# 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 = 6 sizeStates = 4 sizeConstants = 7 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_algebraic[0] = "v_1 in component main (mol_per_s)" legend_algebraic[2] = "v_2 in component main (mol_per_s)" legend_algebraic[3] = "v_SS in component main (mol_per_s)" legend_algebraic[5] = "v_MM in component main (mol_per_s)" legend_constants[0] = "K_1 in component main (per_mol)" legend_constants[1] = "K_2 in component main (per_mol)" legend_constants[2] = "K_3 in component main (per_mol)" legend_constants[3] = "K_4 in component main (per_mol)" legend_constants[4] = "kappa_1 in component main (mol_per_s)" legend_constants[5] = "kappa_2 in component main (mol_per_s)" legend_algebraic[1] = "E_0 in component main (mole)" legend_constants[6] = "k_m in component main (mole)" legend_algebraic[4] = "v_max 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)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 30 states[1] = 0 states[2] = 10 states[3] = 0 constants[0] = 0.1 constants[1] = 0.1 constants[2] = 0.1 constants[3] = 0.1 constants[4] = 10 constants[5] = 10 constants[6] = ((constants[4]+constants[5])*constants[3])/(constants[4]*constants[0]*constants[2]) return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[0] = constants[4]*(constants[0]*states[0]*constants[2]*states[2]-constants[3]*states[3]) rates[0] = -algebraic[0] algebraic[2] = constants[5]*(constants[3]*states[3]-constants[1]*states[1]*constants[2]*states[2]) rates[1] = algebraic[2] rates[2] = algebraic[2]-algebraic[0] rates[3] = algebraic[0]-algebraic[2] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = constants[4]*(constants[0]*states[0]*constants[2]*states[2]-constants[3]*states[3]) algebraic[2] = constants[5]*(constants[3]*states[3]-constants[1]*states[1]*constants[2]*states[2]) algebraic[1] = states[2]+states[3] algebraic[3] = (algebraic[1]*constants[4]*constants[5]*constants[2]*constants[3]*(constants[0]*states[0]-constants[1]*states[1]))/(constants[3]*(constants[4]+constants[5])+constants[4]*constants[0]*constants[2]*states[0]+constants[5]*constants[1]*constants[2]*states[1]) algebraic[4] = algebraic[1]*constants[5]*constants[3] algebraic[5] = algebraic[4]*(states[0]/(constants[6]+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)