Missed the IntFire in pymoose in last commit.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1083 d1858a74-f715-0410-99c9-c66fe9cce3d6
update in HHGate2D to create 2D interpols, instead of 1D.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1084 d1858a74-f715-0410-99c9-c66fe9cce3d6
PyMOOSE working - minor bug fixes.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1085 d1858a74-f715-0410-99c9-c66fe9cce3d6
Correction in IzhikevichNrn: earlier version assumed dt=1, now
corrected.
Added the Python demo and comparison with direct computation using
numpy and matplotlib.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1086 d1858a74-f715-0410-99c9-c66fe9cce3d6
Updated the example to run all 20 models described by Izhikevich. The
inputs are yet to be set up correctly for each neuron type.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1087 d1858a74-f715-0410-99c9-c66fe9cce3d6
In ReadCell, *start_cell wouldn't work if the given path had a global parent
object (e.g.: /library).

Fixed by requesting Shell to create the object on all nodes.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1088 d1858a74-f715-0410-99c9-c66fe9cce3d6
Ability to perform file2tab on interpols contained within HHChannels.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1089 d1858a74-f715-0410-99c9-c66fe9cce3d6
Added a nice GUI to Izhikevich model.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1090 d1858a74-f715-0410-99c9-c66fe9cce3d6
Fix in IdManager.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1091 d1858a74-f715-0410-99c9-c66fe9cce3d6
A little more refined version of Izhikevich model.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1092 d1858a74-f715-0410-99c9-c66fe9cce3d6
Option to pause moose right at startup using either an infinite loop, or by
waiting for keyboard command.

Notes:
Keyboard command more convenient usually, but sometimes the program just
won't wait for keyboard input. e.g.: when moose processes are spawned by music.
The infinite loop helps in debugging then.

To wait using keyboard input, give "-m" as _last_ argument.
To wait using the infinite loop, give "-mi" as the last argument.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1093 d1858a74-f715-0410-99c9-c66fe9cce3d6
Added an extra function for listing all fields of a PyMOOSE class.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1094 d1858a74-f715-0410-99c9-c66fe9cce3d6
implemented sumTotal and intercompartmental reaction

git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1095 d1858a74-f715-0410-99c9-c66fe9cce3d6
Introducing IdGenerator as a solution to ensure aligned Ids
for many global objects created with a single command.

Examples: ReadCell, copy (into a global path)

git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1096 d1858a74-f715-0410-99c9-c66fe9cce3d6
Fixed broken compile.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1097 d1858a74-f715-0410-99c9-c66fe9cce3d6
Load balancing during copy.



git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1098 d1858a74-f715-0410-99c9-c66fe9cce3d6
HHGate: Added initial value setting for X, Y and Z states
variables. The default is still lookup from table. But now one can
explicitly set X, Y, Z to arbitrary initial values. This was required
for handling KA channel by Traub et al (J Neurophysiol 89:909-921, 2003).


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1099 d1858a74-f715-0410-99c9-c66fe9cce3d6
Corrected pymoose code to properly set and get initX/Y/Z.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1100 d1858a74-f715-0410-99c9-c66fe9cce3d6
modified SbmlReader to handle intercompartmental reaction

git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1101 d1858a74-f715-0410-99c9-c66fe9cce3d6
Simplified HHChannel state variable initialization with boolean
flags. Now, instead of initX/Y/Z, one can just set the values
explicitly to flag that they have been manually overridden. Then
reset() will not reset these variables.


git-svn-id: https://svn.code.sf.net/p/moose/code/moose/trunk@1102 d1858a74-f715-0410-99c9-c66fe9cce3d6