# 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 = 5 sizeStates = 2 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 (second)" legend_algebraic[0] = "H_int in component concentrations (mM)" legend_algebraic[1] = "H_ext in component concentrations (mM)" legend_constants[0] = "psi_int in component concentrations (volt)" legend_constants[1] = "psi_ext in component concentrations (volt)" legend_constants[9] = "psi in component concentrations (volt)" legend_states[0] = "pH_int in component concentrations (dimensionless)" legend_states[1] = "pH_ext in component concentrations (dimensionless)" legend_constants[2] = "J_Vtype_H_Max in component H_ATPase (mM_per_s)" legend_algebraic[3] = "J_Vtype_H in component H_ATPase (mM_per_s)" legend_algebraic[4] = "plot in component fluxes (dimensionless)" legend_algebraic[2] = "mu_H in component H_ATPase (joule_per_mmole)" legend_constants[3] = "mu_0 in component H_ATPase (joule_per_mmole)" legend_constants[4] = "xi in component H_ATPase (mmole_per_joule)" legend_constants[5] = "F in component H_ATPase (coulomb_per_mmole)" legend_constants[6] = "R in component H_ATPase (joule_per_mmole_kelvin)" legend_constants[7] = "T in component H_ATPase (kelvin)" legend_constants[8] = "z in component H_ATPase (dimensionless)" legend_rates[0] = "d/dt pH_int in component concentrations (dimensionless)" legend_rates[1] = "d/dt pH_ext in component concentrations (dimensionless)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; constants[0] = -0.03 constants[1] = 0.0 states[0] = 7.5 states[1] = 4.0 constants[2] = 1.8 constants[3] = 4.0 constants[4] = 0.4 constants[5] = 96.5 constants[6] = 0.008315 constants[7] = 300 constants[8] = -1.57 constants[9] = constants[1]-constants[0] constants[10] = 0.00000 constants[11] = 0.100000 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = constants[10] rates[1] = constants[11] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = 1000.00*(power(10.0000, -states[0])) algebraic[1] = 1000.00*(power(10.0000, -states[1])) algebraic[2] = constants[6]*constants[7]*log(algebraic[1]/algebraic[0])+constants[8]*constants[5]*constants[9] algebraic[3] = constants[2]/(1.00000+exp(constants[4]*(algebraic[2]-constants[3]))) algebraic[4] = algebraic[3]/constants[2] 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)