Generated Code

# Size of variable arrays:
sizeAlgebraic = 7
sizeStates = 5
sizeConstants = 43
from math import *
from numpy import *

def createLegends():
    legend_states = [""] * sizeStates
    legend_rates = [""] * sizeStates
    legend_algebraic = [""] * sizeAlgebraic
    legend_voi = ""
    legend_constants = [""] * sizeConstants
    legend_constants[0] = "V_init in component Vstim_para (mV)"
    legend_constants[1] = "V_rate in component Vstim_para (mV_per_s)"
    legend_constants[2] = "Nai in component control_para (mM)"
    legend_constants[3] = "Cai in component control_para (mM)"
    legend_constants[4] = "inhPump in component control_para (dimensionless)"
    legend_constants[5] = "K_Cahalf in component control_para (mV)"
    legend_voi = "time in component time_s (second)"
    legend_states[0] = "V in component vramp_protocol_s (mV)"
    legend_algebraic[6] = "J_VOCC in component J_VOCC (mM_per_s)"
    legend_constants[34] = "J_CaPump in component J_CaPump (mM_per_s)"
    legend_algebraic[0] = "J_NaCa in component J_NaCa (mM_per_s)"
    legend_algebraic[3] = "rho_vCa in component J_VOCC (dimensionless)"
    legend_constants[35] = "K_1 in component K_1 (per_s)"
    legend_algebraic[1] = "stress in component CB4HM (dimensionless)"
    legend_algebraic[2] = "phosphorylation in component CB4HM (dimensionless)"
    legend_constants[6] = "R in component constants (J_per_K_mol)"
    legend_constants[7] = "F in component constants (C_per_mmol)"
    legend_constants[8] = "T in component model_para (kelvin)"
    legend_constants[9] = "Nao in component model_para (mM)"
    legend_constants[10] = "Cao in component model_para (mM)"
    legend_constants[11] = "V_cell in component model_para (fm3)"
    legend_constants[12] = "V_Cahalf in component model_para (mV)"
    legend_constants[13] = "g_mCa in component model_para (nS)"
    legend_constants[14] = "V_pmax in component model_para (mM_per_s)"
    legend_constants[15] = "n in component model_para (dimensionless)"
    legend_constants[16] = "K_ph in component model_para (mM)"
    legend_constants[17] = "K_NaCa in component model_para (mM)"
    legend_constants[18] = "G_NaCa in component model_para (mM_per_s_mV)"
    legend_constants[19] = "n_M in component model_para (dimensionless)"
    legend_constants[20] = "Ca_halfMLCK in component model_para (mM)"
    legend_constants[21] = "M_init in component initials (dimensionless)"
    legend_constants[22] = "Mp_init in component initials (dimensionless)"
    legend_constants[23] = "AM_init in component initials (dimensionless)"
    legend_constants[24] = "AMp_init in component initials (dimensionless)"
    legend_constants[25] = "K_7 in component model_para (per_s)"
    legend_constants[26] = "K_2 in component model_para (per_s)"
    legend_constants[27] = "K_3 in component model_para (per_s)"
    legend_constants[28] = "Nai in component model_para (mM)"
    legend_constants[29] = "K_Cahalf in component model_para (mV)"
    legend_constants[30] = "inhPump in component model_para (dimensionless)"
    legend_constants[31] = "Cai_init in component initials (mM)"
    legend_constants[32] = "z_Ca in component E_Ca (dimensionless)"
    legend_constants[39] = "E in component Nernst_potential (mV)"
    legend_constants[33] = "z_Na in component E_Na (dimensionless)"
    legend_constants[36] = "E in component Nernst_potential (mV)"
    legend_algebraic[5] = "I in component Ionic_currents (pA)"
    legend_constants[41] = "V_mNaCa in component J_NaCa (mV)"
    legend_constants[37] = "K_4 in component CB4HM (per_s)"
    legend_constants[38] = "K_5 in component CB4HM (per_s)"
    legend_constants[40] = "K_6 in component CB4HM (per_s)"
    legend_algebraic[4] = "norm in component CB4HM (dimensionless)"
    legend_states[1] = "M in component CB4HM (dimensionless)"
    legend_states[2] = "Mp in component CB4HM (dimensionless)"
    legend_states[3] = "AM in component CB4HM (dimensionless)"
    legend_states[4] = "AMp in component CB4HM (dimensionless)"
    legend_rates[0] = "d/dt V in component vramp_protocol_s (mV)"
    legend_rates[1] = "d/dt M in component CB4HM (dimensionless)"
    legend_rates[2] = "d/dt Mp in component CB4HM (dimensionless)"
    legend_rates[3] = "d/dt AM in component CB4HM (dimensionless)"
    legend_rates[4] = "d/dt AMp in component CB4HM (dimensionless)"
    return (legend_states, legend_algebraic, legend_voi, legend_constants)

def initConsts():
    constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
    constants[0] = -100
    constants[1] = 1
    constants[2] = 16.55
    constants[3] = 0.0001
    constants[4] = 1
    constants[5] = 11
    constants[6] = 8.314
    constants[7] = 96.48534
    constants[8] = 310
    constants[9] = 140
    constants[10] = 2
    constants[11] = 21
    constants[12] = -27
    constants[13] = 0.046842
    constants[14] = 5.1449e-4
    constants[15] = 1.9015
    constants[16] = 0.6e-3
    constants[17] = 7e-3
    constants[18] = 5.7297e-5
    constants[19] = 8.7613
    constants[20] = 256.98e-6
    constants[21] = 1
    constants[22] = 0
    constants[23] = 0
    constants[24] = 0
    constants[25] = 0.0378
    constants[26] = 1.2387
    constants[27] = 0.1419
    constants[28] = 2.9836
    constants[29] = 11
    constants[30] = 1
    constants[31] = 0.1e-6
    constants[32] = 2
    constants[33] = 1
    constants[34] = (-constants[14]*(power(constants[3], constants[15])))/(power(constants[16], constants[15])+power(constants[3], constants[15]))
    constants[35] = ((power(constants[3], constants[19]))/(power(constants[20], constants[19])+power(constants[3], constants[19])))*1.00000
    constants[36] = ((constants[6]*constants[8])/(constants[33]*constants[7]))*log(constants[9]/constants[2])
    constants[37] = constants[27]/4.00000
    constants[38] = constants[26]
    constants[42] = constants[1]
    constants[39] = ((constants[6]*constants[8])/(constants[32]*constants[7]))*log(constants[10]/constants[3])
    constants[40] = constants[35]
    constants[41] = 3.00000*constants[36]-2.00000*constants[39]
    states[0] = constants[0]
    states[1] = constants[21]
    states[2] = constants[22]
    states[3] = constants[23]
    states[4] = constants[24]
    return (states, constants)

def computeRates(voi, states, constants):
    rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
    rates[0] = constants[42]
    algebraic[4] = states[1]+states[2]+states[3]+states[4]
    rates[1] = (-constants[35]*states[1])/algebraic[4]+(constants[26]*states[2])/algebraic[4]+(constants[25]*states[3])/algebraic[4]
    rates[2] = ((constants[37]*states[4])/algebraic[4]+(constants[35]*states[1])/algebraic[4])-((constants[26]+constants[27])*states[2])/algebraic[4]
    rates[3] = (constants[38]*states[4])/algebraic[4]-((constants[40]+constants[25])*states[3])/algebraic[4]
    rates[4] = ((constants[27]*states[2])/algebraic[4]+(constants[40]*states[3])/algebraic[4])-((constants[37]+constants[38])*states[4])/algebraic[4]
    return(rates)

def computeAlgebraic(constants, states, voi):
    algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
    states = array(states)
    voi = array(voi)
    algebraic[4] = states[1]+states[2]+states[3]+states[4]
    algebraic[0] = ((constants[18]*constants[3])/(constants[3]+constants[17]))*(states[0]-constants[41])
    algebraic[1] = states[4]+states[3]
    algebraic[2] = states[4]+states[2]
    algebraic[3] = 1.00000/(1.00000+exp((constants[12]-states[0])/constants[5]))
    algebraic[5] = constants[13]*algebraic[3]*(states[0]-constants[39])
    algebraic[6] = -algebraic[5]/(2.00000*constants[11]*constants[7])
    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)