# 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 = 3 sizeStates = 2 sizeConstants = 15 from math import * from numpy import * def createLegends(): legend_states = [""] * sizeStates legend_rates = [""] * sizeStates legend_algebraic = [""] * sizeAlgebraic legend_voi = "" legend_constants = [""] * sizeConstants legend_algebraic[0] = "time in component environment (second)" legend_voi = "tau in component environment (dimensionless)" legend_constants[12] = "C_0 in component reaction_constants (per_second)" legend_algebraic[1] = "A in component a (molar)" legend_states[0] = "a in component a (dimensionless)" legend_constants[0] = "alpha in component reaction_constants (dimensionless)" legend_constants[1] = "beta in component reaction_constants (dimensionless)" legend_constants[2] = "K in component reaction_constants (dimensionless)" legend_constants[13] = "C_1 in component reaction_constants (molar)" legend_states[1] = "g in component g (dimensionless)" legend_algebraic[2] = "G in component g (molar)" legend_constants[3] = "gamma in component reaction_constants (dimensionless)" legend_constants[4] = "L in component reaction_constants (dimensionless)" legend_constants[14] = "C_2 in component reaction_constants (molar)" legend_constants[5] = "k2 in component reaction_constants (per_second)" legend_constants[6] = "k3 in component reaction_constants (per_second)" legend_constants[7] = "k6 in component reaction_constants (per_second)" legend_constants[8] = "k7 in component reaction_constants (per_second)" legend_constants[9] = "k0 in component reaction_constants (molar_per_second)" legend_constants[10] = "k4 in component reaction_constants (per_molar2_per_second)" legend_constants[11] = "km in component reaction_constants (molar_per_second)" legend_rates[0] = "d/dt a in component a (dimensionless)" legend_rates[1] = "d/dt g in component g (dimensionless)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 4.39927 constants[0] = 0.008 constants[1] = 1.485 constants[2] = 30 states[1] = 1.96477 constants[3] = 11.385 constants[4] = 0.1 constants[5] = 6e-4 constants[6] = 0.0000048 constants[7] = 0.000891 constants[8] = 0.006831 constants[9] = 8.7831e-11 constants[10] = 2.1e12 constants[11] = 6.9001e-14 constants[12] = constants[5] constants[13] = power(constants[5]/constants[10], 1.0/2) constants[14] = power(constants[5]/constants[10], 1.0/2) return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = constants[2]-((1.00000+constants[0]+constants[1])*states[0]+states[0]*(power(states[1], 2.00000))) rates[1] = ((1.00000-constants[0])*states[0]+states[0]*(power(states[1], 2.00000)))-(constants[4]+constants[3]*states[1]) return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = voi/constants[12] algebraic[1] = constants[13]*states[0] algebraic[2] = constants[14]*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)