# 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 = 2 sizeStates = 3 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] = "R in component R (ng_ml)" legend_constants[0] = "h in component R (first_order_rate_constant)" legend_constants[1] = "c in component R (ng_ml_hr)" legend_constants[2] = "b1 in component R (first_order_rate_constant)" legend_algebraic[1] = "H in component R (dimensionless)" legend_algebraic[0] = "x in component R (ng_ml)" legend_states[1] = "T in component T (ng_ml)" legend_states[2] = "L in component L (ng_ml)" legend_constants[3] = "g1 in component L (first_order_rate_constant)" legend_constants[4] = "b2 in component L (first_order_rate_constant)" legend_constants[5] = "g2 in component T (first_order_rate_constant)" legend_constants[6] = "b3 in component T (first_order_rate_constant)" legend_rates[0] = "d/dt R in component R (ng_ml)" legend_rates[2] = "d/dt L in component L (ng_ml)" legend_rates[1] = "d/dt T in component T (ng_ml)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0.5 constants[0] = 12 constants[1] = 100 constants[2] = 1.29 states[1] = 15 states[2] = 22 constants[3] = 10 constants[4] = 0.97 constants[5] = 0.7 constants[6] = 1.39 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[2] = constants[3]*states[0]-constants[4]*states[2] rates[1] = constants[5]*states[2]-constants[6]*states[1] algebraic[0] = states[1]-constants[1]/constants[0] algebraic[1] = custom_piecewise([greater(algebraic[0] , 0.00000), 1.00000 , True, 0.00000]) rates[0] = (constants[1]-constants[0]*states[1])*(1.00000-algebraic[1])-constants[2]*states[0] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = states[1]-constants[1]/constants[0] algebraic[1] = custom_piecewise([greater(algebraic[0] , 0.00000), 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)