# 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 = 13 sizeStates = 2 sizeConstants = 30 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_algebraic[10] = "P_CE in component equations (dimensionless)" legend_algebraic[5] = "P_PE in component equations (dimensionless)" legend_algebraic[6] = "P_SE in component equations (dimensionless)" legend_algebraic[0] = "Ca in component equations (dimensionless)" legend_algebraic[12] = "C_2 in component equations (per_millisec)" legend_algebraic[1] = "phi_A_1 in component equations (dimensionless)" legend_algebraic[11] = "pi_n in component equations (dimensionless)" legend_algebraic[8] = "A in component equations (dimensionless)" legend_states[0] = "A_1 in component equations (dimensionless)" legend_algebraic[3] = "S in component equations (um)" legend_algebraic[9] = "n in component equations (dimensionless)" legend_algebraic[7] = "n_1 in component equations (dimensionless)" legend_states[1] = "n_2 in component equations (dimensionless)" legend_constants[27] = "G_V in component equations (dimensionless)" legend_constants[26] = "q_V in component equations (per_millisec)" legend_constants[25] = "V in component equations (um_per_millisec)" legend_constants[28] = "F_V in component equations (dimensionless)" legend_constants[29] = "p_V in component equations (dimensionless)" legend_constants[0] = "alpha_1 in component equations (per_um)" legend_constants[1] = "alpha_2 in component equations (per_um)" legend_constants[2] = "beta_1 in component equations (dimensionless)" legend_constants[3] = "beta_2 in component equations (dimensionless)" legend_constants[4] = "lambda in component equations (per_um)" legend_constants[5] = "V_max in component equations (um_per_millisec)" legend_constants[6] = "Ca_m in component equations (dimensionless)" legend_constants[7] = "t_d in component equations (millisecond)" legend_constants[8] = "a_c in component equations (per_millisec2)" legend_constants[9] = "b_c in component equations (per_millisec2)" legend_constants[10] = "C_1 in component equations (per_millisec)" legend_constants[11] = "C_20 in component equations (per_millisec)" legend_constants[12] = "q_k in component equations (dimensionless)" legend_constants[24] = "V_1 in component equations (um_per_millisec)" legend_constants[13] = "a in component equations (dimensionless)" legend_constants[14] = "m_0 in component equations (dimensionless)" legend_constants[15] = "g_1 in component equations (per_um)" legend_constants[16] = "g_2 in component equations (dimensionless)" legend_constants[17] = "pi_min in component equations (dimensionless)" legend_constants[18] = "S_0 in component equations (um)" legend_constants[19] = "q_1 in component equations (per_millisec)" legend_constants[20] = "q_2 in component equations (per_millisec)" legend_constants[21] = "q_3 in component equations (per_millisec)" legend_constants[22] = "TnC in component equations (dimensionless)" legend_algebraic[2] = "l_1 in component user_defined (um)" legend_algebraic[4] = "l_2 in component user_defined (um)" legend_constants[23] = "dl_1_dt in component user_defined (um_per_millisec)" legend_rates[0] = "d/dt A_1 in component equations (dimensionless)" legend_rates[1] = "d/dt n_2 in component equations (dimensionless)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0 states[1] = 0 constants[0] = 14.6 constants[1] = 14.6 constants[2] = 1 constants[3] = 0.0012 constants[4] = 30 constants[5] = 0.0043 constants[6] = 45e-3 constants[7] = 170 constants[8] = 2.4e-4 constants[9] = 5e-4 constants[10] = 2.9e-2 constants[11] = 0.2 constants[12] = 4 constants[13] = 0.25 constants[14] = 0.87 constants[15] = 0.4 constants[16] = 0.6 constants[17] = 5e-2 constants[18] = 0.77 constants[19] = 0.017 constants[20] = 0.26 constants[21] = 0.03 constants[22] = 1 constants[23] = 0.00000 constants[24] = 0.100000*constants[5] constants[25] = -constants[23] constants[26] = custom_piecewise([less_equal(constants[25] , 0.00000), constants[19]-(constants[20]*constants[25])/constants[5] , True, constants[21]]) constants[27] = 1.00000+(0.600000*constants[25])/constants[5] constants[28] = (constants[13]*(1.00000+constants[25]/constants[5]))/(constants[13]-constants[25]/constants[5]) constants[29] = constants[28]/constants[27] return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[1] = constants[26]*(constants[14]*constants[27]-states[1]) algebraic[0] = custom_piecewise([less_equal(voi , constants[7]), constants[6]*(power(1.00000-exp(-constants[8]*(power(voi, 2.00000))), 2.00000)) , True, constants[6]*(power((1.00000-exp(-constants[8]*(power(voi, 2.00000))))*exp(-constants[9]*(power(voi-constants[7], 2.00000))), 2.00000))]) algebraic[1] = exp(-constants[12]*states[0]) algebraic[2] = custom_piecewise([less_equal(200.000 , voi) & less_equal(voi , 201.000), 0.00000 , True, 0.00000]) algebraic[7] = custom_piecewise([less(constants[15]*algebraic[2]+constants[16] , 0.00000), 0.00000 , less_equal(0.00000 , constants[15]*algebraic[2]+constants[16]) & less_equal(constants[15]*algebraic[2]+constants[16] , 1.00000), constants[15]*algebraic[2]+constants[16] , True, 1.00000]) algebraic[9] = algebraic[7]*states[1] algebraic[11] = custom_piecewise([less_equal(0.750000 , algebraic[9]) & less_equal(algebraic[9] , 1.00000), constants[17] , less_equal(0.250000 , algebraic[9]) & less(algebraic[9] , 0.750000), power(constants[17], 2.00000*algebraic[9]-0.500000) , True, 1.00000]) rates[0] = constants[10]*algebraic[0]*(constants[22]-states[0])-constants[11]*algebraic[11]*algebraic[1]*states[0] 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_equal(voi , constants[7]), constants[6]*(power(1.00000-exp(-constants[8]*(power(voi, 2.00000))), 2.00000)) , True, constants[6]*(power((1.00000-exp(-constants[8]*(power(voi, 2.00000))))*exp(-constants[9]*(power(voi-constants[7], 2.00000))), 2.00000))]) algebraic[1] = exp(-constants[12]*states[0]) algebraic[2] = custom_piecewise([less_equal(200.000 , voi) & less_equal(voi , 201.000), 0.00000 , True, 0.00000]) algebraic[7] = custom_piecewise([less(constants[15]*algebraic[2]+constants[16] , 0.00000), 0.00000 , less_equal(0.00000 , constants[15]*algebraic[2]+constants[16]) & less_equal(constants[15]*algebraic[2]+constants[16] , 1.00000), constants[15]*algebraic[2]+constants[16] , True, 1.00000]) algebraic[9] = algebraic[7]*states[1] algebraic[11] = custom_piecewise([less_equal(0.750000 , algebraic[9]) & less_equal(algebraic[9] , 1.00000), constants[17] , less_equal(0.250000 , algebraic[9]) & less(algebraic[9] , 0.750000), power(constants[17], 2.00000*algebraic[9]-0.500000) , True, 1.00000]) algebraic[3] = 0.500000*algebraic[2]+constants[18] algebraic[4] = algebraic[2]+1.87000 algebraic[5] = constants[3]*(exp(constants[1]*algebraic[4])-1.00000) algebraic[6] = constants[2]*(exp(constants[0]*(algebraic[4]-algebraic[2]))-1.00000) algebraic[8] = (states[0]*algebraic[3])/1.00000 algebraic[10] = constants[4]*algebraic[3]*states[0]*algebraic[9]*constants[29] algebraic[12] = constants[11]*algebraic[11]*algebraic[1] 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)