Generated Code
The following is python code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 19
sizeStates = 7
sizeConstants = 17
from math import *
from numpy import *
def createLegends():
legend_states = [""] * sizeStates
legend_rates = [""] * sizeStates
legend_algebraic = [""] * sizeAlgebraic
legend_voi = ""
legend_constants = [""] * sizeConstants
legend_voi = "time in component environment (second)"
legend_constants[0] = "C_m in component environment (fF)"
legend_states[0] = "q_K_o in component environment (fmol)"
legend_states[1] = "q_K_i in component environment (fmol)"
legend_states[2] = "q_Na_o in component environment (fmol)"
legend_states[3] = "q_Na_i in component environment (fmol)"
legend_states[4] = "q_x0_funny in component environment (fmol)"
legend_states[5] = "q_x1_funny in component environment (fmol)"
legend_states[6] = "q_mem in component environment (fC)"
legend_constants[1] = "R in component environment (J_per_K_per_mol)"
legend_constants[2] = "T in component environment (kelvin)"
legend_constants[3] = "F in component environment (C_per_mol)"
legend_algebraic[13] = "v_funny_K in component funny (fmol_per_sec)"
legend_algebraic[14] = "v_funny_Na in component funny (fmol_per_sec)"
legend_algebraic[18] = "I_mem_funny in component funny (fA)"
legend_constants[4] = "kappa_funny_Na in component funny_parameters (fmol_per_sec)"
legend_constants[5] = "kappa_funny_K in component funny_parameters (fmol_per_sec)"
legend_constants[6] = "kappa_R_xf in component funny_parameters (fmol_per_sec)"
legend_constants[7] = "K_Na_i in component funny_parameters (per_fmol)"
legend_constants[8] = "K_Na_o in component funny_parameters (per_fmol)"
legend_constants[9] = "K_K_i in component funny_parameters (per_fmol)"
legend_constants[10] = "K_K_o in component funny_parameters (per_fmol)"
legend_constants[11] = "K_x0_funny in component funny_parameters (per_fmol)"
legend_constants[12] = "K_x1_funny in component funny_parameters (per_fmol)"
legend_constants[13] = "zNa in component funny_parameters (dimensionless)"
legend_constants[14] = "zK in component funny_parameters (dimensionless)"
legend_constants[15] = "z_xff in component funny_parameters (dimensionless)"
legend_constants[16] = "z_xfr in component funny_parameters (dimensionless)"
legend_algebraic[0] = "mu_K_i in component funny (J_per_mol)"
legend_algebraic[1] = "mu_K_o in component funny (J_per_mol)"
legend_algebraic[2] = "mu_Na_i in component funny (J_per_mol)"
legend_algebraic[3] = "mu_Na_o in component funny (J_per_mol)"
legend_algebraic[4] = "V_mem in component funny (J_per_C)"
legend_algebraic[6] = "Am_Na in component funny (J_per_mol)"
legend_algebraic[5] = "Am_K in component funny (J_per_mol)"
legend_algebraic[9] = "Af_K in component funny (J_per_mol)"
legend_algebraic[10] = "Ar_K in component funny (J_per_mol)"
legend_algebraic[11] = "Af_Na in component funny (J_per_mol)"
legend_algebraic[12] = "Ar_Na in component funny (J_per_mol)"
legend_algebraic[7] = "mu_x0_funny in component funny (J_per_mol)"
legend_algebraic[8] = "mu_x1_funny in component funny (J_per_mol)"
legend_algebraic[15] = "Af_R_xf in component funny (J_per_mol)"
legend_algebraic[16] = "Ar_R_xf in component funny (J_per_mol)"
legend_algebraic[17] = "v_xf in component funny (fmol_per_sec)"
legend_rates[1] = "d/dt q_K_i in component environment (fmol)"
legend_rates[0] = "d/dt q_K_o in component environment (fmol)"
legend_rates[3] = "d/dt q_Na_i in component environment (fmol)"
legend_rates[2] = "d/dt q_Na_o in component environment (fmol)"
legend_rates[6] = "d/dt q_mem in component environment (fC)"
legend_rates[4] = "d/dt q_x0_funny in component environment (fmol)"
legend_rates[5] = "d/dt q_x1_funny in component environment (fmol)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 153400
states[0] = 27.9828
states[1] = 5510
states[2] = 9.3276
states[3] = 0.00456
states[4] = 5.4799070E-06
states[5] = 5.4799070E-06
states[6] = -8.5e4
constants[1] = 8.31
constants[2] = 310
constants[3] = 96500
constants[4] = 45.0247
constants[5] = 91.4974
constants[6] = 0.188833
constants[7] = 1.80864
constants[8] = 13.2633
constants[9] = 2.57828
constants[10] = 18.9074
constants[11] = 0.00306604
constants[12] = 61.5887
constants[13] = 1
constants[14] = 1
constants[15] = -1.8309039
constants[16] = 0.787348905
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[4] = states[6]/constants[0]
algebraic[5] = constants[14]*constants[3]*algebraic[4]
algebraic[0] = constants[1]*constants[2]*log(constants[9]*states[1])
algebraic[8] = constants[1]*constants[2]*log(constants[12]*states[5])
algebraic[9] = algebraic[8]+algebraic[0]+algebraic[5]
algebraic[1] = constants[1]*constants[2]*log(constants[10]*states[0])
algebraic[10] = algebraic[8]+algebraic[1]
algebraic[13] = custom_piecewise([equal(algebraic[5] , 0.00000), 1.00000*constants[5]*(exp(algebraic[9]/(constants[1]*constants[2]))-exp(algebraic[10]/(constants[1]*constants[2]))) , True, (((1.00000*constants[5]*algebraic[5])/(constants[1]*constants[2]))/(exp(algebraic[5]/(constants[1]*constants[2]))-1.00000))*(exp(algebraic[9]/(constants[1]*constants[2]))-exp(algebraic[10]/(constants[1]*constants[2])))])
rates[1] = -algebraic[13]
rates[0] = algebraic[13]
algebraic[6] = constants[13]*constants[3]*algebraic[4]
algebraic[2] = constants[1]*constants[2]*log(constants[7]*states[3])
algebraic[11] = algebraic[8]+algebraic[2]+algebraic[6]
algebraic[3] = constants[1]*constants[2]*log(constants[8]*states[2])
algebraic[12] = algebraic[8]+algebraic[3]
algebraic[14] = custom_piecewise([equal(algebraic[6] , 0.00000), 1.00000*constants[4]*(exp(algebraic[11]/(constants[1]*constants[2]))-exp(algebraic[12]/(constants[1]*constants[2]))) , True, (((1.00000*constants[4]*algebraic[6])/(constants[1]*constants[2]))/(exp(algebraic[6]/(constants[1]*constants[2]))-1.00000))*(exp(algebraic[11]/(constants[1]*constants[2]))-exp(algebraic[12]/(constants[1]*constants[2])))])
rates[3] = -algebraic[14]
rates[2] = algebraic[14]
algebraic[7] = constants[1]*constants[2]*log(constants[11]*states[4])
algebraic[15] = algebraic[7]+constants[15]*constants[3]*algebraic[4]
algebraic[16] = algebraic[8]+constants[16]*constants[3]*algebraic[4]
algebraic[17] = constants[6]*(exp(algebraic[15]/(constants[1]*constants[2]))-exp(algebraic[16]/(constants[1]*constants[2])))
rates[4] = -algebraic[17]
rates[5] = algebraic[17]
algebraic[18] = constants[3]*((-constants[14]*algebraic[13]+constants[13]*algebraic[14]+constants[16]*algebraic[17])-constants[15]*algebraic[17])
rates[6] = algebraic[18]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[4] = states[6]/constants[0]
algebraic[5] = constants[14]*constants[3]*algebraic[4]
algebraic[0] = constants[1]*constants[2]*log(constants[9]*states[1])
algebraic[8] = constants[1]*constants[2]*log(constants[12]*states[5])
algebraic[9] = algebraic[8]+algebraic[0]+algebraic[5]
algebraic[1] = constants[1]*constants[2]*log(constants[10]*states[0])
algebraic[10] = algebraic[8]+algebraic[1]
algebraic[13] = custom_piecewise([equal(algebraic[5] , 0.00000), 1.00000*constants[5]*(exp(algebraic[9]/(constants[1]*constants[2]))-exp(algebraic[10]/(constants[1]*constants[2]))) , True, (((1.00000*constants[5]*algebraic[5])/(constants[1]*constants[2]))/(exp(algebraic[5]/(constants[1]*constants[2]))-1.00000))*(exp(algebraic[9]/(constants[1]*constants[2]))-exp(algebraic[10]/(constants[1]*constants[2])))])
algebraic[6] = constants[13]*constants[3]*algebraic[4]
algebraic[2] = constants[1]*constants[2]*log(constants[7]*states[3])
algebraic[11] = algebraic[8]+algebraic[2]+algebraic[6]
algebraic[3] = constants[1]*constants[2]*log(constants[8]*states[2])
algebraic[12] = algebraic[8]+algebraic[3]
algebraic[14] = custom_piecewise([equal(algebraic[6] , 0.00000), 1.00000*constants[4]*(exp(algebraic[11]/(constants[1]*constants[2]))-exp(algebraic[12]/(constants[1]*constants[2]))) , True, (((1.00000*constants[4]*algebraic[6])/(constants[1]*constants[2]))/(exp(algebraic[6]/(constants[1]*constants[2]))-1.00000))*(exp(algebraic[11]/(constants[1]*constants[2]))-exp(algebraic[12]/(constants[1]*constants[2])))])
algebraic[7] = constants[1]*constants[2]*log(constants[11]*states[4])
algebraic[15] = algebraic[7]+constants[15]*constants[3]*algebraic[4]
algebraic[16] = algebraic[8]+constants[16]*constants[3]*algebraic[4]
algebraic[17] = constants[6]*(exp(algebraic[15]/(constants[1]*constants[2]))-exp(algebraic[16]/(constants[1]*constants[2])))
algebraic[18] = constants[3]*((-constants[14]*algebraic[13]+constants[13]*algebraic[14]+constants[16]*algebraic[17])-constants[15]*algebraic[17])
return algebraic
def custom_piecewise(cases):
"""Compute result of a piecewise function"""
return select(cases[0::2],cases[1::2])
def solve_model():
"""Solve model with ODE solver"""
from scipy.integrate import ode
# Initialise constants and state variables
(init_states, constants) = initConsts()
# Set timespan to solve over
voi = linspace(0, 10, 500)
# Construct ODE object to solve
r = ode(computeRates)
r.set_integrator('vode', method='bdf', atol=1e-06, rtol=1e-06, max_step=1)
r.set_initial_value(init_states, voi[0])
r.set_f_params(constants)
# Solve model
states = array([[0.0] * len(voi)] * sizeStates)
states[:,0] = init_states
for (i,t) in enumerate(voi[1:]):
if r.successful():
r.integrate(t)
states[:,i+1] = r.y
else:
break
# Compute algebraic variables
algebraic = computeAlgebraic(constants, states, voi)
return (voi, states, algebraic)
def plot_model(voi, states, algebraic):
"""Plot variables against variable of integration"""
import pylab
(legend_states, legend_algebraic, legend_voi, legend_constants) = createLegends()
pylab.figure(1)
pylab.plot(voi,vstack((states,algebraic)).T)
pylab.xlabel(legend_voi)
pylab.legend(legend_states + legend_algebraic, loc='best')
pylab.show()
if __name__ == "__main__":
(voi, states, algebraic) = solve_model()
plot_model(voi, states, algebraic)