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<h1> Docs: Changes: 3.1</h1>
<p align="center"><font color="#ff0000" size="5"><a name="CHANGES">CHANGES</a>
in the PETSc 3.1</font></p>
<p><u><b>General:</b></u></p>
<ul>
<li>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()</li>
<li>Added configure option --with-single-library that causes
all PETSc code to be compiled into the single library libpetsc.XXX</li>
<li>PetscMap changed to PetscLayout and PetscMapInitialize()
changed to PetscLayoutCreate() and it now allocates the space of
the object.</li>
<li>In makefiles include ${PETSC_DIR}/conf/base is replaced
with two lines include ${PETSC_DIR}/conf/variables and include
${PETSC_DIR}/conf/rules</li>
<li>BlockSolve95 interface is removed</li>
<li>petsc.h and petscdef.h are replaced with petscsys.h and
petscsysdef.h; while petsc.h now includes ALL PETSc include files.</li>
<li>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.</li>
</ul>
<ul>
</ul>
<u><b>Logging:<br>
</b></u>
<ul>
<li>PetscLogFlops(int) ->PetscLogFlops(PetscLogDouble).
[check fortran usage]<br>
</li>
</ul>
<u><b>config/configure.py:<br>
</b></u>
<ul>
<li>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-</li>
</ul>
<u><b></b></u>
<ul>
</ul>
<p><u><b>IS:</b></u></p>
<p><u><b>Vec: <br>
</b></u></p>
<p><u><b>VecScatter:<br>
</b></u></p>
<ul>
</ul>
<p><u><b>Mat:</b></u></p>
<ul>
<li>MatGetSubMatrix
<dl>
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.
</dl>
</li>
<li>MatGetSubMatrixRaw
<dl>
Removed, use MatGetSubMatrix
</dl>
</li>
<li>Changed name of option MAT_KEEP_ZEROED_ROWS to
MAT_KEEP_NONZERO_PATTERN to more clearly indicate what it does.</li>
<li>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.</li>
<li>The function provided to MatNullSpaceSetFunction() now
takes a MatNullSpace() as the first argument. Added Fortran interface
for this function as well.</li>
<li>Removed MatPBRelax() merged its functionality into
MatRelax()</li>
<li>Changed MatRelax() to MatSOR() to match MatSORType() and
PCSOR</li>
<li>Removed requirement that rows be sorted in
MatCreateMPIAIJWithArrays() and MatMPIAIJSetPreallocationCSR().</li>
<li>Changed MATOP_DIAGONAL_SHIFT to MATOP_DIAGONAL_SET to match
function name MatDiagonalSet().</li>
<li>MATMPIROWBS i.e BlockSolve95 interface is now removed.</li>
</ul>
<u><b>PC:</b></u>
<ul>
<li>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.</li>
<li>Removed -pc_asm_in_place and PCASMSetUseInPlace() since the
option made no sense</li>
<li>PCApplyRichardson() has an additional argument indicating
if the initial guess being passed in is nonzero. SOR will save some
work if it is zero.</li>
<li>MatSetBlockSize() is no longer an error for BAIJ matrices,
but the argument must be the same as when the matrix was preallocated. </li>
<li>PCFactorSetPivoting() renamed to PCFactorSetColumnPivot()</li>
<li>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>.
</shiftamount></shifttype></li>
<li>Added PCREDISTRIBUTE for load balancing and removal of Dirichlet degrees of freedom.</li>
</ul>
<p><u><b>KSP:</b></u></p>
<ul>
<li>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.<br>
</li>
<li>Added KSPGCR (Generalized Conjugate Residuals), a flexible
method (like FGMRES) providing inexpensive residuals.</li>
</ul>
<ul>
</ul>
<ul>
</ul>
<ul>
</ul>
<p><u><b>SNES:</b></u></p>
<p><u><b>TS:</b></u></p>
<ul>
<li>Rename TS_EULER, TS_BEULER, etc like TSEULER for
consistency with other packages.</li>
<li>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().</li>
<li>Add TSSSP which implements optimal strong stability
preserving time integrators of order 2, 3, and 4 using a low-storage
explicit Runge-Kutta scheme.</li>
<li>Change TSSetPreStep() and TSSetPostStep() to run before and
after each step instead of before and after each solve.</li>
</ul>
<p><u><b>DA:</b></u></p>
<ul>
<li>DAGetColoring() now takes a MatType as an additional
argument, should be MATAIJ or MATBAIJ</li>
<li>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.</li>
<li>DASetCoordinates() now references the vector, so the user
should release their reference by calling VecDestroy().</li>
</ul>
<p><u><b>DMMG:</b></u></p>
<ul>
</ul>
<u><b>PetscViewer: <br>
</b></u>
<ul>
</ul>
<ul>
</ul>
<p><u><b>SYS:</b></u></p>
<ul>
<li>PetscSleep(), PetscDrawGetPause(), and PetscDrawSetPause()
now take PetscReal instead of int. Also, -draw_pause takes a real value.</li>
<li>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.</li>
</ul>
<p><u><b>AO:<br>
</b></u></p>
<p><u><b>Sieve:</b></u></p>
<p><u><b>Fortran:<br>
</b></u></p>
<ul>
<li>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]<br>
</li>
<li>use petsc and use petscdef are now use petscsys and use
petscsysdef<br>
</li>
</ul>
<p> </p>
<br>
<p></p>
<ul>
</ul>
<p><u><b><a
href="http://www.mcs.anl.gov/petsc/petsc-as/miscellaneous/external.html">ExternalPackages</a>:</b></u></p>
<ul>
<li>Added MATORDERING_AMD for Tim Davis' Approximate Minimum
Degree package.</li>
</ul>
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