Generated Code

# Size of variable arrays:
sizeAlgebraic = 0
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 (dimensionless)"
    legend_states[0] = "x in component x (dimensionless)"
    legend_constants[0] = "a1 in component model_parameters (dimensionless)"
    legend_constants[1] = "k1 in component model_parameters (dimensionless)"
    legend_constants[2] = "b1 in component model_parameters (dimensionless)"
    legend_constants[3] = "kp in component model_parameters (dimensionless)"
    legend_states[1] = "y in component y (dimensionless)"
    legend_constants[4] = "epsilon in component model_parameters (dimensionless)"
    legend_constants[5] = "a2 in component model_parameters (dimensionless)"
    legend_constants[6] = "a3 in component model_parameters (dimensionless)"
    legend_constants[7] = "k2 in component model_parameters (dimensionless)"
    legend_constants[8] = "b2 in component model_parameters (dimensionless)"
    legend_states[2] = "z in component z (dimensionless)"
    legend_constants[9] = "delta in component model_parameters (dimensionless)"
    legend_constants[10] = "a4 in component model_parameters (dimensionless)"
    legend_constants[11] = "a5 in component model_parameters (dimensionless)"
    legend_constants[12] = "k3 in component model_parameters (dimensionless)"
    legend_constants[13] = "b3 in component model_parameters (dimensionless)"
    legend_rates[0] = "d/dt x in component x (dimensionless)"
    legend_rates[1] = "d/dt y in component y (dimensionless)"
    legend_rates[2] = "d/dt z in component z (dimensionless)"
    return (legend_states, legend_algebraic, legend_voi, legend_constants)

def initConsts():
    constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
    states[0] = 2.0
    constants[0] = 0.05
    constants[1] = 0.1
    constants[2] = 0.1
    constants[3] = 0.5
    states[1] = 1.0
    constants[4] = 0.1
    constants[5] = 0.009
    constants[6] = 0.675
    constants[7] = 0.5
    constants[8] = 0.3
    states[2] = 0.15
    constants[9] = 0.9
    constants[10] = 0.01
    constants[11] = 0.005
    constants[12] = 0.025
    constants[13] = 0.01
    return (states, constants)

def computeRates(voi, states, constants):
    rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
    rates[0] = custom_piecewise([greater_equal(voi , 0.00000) & less(voi , 10000.0), constants[0]/(constants[1]+states[1])-constants[2]*states[0] , greater_equal(voi , 10000.0) & less(voi , 10360.0), (constants[0]/(constants[1]+states[1])-constants[2]*states[0])+constants[3] , greater_equal(voi , 10360.0) & less(voi , 11440.0), constants[0]/(constants[1]+states[1])-constants[2]*states[0] , greater_equal(voi , 11440.0) & less(voi , 11800.0), (constants[0]/(constants[1]+states[1])-constants[2]*states[0])+constants[3] , greater_equal(voi , 11800.0) & less(voi , 12880.0), constants[0]/(constants[1]+states[1])-constants[2]*states[0] , greater_equal(voi , 12880.0) & less(voi , 13240.0), (constants[0]/(constants[1]+states[1])-constants[2]*states[0])+constants[3] , greater_equal(voi , 13240.0) & less(voi , 14320.0), constants[0]/(constants[1]+states[1])-constants[2]*states[0] , greater_equal(voi , 14320.0) & less(voi , 14680.0), (constants[0]/(constants[1]+states[1])-constants[2]*states[0])+constants[3] , greater_equal(voi , 14680.0) & less(voi , 15760.0), constants[0]/(constants[1]+states[1])-constants[2]*states[0] , greater_equal(voi , 15760.0) & less(voi , 16120.0), (constants[0]/(constants[1]+states[1])-constants[2]*states[0])+constants[3] , True, float('nan')])
    rates[1] = constants[4]*(((constants[5]+constants[6]*states[0])*states[1]*states[2])/(constants[7]+power(states[0], 2.00000))-constants[8]*states[1])
    rates[2] = constants[4]*constants[9]*(constants[10]*states[0]-((constants[11]*states[0]*states[2])/(constants[12]+states[0])+constants[13]*states[2]))
    return(rates)

def computeAlgebraic(constants, states, voi):
    algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
    states = array(states)
    voi = array(voi)
    return algebraic

def custom_piecewise(cases):
    """Compute result of a piecewise function"""
    return select(cases[0::2],cases[1::2])

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)