interface:

• Added Fortran 90 interface support for HP Convex  and Solaris.machine.