def main(standalone=False):
mfile = os.path.join(os.path.dirname(__file__), 'OSC_diff_vols.g')
runtime = 4000.0
modelId = moose.loadModel(mfile, 'model', 'ee')
kin = moose.element('/model/kinetics')
compt1 = moose.element('/model/compartment_1')
compt1.x1 += kin.x1
compt1.x0 += kin.x1
fixXreacs.fixXreacs('/model')
#fixXreacs.restoreXreacs( '/model' )
#fixXreacs.fixXreacs( '/model' )
ks1 = moose.Ksolve('/model/kinetics/ksolve')
ds1 = moose.Dsolve('/model/kinetics/dsolve')
s1 = moose.Stoich('/model/kinetics/stoich')
s1.compartment = moose.element('/model/kinetics')
s1.ksolve = ks1
s1.dsolve = ds1
s1.path = '/model/kinetics/##'
ks2 = moose.Ksolve('/model/compartment_1/ksolve')
ds2 = moose.Dsolve('/model/compartment_1/dsolve')
s2 = moose.Stoich('/model/compartment_1/stoich')
s2.compartment = moose.element('/model/compartment_1')
s2.ksolve = ks2
s2.dsolve = ds2
s2.path = '/model/compartment_1/##'
ds2.buildMeshJunctions(ds1)
moose.reinit()
moose.start(runtime)
# I don't have an analytic way to assess oscillations
assert (countCrossings('/model/graphs/conc2/M.Co', 0.001) == 4)
moose.delete('/model')
def makeModel():
# create container for model
num = 1 # number of compartments
model = moose.Neutral( '/model' )
compartment = moose.CylMesh( '/model/compartment' )
compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
# create molecules and reactions
s = moose.Pool( '/model/compartment/s' )
#####################################################################
# Put in endo compartment. Add molecule s
endo = moose.EndoMesh( '/model/endo' )
endo.isMembraneBound = True
endo.surround = compartment
es = moose.Pool( '/model/endo/s' )
rXfer = moose.Reac( '/model/endo/rXfer' )
#####################################################################
moose.connect( rXfer, 'sub', s, 'reac' )
moose.connect( rXfer, 'prd', es, 'reac' )
volRatio = compartment.volume / endo.volume
rXfer.Kf = 0.04 # 0.04/sec
rXfer.Kb = 0.02 # 0.02/sec
#####################################################################
fixXreacs.fixXreacs( '/model' )
#fixXreacs.restoreXreacs( '/model' )
#fixXreacs.fixXreacs( '/model' )
#####################################################################
# Make solvers
ksolve = moose.Ksolve( '/model/compartment/ksolve' )
dsolve = moose.Dsolve( '/model/dsolve' )
eksolve = moose.Ksolve( '/model/endo/ksolve' )
edsolve = moose.Dsolve( '/model/endo/dsolve' )
stoich = moose.Stoich( '/model/compartment/stoich' )
stoich.compartment = compartment
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.path = "/model/compartment/##"
assert( dsolve.numPools == 1 )
s.vec.concInit = [1]*num
estoich = moose.Stoich( '/model/endo/stoich' )
estoich.compartment = endo
estoich.ksolve = eksolve
estoich.dsolve = edsolve
estoich.path = "/model/endo/##"
assert( edsolve.numPools == 2 )
edsolve.buildMeshJunctions( dsolve )
plot1 = moose.Table2( '/model/plot1' )
plot2 = moose.Table2( '/model/plot2' )
moose.connect( '/model/plot1', 'requestOut', s, 'getN' )
moose.connect( '/model/plot2', 'requestOut', es, 'getN' )
plot3 = moose.Table2( '/model/plot3' )
plot4 = moose.Table2( '/model/plot4' )
moose.connect( '/model/plot3', 'requestOut', s, 'getConc' )
moose.connect( '/model/plot4', 'requestOut', es, 'getConc' )
def main():
"""
This example illustrates loading and running a reaction system that
spans two volumes, that is, is in different compartments. It uses a
kkit model file. You can tell if it is working if you see nice
relaxation oscillations.
"""
# the kkit reader doesn't know how to do multicompt solver setup.
solver = "ee"
mfile = '../Genesis_files/OSC_diff_vols.g'
runtime = 3000.0
simDt = 1.0
modelId = moose.loadModel(mfile, 'model', solver)
#moose.delete( '/model/kinetics/A/Stot' )
compt0 = moose.element('/model/kinetics')
compt1 = moose.element('/model/compartment_1')
assert (deq(compt0.volume, 2e-20))
assert (deq(compt1.volume, 1e-20))
dy = compt0.dy
compt1.y1 += dy
compt1.y0 = dy
assert (deq(compt1.volume, 1e-20))
# We now have two cubes adjacent to each other. Compt0 has 2x vol.
# Compt1 touches it.
stoich0 = moose.Stoich('/model/kinetics/stoich')
stoich1 = moose.Stoich('/model/compartment_1/stoich')
ksolve0 = moose.Ksolve('/model/kinetics/ksolve')
ksolve1 = moose.Ksolve('/model/compartment_1/ksolve')
stoich0.compartment = compt0
stoich0.ksolve = ksolve0
stoich0.path = '/model/kinetics/##'
stoich1.compartment = compt1
stoich1.ksolve = ksolve1
stoich1.path = '/model/compartment_1/##'
#stoich0.buildXreacs( stoich1 )
print ksolve0.numLocalVoxels, ksolve0.numPools, stoich0.numAllPools
assert (ksolve0.numLocalVoxels == 1)
assert (ksolve0.numPools == 7)
assert (stoich0.numAllPools == 6)
print len(stoich0.proxyPools[stoich1]),
print len(stoich1.proxyPools[stoich0])
assert (len(stoich0.proxyPools[stoich1]) == 1)
assert (len(stoich1.proxyPools[stoich0]) == 1)
print ksolve1.numLocalVoxels, ksolve1.numPools, stoich1.numAllPools
assert (ksolve1.numLocalVoxels == 1)
assert (ksolve1.numPools == 6)
assert (stoich1.numAllPools == 5)
stoich0.buildXreacs(stoich1)
print moose.element('/model/kinetics/endo')
print moose.element('/model/compartment_1/exo')
moose.le('/model/compartment_1')
moose.reinit()
moose.start(runtime)
# Display all plots.
for x in moose.wildcardFind('/model/#graphs/conc#/#'):
t = numpy.arange(0, x.vector.size, 1) * simDt
pylab.plot(t, x.vector, label=x.name)
pylab.legend()
pylab.show()
def _configureSolvers(self):
if not hasattr(self, 'chemid'):
return
if not hasattr(self, 'dendCompt'):
raise BuildError("configureSolvers: no chem meshes defined.")
dmksolve = moose.Ksolve(self.dendCompt.path + '/ksolve')
dmdsolve = moose.Dsolve(self.dendCompt.path + '/dsolve')
dmstoich = moose.Stoich(self.dendCompt.path + '/stoich')
dmstoich.compartment = self.dendCompt
dmstoich.ksolve = dmksolve
dmstoich.dsolve = dmdsolve
dmstoich.path = self.dendCompt.path + "/##"
# Below we have code that only applies if there are spines
# Put in spine solvers. Note that these get info from the dendCompt
if hasattr(self, 'spineCompt'):
if self.useGssa:
smksolve = moose.Gsolve(self.spineCompt.path + '/ksolve')
else:
smksolve = moose.Ksolve(self.spineCompt.path + '/ksolve')
smdsolve = moose.Dsolve(self.spineCompt.path + '/dsolve')
smstoich = moose.Stoich(self.spineCompt.path + '/stoich')
smstoich.compartment = self.spineCompt
smstoich.ksolve = smksolve
smstoich.dsolve = smdsolve
smstoich.path = self.spineCompt.path + "/##"
# Put in PSD solvers. Note that these get info from the dendCompt
if self.useGssa:
pmksolve = moose.Gsolve(self.psdCompt.path + '/ksolve')
else:
pmksolve = moose.Ksolve(self.psdCompt.path + '/ksolve')
pmdsolve = moose.Dsolve(self.psdCompt.path + '/dsolve')
pmstoich = moose.Stoich(self.psdCompt.path + '/stoich')
pmstoich.compartment = self.psdCompt
pmstoich.ksolve = pmksolve
pmstoich.dsolve = pmdsolve
pmstoich.path = self.psdCompt.path + "/##"
# Put in cross-compartment diffusion between ksolvers
dmdsolve.buildNeuroMeshJunctions(smdsolve, pmdsolve)
# Put in cross-compartment reactions between ksolvers
smstoich.buildXreacs(pmstoich)
#pmstoich.buildXreacs( smstoich )
smstoich.buildXreacs(dmstoich)
dmstoich.filterXreacs()
smstoich.filterXreacs()
pmstoich.filterXreacs()
# set up the connections so that the spine volume scaling can happen
self.elecid.setSpineAndPsdMesh(self.spineCompt, self.psdCompt)
self.elecid.setSpineAndPsdDsolve(smdsolve, pmdsolve)
def test_xreac2():
mfile = os.path.join(os.path.dirname(__file__), 'OSC_diff_vols.g')
runtime = 4000.0
modelId = moose.loadModel(mfile, 'model', 'ee')
kin = moose.element('/model/kinetics')
compt1 = moose.element('/model/compartment_1')
compt1.x1 += kin.x1
compt1.x0 += kin.x1
# for r in moose.wildcardFind('/##[TYPE=Reac]'):
# print("---", r)
# print(r.neighbors['sub'])
# print(r.neighbors['prd'])
fixXreacs.fixXreacs('/model')
#fixXreacs.restoreXreacs( '/model' )
#fixXreacs.fixXreacs( '/model' )
print('After fixing...')
for r in moose.wildcardFind('/##[TYPE=Reac]'):
print("---", r)
print(r.neighbors['sub'])
print(r.neighbors['prd'])
ks1 = moose.Ksolve('/model/kinetics/ksolve')
ds1 = moose.Dsolve('/model/kinetics/dsolve')
s1 = moose.Stoich('/model/kinetics/stoich')
s1.compartment = moose.element('/model/kinetics')
s1.ksolve = ks1
s1.dsolve = ds1
s1.path = '/model/kinetics/##'
ks2 = moose.Ksolve('/model/compartment_1/ksolve')
ds2 = moose.Dsolve('/model/compartment_1/dsolve')
s2 = moose.Stoich('/model/compartment_1/stoich')
s2.compartment = moose.element('/model/compartment_1')
s2.ksolve = ks2
s2.dsolve = ds2
s2.path = '/model/compartment_1/##'
print(ds1)
ds2.buildMeshJunctions(ds1)
moose.reinit()
moose.start(runtime)
# I don't have an analytic way to assess oscillations
nCrossings = countCrossings('/model/graphs/conc2/M.Co', 0.001)
assert (nCrossings == 4), "Expected 4, got %d" % nCrossings
moose.delete('/model')
def main():
makeModel()
'''
'''
ksolve = moose.Ksolve('/model/compartment/ksolve')
stoich = moose.Stoich('/model/compartment/stoich')
stoich.compartment = moose.element('/model/compartment')
stoich.ksolve = ksolve
stoich.path = "/model/compartment/##"
#solver.method = "rk5"
#mesh = moose.element( "/model/compartment/mesh" )
#moose.connect( mesh, "remesh", solver, "remesh" )
'''
moose.setClock( 5, 1.0 ) # clock for the solver
moose.useClock( 5, '/model/compartment/ksolve', 'process' )
'''
moose.reinit()
moose.start(100.0) # Run the model for 100 seconds.
func = moose.element('/model/compartment/d/func')
if useY:
func.expr = "-y0 + 10*y1"
else:
func.expr = "-x0 + 10*x1"
moose.start(100.0) # Run the model for 100 seconds.
#moose.showfields( '/model/compartment/d' )
#moose.showfields( '/model/compartment/d/func' )
print((func.x.value))
print((moose.element('/model/compartment/b').n))
# Iterate through all plots, dump their contents to data.plot.
displayPlots()
quit()
def setup_solvers():
global compt_
s = moose.Stoich('%s/stoich' % compt_.path)
k = moose.Ksolve('%s/ksolve' % compt_.path)
s.ksolve = k
s.compartment = compt_
s.path = '%s/##' % compt_.path
def singleCompt(name, params):
mod = moose.copy('/library/' + name + '/' + name, '/model')
A = moose.element(mod.path + '/A')
Z = moose.element(mod.path + '/Z')
Z.nInit = 1
Ca = moose.element(mod.path + '/Ca')
CaStim = moose.element(Ca.path + '/CaStim')
runtime = params['preStimTime'] + params['stimWidth'] + params[
'postStimTime']
steptime = 100
CaStim.expr += ' + x2 * (t > ' + str(runtime) + ' ) * ( t < ' + str(
runtime + steptime) + ' )'
print CaStim.expr
tab = moose.Table2('/model/' + name + '/Atab')
#for i in range( 10, 19 ):
#moose.setClock( i, 0.01 )
ampl = moose.element(mod.path + '/ampl')
phase = moose.element(mod.path + '/phase')
moose.connect(tab, 'requestOut', A, 'getN')
ampl.nInit = params['stimAmplitude'] * 1
phase.nInit = params['preStimTime']
ksolve = moose.Ksolve(mod.path + '/ksolve')
stoich = moose.Stoich(mod.path + '/stoich')
stoich.compartment = mod
stoich.ksolve = ksolve
stoich.path = mod.path + '/##'
runtime += 2 * steptime
moose.reinit()
moose.start(runtime)
t = np.arange(0, runtime + 1e-9, tab.dt)
return name, t, tab.vector
def singleCompt(name, params):
print('=============')
print('[INFO] Making compartment %s' % name)
mod = moose.copy('/library/' + name + '/' + name, '/model')
A = moose.element(mod.path + '/A')
Z = moose.element(mod.path + '/Z')
Z.nInit = 1
Ca = moose.element(mod.path + '/Ca')
CaStim = moose.element(Ca.path + '/CaStim')
print('\n\n[INFO] CaStim %s' % CaStim.path)
runtime = params['preStimTime'] + params['postStimTime']
steptime = 50
CaStim.expr += '+x2*(t>100+' + str(runtime) + ')*(t<100+' + str(
runtime + steptime) + ')'
print("[INFO] CaStim.expr = %s" % CaStim.expr)
tab = moose.Table2('/model/' + name + '/Atab')
ampl = moose.element(mod.path + '/ampl')
phase = moose.element(mod.path + '/phase')
moose.connect(tab, 'requestOut', A, 'getN')
ampl.nInit = params['stimAmplitude'] * 1
phase.nInit = params['preStimTime']
ksolve = moose.Ksolve(mod.path + '/ksolve')
stoich = moose.Stoich(mod.path + '/stoich')
stoich.compartment = mod
stoich.ksolve = ksolve
stoich.path = mod.path + '/##'
print('REINIT AND START')
moose.reinit()
runtime += 100 + steptime * 2
moose.start(runtime)
t = np.arange(0, runtime + 1e-9, tab.dt)
return name, t, tab.vector
def setupSteadyState(simdt, plotDt):
stoich = moose.Stoich('/model/kinetics/stoich')
ksolve = moose.Ksolve('/model/kinetics/ksolve')
stoich.compartment = moose.element('/model/kinetics')
stoich.ksolve = ksolve
#ksolve.stoich = stoich
stoich.path = "/model/kinetics/##"
state = moose.SteadyState('/model/kinetics/state')
#### Set clocks here
#moose.useClock(4, "/model/kinetics/##[]", "process")
#moose.setClock(4, float(simdt))
#moose.setClock(5, float(simdt))
#moose.useClock(5, '/model/kinetics/ksolve', 'process' )
#moose.useClock(8, '/model/graphs/#', 'process' )
#moose.setClock(8, float(plotDt))
moose.reinit()
state.stoich = stoich
state.showMatrices()
state.convergenceCriterion = 1e-8
return ksolve, state
def main():
makeModel()
ksolve = moose.Ksolve('/model/compartment/ksolve')
stoich = moose.Stoich('/model/compartment/stoich')
stoich.compartment = moose.element('/model/compartment')
stoich.ksolve = ksolve
stoich.path = "/model/compartment/##"
#solver.method = "rk5"
#mesh = moose.element( "/model/compartment/mesh" )
#moose.connect( mesh, "remesh", solver, "remesh" )
'''
moose.setClock( 5, 1.0 ) # clock for the solver
moose.useClock( 5, '/model/compartment/ksolve', 'process' )
'''
moose.reinit()
moose.start(100.0) # Run the model for 100 seconds.
a = moose.element('/model/compartment/a')
b = moose.element('/model/compartment/b')
# move most molecules over to b
b.conc = b.conc + a.conc * 0.9
a.conc = a.conc * 0.1
moose.start(100.0) # Run the model for 100 seconds.
# move most molecules back to a
a.conc = a.conc + b.conc * 0.99
b.conc = b.conc * 0.01
moose.start(100.0) # Run the model for 100 seconds.
# Iterate through all plots, dump their contents to data.plot.
displayPlots()
quit()
def main():
"""
This example implements a reaction-diffusion like system which is
bistable and propagates losslessly. It is based on the NEURON example
rxdrun.py, but incorporates more compartments and runs for a longer time.
The system is implemented in a function rather than as a proper system
of chemical reactions. Please see rxdReacDiffusion.py for a variant that
uses a reaction plus a function object to control its rates.
"""
dt = 0.1
# define the geometry
compt = moose.CylMesh('/cylinder')
compt.r0 = compt.r1 = 1
compt.diffLength = 0.2
compt.x1 = 100
assert (compt.numDiffCompts == compt.x1 / compt.diffLength)
#define the molecule. Its geometry is defined by its parent volume, cylinder
c = moose.Pool('/cylinder/pool')
c.diffConst = 1 # define diffusion constant
# Here we set up a function calculation
func = moose.Function('/cylinder/pool/func')
func.expr = "-x0 * (0.3 - x0) * (1 - x0)"
func.x.num = 1 #specify number of input variables.
#Connect the molecules to the func
moose.connect(c, 'nOut', func.x[0], 'input')
#Connect the function to the pool
moose.connect(func, 'valueOut', c, 'increment')
#Set up solvers
ksolve = moose.Ksolve('/cylinder/ksolve')
dsolve = moose.Dsolve('/cylinder/dsolve')
stoich = moose.Stoich('/cylinder/stoich')
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.compartment = compt
stoich.reacSystemPath = '/cylinder/##'
#initialize
x = numpy.arange(0, compt.x1, compt.diffLength)
c.vec.nInit = [(q < 0.2 * compt.x1) for q in x]
# Run and plot it.
moose.reinit()
updateDt = 50
runtime = updateDt * 4
plt = pylab.plot(x, c.vec.n, label='t = 0 ')
t1 = time.time()
for t in range(0, runtime - 1, updateDt):
moose.start(updateDt)
plt = pylab.plot(x, c.vec.n, label='t = ' + str(t + updateDt))
print(("Time = %f " % (time.time() - t1)))
print(("Time = %s " % (time.time() - t1)))
pylab.ylim(0, 1.05)
pylab.legend()
pylab.show()
def makeModel():
if len(sys.argv) == 1:
useGsolve = True
else:
useGsolve = (sys.argv[1] == 'True')
# create container for model
model = moose.Neutral('model')
compartment = moose.CubeMesh('/model/compartment')
compartment.volume = 1e-22
# the mesh is created automatically by the compartment
moose.le('/model/compartment')
mesh = moose.element('/model/compartment/mesh')
# create molecules and reactions
a = moose.Pool('/model/compartment/a')
b = moose.Pool('/model/compartment/b')
# create functions of time
f1 = moose.Function('/model/compartment/f1')
f2 = moose.Function('/model/compartment/f2')
# connect them up for reactions
moose.connect(f1, 'valueOut', a, 'setConc')
moose.connect(f2, 'valueOut', b, 'increment')
# Assign parameters
a.concInit = 0
b.concInit = 1
#f1.numVars = 1
#f2.numVars = 1
f1.expr = '1 + sin(t)'
f2.expr = '10 * cos(t)'
# Create the output tables
graphs = moose.Neutral('/model/graphs')
outputA = moose.Table2('/model/graphs/nA')
outputB = moose.Table2('/model/graphs/nB')
# connect up the tables
moose.connect(outputA, 'requestOut', a, 'getN')
moose.connect(outputB, 'requestOut', b, 'getN')
# Set up the solvers
if useGsolve:
gsolve = moose.Gsolve('/model/compartment/gsolve')
gsolve.useClockedUpdate = True
else:
gsolve = moose.Ksolve('/model/compartment/gsolve')
stoich = moose.Stoich('/model/compartment/stoich')
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):
moose.setClock(i, 0.1) # for computational objects
def _configureSolvers(self):
dmksolve = moose.Ksolve(self.dendCompt.path + '/ksolve')
dmdsolve = moose.Dsolve(self.dendCompt.path + '/dsolve')
dmstoich = moose.Stoich(self.dendCompt.path + '/stoich')
dmstoich.compartment = self.dendCompt
dmstoich.ksolve = dmksolve
dmstoich.dsolve = dmdsolve
dmstoich.path = self.dendCompt.path + "/##"
print 'Dend solver: numPools = ', dmdsolve.numPools, \
', nvox= ', self.dendCompt.mesh.num, dmksolve.numAllVoxels
# Put in spine solvers. Note that these get info from the dendCompt
if self.useGssa:
smksolve = moose.Gsolve(self.spineCompt.path + '/ksolve')
else:
smksolve = moose.Ksolve(self.spineCompt.path + '/ksolve')
smdsolve = moose.Dsolve(self.spineCompt.path + '/dsolve')
smstoich = moose.Stoich(self.spineCompt.path + '/stoich')
smstoich.compartment = self.spineCompt
smstoich.ksolve = smksolve
smstoich.dsolve = smdsolve
smstoich.path = self.spineCompt.path + "/##"
print 'spine num Pools = ', smstoich.numAllPools, \
', nvox= ', self.spineCompt.mesh.num, smksolve.numAllVoxels
# Put in PSD solvers. Note that these get info from the dendCompt
if self.useGssa:
pmksolve = moose.Gsolve(self.psdCompt.path + '/ksolve')
else:
pmksolve = moose.Ksolve(self.psdCompt.path + '/ksolve')
pmdsolve = moose.Dsolve(self.psdCompt.path + '/dsolve')
pmstoich = moose.Stoich(self.psdCompt.path + '/stoich')
pmstoich.compartment = self.psdCompt
pmstoich.ksolve = pmksolve
pmstoich.dsolve = pmdsolve
pmstoich.path = self.psdCompt.path + "/##"
print 'psd num Pools = ', pmstoich.numAllPools, \
', voxels=', self.psdCompt.mesh.num, pmksolve.numAllVoxels
# Put in cross-compartment diffusion between ksolvers
dmdsolve.buildNeuroMeshJunctions(smdsolve, pmdsolve)
# Put in cross-compartment reactions between ksolvers
smstoich.buildXreacs(pmstoich)
smstoich.buildXreacs(dmstoich)
#smstoich.buildXreacs( pmstoich )
dmstoich.filterXreacs()
smstoich.filterXreacs()
pmstoich.filterXreacs()
def makeModel():
# create container for model
r0 = 2e-6 # m
r1 = 1e-6 # m
num = 100
diffLength = 1e-6 # m
len = num * diffLength # m
diffConst = 10e-12 # m^2/sec
motorRate = 10e-6 # m/sec
concA = 1 # millimolar
model = moose.Neutral( 'model' )
compartment = moose.CylMesh( '/model/compartment' )
compartment.r0 = r0
compartment.r1 = r1
compartment.x0 = 0
compartment.x1 = len
compartment.diffLength = diffLength
assert( compartment.numDiffCompts == num )
# create molecules and reactions
a = moose.Pool( '/model/compartment/a' )
b = moose.Pool( '/model/compartment/b' )
c = moose.Pool( '/model/compartment/c' )
d = moose.BufPool( '/model/compartment/d' )
r1 = moose.Reac( '/model/compartment/r1' )
moose.connect( r1, 'sub', b, 'reac' )
moose.connect( r1, 'sub', d, 'reac' )
moose.connect( r1, 'prd', c, 'reac' )
r1.Kf = 1.0 # 1/(mM.sec)
r1.Kb = 1.0 # 1/sec
# Assign parameters
a.diffConst = diffConst
b.diffConst = diffConst / 2.0
b.motorConst = motorRate
c.diffConst = 0
d.diffConst = diffConst
# Make solvers
ksolve = moose.Ksolve( '/model/compartment/ksolve' )
dsolve = moose.Dsolve( '/model/compartment/dsolve' )
stoich = moose.Stoich( '/model/compartment/stoich' )
stoich.compartment = compartment
stoich.ksolve = ksolve
stoich.dsolve = dsolve
os.kill( PID, signal.SIGUSR1 )
stoich.path = "/model/compartment/##"
print((dsolve.numPools))
assert( dsolve.numPools == 3 )
a.vec[0].concInit = concA
b.vec[0].concInit = concA
c.vec[0].concInit = concA
d.vec.concInit = concA / 5.0
d.vec[num-1].concInit = concA
def main():
"""
funcRateHarmonicOsc illustrates the use of function objects to
directly define the rates of change of pool concentration. This
example shows how to set up a simple harmonic oscillator system
of differential equations using the script. In normal use one would
prefer to use SBML.
The equations are ::
p' = v - offset1
v' = -k(p - offset2)
where the rates for Pools p and v are computed using Functions.
Note the use of offsets. This is because MOOSE chemical
systems cannot have negative concentrations.
The model is set up to run using default Exponential Euler
integration, and then using the GSL deterministic solver.
"""
makeModel()
for i in range( 11, 18 ):
moose.setClock( i, 0.01 )
moose.setClock( 18, 0.1 )
moose.reinit()
moose.start( runtime ) # Run the model
# Iterate through all plots, dump their contents to data.plot.
for x in moose.wildcardFind( '/model/graphs/#' ):
#x.xplot( 'scriptKineticModel.plot', x.name )
t = numpy.arange( 0, x.vector.size, 1 ) * x.dt # sec
pylab.plot( t, x.vector, label=x.name )
pylab.suptitle( "Integration using ee" )
pylab.legend()
pylab.figure()
compt = moose.element( '/model/harmonic' )
ksolve = moose.Ksolve( '/model/harmonic/ksolve' )
stoich = moose.Stoich( '/model/harmonic/stoich' )
stoich.compartment = compt
stoich.ksolve = ksolve
stoich.path = '/model/harmonic/##'
for i in range( 11, 18 ):
moose.setClock( i, 0.1 )
moose.reinit()
moose.start( runtime ) # Run the model
for x in moose.wildcardFind( '/model/graphs/#' ):
t = numpy.arange( 0, x.vector.size, 1 ) * x.dt # sec
pylab.plot( t, x.vector, label=x.name )
pylab.suptitle( "Integration using gsl" )
pylab.legend()
pylab.show()
quit()
def loadChem():
chem = moose.Neutral('/model/chem')
modelId = moose.loadModel(
os.path.join(scriptDir, '..', 'genesis', 'chanPhosphByCaMKII.g'),
'/model/chem', 'ee')
stoich = moose.Stoich('/model/chem/kinetics/stoich')
ksolve = moose.Ksolve('/model/chem/kinetics/ksolve')
stoich.compartment = moose.element('/model/chem/kinetics')
stoich.ksolve = ksolve
stoich.path = "/model/chem/##"
def main(standalone=False):
mfile = os.path.join(os.path.dirname(__file__), 'OSC_diff_vols.g')
runtime = 4000.0
modelId = moose.loadModel(mfile, 'model', 'ee')
kin = moose.element('/model/kinetics')
compt1 = moose.element('/model/compartment_1')
compt1.x1 += kin.x1
compt1.x0 += kin.x1
fixXreacs.fixXreacs('/model')
#fixXreacs.restoreXreacs( '/model' )
#fixXreacs.fixXreacs( '/model' )
ks1 = moose.Ksolve('/model/kinetics/ksolve')
ds1 = moose.Dsolve('/model/kinetics/dsolve')
s1 = moose.Stoich('/model/kinetics/stoich')
s1.compartment = moose.element('/model/kinetics')
s1.ksolve = ks1
s1.dsolve = ds1
s1.path = '/model/kinetics/##'
ks2 = moose.Ksolve('/model/compartment_1/ksolve')
ds2 = moose.Dsolve('/model/compartment_1/dsolve')
s2 = moose.Stoich('/model/compartment_1/stoich')
s2.compartment = moose.element('/model/compartment_1')
s2.ksolve = ks2
s2.dsolve = ds2
s2.path = '/model/compartment_1/##'
ds2.buildMeshJunctions(ds1)
moose.reinit()
moose.start(runtime)
# I don't have an analytic way to assess oscillations
assert (countCrossings('/model/graphs/conc2/M.Co', 0.001) == 4)
if standalone:
# Display all plots.
for x in moose.wildcardFind('/model/#graphs/conc#/#'):
t = np.arange(0, x.vector.size, 1) * x.dt
plt.plot(t, x.vector, label=x.name)
plt.legend()
plt.show()
moose.delete('/model')
def setCompartmentSolver(modelRoot, solver):
comptlist = dict(
(c, c.volume)
for c in moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]'))
comptVol = {}
compts = []
vol = [v for k, v in comptlist.items()]
volumeSort = sorted(vol)
for k, v in comptlist.items():
comptVol[k] = v
for volSor in volumeSort:
for a, b in comptVol.items():
if b == volSor:
compts.append(a)
#compts = [key for key, value in sorted(comptlist.items(), key=lambda (k,v): (v,k))]
if (len(compts) == '0'):
print("Atleast one compartment is required ")
return
else:
if (len(compts) > 3):
print("Warning: setSolverOnCompt Cannot handle ", len(compts),
" chemical compartments\n")
return
elif (len(compts) > 1):
positionCompt(compts)
if solver != 'ee' or solver != "Exponential Euler":
fixXreacs(modelRoot)
for compt in compts:
if solver != 'ee':
if (solver == 'gsl') or (solver == 'Runge Kutta'):
ksolve = moose.Ksolve(compt.path + '/ksolve')
if (solver == 'gssa') or (solver == 'Gillespie'):
ksolve = moose.Gsolve(compt.path + '/gsolve')
dsolve = moose.Dsolve(compt.path + '/dsolve')
stoich = moose.Stoich(compt.path + '/stoich')
stoich.compartment = compt
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.path = compt.path + "/##"
ksolveList = moose.wildcardFind(modelRoot + '/##[ISA=Ksolve]')
dsolveList = moose.wildcardFind(modelRoot + '/##[ISA=Dsolve]')
stoichList = moose.wildcardFind(modelRoot + '/##[ISA=Stoich]')
i = 0
while (i < len(dsolveList) - 1):
dsolveList[i + 1].buildMeshJunctions(dsolveList[i])
i += 1
print("Solver is added to model path %s" % modelRoot)
'''
def makeModel():
model = moose.Neutral('/model')
# Make neuronal model. It has no channels, just for geometry
cell = moose.loadModel('./branching.p', '/model/cell', 'Neutral')
# We don't want the cell to do any calculations. Disable everything.
for i in moose.wildcardFind('/model/cell/##'):
i.tick = -1
# create container for model
model = moose.element('/model')
chem = moose.Neutral('/model/chem')
# The naming of the compartments is dicated by the places that the
# chem model expects to be loaded.
compt0 = moose.NeuroMesh('/model/chem/compt0')
compt0.separateSpines = 0
compt0.geometryPolicy = 'cylinder'
#reacSystem = moose.loadModel( 'simpleOsc.g', '/model/chem', 'ee' )
makeChemModel(compt0) # Populate all compt with the chem system.
compt0.diffLength = 1e-6 # This will be over 100 compartments.
# This is the magic command that configures the diffusion compartments.
compt0.subTreePath = "/model/cell/#"
#compt0.cell = cell
# Build the solvers. No need for diffusion in this version.
ksolve0 = moose.Ksolve('/model/chem/compt0/ksolve')
dsolve0 = moose.Dsolve('/model/chem/compt0/dsolve')
stoich0 = moose.Stoich('/model/chem/compt0/stoich')
# Configure solvers
stoich0.compartment = compt0
stoich0.ksolve = ksolve0
stoich0.dsolve = dsolve0
stoich0.path = '/model/chem/compt0/#'
assert (stoich0.numVarPools == 2)
assert (stoich0.numProxyPools == 0)
assert (stoich0.numRates == 0)
moose.element('/model/chem/compt0/a[0]').concInit = aConcInit
twigs = findTwigs(compt0)
print(('twigs = ', twigs))
for i in twigs:
e = moose.element('/model/chem/compt0/b[' + str(i) + ']')
e.concInit = bConcInit
# Create the output tables
graphs = moose.Neutral('/model/graphs')
makeTab('a_soma', '/model/chem/compt0/a[0]')
makeTab('b_soma', '/model/chem/compt0/b[0]')
num = twigs[0]
makeTab('a_apical', '/model/chem/compt0/a[' + str(num) + ']')
makeTab('b_apical', '/model/chem/compt0/b[' + str(num) + ']')
def makeModel():
# create container for model
r0 = 1e-6 # m
r1 = 0.5e-6 # m. Note taper.
num = 200
diffLength = 1e-6 # m
comptLength = num * diffLength # m
diffConst = 20e-12 # m^2/sec
concA = 1 # millimolar
diffDt = 0.02 # for the diffusion
chemDt = 0.2 # for the reaction
mfile = '../../genesis/M1719.g'
model = moose.Neutral( 'model' )
compartment = moose.CylMesh( '/model/kinetics' )
# load in model
modelId = moose.loadModel( mfile, '/model', 'ee' )
a = moose.element( '/model/kinetics/a' )
b = moose.element( '/model/kinetics/b' )
c = moose.element( '/model/kinetics/c' )
ac = a.concInit
bc = b.concInit
cc = c.concInit
compartment.r0 = r0
compartment.r1 = r1
compartment.x0 = 0
compartment.x1 = comptLength
compartment.diffLength = diffLength
assert( compartment.numDiffCompts == num )
# Assign parameters
for x in moose.wildcardFind( '/model/kinetics/##[ISA=PoolBase]' ):
#print 'pools: ', x, x.name
x.diffConst = diffConst
# Make solvers
ksolve = moose.Ksolve( '/model/kinetics/ksolve' )
dsolve = moose.Dsolve( '/model/dsolve' )
# Set up clocks.
moose.setClock( 10, diffDt )
for i in range( 11, 17 ):
moose.setClock( i, chemDt )
stoich = moose.Stoich( '/model/kinetics/stoich' )
stoich.compartment = compartment
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.path = "/model/kinetics/##"
print(('dsolve.numPools, num = ', dsolve.numPools, num))
b.vec[num-1].concInit *= 1.01 # Break symmetry.
def makeSolvers():
stoich = moose.Stoich('/model/compartment/stoich')
stoich.compartment = moose.element('/model/compartment')
if (solver == 'gssa'):
gsolve = moose.Gsolve('/model/compartment/ksolve')
stoich.ksolve = gsolve
else:
ksolve = moose.Ksolve('/model/compartment/ksolve')
stoich.ksolve = ksolve
stoich.path = "/model/compartment/##"
moose.setClock(5, 1.0) # clock for the solver
moose.useClock(5, '/model/compartment/ksolve', 'process')
def setCompartmentSolver(modelRoot, solver):
compt = moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]')
if (solver == 'gsl') or (solver == 'Runge Kutta'):
ksolve = moose.Ksolve(compt[0].path + '/ksolve')
if (solver == 'gssa') or (solver == 'Gillespie'):
ksolve = moose.Gsolve(compt[0].path + '/gsolve')
if (solver != 'ee'):
stoich = moose.Stoich(compt[0].path + '/stoich')
stoich.compartment = compt[0]
stoich.ksolve = ksolve
stoich.path = compt[0].path + "/##"
for x in moose.wildcardFind(modelRoot + '/data/graph#/#'):
x.tick = 18
def setupSteadyState(simdt, plotDt):
ksolve = moose.Ksolve('/model/kinetics/ksolve')
stoich = moose.Stoich('/model/kinetics/stoich')
stoich.compartment = moose.element('/model/kinetics')
stoich.ksolve = ksolve
stoich.path = "/model/kinetics/##"
state = moose.SteadyState('/model/kinetics/state')
moose.reinit()
state.stoich = stoich
state.showMatrices()
state.convergenceCriterion = 1e-8
return ksolve, state
def setup_solvers( compt, stochastic ):
global args
stoich = moose.Stoich( "%s/stoich" % compt.path)
if stochastic:
_logger.info("Setting up Stochastic solver in %s" % compt.path )
s = moose.Gsolve('%s/gsolve' % compt.path)
s.useClockedUpdate = True
else:
s = moose.Ksolve('%s/ksolve' % compt.path)
_logger.info( 'Using method %s' % s.method )
stoich.compartment = moose.element(compt.path)
stoich.ksolve = s
stoich.path = '%s/##' % compt.path
def setCompartmentSolver(modelRoot, solver):
"""
If Solver type is 'gsl' or 'gssa' do add Solver
if 'ee' nothing
"""
if solver != 'ee':
comptlist = dict(
(c.volume, c)
for c in moose.wildcardFind(modelRoot + '/##[ISA=ChemCompt]'))
vollist = sorted(comptlist.keys())
compts = [comptlist[key] for key in vollist]
#compts = [key for key, value in sorted(comptlist.items(), key=lambda (k,v): (v,k))]
if (len(compts) > 1):
positionCompt(compts)
fixXreacs(modelRoot)
vollist = sorted(comptlist.keys())
compts = [comptlist[key] for key in vollist]
#compts = [key for key, value in sorted(comptlist.items(), key=lambda (k,v): (v,k))]
for compt in compts:
if solver != 'ee':
if solver.lower() in ['gsl', 'runge kutta', 'lsoda']:
ksolve = moose.Ksolve(compt.path + '/ksolve')
elif solver.lower() in ['gssa', 'gillespie']:
ksolve = moose.Gsolve(compt.path + '/gsolve')
if (len(compts) > 1):
dsolve = moose.Dsolve(compt.path + '/dsolve')
stoich = moose.Stoich(compt.path + '/stoich')
stoich.ksolve = ksolve
if (len(compts) > 1):
stoich.dsolve = dsolve
stoich.compartment = compt
stoich.path = compt.path + "/##"
dsolveList = moose.wildcardFind(modelRoot + '/##[ISA=Dsolve]')
i = 0
while (i < len(dsolveList) - 1):
dsolveList[i + 1].buildMeshJunctions(dsolveList[i])
i += 1
if not modelRoot[:1].startswith('/'):
modelRoot = '/' + modelRoot
print(" Solver is added to model path `%s` with `%s` solver" %
(modelRoot, solver))
def switchSolvers(solver):
if (moose.exists('model/kinetics/stoich')):
moose.delete('/model/kinetics/stoich')
moose.delete('/model/kinetics/ksolve')
compt = moose.element('/model/kinetics')
if (solver == 'gsl'):
ksolve = moose.Ksolve('/model/kinetics/ksolve')
if (solver == 'gssa'):
ksolve = moose.Gsolve('/model/kinetics/ksolve')
if (solver != 'ee'):
stoich = moose.Stoich('/model/kinetics/stoich')
stoich.compartment = compt
stoich.ksolve = ksolve
stoich.path = "/model/kinetics/##"
def main():
"""
This example illustrates how to set up a kinetic solver and kinetic model
using the scripting interface. Normally this would be done using the
Shell::doLoadModel command, and normally would be coordinated by the
SimManager as the base of the entire model.
This example creates a bistable model having two enzymes and a reaction.
One of the enzymes is autocatalytic.
The model is set up to run using Exponential Euler integration.
"""
makeModel()
ksolve = moose.Ksolve('/model/compartment/ksolve')
try:
ksolve.numThreads = 10
except Exception as e:
print('No parallel ksolve')
stoich = moose.Stoich('/model/compartment/stoich')
stoich.compartment = moose.element('/model/compartment')
stoich.ksolve = ksolve
stoich.reacSystemPath = "/model/compartment/##"
#solver.method = "rk5"
#mesh = moose.element( "/model/compartment/mesh" )
#moose.connect( mesh, "remesh", solver, "remesh" )
'''
moose.setClock( 5, 1.0 ) # clock for the solver
moose.useClock( 5, '/model/compartment/ksolve', 'process' )
'''
moose.reinit()
moose.start(100.0) # Run the model for 100 seconds.
a = moose.element('/model/compartment/a')
b = moose.element('/model/compartment/b')
# move most molecules over to b
b.conc = b.conc + a.conc * 0.9
a.conc = a.conc * 0.1
moose.start(100.0) # Run the model for 100 seconds.
# move most molecules back to a
a.conc = a.conc + b.conc * 0.99
b.conc = b.conc * 0.01
moose.start(100.0) # Run the model for 100 seconds.
# Iterate through all plots, dump their contents to data.plot.
displayPlots()
quit()
def makeSolvers(elecDt):
# Put in the solvers, see how they fare.
# Here we kludge in a single chem solver for the whole system.
ksolve = moose.Ksolve('/model/ksolve')
stoich = moose.Stoich('/model/stoich')
stoich.compartment = moose.element('/model/chem/neuroMesh')
stoich.ksolve = ksolve
stoich.path = '/model/chem/##'
moose.useClock(5, '/model/ksolve', 'init')
moose.useClock(6, '/model/ksolve', 'process')
# Here is the elec solver
hsolve = moose.HSolve('/model/hsolve')
moose.useClock(1, '/model/hsolve', 'process')
hsolve.dt = elecDt
hsolve.target = '/model/elec/compt'
def main():
compartment = makeModel()
ksolve = moose.Ksolve('/model/compartment/ksolve')
stoich = moose.Stoich('/model/compartment/stoich')
stoich.compartment = compartment
stoich.ksolve = ksolve
stoich.path = "/model/compartment/##"
state = moose.SteadyState('/model/compartment/state')
moose.reinit()
state.stoich = stoich
state.convergenceCriterion = 1e-6
moose.seed(111) # Used when generating the samples in state space
moose.reinit()
moose.start(10)
plot(10)