Generated Code

# Size of variable arrays:
sizeAlgebraic = 5
sizeStates = 3
sizeConstants = 14
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_states[0] = "V in component membrane (millivolt)"
    legend_constants[0] = "Cm in component membrane (picoF)"
    legend_algebraic[0] = "i_s in component calcium_channel (femtoA)"
    legend_algebraic[2] = "i_K in component potassium_channel (femtoA)"
    legend_algebraic[3] = "i_K_ACh in component acetyl_choline_activated_potassium_channel (femtoA)"
    legend_algebraic[4] = "i_j in component coupling_current (femtoA)"
    legend_constants[1] = "g_s in component calcium_channel (picoS)"
    legend_constants[2] = "V_s in component calcium_channel (millivolt)"
    legend_constants[3] = "V_1 in component calcium_channel (millivolt)"
    legend_constants[4] = "V_2 in component calcium_channel (millivolt)"
    legend_constants[5] = "g_K in component potassium_channel (picoS)"
    legend_constants[6] = "V_K in component potassium_channel (millivolt)"
    legend_states[1] = "w in component potassium_channel_w_gate (dimensionless)"
    legend_constants[7] = "lambda_w in component potassium_channel_w_gate (per_second)"
    legend_constants[8] = "V_3 in component potassium_channel_w_gate (millivolt)"
    legend_constants[9] = "V_4 in component potassium_channel_w_gate (millivolt)"
    legend_states[2] = "u in component acetyl_choline_activated_potassium_channel_u_gate (dimensionless)"
    legend_constants[13] = "alpha in component acetyl_choline_activated_potassium_channel_u_gate (per_second)"
    legend_algebraic[1] = "beta in component acetyl_choline_activated_potassium_channel_u_gate (per_second)"
    legend_constants[10] = "ACh in component acetyl_choline_activated_potassium_channel_u_gate (molar)"
    legend_constants[11] = "g_j in component coupling_current (picoS)"
    legend_constants[12] = "V_B in component coupling_current (millivolt)"
    legend_rates[0] = "d/dt V in component membrane (millivolt)"
    legend_rates[1] = "d/dt w in component potassium_channel_w_gate (dimensionless)"
    legend_rates[2] = "d/dt u in component acetyl_choline_activated_potassium_channel_u_gate (dimensionless)"
    return (legend_states, legend_algebraic, legend_voi, legend_constants)

def initConsts():
    constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
    states[0] = -52.07606
    constants[0] = 60
    constants[1] = 382.9118
    constants[2] = 214.1429
    constants[3] = -35.9358
    constants[4] = 7.8589
    constants[5] = 536.1093
    constants[6] = -259.0783
    states[1] = 0.0008971
    constants[7] = 20.7796
    constants[8] = -27.9375
    constants[9] = 6.321
    states[2] = 0.2344555
    constants[10] = 1e-6
    constants[11] = 0
    constants[12] = -50
    constants[13] = 0.0123320/(1.00000+4.20000e-06/constants[10])
    return (states, constants)

def computeRates(voi, states, constants):
    rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
    rates[1] = constants[7]*cosh((states[0]-constants[8])/(2.00000*constants[9]))*((1.00000/2.00000)*(1.00000+tanh((states[0]-constants[8])/constants[9]))-states[1])
    algebraic[1] = 0.0100000*exp(0.0133000*(states[0]+40.0000))
    rates[2] = constants[13]*(1.00000-states[2])-algebraic[1]*states[2]
    algebraic[0] = (1.00000/2.00000)*constants[1]*(1.00000+tanh((states[0]-constants[3])/constants[4]))*(states[0]-constants[2])
    algebraic[2] = constants[5]*states[1]*(states[0]-constants[6])
    algebraic[3] = 1.00000*0.270000*states[2]*(states[0]+90.0000)
    algebraic[4] = constants[11]*(states[0]-constants[12])
    rates[0] = -(algebraic[0]+algebraic[2]+algebraic[3]+algebraic[4])/constants[0]
    return(rates)

def computeAlgebraic(constants, states, voi):
    algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
    states = array(states)
    voi = array(voi)
    algebraic[1] = 0.0100000*exp(0.0133000*(states[0]+40.0000))
    algebraic[0] = (1.00000/2.00000)*constants[1]*(1.00000+tanh((states[0]-constants[3])/constants[4]))*(states[0]-constants[2])
    algebraic[2] = constants[5]*states[1]*(states[0]-constants[6])
    algebraic[3] = 1.00000*0.270000*states[2]*(states[0]+90.0000)
    algebraic[4] = constants[11]*(states[0]-constants[12])
    return algebraic

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)