Generated Code

# Size of variable arrays:
sizeAlgebraic = 7
sizeStates = 5
sizeConstants = 23
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 main (second)"
    legend_states[0] = "q_1 in component main (mole)"
    legend_states[1] = "q_2 in component main (mole)"
    legend_states[2] = "q_3 in component main (mole)"
    legend_states[3] = "q_4 in component main (mole)"
    legend_states[4] = "q_5 in component main (mole)"
    legend_algebraic[0] = "q_6 in component main (mole)"
    legend_constants[0] = "q_tot in component main (mole)"
    legend_algebraic[3] = "v_1 in component main (mol_per_s)"
    legend_algebraic[4] = "v_2 in component main (mol_per_s)"
    legend_algebraic[5] = "v_3 in component main (mol_per_s)"
    legend_algebraic[6] = "v_4 in component main (mol_per_s)"
    legend_constants[1] = "kappa_1 in component main (mol_per_s)"
    legend_constants[2] = "kappa_2 in component main (mol_per_s)"
    legend_constants[3] = "kappa_3 in component main (mol_per_s)"
    legend_constants[4] = "kappa_4 in component main (mol_per_s)"
    legend_constants[5] = "K_1 in component main (per_mol)"
    legend_constants[6] = "K_2 in component main (per_mol)"
    legend_constants[7] = "K_s in component main (per_mol)"
    legend_constants[8] = "K_3 in component main (per_mol)"
    legend_constants[9] = "K_4 in component main (per_mol)"
    legend_constants[10] = "K_5 in component main (per_mol)"
    legend_constants[11] = "K_6 in component main (per_mol)"
    legend_constants[12] = "K_m in component main (per_mol)"
    legend_constants[13] = "k_m in component main (mole)"
    legend_constants[14] = "v_max in component main (mol_per_s)"
    legend_constants[15] = "k_f_1 in component main (per_mol_per_s)"
    legend_constants[16] = "k_r_1 in component main (per_s)"
    legend_constants[17] = "k_f_2 in component main (per_s)"
    legend_constants[18] = "k_r_2 in component main (per_mol_per_s)"
    legend_constants[19] = "k_f_3 in component main (per_s)"
    legend_constants[20] = "k_r_3 in component main (per_s)"
    legend_constants[21] = "k_f_4 in component main (per_s)"
    legend_constants[22] = "k_r_4 in component main (per_s)"
    legend_algebraic[1] = "v_SF in component main (mol_per_s)"
    legend_algebraic[2] = "v_MM in component main (mol_per_s)"
    legend_rates[0] = "d/dt q_1 in component main (mole)"
    legend_rates[1] = "d/dt q_2 in component main (mole)"
    legend_rates[2] = "d/dt q_3 in component main (mole)"
    legend_rates[3] = "d/dt q_4 in component main (mole)"
    legend_rates[4] = "d/dt q_5 in component main (mole)"
    return (legend_states, legend_algebraic, legend_voi, legend_constants)

def initConsts():
    constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
    states[0] = 100
    states[1] = 0
    states[2] = 0
    states[3] = 0
    states[4] = 0
    constants[0] = 1
    constants[1] = 100
    constants[2] = 100
    constants[3] = 1
    constants[4] = 0.1
    constants[5] = 0.1
    constants[6] = 0.1
    constants[7] = 0.1
    constants[8] = 1
    constants[9] = 1
    constants[10] = 1
    constants[11] = 1
    constants[12] = 1
    constants[13] = 2.00000/(constants[7]*(1.00000+constants[3]/constants[4]))
    constants[14] = (constants[0]*constants[3]*constants[12])/(1.00000+constants[3]/constants[4])
    constants[15] = constants[1]*constants[5]*constants[11]
    constants[16] = constants[1]*constants[8]
    constants[17] = constants[2]*constants[9]
    constants[18] = constants[2]*constants[6]*constants[10]
    constants[19] = constants[3]*constants[8]
    constants[20] = constants[3]*constants[9]
    constants[21] = constants[4]*constants[10]
    constants[22] = constants[4]*constants[11]
    return (states, constants)

def computeRates(voi, states, constants):
    rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
    algebraic[0] = ((constants[0]-states[2])-states[3])-states[4]
    algebraic[3] = constants[15]*states[0]*algebraic[0]-constants[16]*states[2]
    rates[0] = -algebraic[3]
    algebraic[4] = constants[17]*states[3]-constants[18]*states[1]*states[4]
    rates[1] = algebraic[4]-1000.00*states[1]
    algebraic[5] = constants[19]*states[2]-constants[20]*states[3]
    rates[2] = algebraic[3]-algebraic[5]
    rates[3] = algebraic[5]-algebraic[4]
    algebraic[6] = constants[21]*states[4]-constants[22]*algebraic[0]
    rates[4] = algebraic[4]-algebraic[6]
    return(rates)

def computeAlgebraic(constants, states, voi):
    algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
    states = array(states)
    voi = array(voi)
    algebraic[0] = ((constants[0]-states[2])-states[3])-states[4]
    algebraic[3] = constants[15]*states[0]*algebraic[0]-constants[16]*states[2]
    algebraic[4] = constants[17]*states[3]-constants[18]*states[1]*states[4]
    algebraic[5] = constants[19]*states[2]-constants[20]*states[3]
    algebraic[6] = constants[21]*states[4]-constants[22]*algebraic[0]
    algebraic[1] = (constants[0]*constants[3]*constants[4]*constants[12]*constants[7]*(states[0]-states[1]))/(2.00000*constants[4]+(constants[3]+constants[4])*constants[7]*(states[0]+states[1])+2.00000*constants[3]*constants[7]*constants[7]*states[0]*states[1])
    algebraic[2] = (constants[14]*states[0])/(constants[13]+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)