Resolved merge conflict

moose-examples/snippets/intfire.py

+<<<<<<< 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

moose-examples/snippets/loadKineticModel.py

+# 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()