# 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 = 7 sizeStates = 3 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 (millisecond)" legend_states[0] = "V in component V (millivolt)" legend_constants[0] = "C in component V (microF_per_cm2)" legend_constants[1] = "i_app in component V (microA_per_cm2)" legend_algebraic[0] = "i_L in component i_L (microA_per_cm2)" legend_algebraic[3] = "i_Ca in component i_Ca (microA_per_cm2)" legend_algebraic[6] = "i_K in component i_K (microA_per_cm2)" legend_constants[2] = "g_L in component i_L (milliS_per_cm2)" legend_constants[3] = "E_L in component i_L (millivolt)" legend_constants[4] = "E_Ca in component i_Ca (millivolt)" legend_constants[5] = "g_Ca in component i_Ca (milliS_per_cm2)" legend_states[1] = "m in component i_Ca_m_gate (dimensionless)" legend_algebraic[1] = "m_infinity in component i_Ca_m_gate (dimensionless)" legend_algebraic[4] = "lambda_m in component i_Ca_m_gate (per_millisecond)" legend_constants[6] = "lambda_m_bar in component i_Ca_m_gate (per_millisecond)" legend_constants[7] = "V1 in component i_Ca_m_gate (millivolt)" legend_constants[8] = "V2 in component i_Ca_m_gate (millivolt)" legend_constants[9] = "E_K in component i_K (millivolt)" legend_constants[10] = "g_K in component i_K (milliS_per_cm2)" legend_states[2] = "n in component i_K_n_gate (dimensionless)" legend_algebraic[2] = "n_infinity in component i_K_n_gate (dimensionless)" legend_algebraic[5] = "lambda_n in component i_K_n_gate (per_millisecond)" legend_constants[11] = "lambda_n_bar in component i_K_n_gate (per_millisecond)" legend_constants[12] = "V3 in component i_K_n_gate (millivolt)" legend_constants[13] = "V4 in component i_K_n_gate (millivolt)" legend_rates[0] = "d/dt V in component V (millivolt)" legend_rates[1] = "d/dt m in component i_Ca_m_gate (dimensionless)" legend_rates[2] = "d/dt n in component i_K_n_gate (dimensionless)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = -50 constants[0] = 20.0 constants[1] = 540.0 constants[2] = 2.0 constants[3] = -50.00 constants[4] = 100.0 constants[5] = 4.0 states[1] = 0.1 constants[6] = 1.0 constants[7] = 0.0 constants[8] = 15.0 constants[9] = -70.0 constants[10] = 8.0 states[2] = 0.1 constants[11] = 0.1 constants[12] = 10.0 constants[13] = 10.0 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[1] = 0.500000*(1.00000+tanh((states[0]-constants[7])/constants[8])) algebraic[4] = constants[6]*cosh((states[0]-constants[7])/(2.00000*constants[8])) rates[1] = algebraic[4]*(algebraic[1]-states[1]) algebraic[2] = 0.500000*(1.00000+tanh((states[0]-constants[12])/constants[13])) algebraic[5] = constants[11]*cosh((states[0]-constants[12])/(2.00000*constants[13])) rates[2] = algebraic[5]*(algebraic[2]-states[2]) algebraic[0] = constants[2]*(states[0]-constants[3]) algebraic[3] = constants[5]*states[1]*(states[0]-constants[4]) algebraic[6] = constants[10]*states[2]*(states[0]-constants[9]) rates[0] = (constants[1]-(algebraic[0]+algebraic[3]+algebraic[6]))/constants[0] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[1] = 0.500000*(1.00000+tanh((states[0]-constants[7])/constants[8])) algebraic[4] = constants[6]*cosh((states[0]-constants[7])/(2.00000*constants[8])) algebraic[2] = 0.500000*(1.00000+tanh((states[0]-constants[12])/constants[13])) algebraic[5] = constants[11]*cosh((states[0]-constants[12])/(2.00000*constants[13])) algebraic[0] = constants[2]*(states[0]-constants[3]) algebraic[3] = constants[5]*states[1]*(states[0]-constants[4]) algebraic[6] = constants[10]*states[2]*(states[0]-constants[9]) 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)