Specifically, request availability of a read/write access to the
Jacobian matrix, and a means to zeroing the elements of an arbitrary
matrix type (unimplemented 'MatrixZero' template class).
Also, implement a function for zeroing a CSRMatrix, and create a
read/write reference to the underlying matrix. Needed for clearing
the coefficient matrix between each Jacobian assembly.
The statement is only correct during the very first grid pass whilst
constructing the matrix. Source terms are added later, in arbitrary
order, and we cannot know (in assembleBlock) what (block) rows are
affected by such contributions.
While here, allow user to override policies for negating a vector and
zeroing the vector. Moreover, the JacobianSystem no longer assumes
responsibility for solving the Jacobian system of linear equations, so
accept a linear solver parameter in solve().
The class is parametrised on policies for setting the size of
individual vectors, adding two vectors, and assembling local
contributions into the residual vector.
Provide default implementations of these policies, suitable for
base-vectors that implement (some of) the std::vector<T> interface.
Pass the scalar number of rows and non-zeros into .setSize() along
with the number of degrees of freedom per cell. This allows the
assembler to impose block structure in an optimal way for each
particular type of linear system.
For instance, an iterative linear solver is likely to need some kind
of stopping criterion and the implicit solver should not be tasked
with defining the criterion.
Automake 1.11 introduced the concept of "silent build rules" wherein the
build commands are reported as
CC spu_explicit.lo
rather than something along the lines of
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../../../../opmtransport/src -I.. -O3 -DNDEBUG -Wall -Wextra -std=c99 -pedantic -march=native -mtune=native -MT spu_explicit.lo -MD -MP -MF .deps/spu_explicit.Tpo -c -o spu_explicit.lo ../../../../../opmtransport/src/spu_explicit.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../../../../opmtransport/src -I.. -O3 -DNDEBUG -Wall -Wextra -std=c99 -pedantic -march=native -mtune=native -MT spu_explicit.lo -MD -MP -MF .deps/spu_explicit.Tpo -c ../../../../../opmtransport/src/spu_explicit.c -fPIC -DPIC -o .libs/spu_explicit.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../../../../opmtransport/src -I.. -O3 -DNDEBUG -Wall -Wextra -std=c99 -pedantic -march=native -mtune=native -MT spu_explicit.lo -MD -MP -MF .deps/spu_explicit.Tpo -c ../../../../../opmtransport/src/spu_explicit.c -o spu_explicit.o >/dev/null 2>&1
The former is much easier to read and, consequently, more conducive to
visually noticing diagnostics from the toolset (compiler, linker &c).
On the other hand, only fairly recent editions of Automake have the
"silent rule" capability, so enable silent rules only if available. In
particular, Automake 1.10.x (the default Automake version in MacOS X
10.6) does not support the capability. Neither does the default
Automake in CentOS 5.6.
Further details on silent build rules can be found at
http://sources.redhat.com/automake/automake.html#Optionshttp://www.flameeyes.eu/autotools-mythbuster/automake/silent.html
Thanks to Arne Morten Kvarving in Dune Flyspray issue #922
(http://www.dune-project.org/flyspray/index.php?do=details&task_id=922)
for the tip on how to preserve "configure.ac" backwards compatibility
with Automake < 1.11 .
