# 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 = 4 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] = "c in component c (dimensionless)" legend_algebraic[0] = "f in component c (dimensionless)" legend_constants[0] = "kcd in component reaction_constants (first_order_rate_constant)" legend_constants[1] = "ki1 in component reaction_constants (dimensionless)" legend_states[1] = "o in component o (dimensionless)" legend_states[2] = "a in component a (dimensionless)" legend_constants[2] = "kad in component reaction_constants (first_order_rate_constant)" legend_constants[3] = "ki2 in component reaction_constants (first_order_rate_constant)" legend_states[3] = "r in component r (dimensionless)" legend_constants[4] = "kcr in component reaction_constants (first_order_rate_constant)" legend_constants[5] = "krd in component reaction_constants (first_order_rate_constant)" legend_constants[6] = "k in component reaction_constants (dimensionless)" legend_rates[0] = "d/dt c in component c (dimensionless)" legend_rates[2] = "d/dt a in component a (dimensionless)" legend_rates[3] = "d/dt r in component r (dimensionless)" legend_rates[1] = "d/dt o in component o (dimensionless)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0.6 constants[0] = 1.0 constants[1] = 0.1 states[1] = 0.055 states[2] = 0.055 constants[2] = 10.0 constants[3] = 0.1 states[3] = 0.01 constants[4] = 0.05 constants[5] = 0.9 constants[6] = 0.001 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[2] = states[0]/(1.00000+(states[1]*states[3])/constants[3])-constants[2]*states[2] rates[3] = ((power(states[1]*states[3], 2.00000))/(1.00000*(constants[6]+power(states[1]*states[3], 2.00000)))+constants[4])-constants[5]*states[3] rates[1] = 1.00000*(states[2]-states[1]) algebraic[0] = custom_piecewise([greater(voi , 0.00000) & less(voi , 1.00000) | greater(voi , 4.00000) & less(voi , 5.00000) | greater(voi , 8.00000) & less(voi , 9.00000) | greater(voi , 12.0000) & less(voi , 13.0000) | greater(voi , 16.0000) & less(voi , 17.0000), 1.00000 , True, 0.00000]) rates[0] = 1.00000*((1.00000+algebraic[0])/(1.00000+states[1]/constants[1]))-constants[0]*states[0] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = custom_piecewise([greater(voi , 0.00000) & less(voi , 1.00000) | greater(voi , 4.00000) & less(voi , 5.00000) | greater(voi , 8.00000) & less(voi , 9.00000) | greater(voi , 12.0000) & less(voi , 13.0000) | greater(voi , 16.0000) & less(voi , 17.0000), 1.00000 , True, 0.00000]) return algebraic def custom_piecewise(cases): """Compute result of a piecewise function""" return select(cases[0::2],cases[1::2]) 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)