diff --git a/moose-examples/snippets/RandSpikeStats.py b/moose-examples/snippets/RandSpikeStats.py
index 377dc18b9659f1ad0c90b8a851aace2949605d60..725ae5d0ac9cc29af6fff70178ae2d747d7e4198 100644
--- a/moose-examples/snippets/RandSpikeStats.py
+++ b/moose-examples/snippets/RandSpikeStats.py
@@ -141,8 +141,6 @@ def main():
moose.setClock( i, dt )
moose.useClock( 8, '/plot#', 'process' )
'''
-
-
# Run the 'main' if this script is executed standalone.
if __name__ == '__main__':
main()
diff --git a/moose-examples/snippets/analogStimTable.py b/moose-examples/snippets/analogStimTable.py
index f7ce328caa05764ced9b49b6cccaf98204393e79..941de47ec9cf8bb309eee68a50e5cefa2d35dfc1 100644
--- a/moose-examples/snippets/analogStimTable.py
+++ b/moose-examples/snippets/analogStimTable.py
@@ -95,5 +95,6 @@ if __name__ == '__main__':
main()
>>>>>>> 0e491aa41584cf7a66c0e242374d8ee61660eb7b
+
#
# stimtable.py ends here
diff --git a/moose-examples/snippets/crossComptSimpleReac.py b/moose-examples/snippets/crossComptSimpleReac.py
index ddfea60bcdd8bedc6b1a615e371da0334e25706b..e3fffe80d3887f62251259dc95bd25a83a08c617 100644
--- a/moose-examples/snippets/crossComptSimpleReac.py
+++ b/moose-examples/snippets/crossComptSimpleReac.py
@@ -11,84 +11,84 @@
import math
import matplotlib.pyplot as plt
-import numpy
+import numpy as np
import moose
def makeModel():
- # create container for model
- model = moose.Neutral( 'model' )
- compt0 = moose.CubeMesh( '/model/compt0' )
- compt0.volume = 1e-15
- compt1 = moose.CubeMesh( '/model/compt1' )
- compt1.volume = 1e-16
- compt2 = moose.CubeMesh( '/model/compt2' )
- compt2.volume = 1e-17
-
- # Position containers so that they abut each other, with
- # compt1 in the middle.
- side = compt1.dy
- compt0.y1 += side
- compt0.y0 += side
- compt2.x1 += side
- compt2.x0 += side
- print(('Volumes = ', compt0.volume, compt1.volume, compt2.volume))
-
- # create molecules and reactions
- a = moose.Pool( '/model/compt0/a' )
- b = moose.Pool( '/model/compt1/b' )
- c = moose.Pool( '/model/compt2/c' )
- reac0 = moose.Reac( '/model/compt1/reac0' )
- reac1 = moose.Reac( '/model/compt1/reac1' )
-
- # connect them up for reactions
- moose.connect( reac0, 'sub', a, 'reac' )
- moose.connect( reac0, 'prd', b, 'reac' )
- moose.connect( reac1, 'sub', b, 'reac' )
- moose.connect( reac1, 'prd', c, 'reac' )
-
- # Assign parameters
- a.concInit = 1
- b.concInit = 12.1
- c.concInit = 1
- reac0.Kf = 0.1
- reac0.Kb = 0.1
- reac1.Kf = 0.1
- reac1.Kb = 0.1
-
- # Create the output tables
- graphs = moose.Neutral( '/model/graphs' )
- outputA = moose.Table2 ( '/model/graphs/concA' )
- outputB = moose.Table2 ( '/model/graphs/concB' )
- outputC = moose.Table2 ( '/model/graphs/concC' )
-
- # connect up the tables
- moose.connect( outputA, 'requestOut', a, 'getConc' );
- moose.connect( outputB, 'requestOut', b, 'getConc' );
- moose.connect( outputC, 'requestOut', c, 'getConc' );
-
- # Build the solvers. No need for diffusion in this version.
- ksolve0 = moose.Ksolve( '/model/compt0/ksolve0' )
- ksolve1 = moose.Ksolve( '/model/compt1/ksolve1' )
- ksolve2 = moose.Ksolve( '/model/compt2/ksolve2' )
- stoich0 = moose.Stoich( '/model/compt0/stoich0' )
- stoich1 = moose.Stoich( '/model/compt1/stoich1' )
- stoich2 = moose.Stoich( '/model/compt2/stoich2' )
-
- # Configure solvers
- stoich0.compartment = compt0
- stoich1.compartment = compt1
- stoich2.compartment = compt2
- stoich0.ksolve = ksolve0
- stoich1.ksolve = ksolve1
- stoich2.ksolve = ksolve2
- stoich0.path = '/model/compt0/#'
- stoich1.path = '/model/compt1/#'
- stoich2.path = '/model/compt2/#'
- stoich1.buildXreacs( stoich0 )
- stoich1.buildXreacs( stoich2 )
- stoich0.filterXreacs()
- stoich1.filterXreacs()
- stoich2.filterXreacs()
+ # create container for model
+ model = moose.Neutral( 'model' )
+ compt0 = moose.CubeMesh( '/model/compt0' )
+ compt0.volume = 1e-15
+ compt1 = moose.CubeMesh( '/model/compt1' )
+ compt1.volume = 1e-16
+ compt2 = moose.CubeMesh( '/model/compt2' )
+ compt2.volume = 1e-17
+
+ # Position containers so that they abut each other, with
+ # compt1 in the middle.
+ side = compt1.dy
+ compt0.y1 += side
+ compt0.y0 += side
+ compt2.x1 += side
+ compt2.x0 += side
+ print(('Volumes = ', compt0.volume, compt1.volume, compt2.volume))
+
+ # create molecules and reactions
+ a = moose.Pool( '/model/compt0/a' )
+ b = moose.Pool( '/model/compt1/b' )
+ c = moose.Pool( '/model/compt2/c' )
+ reac0 = moose.Reac( '/model/compt1/reac0' )
+ reac1 = moose.Reac( '/model/compt1/reac1' )
+
+ # connect them up for reactions
+ moose.connect( reac0, 'sub', a, 'reac' )
+ moose.connect( reac0, 'prd', b, 'reac' )
+ moose.connect( reac1, 'sub', b, 'reac' )
+ moose.connect( reac1, 'prd', c, 'reac' )
+
+ # Assign parameters
+ a.concInit = 1
+ b.concInit = 12.1
+ c.concInit = 1
+ reac0.Kf = 0.1
+ reac0.Kb = 0.1
+ reac1.Kf = 0.1
+ reac1.Kb = 0.1
+
+ # Create the output tables
+ graphs = moose.Neutral( '/model/graphs' )
+ outputA = moose.Table2 ( '/model/graphs/concA' )
+ outputB = moose.Table2 ( '/model/graphs/concB' )
+ outputC = moose.Table2 ( '/model/graphs/concC' )
+
+ # connect up the tables
+ moose.connect( outputA, 'requestOut', a, 'getConc' );
+ moose.connect( outputB, 'requestOut', b, 'getConc' );
+ moose.connect( outputC, 'requestOut', c, 'getConc' );
+
+ # Build the solvers. No need for diffusion in this version.
+ ksolve0 = moose.Ksolve( '/model/compt0/ksolve0' )
+ ksolve1 = moose.Ksolve( '/model/compt1/ksolve1' )
+ ksolve2 = moose.Ksolve( '/model/compt2/ksolve2' )
+ stoich0 = moose.Stoich( '/model/compt0/stoich0' )
+ stoich1 = moose.Stoich( '/model/compt1/stoich1' )
+ stoich2 = moose.Stoich( '/model/compt2/stoich2' )
+
+ # Configure solvers
+ stoich0.compartment = compt0
+ stoich1.compartment = compt1
+ stoich2.compartment = compt2
+ stoich0.ksolve = ksolve0
+ stoich1.ksolve = ksolve1
+ stoich2.ksolve = ksolve2
+ stoich0.path = '/model/compt0/#'
+ stoich1.path = '/model/compt1/#'
+ stoich2.path = '/model/compt2/#'
+ stoich1.buildXreacs( stoich0 )
+ stoich1.buildXreacs( stoich2 )
+ stoich0.filterXreacs()
+ stoich1.filterXreacs()
+ stoich2.filterXreacs()
@@ -142,13 +142,17 @@ def main():
# FIXME: Plotting causes seg-fault.
## Iterate through all plots, dump their contents to data.plot.
- #for x in moose.wildcardFind( '/model/graphs/conc#' ):
- # t = numpy.linspace( 0, runtime, x.vector.size ) # sec
- # plt.plot( t, x.vector, label=x.name )
- #plt.legend()
- #plt.show()
- #quit()
-
+ ### Temp fix, if try to save and plot the graph doesn't give seg fault
+ for x in moose.wildcardFind( '/model/graphs/conc#' ):
+ t = np.arange( 0, x.vector.size, 1) # sec
+ graphpath = x.name+".csv"
+ #t = np.linspace( 0, runtime,x.vector.size) # sec
+ f = open(graphpath, "w")
+ np.savetxt(graphpath, np.vstack((t*plotdt,x.vector)))
+ plt.plot( t, x.vector, label=x.name )
+ plt.legend()
+ plt.show()
+ quit()
# Run the 'main' if this script is executed standalone.
if __name__ == '__main__':
main()
diff --git a/moose-examples/snippets/cspaceSteadyState.py b/moose-examples/snippets/cspaceSteadyState.py
index 12ebb3b87ec413a3f6f29fd4b74f826a49041989..7cd2f012fa2b0b359d8f6aa3e515c9fc0976d0d1 100644
--- a/moose-examples/snippets/cspaceSteadyState.py
+++ b/moose-examples/snippets/cspaceSteadyState.py
@@ -13,28 +13,28 @@ import numpy
import moose
def displayPlots():
- for x in moose.wildcardFind( '/model/graphs/#' ):
- t = numpy.arange( 0, x.vector.size, 1 ) #sec
- pylab.plot( t, x.vector, label=x.name )
- pylab.legend()
- pylab.show()
+ for x in moose.wildcardFind( '/model/graphs/#' ):
+ t = numpy.arange( 0, x.vector.size, 1 ) #sec
+ pylab.plot( t, x.vector, label=x.name )
+ pylab.legend()
+ pylab.show()
def getState( ksolve, state ):
- state.randomInit()
- moose.start( 0.1 ) # Run the model for 2 seconds.
- state.settle()
- '''
- scale = 1.0 / ( 1e-15 * 6.022e23 )
- for x in ksolve.nVec[0]:
- print x * scale,
- # print ksolve.nVec[0]
- print state.nIter, state.status, state.stateType, state.nNegEigenvalues, state.nPosEigenvalues, state.solutionStatus
- '''
- moose.start( 20.0 ) # Run model for 10 seconds, just for display
+ state.randomInit()
+ moose.start( 0.1 ) # Run the model for 2 seconds.
+ state.settle()
+ '''
+ scale = 1.0 / ( 1e-15 * 6.022e23 )
+ for x in ksolve.nVec[0]:
+ print x * scale,
+ # print ksolve.nVec[0]
+ print state.nIter, state.status, state.stateType, state.nNegEigenvalues, state.nPosEigenvalues, state.solutionStatus
+ '''
+ moose.start( 20.0 ) # Run model for 10 seconds, just for display
def main():
- """
+ """
This example sets up the kinetic solver and steady-state finder, on
a bistable model.
It looks for the fixed points 100 times, as follows:
@@ -91,53 +91,53 @@ def main():
this algorithm!
You may wish to sample concentration space logarithmically rather than
linearly.
- """
- # The wildcard uses # for single level, and ## for recursive.
- #compartment = makeModel()
- moose.loadModel( '../genesis/M1719.cspace', '/model', 'ee' )
- compartment = moose.element( 'model/kinetics' )
- compartment.name = 'compartment'
- ksolve = moose.Ksolve( '/model/compartment/ksolve' )
- stoich = moose.Stoich( '/model/compartment/stoich' )
- stoich.compartment = compartment
- stoich.ksolve = ksolve
- #ksolve.stoich = stoich
- stoich.path = "/model/compartment/##"
- state = moose.SteadyState( '/model/compartment/state' )
-
- moose.reinit()
- state.stoich = stoich
- #state.showMatrices()
- state.convergenceCriterion = 1e-7
-
- moose.le( '/model/graphs' )
- a = moose.element( '/model/compartment/a' )
- b = moose.element( '/model/compartment/b' )
- c = moose.element( '/model/compartment/c' )
-
- for i in range( 0, 100 ):
- getState( ksolve, state )
-
- moose.start( 100.0 ) # Run the model for 100 seconds.
-
- b = moose.element( '/model/compartment/b' )
- c = moose.element( '/model/compartment/c' )
-
- # move most molecules over to b
- b.conc = b.conc + c.conc * 0.95
- c.conc = c.conc * 0.05
- moose.start( 100.0 ) # Run the model for 100 seconds.
-
- # move most molecules back to a
- c.conc = c.conc + b.conc * 0.95
- b.conc = b.conc * 0.05
- moose.start( 100.0 ) # Run the model for 100 seconds.
-
- # Iterate through all plots, dump their contents to data.plot.
- displayPlots()
-
- quit()
+ """
+ # The wildcard uses # for single level, and ## for recursive.
+ #compartment = makeModel()
+ moose.loadModel( '../genesis/M1719.cspace', '/model', 'ee' )
+ compartment = moose.element( 'model/kinetics' )
+ compartment.name = 'compartment'
+ ksolve = moose.Ksolve( '/model/compartment/ksolve' )
+ stoich = moose.Stoich( '/model/compartment/stoich' )
+ stoich.compartment = compartment
+ stoich.ksolve = ksolve
+ #ksolve.stoich = stoich
+ stoich.path = "/model/compartment/##"
+ state = moose.SteadyState( '/model/compartment/state' )
+
+ moose.reinit()
+ state.stoich = stoich
+ #state.showMatrices()
+ state.convergenceCriterion = 1e-7
+
+ moose.le( '/model/graphs' )
+ a = moose.element( '/model/compartment/a' )
+ b = moose.element( '/model/compartment/b' )
+ c = moose.element( '/model/compartment/c' )
+
+ for i in range( 0, 100 ):
+ getState( ksolve, state )
+
+ moose.start( 100.0 ) # Run the model for 100 seconds.
+
+ b = moose.element( '/model/compartment/b' )
+ c = moose.element( '/model/compartment/c' )
+
+ # move most molecules over to b
+ b.conc = b.conc + c.conc * 0.95
+ c.conc = c.conc * 0.05
+ moose.start( 100.0 ) # Run the model for 100 seconds.
+
+ # move most molecules back to a
+ c.conc = c.conc + b.conc * 0.95
+ b.conc = b.conc * 0.05
+ moose.start( 100.0 ) # Run the model for 100 seconds.
+
+ # Iterate through all plots, dump their contents to data.plot.
+ displayPlots()
+
+ quit()
# Run the 'main' if this script is executed standalone.
if __name__ == '__main__':
- main()
+ main()
diff --git a/moose-examples/snippets/funcInputToPools.py b/moose-examples/snippets/funcInputToPools.py
index 3a8d06fa28d574001d48d4282f01c713e4c9d4fe..45f5c1da9d4f826fe92e3fc5207852e698fef3e7 100644
--- a/moose-examples/snippets/funcInputToPools.py
+++ b/moose-examples/snippets/funcInputToPools.py
@@ -154,9 +154,6 @@ def makeModel():
stoich.compartment = compartment
stoich.ksolve = gsolve
stoich.path = '/model/compartment/##'
- '''
- '''
-
# We need a finer timestep than the default 0.1 seconds,
# in order to get numerical accuracy.
for i in range (10, 19 ):
@@ -164,27 +161,27 @@ def makeModel():
def main():
"""
- This example describes the special (and discouraged) use case where
- functions provide input to a reaction system. Here we have two functions of
- time which control the pool # and pool rate of change, respectively::
+This example describes the special (and discouraged) use case where
+functions provide input to a reaction system. Here we have two functions of
+time which control the pool # and pool rate of change, respectively::
- number of molecules of a = 1 + sin(t)
- rate of change of number of molecules of b = 10 * cos(t)
+number of molecules of a = 1 + sin(t)
+rate of change of number of molecules of b = 10 * cos(t)
- In the stochastic case one must set a special flag *useClockedUpdate*
- in order to achieve clock-triggered updates from the functions. This is
- needed because the functions do not have reaction events to trigger them,
- and even if there were reaction events they might not be frequent enough to
- track the periodic updates. The use of this flag slows down the calculations,
- so try to use a table to control a pool instead.
+In the stochastic case one must set a special flag *useClockedUpdate*
+in order to achieve clock-triggered updates from the functions. This is
+needed because the functions do not have reaction events to trigger them,
+and even if there were reaction events they might not be frequent enough to
+track the periodic updates. The use of this flag slows down the calculations,
+so try to use a table to control a pool instead.
- To run in stochastic mode::
+To run in stochastic mode::
- ''python funcInputToPools''
+ ''python funcInputToPools''
- To run in deterministic mode::
+To run in deterministic mode::
- ''python funcInputToPools false''
+ ''python funcInputToPools false''
"""
@@ -222,4 +219,4 @@ def main():
# Run the 'main' if this script is executed standalone.
if __name__ == '__main__':
- main()
+ main()
\ No newline at end of file
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()