# 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 = 10 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_voi = "time in component environment (hour)" legend_states[0] = "c11 in component c11 (per_millilitre)" legend_constants[0] = "p1 in component model_parameters (per_hour)" legend_constants[1] = "p2 in component model_parameters (per_hour)" legend_constants[2] = "p5 in component model_parameters (per_hour)" legend_constants[3] = "p6 in component model_parameters (per_hour)" legend_states[1] = "c12 in component c12 (per_millilitre)" legend_states[2] = "c21 in component c21 (per_millilitre)" legend_constants[4] = "p4 in component model_parameters (per_hour)" legend_constants[5] = "p11 in component model_parameters (per_hour)" legend_constants[6] = "p12 in component model_parameters (per_hour)" legend_states[3] = "c22 in component c22 (per_millilitre)" legend_states[4] = "c31 in component c31 (per_millilitre)" legend_constants[7] = "p3 in component model_parameters (per_hour)" legend_constants[8] = "p7 in component model_parameters (per_hour)" legend_constants[9] = "p8 in component model_parameters (per_hour)" legend_states[5] = "c32 in component c32 (per_millilitre)" legend_states[6] = "c41 in component c41 (per_millilitre)" legend_constants[10] = "p9 in component model_parameters (per_hour)" legend_constants[11] = "p10 in component model_parameters (per_hour)" legend_states[7] = "c42 in component c42 (per_millilitre)" legend_states[8] = "c51 in component c51 (per_millilitre)" legend_constants[12] = "p13 in component model_parameters (per_hour)" legend_constants[13] = "p14 in component model_parameters (per_hour)" legend_constants[14] = "p15 in component model_parameters (per_hour)" legend_states[9] = "c52 in component c52 (per_millilitre)" legend_rates[0] = "d/dt c11 in component c11 (per_millilitre)" legend_rates[2] = "d/dt c21 in component c21 (per_millilitre)" legend_rates[4] = "d/dt c31 in component c31 (per_millilitre)" legend_rates[6] = "d/dt c41 in component c41 (per_millilitre)" legend_rates[8] = "d/dt c51 in component c51 (per_millilitre)" legend_rates[1] = "d/dt c12 in component c12 (per_millilitre)" legend_rates[3] = "d/dt c22 in component c22 (per_millilitre)" legend_rates[5] = "d/dt c32 in component c32 (per_millilitre)" legend_rates[7] = "d/dt c42 in component c42 (per_millilitre)" legend_rates[9] = "d/dt c52 in component c52 (per_millilitre)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 9000 constants[0] = 0.032044 constants[1] = 0.016630 constants[2] = 6.363016 constants[3] = 7.574118 states[1] = 12000 states[2] = 0 constants[4] = 0.019571 constants[5] = 4.881967 constants[6] = 5.356513 states[3] = 0 states[4] = 0 constants[7] = 0.001885 constants[8] = 1.140535 constants[9] = 1.429125 states[5] = 0 states[6] = 0 constants[10] = 9.768637 constants[11] = 5.3640806 states[7] = 0 states[8] = 0 constants[12] = 0.052968 constants[13] = 0.443166 constants[14] = 0.103700 states[9] = 0 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = -constants[0]*states[0]-constants[1]*states[0]-constants[2]*states[0]+constants[3]*states[1] rates[2] = constants[0]*states[0]-constants[4]*states[2]-constants[5]*states[2]+constants[6]*states[3] rates[4] = constants[1]*states[0]-constants[7]*states[4]-constants[8]*states[4]+constants[9]*states[5] rates[6] = constants[7]*states[4]+constants[4]*states[2]-constants[10]*states[6]+constants[11]*states[7] rates[8] = constants[12]*states[0]-constants[13]*states[8]+constants[14]*states[9] rates[1] = constants[2]*states[0]-constants[3]*states[1] rates[3] = constants[5]*states[2]-constants[6]*states[3] rates[5] = constants[8]*states[4]-constants[9]*states[5] rates[7] = constants[10]*states[6]-constants[11]*states[7] rates[9] = constants[13]*states[8]-constants[14]*states[9] 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)