diff --git a/moose-examples/snippets/intfire.py b/moose-examples/snippets/intfire.py deleted file mode 100644 index 35f8fcb9ea245df9b65b40afe7e5ee96ccb5115c..0000000000000000000000000000000000000000 --- a/moose-examples/snippets/intfire.py +++ /dev/null @@ -1,128 +0,0 @@ -<<<<<<< HEAD - -======= ->>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b -# intfire.py --- -# -# Filename: intfire.py -# Description: -# Author:Subhasis Ray -# Maintainer: -# Created: Thu Jun 21 16:40:25 2012 (+0530) -# Version: -# Last-Updated: Sat Jun 23 13:44:10 2012 (+0530) -# By: subha -# Update #: 35 -# URL: -# Keywords: -# Compatibility: -# -# - -# Commentary: -# -# Code snippet to show some operations on IntFire. -# -# - -# Change log: -# -# -# -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License as -# published by the Free Software Foundation; either version 3, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; see the file COPYING. If not, write to -# the Free Software Foundation, Inc., 51 Franklin Street, Fifth -# Floor, Boston, MA 02110-1301, USA. -# -# - -# Code: - -import moose - -def connect_two_intfires(): - """ -Connect two IntFire neurons so that spike events in one gets -transmitted to synapse of the other. -<<<<<<< HEAD -======= - ->>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b - """ - if1 = moose.IntFire('if1') - if2 = moose.IntFire('if2') - sf1 = moose.SimpleSynHandler( 'if1/sh' ) - moose.connect( sf1, 'activationOut', if1, 'activation' ) - sf1.synapse.num = 1 - syn1 = moose.element(sf1.synapse) - # Connect the spike message of if2 to the first synapse on if1 - moose.connect(if2, 'spikeOut', syn1, 'addSpike') - -def connect_spikegen(): - """ -Connect a SpikeGen object to an IntFire neuron such that spike -events in spikegen get transmitted to the synapse of the IntFire -neuron. - -<<<<<<< HEAD - """ - if3 = moose.IntFire('if3') -======= -if3 = moose.IntFire('if3') - """ ->>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b - sf3 = moose.SimpleSynHandler( 'if3/sh' ) - moose.connect( sf3, 'activationOut', if3, 'activation' ) - sf3.synapse.num = 1 - sg = moose.SpikeGen('sg') - syn = moose.element(sf3.synapse) - moose.connect(sg, 'spikeOut', syn, 'addSpike') - -def setup_synapse(): - """ -Create an intfire object and create two synapses on it. -<<<<<<< HEAD -======= - ->>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b - """ - if4 = moose.IntFire('if4') - sf4 = moose.SimpleSynHandler( 'if4/sh' ) - sg1 = moose.SpikeGen('sg1') - sg2 = moose.SpikeGen('sg2') - sf4.synapse.num = 2 # set synapse count to 2 - sf4.synapse[0].weight = 0.5 - sf4.synapse[0].delay = 1e-3 - sf4.synapse[1].weight = 2.0 - sf4.synapse[1].delay = 2e-3 - moose.connect(sg1, 'spikeOut', sf4.synapse[0], 'addSpike') - moose.connect(sg2, 'spikeOut', sf4.synapse[1], 'addSpike') - -def main(): - """ -Demonstrates connection between 2 IntFire neurons to observe -spike generation. -<<<<<<< HEAD -======= - ->>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b - """ - connect_two_intfires() - connect_spikegen() - setup_synapse() - -if __name__ == '__main__': - main() -# -# intfire.py ends here diff --git a/moose-examples/snippets/loadKineticModel.py b/moose-examples/snippets/loadKineticModel.py deleted file mode 100644 index 25c3f69e5144bc7419ca827e16314e41d1b4c0cb..0000000000000000000000000000000000000000 --- a/moose-examples/snippets/loadKineticModel.py +++ /dev/null @@ -1,100 +0,0 @@ -# loadKineticModel.py --- -# -# Filename: loadKineticModel.py -# Description: -# Author: Upi Bhalla -# Maintainer: -# Created: Sat Oct 04 12:14:15 2014 (+0530) -# Version: -# Last-Updated: -# By: -# Update #: 0 -# URL: -# Keywords: -# Compatibility: -# -# - -# Commentary: -# -# -# -# - -# Change log: -# -# -# -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License as -# published by the Free Software Foundation; either version 3, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; see the file COPYING. If not, write to -# the Free Software Foundation, Inc., 51 Franklin Street, Fifth -# Floor, Boston, MA 02110-1301, USA. -# -# -# Code: - -import moose -import pylab -import numpy -import sys - -def main(): - """ - This example illustrates loading, running, and saving a kinetic - model defined in kkit format. It uses a default kkit model but - you can specify another using the command line -<<<<<<< HEAD - - ``python filename runtime solver``. - -======= - ``python filename runtime solver``. ->>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b - We use the gsl solver here. - The model already defines a couple of plots and sets the runtime 20 secs. - - """ - solver = "gsl" # Pick any of gsl, gssa, ee.. - mfile = '../genesis/kkit_objects_example.g' - runtime = 20.0 - if ( len( sys.argv ) >= 3 ): - if sys.argv[1][0] == '/': - mfile = sys.argv[1] - else: - mfile = '../genesis/' + sys.argv[1] - runtime = float( sys.argv[2] ) - if ( len( sys.argv ) == 4 ): - solver = sys.argv[3] - modelId = moose.loadModel( mfile, 'model', solver ) - # Increase volume so that the stochastic solver gssa - # gives an interesting output - #compt = moose.element( '/model/kinetics' ) - #compt.volume = 1e-19 - - moose.reinit() - moose.start( runtime ) - - - # Display all plots. - for x in moose.wildcardFind( '/model/#graphs/conc#/#' ): - t = numpy.arange( 0, x.vector.size, 1 ) * x.dt - pylab.plot( t, x.vector, label=x.name ) - pylab.legend() - pylab.show() - - quit() - -# Run the 'main' if this script is executed standalone. -if __name__ == '__main__': - main()