"""This module contains a Fenton_karma_1998_BR_altered cardiac cell model
The module was autogenerated from a gotran ode file
"""
from __future__ import division
from collections import OrderedDict
import ufl
from cbcbeat.dolfinimport import *
from cbcbeat.cellmodels import CardiacCellModel
[docs]class Fenton_karma_1998_BR_altered(CardiacCellModel):
def __init__(self, params=None, init_conditions=None):
"""
Create cardiac cell model
*Arguments*
params (dict, :py:class:`dolfin.Mesh`, optional)
optional model parameters
init_conditions (dict, :py:class:`dolfin.Mesh`, optional)
optional initial conditions
"""
CardiacCellModel.__init__(self, params, init_conditions)
@staticmethod
[docs] def default_parameters():
"Set-up and return default parameters."
params = OrderedDict([("u_c", 0.13),
("u_v", 0.04),
("g_fi_max", 4),
("tau_v1_minus", 1250),
("tau_v2_minus", 19.6),
("tau_v_plus", 3.33),
("tau_0", 12.5),
("tau_r", 33.33),
("k", 10),
("tau_si", 29),
("u_csi", 0.85),
("tau_w_minus", 41),
("tau_w_plus", 870),
("IstimAmplitude", -0.2),
("IstimEnd", 50000),
("IstimPeriod", 1000),
("IstimPulseDuration", 1),
("IstimStart", 10),
("Cm", 1),
("V_0", -85),
("V_fi", 15)])
return params
@staticmethod
[docs] def default_initial_conditions():
"Set-up and return default initial conditions."
ic = OrderedDict([("V", -85),
("v", 1),
("w", 1)])
return ic
def _I(self, v, s, time):
"""
Original gotran transmembrane current dV/dt
"""
time = time if time else Constant(0.0)
# Assign states
V = v
assert(len(s) == 2)
v, w = s
# Assign parameters
u_c = self._parameters["u_c"]
g_fi_max = self._parameters["g_fi_max"]
tau_0 = self._parameters["tau_0"]
tau_r = self._parameters["tau_r"]
k = self._parameters["k"]
tau_si = self._parameters["tau_si"]
u_csi = self._parameters["u_csi"]
Cm = self._parameters["Cm"]
V_0 = self._parameters["V_0"]
V_fi = self._parameters["V_fi"]
# Init return args
current = [ufl.zero()]*1
# Expressions for the p component
p = ufl.conditional(ufl.lt((-V_0 + V)/(V_fi - V_0), u_c), 0, 1)
# Expressions for the Fast inward current component
tau_d = Cm/g_fi_max
J_fi = -(1 - (-V_0 + V)/(V_fi - V_0))*(-u_c + (-V_0 + V)/(V_fi -\
V_0))*p*v/tau_d
# Expressions for the Slow outward current component
J_so = p/tau_r + (1 - p)*(-V_0 + V)/(tau_0*(V_fi - V_0))
# Expressions for the Slow inward current component
J_si = -(1 + ufl.tanh(k*(-u_csi + (-V_0 + V)/(V_fi -\
V_0))))*w/(2*tau_si)
# Expressions for the Stimulus protocol component
J_stim = 0
# Expressions for the Membrane component
current[0] = (V_0 - V_fi)*(J_stim + J_fi + J_si + J_so)
# Return results
return current[0]
[docs] def I(self, v, s, time=None):
"""
Transmembrane current
I = -dV/dt
"""
return -self._I(v, s, time)
[docs] def F(self, v, s, time=None):
"""
Right hand side for ODE system
"""
time = time if time else Constant(0.0)
# Assign states
V = v
assert(len(s) == 2)
v, w = s
# Assign parameters
u_c = self._parameters["u_c"]
u_v = self._parameters["u_v"]
tau_v1_minus = self._parameters["tau_v1_minus"]
tau_v2_minus = self._parameters["tau_v2_minus"]
tau_v_plus = self._parameters["tau_v_plus"]
tau_w_minus = self._parameters["tau_w_minus"]
tau_w_plus = self._parameters["tau_w_plus"]
V_0 = self._parameters["V_0"]
V_fi = self._parameters["V_fi"]
# Init return args
F_expressions = [ufl.zero()]*2
# Expressions for the p component
p = ufl.conditional(ufl.lt((-V_0 + V)/(V_fi - V_0), u_c), 0, 1)
# Expressions for the q component
q = ufl.conditional(ufl.lt((-V_0 + V)/(V_fi - V_0), u_v), 0, 1)
# Expressions for the v gate component
tau_v_minus = tau_v1_minus*q + tau_v2_minus*(1 - q)
F_expressions[0] = (1 - p)*(1 - v)/tau_v_minus - p*v/tau_v_plus
# Expressions for the w gate component
F_expressions[1] = (1 - p)*(1 - w)/tau_w_minus - p*w/tau_w_plus
# Return results
return dolfin.as_vector(F_expressions)
[docs] def num_states(self):
return 2
def __str__(self):
return 'Fenton_karma_1998_BR_altered cardiac cell model'