From 0015fd23ea492c7c08f04a5b08aa27b88b7695f6 Mon Sep 17 00:00:00 2001
From: HarshaRani <ranishashi@gmail.com>
Date: Fri, 14 Apr 2017 18:52:59 +0530
Subject: [PATCH] Resolved merge conflict
---
moose-examples/snippets/intfire.py | 128 ++++++++++++++++++++
moose-examples/snippets/loadKineticModel.py | 100 +++++++++++++++
2 files changed, 228 insertions(+)
create mode 100644 moose-examples/snippets/intfire.py
create mode 100644 moose-examples/snippets/loadKineticModel.py
diff --git a/moose-examples/snippets/intfire.py b/moose-examples/snippets/intfire.py
new file mode 100644
index 00000000..35f8fcb9
--- /dev/null
+++ b/moose-examples/snippets/intfire.py
@@ -0,0 +1,128 @@
+<<<<<<< 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
new file mode 100644
index 00000000..25c3f69e
--- /dev/null
+++ b/moose-examples/snippets/loadKineticModel.py
@@ -0,0 +1,100 @@
+# 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()
--
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