# 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 = 9 sizeStates = 2 sizeConstants = 13 from math import * from numpy import * def createLegends(): legend_states = [""] * sizeStates legend_rates = [""] * sizeStates legend_algebraic = [""] * sizeAlgebraic legend_voi = "" legend_constants = [""] * sizeConstants legend_voi = "t in component main (second)" legend_constants[0] = "V_m in component main (J_per_C)" legend_constants[1] = "RTF in component main (J_per_C)" legend_constants[10] = "epsilon in component main (dimensionless)" legend_states[0] = "TA_i in component main (mol_per_m3)" legend_algebraic[0] = "CO2_o in component main (mol_per_m3)" legend_algebraic[5] = "CO2_i in component main (mol_per_m3)" legend_algebraic[7] = "HCO3_i in component main (mol_per_m3)" legend_algebraic[1] = "HCO3_o in component main (mol_per_m3)" legend_states[1] = "H_i in component main (mol_per_m3)" legend_constants[2] = "H_o in component main (mol_per_m3)" legend_constants[3] = "H_Lim in component main (mol_per_m3)" legend_algebraic[6] = "M_CO2 in component main (mol_per_m2_s)" legend_algebraic[8] = "M_HCO3 in component main (mol_per_m2_s)" legend_algebraic[3] = "M_H in component main (mol_per_m2_s)" legend_algebraic[2] = "pH_i in component main (dimensionless)" legend_constants[11] = "pH_o in component main (dimensionless)" legend_constants[12] = "pH_Lim in component main (dimensionless)" legend_constants[4] = "P_CO2 in component main (m_per_s)" legend_constants[5] = "P_HCO3 in component main (m_per_s)" legend_constants[6] = "k in component main (m_per_s)" legend_constants[7] = "K_A in component main (mol_per_m3)" legend_constants[8] = "rho in component main (per_m)" legend_algebraic[4] = "alpha_i in component main (dimensionless)" legend_constants[9] = "beta in component main (mol_per_m3)" legend_rates[0] = "d/dt TA_i in component main (mol_per_m3)" legend_rates[1] = "d/dt H_i in component main (mol_per_m3)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; constants[0] = -0.057 constants[1] = 0.0256796 states[0] = 0.0 states[1] = 3.981071705534970e-05 constants[2] = 1.995262314968879e-05 constants[3] = 3.981071705534970e-05 constants[4] = 6e-5 constants[5] = 5e-9 constants[6] = 0.0375 constants[7] = 1e-3 constants[8] = 8000 constants[9] = -26 constants[10] = exp(-constants[0]/constants[1]) constants[11] = -log(0.00100000*constants[2], 10) constants[12] = -log(0.00100000*constants[3], 10) return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[0] = custom_piecewise([less(voi , 100.000), 0.00000 , less(voi , 2800.00), 1.18770 , True, 0.00000]) algebraic[4] = states[1]/(states[1]+constants[7]) algebraic[5] = algebraic[4]*states[0] algebraic[6] = constants[4]*(algebraic[0]-algebraic[5]) algebraic[7] = (1.00000-algebraic[4])*states[0] algebraic[1] = (constants[7]*algebraic[0])/constants[2] algebraic[8] = (((constants[5]*constants[0])/constants[1])*(algebraic[1]-algebraic[7]*constants[10]))/(1.00000-constants[10]) rates[0] = constants[8]*(algebraic[6]+algebraic[8]) algebraic[2] = -log(0.00100000*states[1], 10) algebraic[3] = custom_piecewise([less(algebraic[2] , constants[12]), constants[6]*(states[1]-constants[3]) , True, 0.00000]) rates[1] = ((-2.30300*states[1])/constants[9])*constants[8]*(((1.00000-algebraic[4])*algebraic[6]-algebraic[4]*algebraic[8])-algebraic[3]) return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = custom_piecewise([less(voi , 100.000), 0.00000 , less(voi , 2800.00), 1.18770 , True, 0.00000]) algebraic[4] = states[1]/(states[1]+constants[7]) algebraic[5] = algebraic[4]*states[0] algebraic[6] = constants[4]*(algebraic[0]-algebraic[5]) algebraic[7] = (1.00000-algebraic[4])*states[0] algebraic[1] = (constants[7]*algebraic[0])/constants[2] algebraic[8] = (((constants[5]*constants[0])/constants[1])*(algebraic[1]-algebraic[7]*constants[10]))/(1.00000-constants[10]) algebraic[2] = -log(0.00100000*states[1], 10) algebraic[3] = custom_piecewise([less(algebraic[2] , constants[12]), constants[6]*(states[1]-constants[3]) , 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)