# 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 = 1 sizeStates = 2 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 = "time in component environment (hour)" legend_states[0] = "O2 in component O2 (CONCENTRATIONO2)" legend_constants[0] = "p1 in component O2 (CONFIRMp1)" legend_constants[1] = "F1 in component O2 (dimensionless)" legend_constants[2] = "p2 in component model_parameters (per_day)" legend_states[1] = "H2O2 in component H2O2 (CONCENTRATIONH2O2)" legend_constants[3] = "p3 in component H2O2 (per_day)" legend_constants[4] = "p4 in component H2O2 (per_day)" legend_algebraic[0] = "V in component V (CONFIRMV)" legend_constants[5] = "Vmax in component V (microgram_per_hour)" legend_constants[6] = "ki in component V (CONFIRMki)" legend_rates[0] = "d/dt O2 in component O2 (CONCENTRATIONO2)" legend_rates[1] = "d/dt H2O2 in component H2O2 (CONCENTRATIONH2O2)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0.00235897 constants[0] = 0.0000143385 constants[1] = 20 constants[2] = 0.117425199 states[1] = 0.000027947 constants[3] = 2.552293418 constants[4] = 8.379310334 constants[5] = 10400000 constants[6] = 0.000008982 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = constants[0]*constants[1]-constants[2]*states[0] rates[1] = (constants[2]*states[0]-constants[3]*states[1])-constants[4]*states[1] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = constants[5]*(constants[6]/(constants[6]+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)