def makeChemProto(name='hydra'):
chem = moose.Neutral('/library/' + name)
compt = moose.CubeMesh('/library/' + name + '/' + name)
A = moose.Pool(compt.path + '/A')
B = moose.Pool(compt.path + '/B')
C = moose.Pool(compt.path + '/C')
#A.diffConst=params['diffA']
#B.diffConst=params['diffB']
Adot = moose.Function(A.path + '/Adot')
Bdot = moose.Function(B.path + '/Bdot')
Cdot = moose.Function(C.path + '/Cdot')
#Adot.expr="0.001*((x0^2/x1)+1)-1*x0+0.5*x0"
#Bdot.expr="0*x0+0.001*x0^2-1*x1+1*x1"
Adot.expr = "-0.1*x0+((0.1*x0^2)/(x1+x2))"
Bdot.expr = "0*x0-0.1*x1+0.1*x2+0.1*x0^2-0.1*(x1+x2)"
Cdot.expr = "0*x0+0.1*x1-0.1*x2+0.1*x0^2-0.1*(x1+x2)"
print "$$$$> ", Adot, Bdot, Cdot
print Adot.expr, Bdot.expr, Cdot.expr
print moose.showmsg(Adot)
Adot.x.num = 3 #2
Bdot.x.num = 3 #2
Cdot.x.num = 3
#A.nInit=10
#B.nInit=5
A.nInit = 1
B.nInit = 1
C.nInit = 1
moose.connect(A, 'nOut', Adot.x[0], 'input')
moose.connect(B, 'nOut', Adot.x[1], 'input')
moose.connect(C, 'nOut', Adot.x[2], 'input')
moose.connect(Adot, 'valueOut', A, 'increment')
moose.connect(A, 'nOut', Bdot.x[0], 'input')
moose.connect(B, 'nOut', Bdot.x[1], 'input')
moose.connect(C, 'nOut', Bdot.x[2], 'input')
moose.connect(Bdot, 'valueOut', B, 'increment')
moose.connect(A, 'nOut', Cdot.x[0], 'input')
moose.connect(B, 'nOut', Cdot.x[1], 'input')
moose.connect(C, 'nOut', Cdot.x[2], 'input')
moose.connect(Cdot, 'valueOut', C, 'increment')
return compt
def test_print():
a = moose.Function('f', expr='sqrt(sin(x0))+cos(x1)^2+ln(20+sin(t))')
# Get equivalent sympy expression. And do whatever you like with it.
try:
sympyExpr = a.sympyExpr()
print('Sympy expression is:', sympyExpr)
# Or pretty-print using sympy
a.printUsingSympy()
except ImportError:
pass
def test_var_order():
"""The y values are one step behind the x values because of
scheduling sequences"""
moose.delete( '/' )
nsteps = 5
simtime = nsteps
dt = 1.0
# fn0 = moose.Function('/fn0')
fn1 = moose.Function('/fn1')
fn1.x.num = 2
fn1.expr = 'y1+y0+x1+x0'
fn1.mode = 1
inputs = np.arange(0, nsteps+1, 1.0)
x0 = moose.StimulusTable('/x0')
x0.vector = inputs
x0.startTime = 0.0
x0.stopTime = simtime
x0.stepPosition = 0.0
inputs /= 10
x1 = moose.StimulusTable('/x1')
x1.vector = inputs
x1.startTime = 0.0
x1.stopTime = simtime
x1.stepPosition = 0.0
inputs /= 10
y0 = moose.StimulusTable('/y0')
y0.vector = inputs
y0.startTime = 0.0
y0.stopTime = simtime
y0.stepPosition = 0.0
inputs /= 10
y1 = moose.StimulusTable('/y1')
y1.vector = inputs
y1.startTime = 0.0
y1.startTime = 0.0
y1.stopTime = simtime
y1.stepPosition = 0.0
# print( fn1, type(fn1) )
# print( moose.showmsg(fn1.x) )
moose.connect(x0, 'output', fn1.x[0], 'input')
moose.connect(x1, 'output', fn1.x[1], 'input')
moose.connect(fn1, 'requestOut', y0, 'getOutputValue')
moose.connect(fn1, 'requestOut', y1, 'getOutputValue')
z1 = moose.Table('/z1')
moose.connect(z1, 'requestOut', fn1, 'getValue')
for ii in range(32):
moose.setClock(ii, dt)
moose.reinit()
moose.start(simtime)
expected = [0, 1.1, 2.211, 3.322, 4.433, 5.544]
assert np.allclose(z1.vector, expected), "Excepted %s, got %s" % (expected, z1.vector )
print( 'Passed order vars' )
def remove_extra( pool, limit ):
null = moose.BufPool( '%s/null' % pool.path )
null.nInit = 0.0
nullReac = moose.Reac( '%s/null_reac' % pool.path )
nullReac.numKb = 0.0
moose.connect( nullReac, 'sub', pool, 'reac' )
moose.connect( nullReac, 'prd', null, 'reac' )
nullF = moose.Function( '%s/func_null' % pool.path )
nullF.expr = '(x0 > %f)?1e-2:0' % limit
_logger.debug( 'Removing extra from pool %s' % pool.path )
_logger.debug( '\tExpression on nullR %s' % nullF.expr )
moose.connect( pool, 'nOut', nullF.x[0], 'input' )
moose.connect( nullF, 'valueOut', nullReac, 'setNumKf' )
def makeModel():
# create container for model
model = moose.Neutral('model')
harmonic = moose.CubeMesh('/model/harmonic')
harmonic.volume = 1e-15
lotka = moose.CubeMesh('/model/lotka')
lotka.volume = 1e-15
# create molecules and reactions
p = moose.Pool('/model/harmonic/p')
v = moose.Pool('/model/harmonic/v')
pdot = moose.Function('/model/harmonic/p/func')
vdot = moose.Function('/model/harmonic/v/func')
# Parameters
offset1 = 1.0
offset2 = 1.0
k = 0.1
p.nInit = offset1
v.nInit = offset2 + 0.1
pdot.x.num = 1
vdot.x.num = 1
pdot.expr = "x0 - " + str(offset1)
vdot.expr = "-" + str(k) + " * (x0 - " + str(offset2) + ")"
# connect them up for reactions
moose.connect(p, 'nOut', vdot.x[0], 'input')
moose.connect(v, 'nOut', pdot.x[0], 'input')
moose.connect(vdot, 'valueOut', v, 'increment')
moose.connect(pdot, 'valueOut', p, 'increment')
# Create the output tables
graphs = moose.Neutral('/model/graphs')
pplot = moose.Table2('/model/graphs/p')
vplot = moose.Table2('/model/graphs/v')
# connect up the tables
moose.connect(pplot, 'requestOut', p, 'getN')
moose.connect(vplot, 'requestOut', v, 'getN')
def test_var_order():
"""The y values are one step behind the x values because of
scheduling sequences"""
nsteps = 5
simtime = nsteps
dt = 1.0
# fn0 = moose.Function('/fn0')
# fn0.x.num = 2
# fn0.expr = 'x0 + x1'
# fn0.mode = 1
fn1 = moose.Function('/fn1')
fn1.x.num = 2
fn1.expr = 'y1 + y0 + x1 + x0'
fn1.mode = 1
inputs = np.arange(0, nsteps+1, 1.0)
x0 = moose.StimulusTable('/x0')
x0.vector = inputs
x0.startTime = 0.0
x0.stopTime = simtime
x0.stepPosition = 0.0
inputs /= 10
x1 = moose.StimulusTable('/x1')
x1.vector = inputs
x1.startTime = 0.0
x1.stopTime = simtime
x1.stepPosition = 0.0
inputs /= 10
y0 = moose.StimulusTable('/y0')
y0.vector = inputs
y0.startTime = 0.0
y0.stopTime = simtime
y0.stepPosition = 0.0
inputs /= 10
y1 = moose.StimulusTable('/y1')
y1.vector = inputs
y1.startTime = 0.0
y1.startTime = 0.0
y1.stopTime = simtime
y1.stepPosition = 0.0
moose.connect(x0, 'output', fn1.x[0], 'input')
moose.connect(x1, 'output', fn1.x[1], 'input')
moose.connect(fn1, 'requestOut', y0, 'getOutputValue')
moose.connect(fn1, 'requestOut', y1, 'getOutputValue')
z1 = moose.Table('/z1')
moose.connect(z1, 'requestOut', fn1, 'getValue')
for ii in range(32):
moose.setClock(ii, dt)
moose.reinit()
moose.start(simtime)
for ii in range(len(z1.vector)):
print ii, z1.vector[ii]
def makeChemProto(name='hydra'):
chem = moose.Neutral('/library/' + name)
compt = moose.CubeMesh('/library/' + name + '/' + name)
A = moose.Pool(compt.path + '/A')
B = moose.Pool(compt.path + '/B')
C = moose.Pool(compt.path + '/C')
space = moose.Pool(compt.path + '/space')
#A.diffConst=params['diffA']
#B.diffConst=params['diffB']
Adot = moose.Function(A.path + '/Adot')
Bdot = moose.Function(B.path + '/Bdot')
Cdot = moose.Function(C.path + '/Cdot')
#Adot.expr="0.001*((x0^2/x1)+1)-1*x0+0.5*x0"
#Bdot.expr="0*x0+0.001*x0^2-1*x1+1*x1"
#Adot.expr="0.5*exp(-1.5*x2/(50*1e-06))*x0^2*x1-(0.1+0.01)*x0+0.01*x1"
#Bdot.expr="-0.5*exp(-1.5*x2/(50*1e-06))*x0^2*x1+0.1*x0-0.01*x1+0.01"
Adot.expr = "0.1*x0^2*x1-(0.1+0.01)*x0+0.01*x1"
Bdot.expr = "-0.1*x0^2*x1+0.1*x0-0.01*x1+0.01"
print moose.showmsg(Adot)
Adot.x.num = 2 #2
Bdot.x.num = 2 #2
#A.nInit=10
#B.nInit=5
A.nInit = 0
B.nInit = 0
moose.connect(A, 'nOut', Adot.x[0], 'input')
moose.connect(B, 'nOut', Adot.x[1], 'input')
#moose.connect( space, 'nOut', Adot.x[2], 'input' )
moose.connect(Adot, 'valueOut', A, 'increment')
moose.connect(A, 'nOut', Bdot.x[0], 'input')
moose.connect(B, 'nOut', Bdot.x[1], 'input')
#moose.connect( space, 'nOut', Bdot.x[2], 'input' )
moose.connect(Bdot, 'valueOut', B, 'increment')
return compt
def makeChemProto(name='hydra'):
chem=moose.Neutral('/library/'+name)
compt=moose.CubeMesh('/library/'+name + '/' + name)
A=moose.Pool(compt.path+'/A')
B=moose.Pool(compt.path+'/B')
A.diffConst=params['diffA']
B.diffConst=params['diffB']
Adot = moose.Function( A.path + '/Adot' )
Bdot = moose.Function( B.path + '/Bdot' )
Adot.expr="-0.28*x0*x1"
Bdot.expr="0.28*x0*x1-0.03*x0"
Adot.x.num = 2 #2
Bdot.x.num = 2
moose.connect( A, 'nOut', Adot.x[0], 'input' )
moose.connect( B, 'nOut', Adot.x[1], 'input' )
moose.connect( Adot, 'valueOut', A, 'increment' )
moose.connect( A, 'nOut', Bdot.x[0], 'input' )
moose.connect( B, 'nOut', Bdot.x[1], 'input' )
moose.connect( Bdot, 'valueOut', B, 'increment' )
return compt
def test_var_order():
nsteps = 5
simtime = nsteps
dt = 1.0
fn1 = moose.Function('/fn1')
fn1.expr = 'B+A+y0+y1'
inputs = np.arange(0, nsteps + 1, 1.0)
x0 = moose.StimulusTable('/x0')
x0.vector = inputs
x0.startTime = 0.0
x0.stopTime = simtime
x0.stepPosition = 0.0
print('x0', x0.vector)
inputs /= 10
x1 = moose.StimulusTable('/x1')
x1.vector = inputs
x1.startTime = 0.0
x1.stopTime = simtime
x1.stepPosition = 0.0
print('x1', x1.vector)
inputs /= 10
y0 = moose.StimulusTable('/y0')
y0.vector = inputs
y0.startTime = 0.0
y0.stopTime = simtime
y0.stepPosition = 0.0
print('y0', y0.vector)
inputs /= 10
y1 = moose.StimulusTable('/y1')
y1.vector = inputs
print('y1', y1.vector)
y1.startTime = 0.0
y1.startTime = 0.0
y1.stopTime = simtime
y1.stepPosition = 0.0
moose.connect(x0, 'output', fn1['A'], 'input')
moose.connect(x1, 'output', fn1['B'], 'input')
moose.connect(fn1, 'requestOut', y0, 'getOutputValue')
moose.connect(fn1, 'requestOut', y1, 'getOutputValue')
z1 = moose.Table('/z1')
moose.connect(z1, 'requestOut', fn1, 'getValue')
for ii in range(32):
moose.setClock(ii, dt)
moose.reinit()
moose.start(simtime)
expected = [0, 1.1, 2.211, 3.322, 4.433, 5.544]
assert np.allclose(z1.vector,
expected), "Excepted %s, got %s" % (expected, z1.vector)
print('Passed order vars')
def makeChemProto(name='hydra'):
chem = moose.Neutral('/library/' + name)
compt = moose.CubeMesh('/library/' + name + '/' + name)
A = moose.Pool(compt.path + '/A')
B = moose.Pool(compt.path + '/B')
#A.diffConst=params['diffA']
#B.diffConst=params['diffB']
Adot = moose.Function(A.path + '/Adot')
Bdot = moose.Function(B.path + '/Bdot')
Adot.expr = "-x0+(x0^2/(1+0.01*x0^2))*x1"
Bdot.expr = "x0-(x0^2/(1+0.01*x0^2))*x1"
print moose.showmsg(Adot)
Adot.x.num = 2 #2
Bdot.x.num = 2 #2
moose.connect(A, 'nOut', Adot.x[0], 'input')
moose.connect(B, 'nOut', Adot.x[1], 'input')
moose.connect(Adot, 'valueOut', A, 'increment')
moose.connect(A, 'nOut', Bdot.x[0], 'input')
moose.connect(B, 'nOut', Bdot.x[1], 'input')
moose.connect(Bdot, 'valueOut', B, 'increment')
def attachStimulus( fname, rdes ):
compts = rdes.elecid.compartments
heads = []
lookupSpineIndexFromCompt = []
for i in compts:
sl = rdes.elecid.spinesOnCompartment[i]
lookupSpineIndexFromCompt.append( len( heads ) )
heads.extend( sl[1::2] )
ampar = moose.wildcardFind( '/model/elec/#/glu' )
assert( len(ampar) == len( heads ) )
moose.RandSpike( '/model/elec/spike', len( heads ) )
spikes = moose.vec( '/model/elec/spike' )
spikes.rate = params['meanSpikeRate']
spikes.refractT = params['refractoryPeriod']
amparSynWeight = params['amparSynapseWeight']
nmdarSynWeight = params['nmdarSynapseWeight']
for j in zip( heads, range( len( heads ) ) ):
sh = moose.element( j[0].path + '/glu/sh' )
sh.numSynapses = 1
sh.synapse[0].weight = amparSynWeight
moose.connect( spikes[j[1]], 'spikeOut', sh.synapse[0], 'addSpike' )
sh = moose.element( j[0].path + '/NMDA/sh' )
sh.numSynapses = 1
sh.synapse[0].weight = nmdarSynWeight
moose.connect( spikes[j[1]], 'spikeOut', sh.synapse[0], 'addSpike' )
thetaGaba = moose.Function( '/model/elec/thetaGabaRhythm' )
timeExpr = 'cos( 6.283 * t * ' + str(params['thetaFreq']/2.0) + ' )^2'
rateExpr = str( 2.0 * params['thetaGabaSpikeRate'])
thetaGaba.expr = str( params['baseGabaSpikeRate']) + ' + ' + rateExpr + ' * ' + timeExpr
print thetaGaba.expr,
gabar = moose.wildcardFind( '/model/elec/#/GABA' )
print " NUM-GABA = ", len(gabar)
rsGabar = moose.RandSpike( '/model/elec/gabaSpike', len( gabar ) )
moose.connect( thetaGaba, 'valueOut', rsGabar, 'setRate', 'OneToAll' )
gabaSpikes = moose.vec( '/model/elec/gabaSpike' )
#spikes.rate = params['meanSpikeRate']
gabaSpikes.refractT = params['refractoryPeriod']
gabarSynWeight = params['gabarSynapseWeight']
for i in range( len(gabar) ):
sh = moose.element( gabar[i].path + '/sh' )
sh.numSynapses = 1
sh.synapse[0].weight = gabarSynWeight
moose.connect( gabaSpikes[i], 'spikeOut', sh.synapse[0], 'addSpike' )
return lookupSpineIndexFromCompt
def phosphorylation_first_step(root, nc):
# CaMKII to x1y0 is slow.
subPool = molecules_[pool_name(root, 'x0y%d' % nc)]
prdPool = molecules_[pool_name(root, 'x1y%d' % (nc - 1))]
r0 = add_reaction('%s/reac_0to1_%d' % (subPool.path, nc))
r0.numKb = 0
moose.connect(r0, 'sub', subPool, 'reac')
moose.connect(r0, 'prd', prdPool, 'reac')
# The rate expression of this reaction depends on Ca++
f = moose.Function('%s/func_kf' % r0.path)
f.expr = '{nc}*{k1}*(x0/{kh1})^6/(1 + (x0/{kh1})^3)^2'.format(
k1=_p.k_1, kh1=conc_to_n(_p.K_H1), nc=nc)
f.x.num = 1
moose.connect(molecules_[pool_name(root, 'ca')], 'nOut', f.x[0], 'input')
moose.connect(f, 'valueOut', r0, 'setNumKf')
_logger.debug('Reaction: %s -> %s' % (subPool.name, prdPool.name))
def ca_input( root ):
"""Input calcium pulse
When using stochastic solver, any event less than 100 or so seconds would
not work.
"""
global args
# Input calcium
ca = moose.BufPool( '%s/ca' % root.path )
ca.nInit = conc_to_n( _p.ca_basal )
ca.name = pool_name( root, ca.name )
molecules_[ ca.name ] = ca
_logger.info("Setting up input calcium : init = %s" % ca.nInit )
# _logger.debug("Baselevel ca conc = %s" % _p.resting_ca_conc)
concFunc = moose.Function( "%s/cafunc" % ca.path )
concFunc.expr = args[ 'ca_expr' ]
moose.connect( concFunc, 'valueOut', ca, 'setConc' )
_logger.info( "Ca conc expression = %s " % concFunc.expr )
def createFunction(fb, inputB, objB, objA):
fapath1 = fb.path.replace(objB, objA)
fapath = fapath1.replace('[0]', '')
if not moose.exists(fapath):
# if fb.parent.className in ['CubeMesh','CyclMesh']:
# des = moose.Function('/'+objA+'/'+fb.parent.name+'/'+fb.name)
# elif fb.parent.className in ['Pool','ZombiePool','BufPool','ZombieBufPool']:
# for akey in list(poolListina[findCompartment(fb).name]):
# if fb.parent.name == akey.name:
# des = moose.Function(akey.path+'/'+fb.name)
des = moose.Function(fapath)
moose.connect(des, 'valueOut', moose.element(fapath).parent, 'setN')
for src in inputB:
pool = ((src.path).replace(objB, objA)).replace('[0]', '')
numVariables = des.numVars
expr = ""
expr = (des.expr + '+' + 'x' + str(numVariables))
expr = expr.lstrip("0 +")
expr = expr.replace(" ", "")
des.expr = expr
moose.connect(pool, 'nOut', des.x[numVariables], 'input')
def makeFuncRate():
model = moose.Neutral('/library')
model = moose.Neutral('/library/chem')
compt = moose.CubeMesh('/library/chem/compt')
compt.volume = 1e-15
A = moose.Pool('/library/chem/compt/A')
B = moose.Pool('/library/chem/compt/B')
C = moose.Pool('/library/chem/compt/C')
reac = moose.Reac('/library/chem/compt/reac')
func = moose.Function('/library/chem/compt/reac/func')
func.x.num = 1
func.expr = "(x0/1e8)^2"
moose.connect(C, 'nOut', func.x[0], 'input')
moose.connect(func, 'valueOut', reac, 'setNumKf')
moose.connect(reac, 'sub', A, 'reac')
moose.connect(reac, 'prd', B, 'reac')
A.concInit = 1
B.concInit = 0
C.concInit = 0
reac.Kb = 1
def pp1_activation( root ):
"""Here we setup the reactions PP1
I1P binds with PP1 and give rise to complex I1PPP1 (which is inavtivated PP1)
I1P + PP1 <- -> I1PPP1
"""
activePP1 = molecules_[pool_name(root, 'PP1')]
i1pPool = molecules_[ pool_name( root, 'I1P' ) ]
inactive_pp1 = molecules_[ pool_name( root, 'I1PPP1' ) ]
r = add_reaction( '%s/reac_inactivate_pp1' % activePP1.path )
moose.connect( r, 'sub', activePP1, 'reac' )
moose.connect( r, 'prd', inactive_pp1, 'reac')
k3, k4, s = 1e5, 0.0001, 1
kfFun = moose.Function( '%s/kffunc' % r.path )
kfFun.expr = '{scale}*{k3}*x0'.format( k3 = k3, scale = s )
moose.connect( i1pPool, 'nOut', kfFun.x[0], 'input' )
moose.connect( kfFun, 'valueOut', r, 'setNumKf' )
r.numKb = s * k4
_logger.debug( 'Reaction: %s + %s -> %s' % ( activePP1.name, i1pPool.name,
inactive_pp1.name ) )
def ShortTermPlas(synapse, index, stp_params, simdt, presyn, msg):
#implements short term plasticity - depression and/or facilitation
synchan = synapse.parent.parent
num_inputs = 0
if stp_params.depress is not None:
dep = facil_depress(synchan.path + NAME_DEPRESS + str(index),
stp_params.depress, simdt, presyn, msg)
log.debug(' ***depress={} {} presyn {}', dep.path, dep.expr,
presyn.path)
num_inputs += 1
source0 = dep
plas_expr = '(init*x0)'
if stp_params.facil is not None:
fac = facil_depress(synchan.path + NAME_FACIL + str(index),
stp_params.facil, simdt, presyn, msg)
log.debug(' ***facil={} {} presyn {}', fac.path, fac.expr, presyn.path)
num_inputs += 1
if num_inputs == 1:
source0 = fac
plas_expr = '(init*x0)'
else:
source1 = fac
plas_expr = '(init*x0*x1)'
#
log.debug('**** STP={} x[0]={} ****', plas_expr, source0.path)
plaspath = synchan.path + NAME_STP + str(index)
plas_func = moose.Function(plaspath)
plas_func.c['init'] = synapse.weight
plas_func.c['dt'] = simdt
plas_func.expr = '(t<2*dt) ? (init) :' + plas_expr
plas_func.x.num = num_inputs
moose.connect(source0, 'valueOut', plas_func.x[0], 'input')
if num_inputs == 2:
moose.connect(source1, 'valueOut', plas_func.x[1], 'input')
# Output the updated weight computed by plasticity function to the synapse
moose.connect(plas_func, 'valueOut', synapse, 'setWeight')
return
def example():
"""Function objects can be used to evaluate expressions with arbitrary
number of variables and constants. We can assign expression of the
form::
f(c0, c1, ..., cM, x0, x1, ..., xN, y0,..., yP )
where `c_i`'s are constants and `x_i`'s and `y_i`'s are variables.
The constants must be defined before setting the expression and
variables are connected via messages. The constants can have any
name, but the variable names must be of the form x{i} or y{i}
where i is increasing integer starting from 0.
The `x_i`'s are field elements and you have to set their number
first (function.x.num = N). Then you can connect any source field
sending out double to the 'input' destination field of the
`x[i]`.
The `y_i`'s are useful when the required variable is a value field
and is not available as a source field. In that case you connect
the `requestOut` source field of the function element to the
`get{Field}` destination field on the target element. The `y_i`'s
are automatically added on connecting. Thus, if you call::
moose.connect(function, 'requestOut', a, 'getSomeField')
moose.connect(function, 'requestOut', b, 'getSomeField')
then ``a.someField`` will be assigned to ``y0`` and
``b.someField`` will be assigned to ``y1``.
In this example we evaluate the expression: ``z = c0 * exp(c1 *
x0) * cos(y0)``
with x0 ranging from -1 to +1 and y0 ranging from -pi to
+pi. These values are stored in two stimulus tables called xtab
and ytab respectively, so that at each timestep the next values of
x0 and y0 are assigned to the function.
Along with the value of the expression itself we also compute its
derivative with respect to y0 and its derivative with respect to
time (rate). The former uses a five-point stencil for the
numerical differentiation and has a glitch at y=0. The latter uses
backward difference divided by dt.
Unlike Func class, the number of variables and constants are
unlimited in Function and you can set all the variables via
messages.
"""
demo = moose.Neutral('/model')
function = moose.Function('/model/function')
function.c['c0'] = 1.0
function.c['c1'] = 2.0
function.x.num = 1
function.expr = 'c0 * exp(c1*x0) * cos(y0) + sin(t)'
# mode 0 - evaluate function value, derivative and rate
# mode 1 - just evaluate function value,
# mode 2 - evaluate derivative,
# mode 3 - evaluate rate
function.mode = 0
function.independent = 'y0'
nsteps = 10000
xarr = np.linspace(0.0, 1.0, nsteps)
# Stimulus tables allow you to store sequences of numbers which
# are delivered via the 'output' message at each time step. This
# is a placeholder and in real scenario you will be using any
# sourceFinfo that sends out a double value.
input_x = moose.StimulusTable('/xtab')
input_x.vector = xarr
input_x.startTime = 0.0
input_x.stepPosition = xarr[0]
input_x.stopTime = simtime
moose.connect(input_x, 'output', function.x[0], 'input')
yarr = np.linspace(-np.pi, np.pi, nsteps)
input_y = moose.StimulusTable('/ytab')
input_y.vector = yarr
input_y.startTime = 0.0
input_y.stepPosition = yarr[0]
input_y.stopTime = simtime
moose.connect(function, 'requestOut', input_y, 'getOutputValue')
# data recording
result = moose.Table('/ztab')
moose.connect(result, 'requestOut', function, 'getValue')
derivative = moose.Table('/zprime')
moose.connect(derivative, 'requestOut', function, 'getDerivative')
rate = moose.Table('/dz_by_dt')
moose.connect(rate, 'requestOut', function, 'getRate')
x_rec = moose.Table('/xrec')
moose.connect(x_rec, 'requestOut', input_x, 'getOutputValue')
y_rec = moose.Table('/yrec')
moose.connect(y_rec, 'requestOut', input_y, 'getOutputValue')
dt = simtime / nsteps
for ii in range(32):
moose.setClock(ii, dt)
moose.reinit()
moose.start(simtime)
# Uncomment the following lines and the import matplotlib.pyplot as plt on top
# of this file to display the plot.
if plot_:
plt.plot(x_rec.vector,
result.vector,
'r-',
label='z = {}'.format(function.expr))
plt.subplot(4, 1, 1)
z = function.c['c0'] * np.exp(
function.c['c1'] * xarr) * np.cos(yarr) + np.sin(
np.arange(len(xarr)) * dt)
zz = result.vector[1:]
err = z[1:] - zz[1:]
assert (np.abs(err) <= 0.05).all(), err
assert (np.mean(err) <= 0.001), np.mean(err)
if plot_:
plt.plot(xarr, z, 'b--', label='numpy computed')
plt.xlabel('x')
plt.ylabel('z')
plt.legend()
if plot_:
plt.subplot(4, 1, 2)
plt.plot(y_rec.vector, derivative.vector, 'r-', label='dz/dy0')
# derivatives computed by putting x values in the analytical formula
dzdy = function.c['c0'] * np.exp(function.c['c1'] * xarr) * (-np.sin(yarr))
err = np.abs(dzdy - derivative.vector[1:])
assert (err < 1e-2).all(), err
assert (np.mean(err) < 1e-3), np.mean(err)
if plot_:
plt.plot(yarr, dzdy, 'b--', label='numpy computed')
plt.xlabel('y')
plt.ylabel('dz/dy')
plt.legend()
if plot_:
plt.subplot(4, 1, 3)
# *** BEWARE *** The first two entries are spurious. Entry 0 is
# *** from reinit sending out the defaults. Entry 2 is because
# *** there is no lastValue for computing real forward difference.
plt.plot(np.arange(2, len(rate.vector), 1) * dt,
rate.vector[2:],
'r-',
label='dz/dt')
dzdt = np.diff(z) / dt
plt.plot(np.arange(0, len(dzdt), 1.0) * dt,
dzdt,
'b--',
label='numpy computed')
plt.xlabel('t')
plt.ylabel('dz/dt')
plt.legend()
plt.tight_layout()
plt.show()
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 = 100e-9
compt.x1 = 100e-9
compt.diffLength = 0.2e-9
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 = 1e-13 # define diffusion constant
# Here we set up a function calculation
func = moose.Function( '/cylinder/pool/func' )
func.expr = "(-x0 * (30e-9 - x0) * (100e-9 - x0))*0.0001"
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.Gsolve( '/cylinder/Gsolve' )
dsolve = moose.Dsolve( '/cylinder/dsolve' )
stoich = moose.Stoich( '/cylinder/stoich' )
stoich.compartment = compt
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.path = '/cylinder/##'
#for i in range( 10, 18 ):
# moose.setClock( i, dt )
#initialize
x = numpy.arange( 0, compt.x1, compt.diffLength )
# c.vec.nInit = [ 100.0 * (q < 0.2 * compt.x1) for q in x ]
c.vec.nInit = [ 100 for q in x ]
# Run and plot it.
moose.reinit()
#print((dir(compt)))
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 = ", time.time() - t1))
pylab.ylim( 0, 105 )
pylab.legend()
pylab.show()
def test_wrapper():
a = moose.Pool('/dadadada', concInit=9.99, nInit=10)
assert a.nInit == 10
f = moose.Function('/fun1', expr='x0+x1+A+B')
assert f.expr == 'x0+x1+A+B'
assert f.numVars == 4, f.numVars
def checkCreate(scene, view, modelpath, mobj, string, ret_string, num,
event_pos, layoutPt):
# The variable 'compt' will be empty when dropping cubeMesh,cyclMesh, but rest it shd be
# compartment
# if modelpath.find('/',1) > -1:
# modelRoot = modelpath[0:modelpath.find('/',1)]
# else:
# modelRoot = modelpath
print "28 ", modelpath
if moose.exists(modelpath + '/info'):
mType = moose.Annotator((moose.element(modelpath + '/info'))).modeltype
itemAtView = view.sceneContainerPt.itemAt(view.mapToScene(event_pos))
pos = view.mapToScene(event_pos)
modelpath = moose.element(modelpath)
if num:
string_num = ret_string + str(num)
else:
string_num = ret_string
if string == "CubeMesh" or string == "CylMesh":
if string == "CylMesh":
mobj = moose.CylMesh(modelpath.path + '/' + string_num)
else:
mobj = moose.CubeMesh(modelpath.path + '/' + string_num)
mobj.volume = 1e-15
mesh = moose.element(mobj.path + '/mesh')
qGItem = ComptItem(scene,
pos.toPoint().x(),
pos.toPoint().y(), 100, 100, mobj)
qGItem.setPen(
QtGui.QPen(Qt.QColor(66, 66, 66, 100), 1, Qt.Qt.SolidLine,
Qt.Qt.RoundCap, Qt.Qt.RoundJoin))
view.sceneContainerPt.addItem(qGItem)
qGItem.cmptEmitter.connect(
qGItem.cmptEmitter,
QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"),
layoutPt.positionChange1)
qGItem.cmptEmitter.connect(
qGItem.cmptEmitter,
QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"),
layoutPt.objectEditSlot)
compartment = qGItem
layoutPt.qGraCompt[mobj] = qGItem
view.emit(QtCore.SIGNAL("dropped"), mobj)
elif string == "Pool" or string == "BufPool":
#getting pos with respect to compartment otherwise if compartment is moved then pos would be wrong
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
if string == "Pool":
poolObj = moose.Pool(mobj.path + '/' + string_num)
else:
poolObj = moose.BufPool(mobj.path + '/' + string_num)
poolinfo = moose.Annotator(poolObj.path + '/info')
#Compartment's one Pool object is picked to get the font size
qGItem = PoolItem(poolObj, itemAtView)
layoutPt.mooseId_GObj[poolObj] = qGItem
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
bgcolor = getRandColor()
qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(),
QtGui.QColor('green'), bgcolor)
poolinfo.color = str(bgcolor.getRgb())
view.emit(QtCore.SIGNAL("dropped"), poolObj)
setupItem(modelpath.path, layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
x, y = roundoff(qGItem.scenePos(), layoutPt)
poolinfo.x = x
poolinfo.y = y
#Dropping is on compartment then update Compart size
if isinstance(mobj, moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mobj)]
updateCompartmentSize(compt)
elif string == "Reac":
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
reacObj = moose.Reac(mobj.path + '/' + string_num)
reacinfo = moose.Annotator(reacObj.path + '/info')
qGItem = ReacItem(reacObj, itemAtView)
qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(), "white",
"white")
#if mType == "new_kkit":
# reacinfo.x = posWrtComp.x()
# reacinfo.y = posWrtComp.y()
layoutPt.mooseId_GObj[reacObj] = qGItem
view.emit(QtCore.SIGNAL("dropped"), reacObj)
setupItem(modelpath.path, layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
#Dropping is on compartment then update Compart size
if isinstance(mobj, moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mobj)]
updateCompartmentSize(compt)
x, y = roundoff(qGItem.scenePos(), layoutPt)
reacinfo.x = x
reacinfo.y = y
elif string == "StimulusTable":
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
tabObj = moose.StimulusTable(mobj.path + '/' + string_num)
tabinfo = moose.Annotator(tabObj.path + '/info')
qGItem = TableItem(tabObj, itemAtView)
qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(),
QtGui.QColor('white'),
QtGui.QColor('white'))
#if mType == "new_kkit":
#tabinfo.x = posWrtComp.x()
#tabinfo.y = posWrtComp.y()
layoutPt.mooseId_GObj[tabObj] = qGItem
view.emit(QtCore.SIGNAL("dropped"), tabObj)
setupItem(modelpath.path, layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
#Dropping is on compartment then update Compart size
if isinstance(mobj, moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mobj)]
updateCompartmentSize(compt)
x, y = roundoff(qGItem.scenePos(), layoutPt)
tabinfo.x = x
tabinfo.y = y
elif string == "Function":
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
funcObj = moose.Function(mobj.path + '/' + string_num)
funcinfo = moose.Annotator(funcObj.path + '/info')
#moose.connect( funcObj, 'valueOut', mobj ,'setN' )
poolclass = ["ZombieBufPool", "BufPool"]
comptclass = ["CubeMesh", "cyclMesh"]
if mobj.className in poolclass:
funcParent = layoutPt.mooseId_GObj[element(mobj.path)]
elif mobj.className in comptclass:
funcParent = layoutPt.qGraCompt[moose.element(mobj)]
posWrtComp = funcParent.mapFromScene(pos).toPoint()
#posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
qGItem = FuncItem(funcObj, funcParent)
#print " function ", posWrtComp.x(),posWrtComp.y()
qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(),
QtGui.QColor('red'), QtGui.QColor('green'))
layoutPt.mooseId_GObj[funcObj] = qGItem
#if mType == "new_kkit":
#funcinfo.x = posWrtComp.x()
#funcinfo.y = posWrtComp.y()
view.emit(QtCore.SIGNAL("dropped"), funcObj)
setupItem(modelpath.path, layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
#Dropping is on compartment then update Compart size
mooseCmpt = findCompartment(mobj)
if isinstance(mooseCmpt, moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mooseCmpt)]
updateCompartmentSize(compt)
x, y = roundoff(qGItem.scenePos(), layoutPt)
funcinfo.x = x
funcinfo.y = y
elif string == "Enz" or string == "MMenz":
#If 2 enz has same pool parent, then pos of the 2nd enz shd be displaced by some position, need to check how to deal with it
posWrtComp = pos
enzPool = layoutPt.mooseId_GObj[mobj]
if ((mobj.parent).className == "Enz"):
QtGui.QMessageBox.information(
None, 'Drop Not possible',
'\'{newString}\' has to have Pool as its parent and not Enzyme Complex'
.format(newString=string), QtGui.QMessageBox.Ok)
return
else:
enzparent = findCompartment(mobj)
parentcompt = layoutPt.qGraCompt[enzparent]
if string == "Enz":
enzObj = moose.Enz(moose.element(mobj).path + '/' + string_num)
enzinfo = moose.Annotator(enzObj.path + '/info')
moose.connect(enzObj, 'enz', mobj, 'reac')
qGItem = EnzItem(enzObj, parentcompt)
layoutPt.mooseId_GObj[enzObj] = qGItem
posWrtComp = pos
bgcolor = getRandColor()
qGItem.setDisplayProperties(posWrtComp.x(),
posWrtComp.y() - 40,
QtGui.QColor('green'), bgcolor)
x, y = roundoff(qGItem.scenePos(), layoutPt)
enzinfo.x = x
enzinfo.y = y
enzinfo.color = str(bgcolor.name())
enzinfo.textColor = str(QtGui.QColor('green').name())
#if mType == "new_kkit":
#enzinfo.x = posWrtComp.x()
#enzinfo.y = posWrtComp.y()
#enzinfo.color = str(bgcolor.name())
e = moose.Annotator(enzinfo)
#e.x = posWrtComp.x()
#e.y = posWrtComp.y()
Enz_cplx = enzObj.path + '/' + string_num + '_cplx'
cplxItem = moose.Pool(Enz_cplx)
cplxinfo = moose.Annotator(cplxItem.path + '/info')
qGEnz = layoutPt.mooseId_GObj[enzObj]
qGItem = CplxItem(cplxItem, qGEnz)
layoutPt.mooseId_GObj[cplxItem] = qGItem
enzboundingRect = qGEnz.boundingRect()
moose.connect(enzObj, 'cplx', cplxItem, 'reac')
qGItem.setDisplayProperties(enzboundingRect.height() / 2,
enzboundingRect.height() - 40,
QtGui.QColor('white'),
QtGui.QColor('white'))
#cplxinfo.x = enzboundingRect.height()/2
#cplxinfo.y = enzboundingRect.height()-60
view.emit(QtCore.SIGNAL("dropped"), enzObj)
else:
enzObj = moose.MMenz(mobj.path + '/' + string_num)
enzinfo = moose.Annotator(enzObj.path + '/info')
moose.connect(mobj, "nOut", enzObj, "enzDest")
qGItem = MMEnzItem(enzObj, parentcompt)
posWrtComp = pos
bgcolor = getRandColor()
qGItem.setDisplayProperties(posWrtComp.x(),
posWrtComp.y() - 30,
QtGui.QColor('green'), bgcolor)
#enzinfo.x = posWrtComp.x()
#enzinfo.y = posWrtComp.y()
enzinfo.color = str(bgcolor.name())
layoutPt.mooseId_GObj[enzObj] = qGItem
view.emit(QtCore.SIGNAL("dropped"), enzObj)
x, y = roundoff(qGItem.scenePos(), layoutPt)
enzinfo.x = x
enzinfo.y = y
setupItem(modelpath.path, layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
#Dropping is on compartment then update Compart size
if isinstance(enzparent, moose.ChemCompt):
updateCompartmentSize(parentcompt)
if view.iconScale != 1:
view.updateScale(view.iconScale)
def makeChemProto(name, stimAmpl=1, diffLength=1e-6, preStim=10.0):
# Parameters
sw = params['stimWidth']
dca = params['diffConstA'] * diffLength * diffLength
dcb = params['diffConstB'] * diffLength * diffLength
num = params['dendLength'] / diffLength
# Objects
chem = moose.Neutral('/library/' + name)
compt = moose.CubeMesh(chem.path + '/dend')
# compt = moose.CylMesh( chem.path + '/dend')
# # for i in range(int(num)):
# compt.x0 = 0
# compt.x1 = params['dendLength']
# compt.r0 = 2*params['dendDiameter']
# compt.r1 = params['dendDiameter']
# compt.diffLength = diffLength
A = moose.Pool(compt.path + '/A')
B = moose.Pool(compt.path + '/B')
Z = moose.BufPool(compt.path + '/Z')
Ca = moose.BufPool(compt.path + '/Ca')
phase = moose.BufPool(compt.path + '/phase')
vel = moose.BufPool(compt.path + '/vel')
ampl = moose.BufPool(compt.path + '/ampl')
Adot = moose.Function(A.path + '/Adot')
Bdot = moose.Function(B.path + '/Bdot')
CaStim = moose.Function(Ca.path + '/CaStim')
A.diffConst = dca
B.diffConst = dcb
# Equations
Adot.expr = 'x3*(' + sp('k0a', '+ ') + sp('k1a', '*x1 + ') + sp(
'k2a', '*x1*x1 + ') + sp('k3a', '*x1*x1*x1 + ') + sp(
'k4a', '*x0*x1/(1+x1+10*x2) + ') + sp('k5a', '*x1*x2') + ')'
Bdot.expr = 'x2*(' + sp('k1b', '*x0*x0 + ') + sp('k2b', '*x1') + ')'
CaStim.expr = 'x2 * exp( -((x0 - t)^2)/(2* ' + str(sw * sw) + ') )'
print Adot.expr
print Bdot.expr
print CaStim.expr
# Connections
Adot.x.num = 4
moose.connect(Ca, 'nOut', Adot.x[0], 'input')
moose.connect(A, 'nOut', Adot.x[1], 'input')
moose.connect(B, 'nOut', Adot.x[2], 'input')
moose.connect(Z, 'nOut', Adot.x[3], 'input')
moose.connect(Adot, 'valueOut', A, 'increment')
Bdot.x.num = 3
moose.connect(A, 'nOut', Bdot.x[0], 'input')
moose.connect(B, 'nOut', Bdot.x[1], 'input')
moose.connect(Z, 'nOut', Bdot.x[2], 'input')
moose.connect(Bdot, 'valueOut', B, 'increment')
CaStim.x.num = 3
moose.connect(phase, 'nOut', CaStim.x[0], 'input')
moose.connect(vel, 'nOut', CaStim.x[1], 'input')
moose.connect(ampl, 'nOut', CaStim.x[2], 'input')
moose.connect(CaStim, 'valueOut', Ca, 'setN')
return compt
def makeChemProto(name='hydra'):
chem = moose.Neutral('/library/' + name)
compt = moose.CubeMesh('/library/' + name + '/' + name)
A = moose.Pool(compt.path + '/A')
B = moose.Pool(compt.path + '/B')
C = moose.Pool(compt.path + '/C')
D = moose.Pool(compt.path + '/D')
E = moose.Pool(compt.path + '/E')
F = moose.Pool(compt.path + '/F')
Z1 = moose.Pool(compt.path + '/Z1')
Z2 = moose.Pool(compt.path + '/Z2')
#A.diffConst=params['diffA']
#B.diffConst=params['diffB']
Adot = moose.Function(A.path + '/Adot')
Bdot = moose.Function(B.path + '/Bdot')
Cdot = moose.Function(C.path + '/Cdot')
Ddot = moose.Function(D.path + '/Ddot')
Edot = moose.Function(E.path + '/Edot')
Fdot = moose.Function(F.path + '/Fdot')
#Zdot = moose.Function( Z.path + '/Zdot' )
#Adot.expr="x6*(1+x7)*(-x0+(5/(1+x1^3))*(2-x0-x3))"
#Bdot.expr="x6*(1+x7)*(0*x0-x1+(3+2*(x2^3/(1+x1^3)))*(1/(1+x0^3))*(2-x1-x4))"
#Cdot.expr="x6*(1+x7)*(0*x0+0*x1-0*x2+0.1*((0.2+0.3*(x0^3/(0.85^3+x0^3)))-x2^2*(0.2+1*x1^3/(0.85^3+x1^3))))"
Adot.expr = "x6*(1+x7)*(-x0+(4.5/(1+x1^3))*(2-x0-x3))"
Bdot.expr = "x6*(1+x7)*(0*x0-x1+(3+0.5*(x2^3/(1+x1^3)))*(1/(1+x0^3))*(2-x1-x4))"
Cdot.expr = "x6*(1+x7)*(0*x0+0*x1-0*x2+0.5*((0.2+0.3*(x0^3/(0.85^3+x0^3)))-x2^2*(0.2+1*x1^3/(0.85^3+x1^3))))"
#Ddot.expr="(1+x6)*x7*(0*x0+0*x1+0*x2-x3+(5/(1+x4^3))*(2-x0-x3))"
#Edot.expr="(1+x6)*x7*(0*x0+0*x1+0*x2+0*x3-x4+(3+2*(x5^3/(1+x4^3)))*(1/(1+x3^3))*(2-x1-x4))"
#Fdot.expr="(1+x6)*x7*(0*x0+0*x1+0*x2+0*x3+0*x4-0*x5+0.1*((0.2+0.3*(x3^3/(0.85^3+x3^3)))-x5^2*(0.2+1*x4^3/(0.85^3+x4^3))))"
Ddot.expr = "(1+x6)*x7*(0*x0+0*x1+0*x2-x3+(4.5/(1+x4^3))*(2-x0-x3))"
Edot.expr = "(1+x6)*x7*(0*x0+0*x1+0*x2+0*x3-x4+(3+0.5*(x5^3/(1+x4^3)))*(1/(1+x3^3))*(2-x1-x4))"
Fdot.expr = "(1+x6)*x7*(0*x0+0*x1+0*x2+0*x3+0*x4-0*x5+0.5*((0.2+0.3*(x3^3/(0.85^3+x3^3)))-x5^2*(0.2+1*x4^3/(0.85^3+x4^3))))"
print moose.showmsg(Adot)
Adot.x.num = 8 #2
Bdot.x.num = 8 #2
Cdot.x.num = 8 #2
Ddot.x.num = 8 #2
Edot.x.num = 8 #2
Fdot.x.num = 8 #2
#A.nInit=10
#B.nInit=5
moose.connect(A, 'nOut', Adot.x[0], 'input')
moose.connect(B, 'nOut', Adot.x[1], 'input')
moose.connect(C, 'nOut', Adot.x[2], 'input')
moose.connect(D, 'nOut', Adot.x[3], 'input')
moose.connect(E, 'nOut', Adot.x[4], 'input')
moose.connect(F, 'nOut', Adot.x[5], 'input')
moose.connect(Z1, 'nOut', Adot.x[6], 'input')
moose.connect(Z2, 'nOut', Adot.x[7], 'input')
moose.connect(Adot, 'valueOut', A, 'increment')
moose.connect(A, 'nOut', Bdot.x[0], 'input')
moose.connect(B, 'nOut', Bdot.x[1], 'input')
moose.connect(C, 'nOut', Bdot.x[2], 'input')
moose.connect(D, 'nOut', Bdot.x[3], 'input')
moose.connect(E, 'nOut', Bdot.x[4], 'input')
moose.connect(F, 'nOut', Bdot.x[5], 'input')
moose.connect(Z1, 'nOut', Bdot.x[6], 'input')
moose.connect(Z2, 'nOut', Bdot.x[7], 'input')
moose.connect(Bdot, 'valueOut', B, 'increment')
moose.connect(A, 'nOut', Cdot.x[0], 'input')
moose.connect(B, 'nOut', Cdot.x[1], 'input')
moose.connect(C, 'nOut', Cdot.x[2], 'input')
moose.connect(D, 'nOut', Cdot.x[3], 'input')
moose.connect(E, 'nOut', Cdot.x[4], 'input')
moose.connect(F, 'nOut', Cdot.x[5], 'input')
moose.connect(Z1, 'nOut', Cdot.x[6], 'input')
moose.connect(Z2, 'nOut', Cdot.x[7], 'input')
moose.connect(Cdot, 'valueOut', C, 'increment')
moose.connect(A, 'nOut', Ddot.x[0], 'input')
moose.connect(B, 'nOut', Ddot.x[1], 'input')
moose.connect(C, 'nOut', Ddot.x[2], 'input')
moose.connect(D, 'nOut', Ddot.x[3], 'input')
moose.connect(E, 'nOut', Ddot.x[4], 'input')
moose.connect(F, 'nOut', Ddot.x[5], 'input')
moose.connect(Z1, 'nOut', Ddot.x[6], 'input')
moose.connect(Z2, 'nOut', Ddot.x[7], 'input')
moose.connect(Ddot, 'valueOut', D, 'increment')
moose.connect(A, 'nOut', Edot.x[0], 'input')
moose.connect(B, 'nOut', Edot.x[1], 'input')
moose.connect(C, 'nOut', Edot.x[2], 'input')
moose.connect(D, 'nOut', Edot.x[3], 'input')
moose.connect(E, 'nOut', Edot.x[4], 'input')
moose.connect(F, 'nOut', Edot.x[5], 'input')
moose.connect(Z1, 'nOut', Edot.x[6], 'input')
moose.connect(Z2, 'nOut', Edot.x[7], 'input')
moose.connect(Edot, 'valueOut', E, 'increment')
moose.connect(A, 'nOut', Fdot.x[0], 'input')
moose.connect(B, 'nOut', Fdot.x[1], 'input')
moose.connect(C, 'nOut', Fdot.x[2], 'input')
moose.connect(D, 'nOut', Fdot.x[3], 'input')
moose.connect(E, 'nOut', Fdot.x[4], 'input')
moose.connect(F, 'nOut', Fdot.x[5], 'input')
moose.connect(Z1, 'nOut', Fdot.x[6], 'input')
moose.connect(Z2, 'nOut', Fdot.x[7], 'input')
moose.connect(Fdot, 'valueOut', F, 'increment')
return compt
def makeChemProto(name='hydra'):
moose.Neutral('/library/')
meshName = '/library/' + name
moose.SBML.mooseReadSBML(os.path.join(sdir_, '..', 'data', 'c_m.xml'),
meshName)
Rad = moose.element('/library/hydra/dend/IRSpGr/Rad')
I_C = moose.element(meshName + '/dend/IRSpGr/IRSp53')
Ca = moose.element(meshName + '/dend/Ca')
rec = moose.Pool(meshName + '/dend/IRSpGr/rec')
conv = moose.Pool(meshName + '/dend/conv')
Cdc42 = moose.element(meshName + '/dend/IRSpGr/Cdc42')
Cdc42_m = moose.element(meshName + '/dend/IRSpGr/Cdc42_m')
Cdc42_GDP = moose.element(meshName + '/dend/Cdc42_GDP')
Rac_GTP = moose.element(meshName + '/dend/Rac_GTP')
Rac_m = moose.element(meshName + '/dend/IRSpGr/Rac_m')
Rac_GDP = moose.element(meshName + '/dend/Rac_GDP')
Eps8 = moose.element(meshName + '/dend/IRSpGr/Eps8')
I_Cact = moose.element(meshName + '/dend/IRSpGr/IRSp53_a')
I_M = moose.element(meshName + '/dend/IRSpGr/IRSp53_m')
Idimer = moose.element(meshName + '/dend/IRSpGr/IRSp53_dimer')
recBAR = moose.Function(meshName + '/dend/IRSpGr/recBAR')
gradBAR = moose.Function(meshName + '/dend/IRSpGr/gradBAR')
Radfun = moose.Function(meshName + '/dend/IRSpGr/Radfun')
Ipool = moose.element(meshName + '/dend/IRSpGr/Ipool')
sort = moose.element(meshName + '/dend/IRSpGr/sort')
detach = moose.element(meshName + '/dend/IRSpGr/detach')
curv_IRSp53 = moose.element(meshName + '/dend/IRSpGr/curv_IRSp53')
tube_IRSp53 = moose.element(meshName + '/dend/IRSpGr/tube_IRSp53')
to_tube_Reac = moose.element(meshName + '/dend/IRSpGr/to_tube_Reac')
Cdc42_breac = moose.element(meshName + '/dend/Cdc42_GTP_GDP_Reac')
Tiam_breac = moose.element(meshName + '/dend/Tiam_Rev_Reac')
store_tube = moose.Pool(meshName + '/dend/IRSpGr/store_tube')
IRSp53_temp = moose.element(meshName + '/dend/IRSpGr/IRSp53_temp')
sigma = moose.Pool(meshName + '/dend/IRSpGr/sigma')
Kv = moose.Pool(meshName + '/dend/IRSpGr/Kv')
dend_vasp = moose.element(meshName + '/dend/IRSpGr/VASP')
dend_gactin = moose.element(meshName + '/dend/IRSpGr/Gactin')
dend_factin = moose.element(meshName + '/dend/IRSpGr/Factin')
GF_Reac = moose.element(meshName + '/dend/IRSpGr/GF_Reac')
sort_func = moose.element(meshName + '/dend/IRSpGr/sort_func')
breacT_fun = moose.Function(meshName + '/dend/breacT_fun')
breacC_fun = moose.Function(meshName + '/dend/breacC_fun')
simpleFun = moose.Function(meshName + '/dend/IRSpGr/simpleFun')
simpleFun1 = moose.Function(meshName + '/dend/IRSpGr/simpleFun1')
simpleFun2 = moose.Function(meshName + '/dend/IRSpGr/simpleFun2')
Kvfun = moose.Function(meshName + '/dend/IRSpGr/Kvfun')
recFun = moose.Function(meshName + '/dend/IRSpGr/recFun')
simpleFun2 = moose.Function(meshName + '/dend/IRSpGr/simpleFun2')
simpleFun3 = moose.Function(meshName + '/dend/IRSpGr/simpleFun3')
mod_sort = moose.element(meshName + '/dend/IRSpGr/mod_sort')
mod_detach = moose.element(meshName + '/dend/IRSpGr/mod_detach')
to_tube_Reac = moose.element(meshName + '/dend/IRSpGr/to_tube_Reac')
conv_fun = moose.Function(meshName + '/dend/IRSpGr/conv_fun')
conv_fun.expr = "1*x0*(x1-1.89191155)+1.89191155"
Kvfun.expr = "1.0"
moose.connect(Kvfun, 'valueOut', Kv, 'setN')
simpleFun.expr = "1.0*x0"
simpleFun1.expr = "1.0*x0"
simpleFun2.expr = "0.1*x0"
simpleFun3.expr = "1.0*x0"
breacT_fun.expr = "5*x0"
breacC_fun.expr = "5*x0"
moose.connect(curv_IRSp53, 'nOut', simpleFun2.x[0], 'input')
moose.connect(simpleFun2, 'valueOut', GF_Reac, 'setNumKf')
moose.connect(sort_func, 'nOut', simpleFun.x[0], 'input')
moose.connect(detach, 'nOut', simpleFun1.x[0], 'input')
moose.connect(store_tube, 'nOut', simpleFun3.x[0], 'input')
recFun.expr = "0.0*x0+(exp(45*54*((" + str(
args_[14]) + "/(x0*1e9))-(1/(2.0*(x0*1e9)*(x0*1e9))))))"
Radfun.expr = "sqrt(((45+12)*4*1e-18)/(2*(x2-0.08*(ln((((1.0*x0+1.0*x1)/(2*3.14*(0.45*0.05)))*1e-6*54))))))*((3*" + str(
float(args_[2])) + "*x3*(x0+1.0*x1)^2)/(1.+3*" + str(float(
args_[2])) + "*x3*(x0+1.0*x1)^2))"
mod_sort.Kf = 0.
mod_sort.Kb = 0.
mod_detach.Kf = 0.
mod_detach.Kb = 0.
moose.connect(curv_IRSp53, 'nOut', Radfun.x[0], 'input')
moose.connect(I_M, 'nOut', Radfun.x[1], 'input')
#moose.connect(tube_IRSp53,'nOut',Radfun.x[2],'input')
moose.connect(sigma, 'nOut', Radfun.x[2], 'input')
moose.connect(Kv, 'nOut', Radfun.x[3], 'input')
moose.connect(Radfun, 'valueOut', Rad, 'setN')
moose.connect(rec, 'nOut', conv_fun.x[0], 'input')
moose.connect(conv, 'nOut', conv_fun.x[1], 'input')
moose.connect(conv_fun, 'valueOut', Ca, 'setN')
moose.connect(simpleFun, 'valueOut', mod_sort, 'setNumKf')
moose.connect(simpleFun1, 'valueOut', mod_detach, 'setNumKf')
moose.connect(Rad, 'nOut', recFun.x[0], 'input')
moose.connect(recFun, 'valueOut', Ipool, 'setN')
### Ipool is further copied to sort to participate in the reaction tube_reac or enz (model version 2.5.3)
I_C.concInit = 0.0012
file_molWt = os.path.join(sdir_, '..', 'data', 'prot_wt.xml')
den = 6.0 * 3.14 * np.cbrt(3.0 / (4.0 * 3.14 * 0.73 * 6.02 * 1e23))
num = 1e3 * 1e6 * 1.38 * 1e-23
co = num / den
# Diffconsts are set here
if int(args_[3]) == 1:
for prot in moose.wildcardFind(meshName + '/dend/#[ISA=Pool]'):
mol_name = ET.parse(file_molWt).find(str(prot.name))
print('Name is %s' % mol_name, end='. ')
molWt = mol_name.text.split()
if float(molWt[1]) <= 0.0:
continue
moose.element(prot).diffConst = co * (
300 / (200.0 * np.cbrt(float(molWt[1]) * 1e3))) * 1e-4
print('-- D', prot.name, moose.element(prot).diffConst)
for prot in moose.wildcardFind(meshName +
'/dend/CaMKII_gr/#[ISA=Pool]'):
mol_name = ET.parse(file_molWt).find(str(prot.name))
print('Name is %s' % mol_name, end='. ')
molWt = mol_name.text.split()
if float(molWt[1]) <= 0.0:
continue
moose.element(prot).diffConst = co * (
300 / (200.0 * np.cbrt(float(molWt[1]) * 1e3))) * 1e-4
print('-- D', prot.name, moose.element(prot).diffConst)
for prot in moose.wildcardFind(meshName + '/dend/Ras_gr/#[ISA=Pool]'):
mol_name = ET.parse(file_molWt).find(str(prot.name))
print('Name is %s' % mol_name, end='. ')
molWt = mol_name.text.split()
if float(molWt[1]) <= 0.0:
continue
moose.element(prot).diffConst = co * (
300 / (200.0 * np.cbrt(float(molWt[1]) * 1e3))) * 1e-4
print('-- D', prot.name, moose.element(prot).diffConst)
Ca.diffConst = float(args_[4])
print('-- D', Ca.name, Ca.diffConst)
print('\t==================== diffConst updated')
print('DIFFUSION FOR IRSp53 GROUP')
I_C.diffConst = co * (300 / (8.0 * np.cbrt(120.0 * 1e3))) * 1e-4
print(I_C.diffConst, end=' + ')
I_Cact.diffConst = co * (300 / (8.0 * np.cbrt(208.0 * 1e3))) * 1e-4
print(I_Cact.diffConst)
Eps8.diffConst = co * (300 / (200.0 * np.cbrt(92.0 * 1e3))) * 1e-4
print(Eps8.diffConst, end=' + ')
Cdc42.diffConst = co * (300 / (8.0 * np.cbrt(22.0 * 1e3))) * 1e-4
Cdc42_m.diffConst = co * (300 / (200.0 * np.cbrt(22.0 * 1e3))) * 1e-4
Cdc42_GDP.diffConst = co * (300 / (8.0 * np.cbrt(22.0 * 1e3))) * 1e-4
print(Cdc42.diffConst, end=' + ')
Rac_GTP.diffConst = co * (300 / (8.0 * np.cbrt(22.0 * 1e3))) * 1e-4
Rac_m.diffConst = co * (300 / (200.0 * np.cbrt(22.0 * 1e3))) * 1e-4
Rac_GDP.diffConst = co * (300 / (8.0 * np.cbrt(22.0 * 1e3))) * 1e-4
I_M.diffConst = 1.0 * co * (300 / (200.0 * np.cbrt(392.0 * 1e3))) * 1e-4
print(I_M.diffConst, end=' + ')
Idimer.diffConst = co * (300 / (8.0 * np.cbrt(120.0 * 1e3))) * 1e-4
print(Idimer.diffConst)
curv_IRSp53.diffConst = float(args_[17])
conv.diffConst = 0.0
rec.diffConst = 0.0
dend_gactin.diffConst = 1e-13
dend_vasp.diffConst = 1e-13
return meshName
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 as a hybrid of a reaction and a function which
sets its rates. Please see rxdFuncDiffusion.py for a variant that uses
just a function object to set up the system.
"""
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
# There is an implicit reaction substrate/product. MOOSE makes it explicit.
buf = moose.BufPool( '/cylinder/buf' )
buf.nInit = 1
# The reaction is something entirely peculiar, not a chemical thing.
reaction = moose.Reac( '/cylinder/reac' )
reaction.Kb = 0
# so here we set up a function calculation to do the same thing.
func = moose.Function( '/cylinder/reac/func' )
func.expr = "(1 - x0) * (0.3 - x0)"
func.x.num = 1 #specify number of input variables.
#Connect the reaction to the pools
moose.connect( reaction, 'sub', c, 'reac' )
moose.connect( reaction, 'prd', buf, 'reac' )
#Connect the function to the reaction
moose.connect( func, 'valueOut', reaction, 'setNumKf' )
#Connect the molecules to the func
moose.connect( c, 'nOut', func.x[0], 'input' )
#Set up solvers
ksolve = moose.Ksolve( '/cylinder/ksolve' )
dsolve = moose.Dsolve( '/cylinder/dsolve' )
stoich = moose.Stoich( '/cylinder/stoich' )
stoich.compartment = compt
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.path = '/cylinder/##'
for i in range( 10, 18 ):
moose.setClock( i, dt )
#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 = ", time.time() - t1))
pylab.ylim( 0, 1.05 )
pylab.legend()
pylab.show()
def makeChemProto(name, stimAmpl=1, diffLength=1e-6, preStim=10.0):
# Parameters
sw = params['stimWidth']
dca = params['diffConstA'] * diffLength * diffLength
dcb = params['diffConstB'] * diffLength * diffLength
# Objects
chem = moose.Neutral('/library/' + name)
compt = moose.CubeMesh(chem.path + '/dend')
A = moose.Pool(compt.path + '/A')
B = moose.Pool(compt.path + '/B')
Z = moose.BufPool(compt.path + '/Z')
Ca = moose.BufPool(compt.path + '/Ca')
phase = moose.BufPool(compt.path + '/phase')
vel = moose.BufPool(compt.path + '/vel')
ampl = moose.BufPool(compt.path + '/ampl')
Adot = moose.Function(A.path + '/Adot')
Bdot = moose.Function(B.path + '/Bdot')
CaStim = moose.Function(Ca.path + '/CaStim')
A.diffConst = dca
B.diffConst = dcb
# Equations
xv0 = '(x0-' + str(params['offsetV']) + ')'
xv1 = '(x1-' + str(params['offsetV']) + ')'
xw1 = '(x1-' + str(params['offsetW']) + ')'
xw2 = '(x2-' + str(params['offsetW']) + ')'
Adot.expr = '5*x3*( 0.0 +' + xv1 + ' - (' + xv1 + '^3)/3 -' + xw2 + ' + x0 )' # x0=Ca, x1=A, x2=B
#Adot.expr = 'x3*( 0.5 + x1 - x1*x1*x1/3 - x2 + x0 )' # x0=Ca, x1=A, x2=B
#Bdot.expr = 'x2*' + str(1.0/params['tau']) + '*(x0 + ' + sp('a', ' - ') + sp( 'b', ' * x1 ' ) + ')'
Bdot.expr = 'x2*' + str(1.0 / params['tau']) + '*(' + xv0 + '+' + sp(
'a', ' - ') + sp('b', ' * ' + xw1) + ')'
CaStim.expr = 'x2 * exp( -((x0 - t)^2)/(2* ' + str(sw * sw) + ') )'
print Adot.expr
print Bdot.expr
print CaStim.expr
# Connections
Adot.x.num = 4
moose.connect(Ca, 'nOut', Adot.x[0], 'input')
moose.connect(A, 'nOut', Adot.x[1], 'input')
moose.connect(B, 'nOut', Adot.x[2], 'input')
moose.connect(Z, 'nOut', Adot.x[3], 'input')
moose.connect(Adot, 'valueOut', A, 'increment')
Bdot.x.num = 3
moose.connect(A, 'nOut', Bdot.x[0], 'input')
moose.connect(B, 'nOut', Bdot.x[1], 'input')
moose.connect(Z, 'nOut', Bdot.x[2], 'input')
moose.connect(Bdot, 'valueOut', B, 'increment')
CaStim.x.num = 3
moose.connect(phase, 'nOut', CaStim.x[0], 'input')
moose.connect(vel, 'nOut', CaStim.x[1], 'input')
moose.connect(ampl, 'nOut', CaStim.x[2], 'input')
moose.connect(CaStim, 'valueOut', Ca, 'setN')
return compt
compt.diffLength = 1 assert( compt.numDiffCompts == 1000 ) #define the molecule. Its geometry is defined by its parent volume, cylinder c = moose.Pool( '/cylinder/pool' ) c.diffConst = 1 # define diffusion constant # There is an implicit reaction substrate/product. MOOSE makes it explicit. buf = moose.BufPool( '/cylinder/buf' ) buf.nInit = 1 # The reaction is something entirely peculiar, not a chemical thing. reaction = moose.Reac( '/cylinder/reac' ) reaction.Kb = 0 # so here we set up a function calculation to do the same thing. func = moose.Function( '/cylinder/reac/func' ) func.expr = "(0.3 - x0) * (1 - x0)" func.x.num = 1 #specify number of input variables. #Connect the reaction to the pools moose.connect( reaction, 'sub', c, 'reac' ) moose.connect( reaction, 'prd', buf, 'reac' ) #Connect the function to the reaction moose.connect( func, 'valueOut', reaction, 'setNumKf' ) #Connect the molecules to the func moose.connect( c, 'nOut', func.x[0], 'input' ) #Set up solvers
def test_ksolver_parallel(nthreads=4):
"""
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 as a hybrid of a reaction and a function which
sets its rates. Please see rxdFuncDiffusion.py for a variant that uses
just a function object to set up the system.
"""
dt = 0.1
# define the geometry
compt = moose.CylMesh('/cylinder')
compt.r0 = compt.r1 = 1
# compt.diffLength = 1e-6
compt.x1 = 1e-2
assert compt.numDiffCompts == int(
compt.x1 / compt.diffLength), (compt.numDiffCompts,
compt.x1 / compt.diffLength)
print('No of compartment %d' % compt.numDiffCompts)
#define the molecule. Its geometry is defined by its parent volume, cylinder
c = moose.Pool('/cylinder/pool')
c.diffConst = 1 # define diffusion constant
# There is an implicit reaction substrate/product. MOOSE makes it explicit.
buf = moose.BufPool('/cylinder/buf')
buf.nInit = 1
# The reaction is something entirely peculiar, not a chemical thing.
reaction = moose.Reac('/cylinder/reac')
reaction.Kb = 0
# so here we set up a function calculation to do the same thing.
func = moose.Function('/cylinder/reac/func')
func.expr = "(1 - x0) * (0.3 - x0)"
func.x.num = 1 #specify number of input variables.
#Connect the reaction to the pools
moose.connect(reaction, 'sub', c, 'reac')
moose.connect(reaction, 'prd', buf, 'reac')
#Connect the function to the reaction
moose.connect(func, 'valueOut', reaction, 'setNumKf')
#Connect the molecules to the func
moose.connect(c, 'nOut', func.x[0], 'input')
#Set up solvers
ksolve = moose.Ksolve('/cylinder/ksolve')
ksolve.numThreads = nthreads
dsolve = moose.Dsolve('/cylinder/dsolve')
stoich = moose.Stoich('/cylinder/stoich')
stoich.compartment = compt
stoich.ksolve = ksolve
stoich.dsolve = dsolve
stoich.reacSystemPath = '/cylinder/##'
assert stoich.reacSystemPath == '/cylinder/##'
for i in range(10, 18):
moose.setClock(i, dt)
#initialize
x = np.arange(0, compt.x1, compt.diffLength)
assert len(c.vec) == 10000, len(c.vec)
nInit = [(float(q < 0.2) * compt.x1) for q in x]
c.vec.nInit = nInit
assert np.allclose(c.vec.nInit, nInit), (c.vec.nInit, nInit)
expected = [(0.01, 0.0), (2.6704795776286974e-07, 1.2678976830753021e-17),
(8.167639617309419e-14, 3.8777269301457245e-24),
(2.498062905267963e-20, 1.1860363878961374e-30),
(7.64029581501609e-27, 3.6273808003690943e-37)]
# Run and plot it.
moose.reinit()
updateDt = 50
runtime = updateDt * 4
yvec = c.vec.n
u1, m1 = np.mean(yvec), np.std(yvec)
print(u1, m1)
assert np.isclose((u1, m1), expected[0],
atol=1e-5).all(), ((u1, m1), expected[0])
t1 = time.time()
for i, t in enumerate(range(0, runtime - 1, updateDt)):
moose.start(updateDt)
yvec = c.vec.n
u1, m1 = np.mean(yvec), np.std(yvec)
print(u1, m1)
np.isclose((u1, m1), expected[i + 1], atol=1e-5).all(), expected[i + 1]
return time.time() - t1
dt = 0.1
# define the geometry
compt = moose.CylMesh('/cylinder')
compt.r0 = compt.r1 = 1
compt.x1 = 100
compt.diffLength = 0.2
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
def createRules(model, specInfoMap, globparameterIdValue):
for r in range(0, model.getNumRules()):
rule = model.getRule(r)
comptvolume = []
if (rule.isAssignment()):
rule_variable = rule.getVariable()
rule_variable = parentSp = str(idBeginWith(rule_variable))
poolList = specInfoMap[rule_variable]["Mpath"].path
poolsCompt = findCompartment(moose.element(poolList))
if not isinstance(moose.element(poolsCompt), moose.ChemCompt):
return -2
else:
if poolsCompt.name not in comptvolume:
comptvolume.append(poolsCompt.name)
funcId = moose.Function(poolList + '/func')
objclassname = moose.element(poolList).className
if objclassname == "BufPool" or objclassname == "ZombieBufPool":
moose.connect(funcId, 'valueOut', poolList, 'setN')
elif objclassname == "Pool" or objclassname == "ZombiePool":
# moose.connect( funcId, 'valueOut', poolList ,'increament' )
moose.connect(funcId, 'valueOut', poolList, 'setN')
elif objclassname == "Reac" or objclassname == "ZombieReac":
moose.connect(funcId, 'valueOut', poolList, 'setNumkf')
ruleMath = rule.getMath()
ruleMemlist = []
speFunXterm = {}
getMembers(ruleMath, ruleMemlist)
for i in ruleMemlist:
if (i in specInfoMap):
i = str(idBeginWith(i))
specMapList = specInfoMap[i]["Mpath"]
poolsCompt = findCompartment(moose.element(specMapList))
if not isinstance(moose.element(poolsCompt),
moose.ChemCompt):
return -2
else:
if poolsCompt.name not in comptvolume:
comptvolume.append(poolsCompt.name)
numVars = funcId.numVars
x = funcId.path + '/x[' + str(numVars) + ']'
speFunXterm[i] = 'x' + str(numVars)
moose.connect(specMapList, 'nOut', x, 'input')
funcId.numVars = numVars + 1
elif not (i in globparameterIdValue):
print("check the variable type ", i)
exp = rule.getFormula()
for mem in ruleMemlist:
if (mem in specInfoMap):
#exp1 = exp.replace(mem, str(speFunXterm[mem]))
exp1 = re.sub(r'\b%s\b' % (mem), speFunXterm[mem], exp)
exp = exp1
elif (mem in globparameterIdValue):
#exp1 = exp.replace(mem, str(globparameterIdValue[mem]))
exp1 = re.sub(r'\b%s\b' % (mem), globparameterIdValue[mem],
exp)
exp = exp1
else:
print("Math expression need to be checked")
exp = exp.replace(" ", "")
funcId.expr = exp.strip(" \t\n\r")
# return True
elif (rule.isRate()):
print("Warning : For now this \"", rule.getVariable(),
"\" rate Rule is not handled in moose ")
# return False
elif (rule.isAlgebraic()):
print("Warning: For now this ", rule.getVariable(),
" Algebraic Rule is not handled in moose")
# return False
if len(comptvolume) > 1:
warning = "\nFunction ", moose.element(
poolList
).name, " has input from different compartment which is depricated in moose and running this model cause moose to crash"
return True