Generated Code

# Size of variable arrays:
sizeAlgebraic = 15
sizeStates = 1
sizeConstants = 18
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 (second)"
    legend_constants[0] = "C_ext_Na in component Concentrations (mM)"
    legend_constants[1] = "C_ext_H in component Concentrations (mM)"
    legend_constants[2] = "C_ext_NH4 in component Concentrations (mM)"
    legend_constants[3] = "C_int_Na in component Concentrations (mM)"
    legend_algebraic[0] = "C_int_H in component Concentrations (mM)"
    legend_constants[4] = "C_int_NH4 in component Concentrations (mM)"
    legend_states[0] = "pH_int in component Concentrations (dimensionless)"
    legend_constants[5] = "XTxP0_NHE3_Na in component NHE3_Parameters (nmol_per_s_per_cm2)"
    legend_constants[6] = "XTxP0_NHE3_H in component NHE3_Parameters (nmol_per_s_per_cm2)"
    legend_constants[7] = "XTxP0_NHE3_NH4 in component NHE3_Parameters (nmol_per_s_per_cm2)"
    legend_constants[8] = "K_NHE3_Na in component NHE3_Parameters (mM)"
    legend_constants[9] = "K_NHE3_H in component NHE3_Parameters (mM)"
    legend_constants[10] = "K_NHE3_NH4 in component NHE3_Parameters (mM)"
    legend_algebraic[2] = "XTxP_NHE3_Na in component NHE3 (nmol_per_s_per_cm2)"
    legend_algebraic[3] = "XTxP_NHE3_H in component NHE3 (nmol_per_s_per_cm2)"
    legend_algebraic[4] = "XTxP_NHE3_NH4 in component NHE3 (nmol_per_s_per_cm2)"
    legend_constants[11] = "alpha_ext_Na in component NHE3 (dimensionless)"
    legend_constants[12] = "beta_ext_H in component NHE3 (dimensionless)"
    legend_constants[13] = "gamma_ext_NH4 in component NHE3 (dimensionless)"
    legend_constants[14] = "alpha_int_Na in component NHE3 (dimensionless)"
    legend_algebraic[1] = "beta_int_H in component NHE3 (dimensionless)"
    legend_constants[15] = "gamma_int_NH4 in component NHE3 (dimensionless)"
    legend_algebraic[5] = "sum_NHE3 in component NHE3 (nmol_per_s_per_cm2)"
    legend_algebraic[6] = "J_NHE3_Na in component NHE3 (nmol_per_s_per_cm2)"
    legend_algebraic[7] = "J_NHE3_H in component NHE3 (nmol_per_s_per_cm2)"
    legend_algebraic[8] = "J_NHE3_NH4 in component NHE3 (nmol_per_s_per_cm2)"
    legend_constants[16] = "J_NHE3_Na_Max in component NHE3 (nmol_per_s_per_cm2)"
    legend_algebraic[10] = "plot in component NHE3 (dimensionless)"
    legend_algebraic[11] = "J_NHE3_Na2 in component NHE3 (nmol_per_s_per_cm2)"
    legend_algebraic[12] = "J_NHE3_H2 in component NHE3 (nmol_per_s_per_cm2)"
    legend_algebraic[13] = "J_NHE3_NH42 in component NHE3 (nmol_per_s_per_cm2)"
    legend_algebraic[9] = "sum0_NHE3 in component NHE3 (nmol_per_s_per_cm2)"
    legend_algebraic[14] = "plot2 in component NHE3 (dimensionless)"
    legend_rates[0] = "d/dt pH_int in component Concentrations (dimensionless)"
    return (legend_states, legend_algebraic, legend_voi, legend_constants)

def initConsts():
    constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
    constants[0] = 1
    constants[1] = 5.4954e-5
    constants[2] = 0
    constants[3] = 0
    constants[4] = 0
    states[0] = 4
    constants[5] = 1.6e-3
    constants[6] = 0.48e-3
    constants[7] = 1.6e-3
    constants[8] = 30
    constants[9] = 72e-6
    constants[10] = 0.027e3
    constants[11] = constants[0]/constants[8]
    constants[17] = 5.00000
    constants[12] = constants[1]/constants[9]
    constants[13] = constants[2]/constants[10]
    constants[14] = constants[3]/constants[8]
    constants[15] = constants[4]/constants[10]
    constants[16] = (constants[5]*constants[6])/(constants[5]+constants[6])
    return (states, constants)

def computeRates(voi, states, constants):
    rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
    rates[0] = constants[17]
    return(rates)

def computeAlgebraic(constants, states, voi):
    algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
    states = array(states)
    voi = array(voi)
    algebraic[0] = 1000.00*(power(10.0000, -states[0]))
    algebraic[1] = algebraic[0]/constants[9]
    algebraic[2] = (constants[5]*2.00000*algebraic[0])/(algebraic[0]+0.00100000)
    algebraic[3] = (constants[6]*2.00000*algebraic[0])/(algebraic[0]+0.00100000)
    algebraic[4] = (constants[7]*2.00000*algebraic[0])/(algebraic[0]+0.00100000)
    algebraic[5] = (1.00000+constants[11]+constants[12]+constants[13])*(algebraic[2]*constants[14]+algebraic[3]*algebraic[1]+algebraic[4]*constants[15])+(1.00000+constants[14]+algebraic[1]+constants[15])*(algebraic[2]*constants[11]+algebraic[3]*constants[12]+algebraic[4]*constants[13])
    algebraic[6] = ((algebraic[2]*algebraic[3])/algebraic[5])*(constants[11]*algebraic[1]-constants[14]*constants[12])+((algebraic[2]*algebraic[4])/algebraic[5])*(constants[11]*constants[15]-constants[14]*constants[13])
    algebraic[7] = ((algebraic[2]*algebraic[3])/algebraic[5])*(constants[14]*constants[12]-constants[11]*algebraic[1])+((algebraic[3]*algebraic[4])/algebraic[5])*(constants[12]*constants[15]-algebraic[1]*constants[13])
    algebraic[8] = ((algebraic[2]*algebraic[4])/algebraic[5])*(constants[14]*constants[13]-constants[11]*constants[15])+((algebraic[3]*algebraic[4])/algebraic[5])*(constants[13]*algebraic[1]-constants[12]*constants[15])
    algebraic[9] = (1.00000+constants[11]+constants[12]+constants[13])*(constants[5]*constants[14]+constants[6]*algebraic[1]+constants[7]*constants[15])+(1.00000+constants[14]+algebraic[1]+constants[15])*(constants[5]*constants[11]+constants[6]*constants[12]+constants[7]*constants[13])
    algebraic[10] = algebraic[6]/constants[16]
    algebraic[11] = ((constants[5]*constants[6])/algebraic[9])*(constants[11]*algebraic[1]-constants[14]*constants[12])+((constants[5]*constants[7])/algebraic[5])*(constants[11]*constants[15]-constants[14]*constants[13])
    algebraic[12] = ((constants[5]*constants[6])/algebraic[9])*(constants[14]*constants[12]-constants[11]*algebraic[1])+((constants[6]*constants[7])/algebraic[5])*(constants[12]*constants[15]-algebraic[1]*constants[13])
    algebraic[13] = ((constants[5]*constants[7])/algebraic[9])*(constants[14]*constants[13]-constants[11]*constants[15])+((constants[6]*constants[7])/algebraic[5])*(constants[13]*algebraic[1]-constants[12]*constants[15])
    algebraic[14] = algebraic[11]/constants[16]
    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)