Some unit tests were failing after the introduction of self-documenting Finfos.
Changing to the new syntax fixed this.

Also disabled the "testKineticManagerGssa()" unit test (part of the KSolve
unit tests) if MPI is present. Currently this test locks up in a parallel run.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@896 d1858a74-f715-0410-99c9-c66fe9cce3d6
Added simulation scripts for the paper PyMOOSE: Interoperable scripting in Python for MOOSE

git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@897 d1858a74-f715-0410-99c9-c66fe9cce3d6
Updated OutputEventPort to reflect changes in Music API.

git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@898 d1858a74-f715-0410-99c9-c66fe9cce3d6
Default values for Music InputEventPort variables. Also gave global flags
to Music ports.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@899 d1858a74-f715-0410-99c9-c66fe9cce3d6
minor change.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@900 d1858a74-f715-0410-99c9-c66fe9cce3d6
test code for bulbchan. pymoose and moose not yet matching.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@901 d1858a74-f715-0410-99c9-c66fe9cce3d6
Fixed bug in OutputEventPort.cpp, where the for-loop did not start at 0.

git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@902 d1858a74-f715-0410-99c9-c66fe9cce3d6
Make KineticManager a subclass of KinCompt, set things up so that it
properly passes on volume scaling requests to the Stoich base
class. This fixes most volume scaling issues for simulations under
solver control.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@903 d1858a74-f715-0410-99c9-c66fe9cce3d6
included MPI on windows

git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@904 d1858a74-f715-0410-99c9-c66fe9cce3d6
Set max_buffered to 1 by default (cant be zero) for OutputEventPort

git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@905 d1858a74-f715-0410-99c9-c66fe9cce3d6
included testHsolve

git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@906 d1858a74-f715-0410-99c9-c66fe9cce3d6
Fixed up GSSA solver. Two problems: 
First, an issue with rate calculations for
reactions where any individual substrate had order >= 2. In such cases
the mol count has to be decremented for successive product terms in
the rate calculation. In the extreme case, the bug could give -ve mol
counts if we had 2A -> B when A started at 1.
Second, an error in the initialization that rounded things the 
wrong way for non-integral initial values of n.

Also added in the GSSA test directory.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@907 d1858a74-f715-0410-99c9-c66fe9cce3d6
Code for regularization of scratch Ids: master node handles requests for promotion
of scratch Ids from worker nodes.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@908 d1858a74-f715-0410-99c9-c66fe9cce3d6
pymoose_vcpp is updated.

git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@909 d1858a74-f715-0410-99c9-c66fe9cce3d6
Moved around code in Shell so it compiles in serial mode.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@910 d1858a74-f715-0410-99c9-c66fe9cce3d6
Adding "reinitClock" calls in ClockJob and Ticks. This reinits the Cj and ticks,
but not simulation objects. Used in pollPostmaster() to reinitialize the sched
system, before calling "step".



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@911 d1858a74-f715-0410-99c9-c66fe9cce3d6
Not filling elementList_ with postmaster ids, when alloting space to slaves.
Alloted space was meant to be left blank. This initialization was leading to
an assertion failure, when creating proxies in this space.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@912 d1858a74-f715-0410-99c9-c66fe9cce3d6
Changed channels_ vector in Music ports to hold Erefs instead of Ids.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@913 d1858a74-f715-0410-99c9-c66fe9cce3d6
Small change in the load-balancing: round-robin is used only if the parent is
root. Earlier it was used even when the parent was on node 0.

Also a small refinement in a hack in IdManager::allotMainIdBlock. This is put in
for the MUSIC demo. Need to fix.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@914 d1858a74-f715-0410-99c9-c66fe9cce3d6
Updated PyMOOSE to include new classes in robots directory.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@915 d1858a74-f715-0410-99c9-c66fe9cce3d6