def _addStates(self, params):
from .. import sim
for label, param in params.items():
# regions
if 'regions' not in param:
print(
' Error creating State %s: "regions" parameter was missing' %
(label))
continue
if not isinstance(param['regions'], list):
param['regions'] = [param['regions']]
try:
nrnRegions = [
self.rxd['regions'][region]['hObj']
for region in param['regions']
if self.rxd['regions'][region]['hObj'] != None
]
except:
print(' Error creating State %s: could not find regions %s' %
(label, param['regions']))
# initial
if 'initial' not in param:
param['initial'] == None
if isinstance(param['initial'], basestring): # string-based func
funcStr = self._replaceRxDStr(param['initial'],
constants=True,
regions=True,
species=False)
# create final function dynamically from string
importStr = ' from neuron import crxd as rxd \n from netpyne import sim'
afterDefStr = 'sim.net.rxd["states"]["%s"]["initialFunc"] = initial' % (
label)
funcStr = 'def initial (node): \n%s \n return %s \n%s' % (
importStr, funcStr, afterDefStr) # convert to lambda function
try:
exec(funcStr, {'rxd': rxd}, {'sim': sim})
initial = sim.net.rxd["species"][label]["initialFunc"]
except:
print(
' Error creating State %s: cannot evaluate "initial" expression -- "%s"'
% (label, param['initial']))
continue
else:
initial = param['initial']
# call rxd method to create Region
if nrnRegions:
self.rxd['states'][label]['hObj'] = rxd.State(regions=nrnRegions,
initial=initial)
else:
self.rxd['states'][label]['hObj'] = None
print(' Created State %s' % (label))
kserca = 0.1 kip3 = 0.15 kact = 0.4 ip3rtau = 2000 h.CVode().active(1) h.cvode.atol(1e-10) # define the regions for the rxd cyt = rxd.Region(h.allsec(), nrn_region='i', geometry=rxd.FractionalVolume(fc, surface_fraction=1)) er = rxd.Region(h.allsec(), geometry=rxd.FractionalVolume(fe)) cyt_er_membrane = rxd.Region(h.allsec(), geometry=rxd.FixedPerimeter(1)) # the species and other states ca = rxd.Species([cyt, er], d=caDiff, name='ca', charge=2, initial=cac_init) ip3 = rxd.Species(cyt, d=ip3Diff, initial=ip3_init) ip3r_gate_state = rxd.State(cyt_er_membrane, initial=0.8) h_gate = ip3r_gate_state[cyt_er_membrane] # pumps and channels between ER and Cytosol serca = rxd.MultiCompartmentReaction(ca[cyt]>ca[er], gserca/((kserca / (1000. * ca[cyt])) ** 2 + 1), membrane=cyt_er_membrane, custom_dynamics=True) leak = rxd.MultiCompartmentReaction(ca[er]!=ca[cyt], gleak, gleak, membrane=cyt_er_membrane) minf = ip3[cyt] * 1000. * ca[cyt] / (ip3[cyt] + kip3) / (1000. * ca[cyt] + kact) k = gip3r * (minf * h_gate) ** 3 ip3r = rxd.MultiCompartmentReaction(ca[er]!=ca[cyt], k, k, membrane=cyt_er_membrane) ip3rg = rxd.Rate(h_gate, (1. / (1 + 1000. * ca[cyt] / (0.3)) - h_gate) / ip3rtau)
charge=1,
initial=init(54.4, 2.5),
ecs_boundary_conditions=2.5)
na = rxd.Species([cyt, mem, ecs],
name='na',
d=1e3,
charge=1,
initial=init(10.0, 140.0),
ecs_boundary_conditions=140)
x = rxd.Species([cyt, mem, ecs], name='x', charge=1)
ki, ko, nai, nao, xi, xo = k[cyt], k[ecs], na[cyt], na[ecs], x[cyt], x[ecs]
# gates
ngate = rxd.State([cyt, mem], name='ngate', initial=0.24458654944007166)
mgate = rxd.State([cyt, mem], name='mgate', initial=0.028905534475191907)
hgate = rxd.State([cyt, mem], name='hgate', initial=0.7540796658225246)
# somaA parameter
pA = rxd.Parameter([cyt, mem],
name='paramA',
initial=lambda nd: 1 if nd.segment in somaA else 0)
#What
# gates
m_gate = rxd.Rate(mgate, (minf - mgate) / mtau)
h_gate = rxd.Rate(hgate, (hinf - hgate) / htau)
n_gate = rxd.Rate(ngate, (ninf - ngate) / ntau)
# Nernst potentials
