# 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 = 8 sizeConstants = 11 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 (second)" legend_states[0] = "R in component R (molar)" legend_constants[0] = "L in component L (molar)" legend_states[1] = "LR in component LR (molar)" legend_states[2] = "R_star in component R_star (molar)" legend_constants[1] = "kf in component model_parameters (second_order_rate_constant)" legend_constants[2] = "kr in component model_parameters (first_order_rate_constant)" legend_constants[3] = "kfR in component model_parameters (first_order_rate_constant)" legend_constants[4] = "Kact in component model_parameters (dimensionless)" legend_states[3] = "LR_star in component LR_star (molar)" legend_constants[5] = "alpha in component model_parameters (dimensionless)" legend_constants[6] = "kds in component model_parameters (first_order_rate_constant)" legend_states[4] = "LR_ds in component LR_ds (molar)" legend_states[5] = "R_ds in component R_ds (molar)" legend_constants[7] = "kf2 in component model_parameters (second_order_rate_constant)" legend_constants[8] = "kr2 in component model_parameters (first_order_rate_constant)" legend_states[6] = "G_star in component G_star (molar)" legend_states[7] = "G in component G (molar)" legend_constants[9] = "ka in component model_parameters (second_order_rate_constant)" legend_constants[10] = "ki in component model_parameters (first_order_rate_constant)" legend_rates[0] = "d/dt R in component R (molar)" legend_rates[2] = "d/dt R_star in component R_star (molar)" legend_rates[1] = "d/dt LR in component LR (molar)" legend_rates[3] = "d/dt LR_star in component LR_star (molar)" legend_rates[4] = "d/dt LR_ds in component LR_ds (molar)" legend_rates[5] = "d/dt R_ds in component R_ds (molar)" legend_rates[6] = "d/dt G_star in component G_star (molar)" legend_rates[7] = "d/dt G in component G (molar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0.01 constants[0] = 1E-12 states[1] = 0.01 states[2] = 0.01 constants[1] = 8.4E7 constants[2] = 0.37 constants[3] = 10 constants[4] = 1E-4 states[3] = 0.01 constants[5] = 1E1 constants[6] = 1E-4 states[4] = 0.01 states[5] = 0.01 constants[7] = 8.4E7 constants[8] = 4.6E-3 states[6] = 0.01 states[7] = 0.01 constants[9] = 1E-7 constants[10] = 2E-1 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = (constants[2]*states[1]+(constants[3]/constants[4])*states[2])-(constants[1]*constants[0]*states[0]+constants[3]*states[0]) rates[2] = (constants[2]*states[3]+constants[3]*states[0])-(constants[5]*constants[1]*constants[0]*states[2]+(constants[3]/constants[4])*states[2]) rates[1] = (constants[1]*constants[0]*states[0]+(constants[3]/(constants[5]*constants[4]))*states[3])-(constants[2]*states[1]+constants[3]*states[1]) rates[3] = (constants[3]*states[1]+constants[5]*constants[1]*constants[0]*states[2])-((constants[3]/(constants[5]*constants[4]))*states[3]+constants[6]*states[3]+constants[2]*states[3]) rates[4] = (constants[6]*states[3]+constants[7]*constants[0]*states[5])-constants[8]*states[4] rates[5] = constants[8]*states[4]-constants[7]*constants[0]*states[5] rates[6] = constants[9]*states[7]*(states[3]+states[2])-constants[10]*states[6] rates[7] = constants[10]*states[6]-constants[9]*states[7]*(states[3]+states[2]) 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)