# 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 = 0 sizeStates = 4 sizeConstants = 13 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 (day)" legend_states[0] = "A in component A (dimensionless)" legend_constants[0] = "v in component A (first_order_rate_constant)" legend_constants[1] = "k in component A (dimensionless)" legend_constants[2] = "f in component A (dimensionless)" legend_constants[3] = "sigma1 in component A (first_order_rate_constant)" legend_constants[4] = "b1 in component A (first_order_rate_constant)" legend_constants[5] = "muA in component A (first_order_rate_constant)" legend_states[1] = "G in component G (dimensionless)" legend_states[2] = "R in component R (dimensionless)" legend_constants[6] = "pi1 in component R (first_order_rate_constant)" legend_constants[7] = "beta in component R (first_order_rate_constant)" legend_constants[8] = "muR in component R (first_order_rate_constant)" legend_states[3] = "E in component E (dimensionless)" legend_constants[9] = "lambdaE in component E (first_order_rate_constant)" legend_constants[10] = "muE in component E (first_order_rate_constant)" legend_constants[11] = "gamma in component G (first_order_rate_constant)" legend_constants[12] = "muG in component G (first_order_rate_constant)" legend_rates[0] = "d/dt A in component A (dimensionless)" legend_rates[2] = "d/dt R in component R (dimensionless)" legend_rates[3] = "d/dt E in component E (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] = 1.0 constants[0] = 1.25e5 constants[1] = 5e7 constants[2] = 1e-4 constants[3] = 3e-6 constants[4] = 0.25 constants[5] = 0.25 states[1] = 1e8 states[2] = 0.0 constants[6] = 0.016 constants[7] = 200.0 constants[8] = 0.25 states[3] = 0.0 constants[9] = 1000.0 constants[10] = 0.25 constants[11] = 2000.0 constants[12] = 5.0 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = (constants[2]*constants[0]*states[1])/(constants[1]+states[1])-((constants[3]*states[2]+constants[4])*states[0]+constants[5]*states[0]) rates[2] = (constants[6]*states[3]+constants[7])*states[0]-constants[8]*states[2] rates[3] = constants[9]*states[0]-constants[10]*states[3] rates[1] = constants[11]*states[3]-((constants[0]*states[1])/(constants[1]+states[1])+constants[12]*states[1]) return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) 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)