Fixed bug with kinetic solver handling of requests to set nInit
and concInit of buffered molecules. The solver failed to do these
assignments. Furthermore, it refused to assign the n or conc values
of buffered molecules either. Fixed.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@935 d1858a74-f715-0410-99c9-c66fe9cce3d6
Bug fix in HSolve rate lookups.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@936 d1858a74-f715-0410-99c9-c66fe9cce3d6
Implemented a rather nasty hack in the solver to handle midstream 
turnon/turnoff of buffering of molecules. Only works for molecules
that start out unbuffered.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@937 d1858a74-f715-0410-99c9-c66fe9cce3d6
Fixed problems with volScale assignments to molecules going 
to the parent KinCompt. This results in lots of warning messages if
a legacy kkit model has different volumes in the same group. Seems
to do the correct thing with the rates.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@938 d1858a74-f715-0410-99c9-c66fe9cce3d6
Improved error reporting for volume mismatches, useful for legacy
kkit models.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@939 d1858a74-f715-0410-99c9-c66fe9cce3d6
Tracked down a problem with MMenzymes. Affects both Stoich and 
GssaStoich, but the latter crashes if the volume is too big. Fixed.
Also set up some tests in TESTS/GSSA.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@940 d1858a74-f715-0410-99c9-c66fe9cce3d6
Generated two tests that show distinct problems with the gsolve class:
rMMenz.g and manyvolsrMMenz.g: Shows problem with MM enzyme E not 
being in the dependency tree for MMenz. 
See assignReac.g and manyvolsAssignReac.g: Shows problem of failure
to update dependency treewhen external functions cause assignments
of substrate values.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@941 d1858a74-f715-0410-99c9-c66fe9cce3d6
Fixed two problems with the gsolve. It now correctly updates 
dependencies of MM enzymes, and it handles dependencies arising out
of assignments of molecules during a simulation.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@942 d1858a74-f715-0410-99c9-c66fe9cce3d6
added a batfile to do regression test on parallel moose

git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@943 d1858a74-f715-0410-99c9-c66fe9cce3d6
Added a naive handling for tables on channels for tab2file for GENESIS compatibility.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@944 d1858a74-f715-0410-99c9-c66fe9cce3d6
Fixed flatline bug in Gsolver. Turned out that mtrand() gives a value
of 0.0 about 1 time in 2^31, and I was taking the negative log if this.
The resulting nan caused a flatline.  Hence in a long simulation it 
was very likely to flatline.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@945 d1858a74-f715-0410-99c9-c66fe9cce3d6
Cinfo self-documentation as key/value pairs.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@946 d1858a74-f715-0410-99c9-c66fe9cce3d6
Adding -DMPICH_IGNORE_CXX_SEEK switch in top-level Makefile by default.

git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@947 d1858a74-f715-0410-99c9-c66fe9cce3d6
Reverted genesis_parser/Makefile to use CFLAGS instead of CXXFLAGS


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@948 d1858a74-f715-0410-99c9-c66fe9cce3d6
inline documentation for Cinfos

git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@949 d1858a74-f715-0410-99c9-c66fe9cce3d6
Fixed PyMOOSE Makefile.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@950 d1858a74-f715-0410-99c9-c66fe9cce3d6
Added Ctrl-D (EOF) processing to quit gracefully in MOOSE
CLI. Reverted Makefile in pymoose and genesis_parser to use CXXFLAGS
instead of CFLAGS (as per Niraj). Sorry for the confusion.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@951 d1858a74-f715-0410-99c9-c66fe9cce3d6
bug fixes on readline

git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@952 d1858a74-f715-0410-99c9-c66fe9cce3d6
Clean up of PyMOOSE. Fixed some error in wrapper-generation code in Cinfo.cpp


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@953 d1858a74-f715-0410-99c9-c66fe9cce3d6
PyMOOSE Cleanup. Converted PyMooseBase.path to a field from a getter
funtion. Added PyMooseBase.className member field.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@954 d1858a74-f715-0410-99c9-c66fe9cce3d6