# Generated Code

The following is python code generated by the CellML API from this CellML file. (Back to language selection)

The raw code is available.

# Size of variable arrays: sizeAlgebraic = 16 sizeStates = 9 sizeConstants = 16 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 (hour)" legend_states[0] = "A in component A (molecules)" legend_algebraic[0] = "RXN1 in component RXN1 (flux)" legend_algebraic[1] = "RXN2 in component RXN2 (flux)" legend_algebraic[4] = "RXN5 in component RXN5 (flux)" legend_algebraic[10] = "RXN11 in component RXN11 (flux)" legend_algebraic[5] = "RXN6 in component RXN6 (flux)" legend_algebraic[9] = "RXN10 in component RXN10 (flux)" legend_algebraic[11] = "RXN12 in component RXN12 (flux)" legend_states[1] = "C in component C (molecules)" legend_algebraic[2] = "RXN3 in component RXN3 (flux)" legend_states[2] = "DA in component DA (molecules)" legend_algebraic[6] = "RXN7 in component RXN7 (flux)" legend_states[3] = "DAp in component DAp (molecules)" legend_algebraic[7] = "RXN8 in component RXN8 (flux)" legend_states[4] = "DR in component DR (molecules)" legend_algebraic[12] = "RXN13 in component RXN13 (flux)" legend_states[5] = "DRP in component DRP (molecules)" legend_algebraic[13] = "RXN14 in component RXN14 (flux)" legend_states[6] = "MA in component MA (molecules)" legend_algebraic[8] = "RXN9 in component RXN9 (flux)" legend_states[7] = "MR in component MR (molecules)" legend_algebraic[14] = "RXN15 in component RXN15 (flux)" legend_algebraic[15] = "RXN16 in component RXN16 (flux)" legend_states[8] = "R in component R (molecules)" legend_algebraic[3] = "RXN4 in component RXN4 (flux)" legend_constants[0] = "Gamma_1 in component RXN1 (second_order_rate)" legend_constants[1] = "Delta_1 in component RXN2 (first_order_rate)" legend_constants[2] = "Delta_2 in component RXN3 (first_order_rate)" legend_constants[3] = "Delta_3 in component RXN4 (first_order_rate)" legend_constants[4] = "Gamma_2 in component RXN5 (second_order_rate)" legend_constants[5] = "Thetha_1 in component RXN6 (first_order_rate)" legend_constants[6] = "Alpha_1 in component RXN7 (first_order_rate)" legend_constants[7] = "Alpha_2 in component RXN8 (first_order_rate)" legend_constants[8] = "Delta_4 in component RXN9 (first_order_rate)" legend_constants[9] = "BetaA_1 in component RXN10 (first_order_rate)" legend_constants[10] = "Gamma_3 in component RXN11 (second_order_rate)" legend_constants[11] = "Theta_2 in component RXN12 (first_order_rate)" legend_constants[12] = "Alpha_3 in component RXN13 (first_order_rate)" legend_constants[13] = "Alpha_4 in component RXN14 (first_order_rate)" legend_constants[14] = "Delta_5 in component RXN15 (first_order_rate)" legend_constants[15] = "BetaR_1 in component RXN16 (first_order_rate)" legend_rates[0] = "d/dt A in component A (molecules)" legend_rates[1] = "d/dt C in component C (molecules)" legend_rates[2] = "d/dt DA in component DA (molecules)" legend_rates[3] = "d/dt DAp in component DAp (molecules)" legend_rates[4] = "d/dt DR in component DR (molecules)" legend_rates[5] = "d/dt DRP in component DRP (molecules)" legend_rates[6] = "d/dt MA in component MA (molecules)" legend_rates[7] = "d/dt MR in component MR (molecules)" legend_rates[8] = "d/dt R in component R (molecules)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0.0 states[1] = 0.0 states[2] = 1 states[3] = 0.0 states[4] = 1 states[5] = 1 states[6] = 0.0 states[7] = 0.0 states[8] = 0.0 constants[0] = 2 constants[1] = 1 constants[2] = 1 constants[3] = 0.2 constants[4] = 1 constants[5] = 50 constants[6] = 50 constants[7] = 500 constants[8] = 10 constants[9] = 50 constants[10] = 1 constants[11] = 100 constants[12] = 0.01 constants[13] = 50 constants[14] = 0.5 constants[15] = 5 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[0] = states[0]*states[8]*constants[0] algebraic[2] = states[1]*constants[2] rates[1] = (1.00000/1.00000)*(-1.00000*algebraic[2]+algebraic[0]) algebraic[4] = states[0]*states[2]*constants[4] algebraic[5] = states[3]*constants[5] algebraic[6] = states[2]*constants[6] rates[2] = (1.00000/1.00000)*(-1.00000*algebraic[4]+-1.00000*algebraic[6]+algebraic[5]+algebraic[6]) algebraic[7] = states[3]*constants[7] rates[3] = (1.00000/1.00000)*(-1.00000*algebraic[5]+-1.00000*algebraic[7]+algebraic[4]+algebraic[7]) algebraic[9] = states[6]*constants[9] algebraic[8] = states[6]*constants[8] rates[6] = (1.00000/1.00000)*(-1.00000*algebraic[8]+-1.00000*algebraic[9]+algebraic[6]+algebraic[7]+algebraic[9]) algebraic[1] = states[0]*constants[1] algebraic[10] = states[0]*states[4]*constants[10] algebraic[11] = states[5]*constants[11] rates[0] = (1.00000/1.00000)*(-1.00000*algebraic[0]+-1.00000*algebraic[1]+-1.00000*algebraic[4]+-1.00000*algebraic[10]+algebraic[5]+algebraic[9]+algebraic[11]) algebraic[12] = states[4]*constants[12] rates[4] = (1.00000/1.00000)*(-1.00000*algebraic[10]+-1.00000*algebraic[12]+algebraic[11]+algebraic[12]) algebraic[13] = states[5]*constants[13] rates[5] = (1.00000/1.00000)*(-1.00000*algebraic[11]+-1.00000*algebraic[13]+algebraic[10]+algebraic[13]) algebraic[14] = states[7]*constants[14] algebraic[15] = states[7]*constants[15] rates[7] = (1.00000/1.00000)*(-1.00000*algebraic[14]+-1.00000*algebraic[15]+algebraic[12]+algebraic[13]+algebraic[15]) algebraic[3] = states[8]*constants[3] rates[8] = (1.00000/1.00000)*(-1.00000*algebraic[0]+-1.00000*algebraic[3]+algebraic[2]+algebraic[15]) return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = states[0]*states[8]*constants[0] algebraic[2] = states[1]*constants[2] algebraic[4] = states[0]*states[2]*constants[4] algebraic[5] = states[3]*constants[5] algebraic[6] = states[2]*constants[6] algebraic[7] = states[3]*constants[7] algebraic[9] = states[6]*constants[9] algebraic[8] = states[6]*constants[8] algebraic[1] = states[0]*constants[1] algebraic[10] = states[0]*states[4]*constants[10] algebraic[11] = states[5]*constants[11] algebraic[12] = states[4]*constants[12] algebraic[13] = states[5]*constants[13] algebraic[14] = states[7]*constants[14] algebraic[15] = states[7]*constants[15] algebraic[3] = states[8]*constants[3] 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)