# 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 = 3 sizeConstants = 12 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] = "Tn in component Tn (cells_per_microlitre)" legend_constants[0] = "sn in component Tn (flux)" legend_constants[1] = "dn in component Tn (first_order_rate_constant)" legend_constants[2] = "kn in component model_parameters (first_order_rate_constant)" legend_constants[3] = "eta in component model_parameters (cells_per_microlitre)" legend_states[1] = "C in component C (cells_per_microlitre)" legend_states[2] = "Te in component Te (cells_per_microlitre)" legend_constants[4] = "alpha_n in component Te (dimensionless)" legend_constants[5] = "alpha_e in component Te (first_order_rate_constant)" legend_constants[6] = "de in component Te (first_order_rate_constant)" legend_constants[7] = "gamma_e in component Te (microlitre_per_cells_day)" legend_constants[8] = "Cmax in component C (cells_per_microlitre)" legend_constants[9] = "rc in component C (first_order_rate_constant)" legend_constants[10] = "dc in component C (first_order_rate_constant)" legend_constants[11] = "gamma_c in component C (microlitre_per_cells_day)" legend_rates[0] = "d/dt Tn in component Tn (cells_per_microlitre)" legend_rates[2] = "d/dt Te in component Te (cells_per_microlitre)" legend_rates[1] = "d/dt C in component C (cells_per_microlitre)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 1510.0 constants[0] = 0.071 constants[1] = 0.050 constants[2] = 0.063 constants[3] = 43.0 states[1] = 9600.0 states[2] = 20.0 constants[4] = 0.56 constants[5] = 0.53 constants[6] = 0.12 constants[7] = 0.0077 constants[8] = 190000 constants[9] = 0.23 constants[10] = 0.68 constants[11] = 0.047 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = constants[0]-(constants[1]*states[0]+constants[2]*states[0]*(states[1]/(states[1]+constants[3]))) rates[2] = (constants[4]*constants[2]*states[0]*(states[1]/(states[1]+constants[3]))+constants[5]*states[2]*(states[1]/(states[1]+constants[3])))-(constants[6]*states[2]+constants[7]*states[1]*states[2]) rates[1] = constants[9]*states[1]*log(constants[8]/states[1])-(constants[10]*states[1]+constants[11]*states[1]*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)