# 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 = 3 sizeStates = 5 sizeConstants = 14 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] = "X in component X (dimensionless)" legend_constants[0] = "mu0 in component X (first_order_rate_constant)" legend_constants[1] = "lamda in component X (first_order_rate_constant)" legend_states[1] = "K in component K (first_order_rate_constant)" legend_states[2] = "V in component V (dimensionless)" legend_states[3] = "Y in component Y (dimensionless)" legend_constants[2] = "mu1 in component Y (first_order_rate_constant)" legend_constants[3] = "a in component Y (dimensionless)" legend_states[4] = "Z in component Z (dimensionless)" legend_algebraic[0] = "CD4 in component CD4 (dimensionless)" legend_constants[4] = "mu2 in component V (first_order_rate_constant)" legend_constants[5] = "beta in component V (first_order_rate_constant)" legend_constants[6] = "b in component V (dimensionless)" legend_constants[7] = "theta in component Z (first_order_rate_constant)" legend_constants[8] = "rho in component Z (first_order_rate_constant)" legend_algebraic[1] = "f_X in component Z (dimensionless)" legend_algebraic[2] = "g_V in component Z (dimensionless)" legend_constants[9] = "C1 in component Z (dimensionless)" legend_constants[10] = "C2 in component Z (dimensionless)" legend_constants[11] = "X0 in component Z (dimensionless)" legend_constants[12] = "omega in component K (first_order_rate_constant)" legend_constants[13] = "Kmax in component K (first_order_rate_constant)" legend_rates[0] = "d/dt X in component X (dimensionless)" legend_rates[3] = "d/dt Y in component Y (dimensionless)" legend_rates[2] = "d/dt V in component V (dimensionless)" legend_rates[4] = "d/dt Z in component Z (dimensionless)" legend_rates[1] = "d/dt K in component K (first_order_rate_constant)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 1.0E11 constants[0] = 4.0E-3 constants[1] = 4.0E8 states[1] = 1.35E-14 states[2] = 1.0 states[3] = 1.0 constants[2] = 0.30 constants[3] = 1.0 states[4] = 0.0 constants[4] = 1.0 constants[5] = 1.0E3 constants[6] = 1.0 constants[7] = 1.0E-6 constants[8] = 0.50 constants[9] = 0.04 constants[10] = 1.0E3 constants[11] = 1.0E11 constants[12] = 1.0E-16 constants[13] = 20.0 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = constants[1]-(constants[0]*states[0]+states[1]*states[2]*states[0]) rates[3] = states[1]*states[2]*states[3]-constants[2]*(1.00000+constants[3]*states[4])*states[3] rates[2] = constants[5]*states[3]-constants[4]*(1.00000+constants[6]*states[4])*states[2] rates[1] = constants[12]*states[2]*(constants[13]-states[1]) algebraic[1] = ((1.00000+constants[9])*(power(states[0]/constants[11], 2.00000)))/(constants[9]+power(states[0]/constants[11], 2.00000)) algebraic[2] = states[2]/(constants[10]+states[2]) rates[4] = constants[7]*algebraic[2]+constants[8]*(algebraic[1]-states[4])*states[4] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[1] = ((1.00000+constants[9])*(power(states[0]/constants[11], 2.00000)))/(constants[9]+power(states[0]/constants[11], 2.00000)) algebraic[2] = states[2]/(constants[10]+states[2]) algebraic[0] = (states[0]+states[3])/1.00000e+11 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)