# 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 = 12 sizeStates = 5 sizeConstants = 31 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 interface (ms)" legend_constants[0] = "Cm in component interface (uFpmmsq)" legend_constants[1] = "Am in component interface (pmm)" legend_algebraic[0] = "Istim in component interface (uApmmcu)" legend_states[0] = "Vm in component membrane (mV)" legend_states[1] = "Vt in component Ttubular_current_Vt_var (mV)" legend_states[2] = "m in component sodium_current_m_gate (dimensionless)" legend_states[3] = "h in component sodium_current_h_gate (dimensionless)" legend_states[4] = "n in component potassium_current_n_gate (dimensionless)" legend_algebraic[4] = "INa in component sodium_current (uApmmsq)" legend_algebraic[9] = "IK in component potassium_current (uApmmsq)" legend_algebraic[10] = "IL in component leak_current (uApmmsq)" legend_algebraic[11] = "IT in component Ttubular_current (uApmmsq)" legend_algebraic[5] = "IStimC in component interface (uApmmcu)" legend_constants[30] = "AmC in component interface (pmm)" legend_constants[2] = "IstimStart in component interface (ms)" legend_constants[3] = "IstimEnd in component interface (ms)" legend_constants[4] = "IstimAmplitude in component interface (uApmmcu)" legend_constants[5] = "IstimPeriod in component interface (ms)" legend_constants[6] = "IstimPulseDuration in component interface (ms)" legend_constants[7] = "gNa_max in component sodium_current (mSpmmsq)" legend_constants[8] = "ENa in component sodium_current (mV)" legend_algebraic[1] = "alpha_m in component sodium_current_m_gate (pms)" legend_algebraic[6] = "beta_m in component sodium_current_m_gate (pms)" legend_constants[9] = "alpha_m_max in component sodium_current_m_gate (pms)" legend_constants[10] = "beta_m_max in component sodium_current_m_gate (pms)" legend_constants[11] = "Em in component sodium_current_m_gate (mV)" legend_constants[12] = "v_alpha_m in component sodium_current_m_gate (dimensionless)" legend_constants[13] = "v_beta_m in component sodium_current_m_gate (mV)" legend_algebraic[2] = "alpha_h in component sodium_current_h_gate (pms)" legend_algebraic[7] = "beta_h in component sodium_current_h_gate (pms)" legend_constants[14] = "alpha_h_max in component sodium_current_h_gate (pms)" legend_constants[15] = "beta_h_max in component sodium_current_h_gate (pms)" legend_constants[16] = "Eh in component sodium_current_h_gate (mV)" legend_constants[17] = "v_alpha_h in component sodium_current_h_gate (mV)" legend_constants[18] = "v_beta_h in component sodium_current_h_gate (mV)" legend_constants[19] = "gK_max in component potassium_current (mSpmmsq)" legend_constants[20] = "EK in component potassium_current (mV)" legend_algebraic[3] = "alpha_n in component potassium_current_n_gate (pms)" legend_algebraic[8] = "beta_n in component potassium_current_n_gate (pms)" legend_constants[21] = "alpha_n_max in component potassium_current_n_gate (pms)" legend_constants[22] = "beta_n_max in component potassium_current_n_gate (pms)" legend_constants[23] = "En in component potassium_current_n_gate (mV)" legend_constants[24] = "v_alpha_n in component potassium_current_n_gate (dimensionless)" legend_constants[25] = "v_beta_n in component potassium_current_n_gate (mV)" legend_constants[26] = "EL in component leak_current (mV)" legend_constants[27] = "gL_max in component leak_current (mSpmmsq)" legend_constants[28] = "Rs in component Ttubular_current (mmsqpmS)" legend_constants[29] = "Ct in component Ttubular_current_Vt_var (uFpmmsq)" legend_rates[0] = "d/dt Vm in component membrane (mV)" legend_rates[2] = "d/dt m in component sodium_current_m_gate (dimensionless)" legend_rates[3] = "d/dt h in component sodium_current_h_gate (dimensionless)" legend_rates[4] = "d/dt n in component potassium_current_n_gate (dimensionless)" legend_rates[1] = "d/dt Vt in component Ttubular_current_Vt_var (mV)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; constants[0] = 0.009 constants[1] = 200.0 states[0] = -95.0 states[1] = -95.0 states[2] = 0.0 states[3] = 1.0 states[4] = 0.0 constants[2] = 10 constants[3] = 50000 constants[4] = 0.5 constants[5] = 1000 constants[6] = 1 constants[7] = 1.8 constants[8] = 50.0 constants[9] = 0.208 constants[10] = 2.081 constants[11] = -42.0 constants[12] = 10.0 constants[13] = 18.0 constants[14] = 0.0156 constants[15] = 3.382 constants[16] = -41.0 constants[17] = 14.7 constants[18] = 7.6 constants[19] = 0.415 constants[20] = -70.0 constants[21] = 0.0229 constants[22] = 0.09616 constants[23] = -40.0 constants[24] = 7.0 constants[25] = 40.0 constants[26] = -95.0 constants[27] = 0.0024 constants[28] = 15.0 constants[29] = 0.04 constants[30] = constants[1] return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[1] = (states[0]-states[1])/(constants[28]*constants[29]) algebraic[1] = (constants[9]*(states[0]-constants[11]))/(1.00000-exp((constants[11]-states[0])/constants[12])) algebraic[6] = constants[10]*exp((constants[11]-states[0])/constants[13]) rates[2] = algebraic[1]*(1.00000-states[2])-algebraic[6]*states[2] algebraic[2] = constants[14]*exp((constants[16]-states[0])/constants[17]) algebraic[7] = constants[15]/(1.00000+exp((constants[16]-states[0])/constants[18])) rates[3] = algebraic[2]*(1.00000-states[3])-algebraic[7]*states[3] algebraic[3] = (constants[21]*(states[0]-constants[23]))/(1.00000-exp((constants[23]-states[0])/constants[24])) algebraic[8] = constants[22]*exp((constants[23]-states[0])/constants[25]) rates[4] = algebraic[3]*(1.00000-states[4])-algebraic[8]*states[4] algebraic[0] = custom_piecewise([greater_equal(voi , constants[2]) & less_equal(voi , constants[3]) & less_equal((voi-constants[2])-floor((voi-constants[2])/constants[5])*constants[5] , constants[6]), constants[4] , True, 0.00000]) algebraic[4] = constants[7]*states[2]*states[2]*states[2]*states[3]*(states[0]-constants[8]) algebraic[9] = constants[19]*states[4]*states[4]*states[4]*states[4]*(states[0]-constants[20]) algebraic[10] = constants[27]*(states[0]-constants[26]) algebraic[11] = (states[0]-states[1])/constants[28] rates[0] = (algebraic[0]-(algebraic[4]+algebraic[9]+algebraic[10]+algebraic[11]))/constants[0] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[1] = (constants[9]*(states[0]-constants[11]))/(1.00000-exp((constants[11]-states[0])/constants[12])) algebraic[6] = constants[10]*exp((constants[11]-states[0])/constants[13]) algebraic[2] = constants[14]*exp((constants[16]-states[0])/constants[17]) algebraic[7] = constants[15]/(1.00000+exp((constants[16]-states[0])/constants[18])) algebraic[3] = (constants[21]*(states[0]-constants[23]))/(1.00000-exp((constants[23]-states[0])/constants[24])) algebraic[8] = constants[22]*exp((constants[23]-states[0])/constants[25]) algebraic[0] = custom_piecewise([greater_equal(voi , constants[2]) & less_equal(voi , constants[3]) & less_equal((voi-constants[2])-floor((voi-constants[2])/constants[5])*constants[5] , constants[6]), constants[4] , True, 0.00000]) algebraic[4] = constants[7]*states[2]*states[2]*states[2]*states[3]*(states[0]-constants[8]) algebraic[9] = constants[19]*states[4]*states[4]*states[4]*states[4]*(states[0]-constants[20]) algebraic[10] = constants[27]*(states[0]-constants[26]) algebraic[11] = (states[0]-states[1])/constants[28] algebraic[5] = algebraic[0] 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)