# 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 = 3 sizeConstants = 28 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] = "R in component R (picomolar)" legend_constants[0] = "DR in component model_parameters (flux)" legend_algebraic[2] = "pi_C in component model_parameters (dimensionless)" legend_constants[23] = "DB in component model_parameters (first_order_rate_constant)" legend_states[1] = "B in component B (picomolar)" legend_algebraic[0] = "f in component B (flux)" legend_constants[1] = "kB in component model_parameters (first_order_rate_constant)" legend_states[2] = "C in component C (picomolar)" legend_constants[2] = "DC in component model_parameters (flux)" legend_algebraic[1] = "pi_L in component pi_L (dimensionless)" legend_constants[3] = "DA in component model_parameters (first_order_rate_constant)" legend_constants[4] = "k1 in component pi_L (second_order_rate_constant)" legend_constants[5] = "k2 in component pi_L (first_order_rate_constant)" legend_constants[6] = "k3 in component pi_L (second_order_rate_constant)" legend_constants[7] = "k4 in component pi_L (first_order_rate_constant)" legend_constants[8] = "K in component pi_L (picomolar)" legend_constants[9] = "ko in component pi_L (first_order_rate_constant)" legend_constants[10] = "Io in component pi_L (flux)" legend_constants[11] = "IL in component pi_L (flux)" legend_constants[12] = "rL in component pi_L (flux)" legend_constants[13] = "KOP in component pi_L (picomole_day_picomole_cells)" legend_constants[14] = "KLP in component pi_L (picomole_picomole_cells)" legend_constants[27] = "pi_P in component model_parameters (dimensionless)" legend_constants[15] = "f0 in component model_parameters (dimensionless)" legend_constants[16] = "dB in component model_parameters (first_order_rate_constant)" legend_constants[17] = "IP in component model_parameters (flux)" legend_constants[18] = "kP in component model_parameters (first_order_rate_constant)" legend_constants[24] = "P in component model_parameters (picomolar)" legend_constants[25] = "P_0 in component model_parameters (picomolar)" legend_constants[26] = "P_s in component model_parameters (picomolar)" legend_constants[19] = "C_s in component model_parameters (picomolar)" legend_constants[20] = "SP in component model_parameters (flux)" legend_constants[21] = "k5 in component model_parameters (second_order_rate_constant)" legend_constants[22] = "k6 in component model_parameters (first_order_rate_constant)" legend_rates[0] = "d/dt R in component R (picomolar)" legend_rates[1] = "d/dt B in component B (picomolar)" legend_rates[2] = "d/dt C in component C (picomolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0.00077 constants[0] = 7E-4 states[1] = 0.00073 constants[1] = 0.189 states[2] = 0.00091 constants[2] = 2.1E-3 constants[3] = 0.7 constants[4] = 1E-2 constants[5] = 10.0 constants[6] = 5.8E-4 constants[7] = 1.7E-2 constants[8] = 10.0 constants[9] = 0.35 constants[10] = 0.0 constants[11] = 0.0 constants[12] = 1E3 constants[13] = 2E5 constants[14] = 3E6 constants[15] = 0.05 constants[16] = 0.7 constants[17] = 0.0 constants[18] = 86.0 constants[19] = 5E-3 constants[20] = 250.0 constants[21] = 0.02 constants[22] = 3.0 constants[23] = constants[15]*constants[16] constants[24] = constants[17]/constants[18] constants[25] = constants[20]/constants[18] constants[26] = constants[22]/constants[21] constants[27] = (constants[24]+constants[25])/(constants[24]+constants[26]) return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[2] = (states[2]+constants[15]*constants[19])/(states[2]+constants[19]) rates[0] = constants[0]*algebraic[2]-(constants[23]/algebraic[2])*states[0] algebraic[0] = custom_piecewise([greater(voi , 20.0000) & less_equal(voi , 80.0000), 0.000100000 , True, 0.00000]) rates[1] = ((constants[23]/algebraic[2])*states[0]-constants[1]*states[1])+algebraic[0] algebraic[1] = (constants[6]/constants[7])*((constants[14]*constants[27]*states[1])/(1.00000+(constants[6]*constants[8])/constants[7]+(constants[4]/(constants[5]*constants[9]))*((constants[13]/constants[27])*states[0]+constants[10])))*(1.00000+constants[11]/constants[12]) rates[2] = constants[2]*algebraic[1]-constants[3]*algebraic[2]*states[2] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[2] = (states[2]+constants[15]*constants[19])/(states[2]+constants[19]) algebraic[0] = custom_piecewise([greater(voi , 20.0000) & less_equal(voi , 80.0000), 0.000100000 , True, 0.00000]) algebraic[1] = (constants[6]/constants[7])*((constants[14]*constants[27]*states[1])/(1.00000+(constants[6]*constants[8])/constants[7]+(constants[4]/(constants[5]*constants[9]))*((constants[13]/constants[27])*states[0]+constants[10])))*(1.00000+constants[11]/constants[12]) 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)