Generated Code

# Size of variable arrays:
sizeAlgebraic = 4
sizeStates = 2
sizeConstants = 13
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 (minute)"
    legend_algebraic[0] = "B in component B (micromolar)"
    legend_constants[0] = "F in component B (micromolar)"
    legend_constants[1] = "n2 in component B (dimensionless)"
    legend_constants[2] = "K2 in component B (per_micromolar)"
    legend_states[0] = "Ca in component Ca (micromolar)"
    legend_algebraic[3] = "R in component R (flux)"
    legend_constants[3] = "Vmax in component R (flux)"
    legend_constants[4] = "Km in component R (micromolar)"
    legend_algebraic[2] = "fu in component R (dimensionless)"
    legend_constants[12] = "ISF in component R (dimensionless)"
    legend_constants[5] = "age in component R (dimensionless)"
    legend_states[1] = "C in component C (micromolar)"
    legend_constants[6] = "Va in component Ca (ml)"
    legend_constants[7] = "Vv in component Ca (ml)"
    legend_constants[8] = "Qc in component model_constants (flow)"
    legend_algebraic[1] = "Cv in component Cv (micromolar)"
    legend_constants[9] = "Q in component model_constants (flow)"
    legend_constants[10] = "P in component model_constants (dimensionless)"
    legend_constants[11] = "V in component C (ml)"
    legend_rates[0] = "d/dt Ca in component Ca (micromolar)"
    legend_rates[1] = "d/dt C in component C (micromolar)"
    return (legend_states, legend_algebraic, legend_voi, legend_constants)

def initConsts():
    constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
    constants[0] = 0.48
    constants[1] = 1
    constants[2] = 0.8532
    states[0] = 6.6685
    constants[3] = 9.433e-3
    constants[4] = 198
    constants[5] = 5
    states[1] = 0
    constants[6] = 2148
    constants[7] = 3431
    constants[8] = 6445.65
    constants[9] = 1221.34
    constants[10] = 15.61
    constants[11] = 1454
    constants[12] = -8.32120+2.04010*constants[5]+4.19620*log(constants[5]*365.000, 10)
    return (states, constants)

def computeRates(voi, states, constants):
    rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
    algebraic[1] = ((constants[9]*states[1])/constants[10])/constants[8]
    rates[0] = (constants[8]*(algebraic[1]-states[0]))/(constants[6]+constants[7])
    algebraic[0] = (constants[0]*constants[1]*constants[2]*states[0])/(1.00000+constants[2]*constants[0])
    algebraic[2] = constants[0]/(constants[0]+algebraic[0])
    algebraic[3] = (constants[12]*constants[3]*algebraic[2]*states[1])/(constants[4]+algebraic[2]*states[1])
    rates[1] = (constants[9]*(states[0]-states[1]/constants[10])-algebraic[3]*1.00000)/constants[11]
    return(rates)

def computeAlgebraic(constants, states, voi):
    algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
    states = array(states)
    voi = array(voi)
    algebraic[1] = ((constants[9]*states[1])/constants[10])/constants[8]
    algebraic[0] = (constants[0]*constants[1]*constants[2]*states[0])/(1.00000+constants[2]*constants[0])
    algebraic[2] = constants[0]/(constants[0]+algebraic[0])
    algebraic[3] = (constants[12]*constants[3]*algebraic[2]*states[1])/(constants[4]+algebraic[2]*states[1])
    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)