# 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 = 0 sizeStates = 12 sizeConstants = 38 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_states[0] = "E in component E (millimolar)" legend_constants[0] = "k23 in component reaction_constants (second_order_rate_constant)" legend_constants[1] = "k24 in component reaction_constants (first_order_rate_constant)" legend_constants[2] = "k17 in component reaction_constants (first_order_rate_constant)" legend_constants[3] = "k18 in component reaction_constants (first_order_rate_constant)" legend_constants[4] = "k1 in component reaction_constants (second_order_rate_constant)" legend_constants[5] = "k2 in component reaction_constants (first_order_rate_constant)" legend_constants[6] = "k3 in component reaction_constants (second_order_rate_constant)" legend_constants[7] = "k4 in component reaction_constants (first_order_rate_constant)" legend_states[1] = "ED in component ED (millimolar)" legend_states[2] = "E_ in component E_ (millimolar)" legend_states[3] = "ENa in component ENa (millimolar)" legend_states[4] = "ECl in component ECl (millimolar)" legend_constants[8] = "D in component reaction_constants (millimolar)" legend_constants[9] = "Na in component reaction_constants (millimolar)" legend_constants[10] = "Cl in component reaction_constants (millimolar)" legend_constants[11] = "k29 in component reaction_constants (second_order_rate_constant)" legend_constants[12] = "k30 in component reaction_constants (first_order_rate_constant)" legend_constants[13] = "k11 in component reaction_constants (second_order_rate_constant)" legend_constants[14] = "k12 in component reaction_constants (first_order_rate_constant)" legend_constants[15] = "k9 in component reaction_constants (second_order_rate_constant)" legend_constants[16] = "k10 in component reaction_constants (first_order_rate_constant)" legend_states[5] = "ED_ in component ED_ (millimolar)" legend_states[6] = "ENa_ in component ENa_ (millimolar)" legend_states[7] = "ECl_ in component ECl_ (millimolar)" legend_constants[17] = "D_ in component reaction_constants (millimolar)" legend_constants[18] = "Na_ in component reaction_constants (millimolar)" legend_constants[19] = "Cl_ in component reaction_constants (millimolar)" legend_constants[20] = "k21 in component reaction_constants (second_order_rate_constant)" legend_constants[21] = "k22 in component reaction_constants (first_order_rate_constant)" legend_states[8] = "ENaD in component ENaD (millimolar)" legend_constants[22] = "k27 in component reaction_constants (second_order_rate_constant)" legend_constants[23] = "k28 in component reaction_constants (first_order_rate_constant)" legend_states[9] = "ENaD_ in component ENaD_ (millimolar)" legend_constants[24] = "k25 in component reaction_constants (second_order_rate_constant)" legend_constants[25] = "k26 in component reaction_constants (first_order_rate_constant)" legend_constants[26] = "k31 in component reaction_constants (second_order_rate_constant)" legend_constants[27] = "k32 in component reaction_constants (first_order_rate_constant)" legend_constants[28] = "k5 in component reaction_constants (second_order_rate_constant)" legend_constants[29] = "k6 in component reaction_constants (first_order_rate_constant)" legend_states[10] = "ENaCl in component ENaCl (millimolar)" legend_constants[30] = "k13 in component reaction_constants (second_order_rate_constant)" legend_constants[31] = "k14 in component reaction_constants (first_order_rate_constant)" legend_states[11] = "ENaCl_ in component ENaCl_ (millimolar)" legend_constants[32] = "k7 in component reaction_constants (second_order_rate_constant)" legend_constants[33] = "k8 in component reaction_constants (first_order_rate_constant)" legend_constants[34] = "k15 in component reaction_constants (second_order_rate_constant)" legend_constants[35] = "k16 in component reaction_constants (first_order_rate_constant)" legend_constants[36] = "k19 in component reaction_constants (first_order_rate_constant)" legend_constants[37] = "k20 in component reaction_constants (first_order_rate_constant)" legend_rates[0] = "d/dt E in component E (millimolar)" legend_rates[2] = "d/dt E_ in component E_ (millimolar)" legend_rates[1] = "d/dt ED in component ED (millimolar)" legend_rates[5] = "d/dt ED_ in component ED_ (millimolar)" legend_rates[8] = "d/dt ENaD in component ENaD (millimolar)" legend_rates[9] = "d/dt ENaD_ in component ENaD_ (millimolar)" legend_rates[3] = "d/dt ENa in component ENa (millimolar)" legend_rates[6] = "d/dt ENa_ in component ENa_ (millimolar)" legend_rates[4] = "d/dt ECl in component ECl (millimolar)" legend_rates[7] = "d/dt ECl_ in component ECl_ (millimolar)" legend_rates[10] = "d/dt ENaCl in component ENaCl (millimolar)" legend_rates[11] = "d/dt ENaCl_ in component ENaCl_ (millimolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0.08333 constants[0] = 1.0E5 constants[1] = 3.192E1 constants[2] = 4.587E5 constants[3] = 1.0E5 constants[4] = 1.0E5 constants[5] = 4.183E5 constants[6] = 1.0E5 constants[7] = 4.928E6 states[1] = 0.08333 states[2] = 0.08333 states[3] = 0.08333 states[4] = 0.08333 constants[8] = 1.0E-6 constants[9] = 50.0 constants[10] = 96.0 constants[11] = 1.0E5 constants[12] = 3.514E-1 constants[13] = 1.0E5 constants[14] = 4.982E6 constants[15] = 1.0E5 constants[16] = 4.183E5 states[5] = 0.08333 states[6] = 0.08333 states[7] = 0.08333 constants[17] = 1.0E-6 constants[18] = 10.0 constants[19] = 40.0 constants[20] = 1.0E5 constants[21] = 4.183E5 states[8] = 0.08333 constants[22] = 1.0E5 constants[23] = 1.389E5 states[9] = 0.08333 constants[24] = 1.0E5 constants[25] = 3.192E1 constants[26] = 1.0E5 constants[27] = 1.166E-1 constants[28] = 1.0E5 constants[29] = 1.065E6 states[10] = 0.08333 constants[30] = 1.0E5 constants[31] = 1.065E6 states[11] = 0.08333 constants[32] = 1.0E5 constants[33] = 8.940E4 constants[34] = 1.0E5 constants[35] = 8.940E4 constants[36] = 1.0E3 constants[37] = 2.180E2 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[0] = (constants[1]*states[1]+constants[3]*states[2]+constants[5]*states[3]+constants[7]*states[4])-(constants[0]*constants[8]*states[0]+constants[2]*states[0]+constants[4]*constants[9]*states[0]+constants[6]*constants[10]*states[0]) rates[2] = (constants[12]*states[5]+constants[2]*states[0]+constants[16]*states[6]+constants[14]*states[7])-(constants[11]*constants[17]*states[2]+constants[3]*states[2]+constants[15]*constants[18]*states[2]+constants[13]*constants[19]*states[2]) rates[1] = (constants[0]*states[0]*constants[8]+constants[21]*states[8])-(constants[1]*states[1]+constants[20]*constants[9]*states[1]) rates[5] = (constants[11]*states[2]*constants[17]+constants[23]*states[9])-(constants[12]*states[5]+constants[22]*constants[18]*states[5]) rates[8] = (constants[20]*constants[9]*states[1]+constants[24]*constants[8]*states[3])-(constants[21]*states[8]+constants[25]*states[8]) rates[9] = (constants[22]*constants[18]*states[5]+constants[26]*constants[17]*states[6])-(constants[23]*states[9]+constants[27]*states[9]) rates[3] = (constants[4]*constants[9]*states[0]+constants[25]*states[8]+constants[29]*states[10])-(constants[5]*states[3]+constants[28]*constants[10]*states[3]+constants[24]*constants[8]*states[3]) rates[6] = (constants[15]*constants[18]*states[2]+constants[27]*states[9]+constants[31]*states[11])-(constants[16]*states[6]+constants[30]*constants[19]*states[6]+constants[26]*constants[17]*states[6]) rates[4] = (constants[6]*constants[10]*states[0]+constants[33]*states[10])-(constants[32]*constants[9]*states[4]+constants[7]*states[4]) rates[7] = (constants[13]*constants[19]*states[2]+constants[35]*states[11])-(constants[34]*constants[18]*states[7]+constants[14]*states[7]) rates[10] = (constants[28]*constants[10]*states[3]+constants[32]*constants[9]*states[4]+constants[37]*states[11])-(constants[29]*states[10]+constants[33]*states[10]+constants[36]*states[10]) rates[11] = (constants[30]*constants[19]*states[6]+constants[34]*constants[18]*states[7]+constants[36]*states[10])-(constants[31]*states[11]+constants[35]*states[11]+constants[37]*states[11]) return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) 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)