# 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 = 2 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_constants[0] = "s in component uninfected (per_day_mm3)" legend_constants[1] = "p in component uninfected (per_day)" legend_constants[2] = "gamma in component uninfected (per_day)" legend_constants[13] = "beta in component uninfected (dimensionless)" legend_constants[3] = "N in component free_virus_particle (dimensionless)" legend_constants[4] = "k_1 in component latently_infected (mm3_per_day)" legend_constants[5] = "k_2 in component actively_infected (per_day)" legend_constants[6] = "k_3 in component latently_infected (per_day)" legend_constants[7] = "mu_V in component free_virus_particle (per_day)" legend_states[0] = "T_1 in component latently_infected (per_mm3)" legend_constants[8] = "mu_b in component actively_infected (per_day)" legend_states[1] = "T in component uninfected (per_mm3)" legend_constants[9] = "k_4 in component latently_infected (per_day)" legend_constants[10] = "T_0 in component latently_infected (per_mm3)" legend_constants[11] = "V_0 in component latently_infected (per_mm3)" legend_constants[12] = "t_min in component latently_infected (day)" legend_algebraic[0] = "T_1_t in component latently_infected (per_mm3)" legend_algebraic[1] = "T_2 in component actively_infected (per_mm3)" legend_algebraic[2] = "V in component free_virus_particle (per_mm3)" legend_rates[1] = "d/dt T in component uninfected (per_mm3)" legend_rates[0] = "d/dt T_1 in component latently_infected (per_mm3)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; constants[0] = 10 constants[1] = 0.01 constants[2] = 2E-5 constants[3] = 1000 constants[4] = 2.4E-5 constants[5] = 3E-3 constants[6] = 0.023 constants[7] = 2.4 states[0] = 0 constants[8] = 0.24 states[1] = 1000 constants[9] = 2.424 constants[10] = 1000 constants[11] = 1E-3 constants[12] = 2 constants[13] = (constants[2]/constants[6])*(1.00000+constants[5]/constants[8]) return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[1] = ((constants[0]+constants[1]*states[1])-constants[2]*(power(states[1], 2.00000)))-(constants[6]*constants[13]+(constants[3]*constants[4]*constants[5])/(constants[4]*states[1]+constants[7]))*states[1]*states[0] algebraic[0] = ((constants[4]*constants[10]*constants[11])/(constants[9]-constants[6]))*(exp(-constants[6]*voi)-exp(-constants[9]*voi)) rates[0] = custom_piecewise([less_equal(voi , constants[12]), algebraic[0] , True, ((constants[3]*constants[4]*constants[5])/(constants[4]*states[1]+constants[7]))*states[1]*states[0]-constants[6]*states[0]]) return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = ((constants[4]*constants[10]*constants[11])/(constants[9]-constants[6]))*(exp(-constants[6]*voi)-exp(-constants[9]*voi)) algebraic[1] = (constants[5]*states[0])/constants[8] algebraic[2] = (constants[3]*constants[5]*states[0])/(constants[4]*states[1]+constants[7]) 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)