Generated Code

# Size of variable arrays:
sizeAlgebraic = 6
sizeStates = 6
sizeConstants = 21
from math import *
from numpy import *

def createLegends():
    legend_states = [""] * sizeStates
    legend_rates = [""] * sizeStates
    legend_algebraic = [""] * sizeAlgebraic
    legend_voi = ""
    legend_constants = [""] * sizeConstants
    legend_voi = "t in component AE1 (second)"
    legend_constants[0] = "RT in component param (kJ_per_mol)"
    legend_constants[1] = "K_Cl_o in component param (per_mol)"
    legend_constants[2] = "K_Cl_i in component param (per_mol)"
    legend_constants[3] = "K_HCO3_i in component param (per_mol)"
    legend_constants[4] = "K_HCO3_o in component param (per_mol)"
    legend_constants[5] = "K_E_o in component param (per_mol)"
    legend_constants[6] = "K_ECl_o in component param (per_mol)"
    legend_constants[7] = "K_ECl_i in component param (per_mol)"
    legend_constants[8] = "K_E_i in component param (per_mol)"
    legend_constants[9] = "K_EHCO3_i in component param (per_mol)"
    legend_constants[10] = "K_EHCO3_o in component param (per_mol)"
    legend_constants[11] = "K_Re1 in component param (mM_per_s)"
    legend_constants[12] = "K_Re2 in component param (mM_per_s)"
    legend_constants[13] = "K_Re3 in component param (mM_per_s)"
    legend_constants[14] = "K_Re4 in component param (mM_per_s)"
    legend_constants[15] = "K_Re5 in component param (mM_per_s)"
    legend_constants[16] = "K_Re6 in component param (mM_per_s)"
    legend_constants[17] = "q_Cl_o in component AE1 (mole)"
    legend_constants[18] = "q_Cl_i in component AE1 (mole)"
    legend_constants[19] = "q_HCO3_i in component AE1 (mole)"
    legend_constants[20] = "q_HCO3_o in component AE1 (mole)"
    legend_states[0] = "q_E_o in component AE1 (mole)"
    legend_states[1] = "q_ECl_o in component AE1 (mole)"
    legend_states[2] = "q_ECl_i in component AE1 (mole)"
    legend_states[3] = "q_E_i in component AE1 (mole)"
    legend_states[4] = "q_EHCO3_i in component AE1 (mole)"
    legend_states[5] = "q_EHCO3_o in component AE1 (mole)"
    legend_algebraic[0] = "v_Re1 in component AE1 (mM_per_s)"
    legend_algebraic[1] = "v_Re2 in component AE1 (mM_per_s)"
    legend_algebraic[2] = "v_Re3 in component AE1 (mM_per_s)"
    legend_algebraic[3] = "v_Re4 in component AE1 (mM_per_s)"
    legend_algebraic[4] = "v_Re5 in component AE1 (mM_per_s)"
    legend_algebraic[5] = "v_Re6 in component AE1 (mM_per_s)"
    legend_rates[0] = "d/dt q_E_o in component AE1 (mole)"
    legend_rates[1] = "d/dt q_ECl_o in component AE1 (mole)"
    legend_rates[2] = "d/dt q_ECl_i in component AE1 (mole)"
    legend_rates[3] = "d/dt q_E_i in component AE1 (mole)"
    legend_rates[4] = "d/dt q_EHCO3_i in component AE1 (mole)"
    legend_rates[5] = "d/dt q_EHCO3_o in component AE1 (mole)"
    return (legend_states, legend_algebraic, legend_voi, legend_constants)

def initConsts():
    constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
    constants[0] = 2.5
    constants[1] = 1.34784535e+00
    constants[2] = 1.34809503e+00
    constants[3] = 8.37243345e-01
    constants[4] = 8.37398440e-01
    constants[5] = 3.42812779e+00
    constants[6] = 2.30943735e+02
    constants[7] = 2.50575623e+01
    constants[8] = 3.71610024e-01
    constants[9] = 6.15805309e+01
    constants[10] = 5.68610961e+02
    constants[11] = 2.16462852e+01
    constants[12] = 2.43394395e+00
    constants[13] = 1.99577523e+02
    constants[14] = 3.21470643e+02
    constants[15] = 2.19265742e+00
    constants[16] = 3.48281500e+01
    constants[17] = 114
    constants[18] = 29
    constants[19] = 0.0
    constants[20] = 26
    states[0] = 0.01738
    states[1] = 0.0396
    states[2] = 0.274
    states[3] = 0.473
    states[4] = 0.0621
    states[5] = 0.00228
    return (states, constants)

def computeRates(voi, states, constants):
    rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
    algebraic[0] = constants[11]*(constants[1]*constants[17]*constants[5]*states[0]-constants[6]*states[1])
    algebraic[1] = constants[12]*(constants[6]*states[1]-constants[7]*states[2])
    rates[1] = algebraic[0]-algebraic[1]
    algebraic[2] = constants[13]*(constants[7]*states[2]-constants[2]*constants[18]*constants[8]*states[3])
    rates[2] = algebraic[1]-algebraic[2]
    algebraic[3] = constants[14]*(constants[3]*constants[19]*constants[8]*states[3]-constants[9]*states[4])
    rates[3] = algebraic[2]-algebraic[3]
    algebraic[4] = constants[15]*(constants[9]*states[4]-constants[10]*states[5])
    rates[4] = algebraic[3]-algebraic[4]
    algebraic[5] = constants[16]*(constants[10]*states[5]-constants[4]*constants[20]*constants[5]*states[0])
    rates[0] = algebraic[5]-algebraic[0]
    rates[5] = algebraic[4]-algebraic[5]
    return(rates)

def computeAlgebraic(constants, states, voi):
    algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
    states = array(states)
    voi = array(voi)
    algebraic[0] = constants[11]*(constants[1]*constants[17]*constants[5]*states[0]-constants[6]*states[1])
    algebraic[1] = constants[12]*(constants[6]*states[1]-constants[7]*states[2])
    algebraic[2] = constants[13]*(constants[7]*states[2]-constants[2]*constants[18]*constants[8]*states[3])
    algebraic[3] = constants[14]*(constants[3]*constants[19]*constants[8]*states[3]-constants[9]*states[4])
    algebraic[4] = constants[15]*(constants[9]*states[4]-constants[10]*states[5])
    algebraic[5] = constants[16]*(constants[10]*states[5]-constants[4]*constants[20]*constants[5]*states[0])
    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)