petscmaster 20150125
Documentation: Changes: 2.0.182.0.21
NEW FEATURES and CHANGES in PETSc 2.0.182.0.21
General:

Complex numbers performance upgrade: Added support for using
optimized Fortran kernels for some key complex numbers numerical
routines (such as matrixvector products, vector norms, etc.) instead
of the default C++ routines. This implementation exploits the
maturity of Fortran compilers while retaining the identical user
interface. For example, on rs6000 machines, the base singlenode
performance when using the Fortran kernels is 45 times faster than
the default C++ code.

Changed the names of various compiler flags, e.g., changed
PETSC_COMPLEX to USE_PETSC_COMPLEX.

Changed
PetscObjectInherit()
to
PetscObjectCompose()
since it really denotes
a "hasa" relationship, not an "isa"
relationship.
AO (Application Orderings):

Changed
AOCreateDebug()
to
AOCreateBasic()
; changed
AOCreateDebugIS()
to
AOCreateBasicIS()
.

Removed the MPI_Comm argument from
AOCreateBasicIS()
since it is contained in the IS arguments.

Now the
AOxxxToxxxXX()
remapping routines will not
map negative entries in the input arrays. This allows, for example,
the mapping of neighbor lists that use negative entries to indicate
nonexistent neighbors due to boundaries, etc.
TS (Timestepping Solvers):
 Added an interface to PVODE, the stiff integrator package of Hindmarsh et al.
SNES (Nonlinear Solvers):

Added support for using matrix colorings within finite difference
Jacobian approximations. See the section "Finite Difference
Jacobian Approximations" of the users manual for more details.
Also see the man pages for
SNESDefaultComputeJacobianWithColoring()
.
 Fixed a bug in method SNES_EQ_NLS.
 Increased the default maximum number of function evaluations to 100000.
SLES (Linear Solvers):
KSP (Krylov Subspace Methods):
 Added the routine
KSPGetResidualNorm()
.
PC (Preconditioners):

Added pc_lu_fill and pc_ilu_fill to replace mat_lu_fill and
mat_ilu_fill; also added the commands
PCLUSetFill()
and PCILUSetFill()
.
 Added
PCLUSetMatReordering()
and PCILUSetMatReordering()
.
MAT (Matrices):

Added support for matrix colorings, which are intended primarily for use in finite
difference Jacobian approximations. See the SNES section above for more info. New routines
include:
 MatFDColoringCreate()
 MatFDColoringSetParameters()
 MatFDColoringSetFrequency()
 MatFDColoringSetFunction()
 MatFDColoringSetFromOptions()
 MatFDColoringView()
 MatFDColoringApply()
 MatFDColoringDestroy()

Added the matrix option
MatSetOption(mat,MAT_NEW_NONZERO_ALLOCATION_ERROR) that will cause an
error if a new entry that has not been preallocated is generated in
a sparse matrix. (currently implemented for AIJ and BAIJ matrices
only). This is a useful flag when debugging memory preallocation.
 Replaced the options mat_lu_fill and mat_ilu_fill with pc_lu_fill and pc_ilu_fill.
 Added the routine MatSetValuesBlockedLocal() for BAIJ matrices.
 Changed the final argument of MatGetTypeFromOptions() from type int* to PetscTruth*.

Added MatCreateSeqAdj() for supplying adjacency matrices to PETSc to
do reordering on (for example RCM to reduce bandwidth and thus get
better cache performance) and eventually partitioners.

MatSetLocalToGlobalMapping() and MatSetLocalToGlobalMappingBlocked()
now take a ISLocalToGlobalMapping object rather than a list of
indices.

Added the routine MatGetSubMatrix(), which extracts a parallel matrix
from a parallel matrix (currently implemented only for the MPIAIJ
format).
DA (Distributed Arrays):

When used with the DA_STENCIL_STAR stencil, type, the routine
DAGetGlobalIndices() returns localtoglobal mapping indices that now
include the inactive corner ghost nodes. This is useful, e.g., when
using MatSetValuesLocal() to set matrix elements, including corner
boundary nodes.
VEC (Vectors):

VecSetLocalToGlobalMapping() now takes a ISLocalToGlobalMapping
object rather than a list of indices.
 Added the routine VecCreateMPIWithArray().

Changed the calling sequence for VecCreateGhost(); added
VecCreateGhostWithArray(), VecGhostUpdate[Begin/End](), and
VecGhost[Get/Restore]LocalRepresentations().
IS (Index Sets):

Added ISGlobalToLocalMappingApply() to allow one to convert lists
that are in the global numbering to a local numbering.
 Added a communicator as the first argument to ISLocalToGlobalMappingCreate().
Draw (Graphics):
 Added routines for drawing simple histograms. See DrawHistCreate().
 Removed the option draw_x_private_colormap and made a private colormap the default.

Added the option draw_x_shared_colormap to indicate not to use
a private colormap. If you use Netscape on your machine and are also
doing contour plots, you generally don't want to use a shared
colormap.
 Improved the colors used in the contour plotting.

Changed some routine names:
 DrawText() to DrawString()
 DrawTextVertical() to DrawStringVertical()
 DrawTextSetSize() to DrawStringSetSize()
 DrawTextGetSize() to DrawStringGetSize()
 DrawSyncClear() to DrawSynchronizedClear()
 DrawSyncFlush() to DrawSynchronizedFlush()
 DrawSyncGetMouseButton() to DrawSynchronizedGetMouseButton().
Viewers:
 Added VIEWER_STDOUT_() and VIEWER_STDERR_().
System Routines:
 Added the routine OptionsClearValue().

Added the option get_resident_set_size that causes the program to
call PetscGetResidentSetSize() at the end of the run and print how
much physical memory each process has used.

Changed OptionsGetProgramName() to PetscGetProgramName() and changed
the calling sequence to match PetscGetHostname(), etc.
 Changed BINARY_INT and BINARY_SCALAR to PETSC_INT and PETSC_SCALAR.
Error Handling:
Event Logging:
Fortran Interface:

Added routines to map between C and Fortran representations of communicators
extern int MPICCommToFortranComm(MPI_Comm,int *);
extern int MPIFortranCommToCComm(int,MPI_Comm*);
These provide the same functionality that
extern int PetscCObjectToFortranObject(void *,int *);
extern int PetscFortranObjectToCObject(int,void *);
do for PETSc objects.

Removed the macros Double, DBLE, PetscDoubleExp as they are no longer
required. PETSc now compiles on the Cray T3D/T3E with the dp option
that correctly handles Fortran code using double precision.

Added support for MatGetRow() MatRestoreRow() from Fortran; see
manpage for Fortran calling sequence.

Added PetscBinaryOpen(), PetscBinaryClose(), PetscBinaryRead() and
PetscBinaryWrite() for binary IO from Fortran; see
src/vec/examples/tests/ex20.F. Most users should not need this
functionality.