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 = 48
sizeStates = 9
sizeConstants = 58
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 params_BG (second)"
legend_constants[0] = "R in component params_BG (J_per_K_mol)"
legend_constants[1] = "T in component params_BG (kelvin)"
legend_constants[2] = "F in component params_BG (C_per_mol)"
legend_constants[3] = "K_Nai in component params_BG (per_fmol)"
legend_constants[45] = "q_Nai in component params_BG (fmol)"
legend_constants[4] = "K_Nao in component params_BG (per_fmol)"
legend_constants[47] = "q_Nao in component params_BG (fmol)"
legend_constants[5] = "K_Cli in component params_BG (per_fmol)"
legend_constants[49] = "q_Cli in component params_BG (fmol)"
legend_constants[6] = "K_Clo in component params_BG (per_fmol)"
legend_constants[51] = "q_Clo in component params_BG (fmol)"
legend_constants[7] = "K_HCO3i in component params_BG (per_fmol)"
legend_constants[53] = "q_HCO3i in component params_BG (fmol)"
legend_constants[8] = "K_HCO3o in component params_BG (per_fmol)"
legend_constants[55] = "q_HCO3o in component params_BG (fmol)"
legend_constants[9] = "K_1 in component params_BG (per_fmol)"
legend_constants[10] = "q_init_1 in component params_BG (fmol)"
legend_constants[11] = "K_2 in component params_BG (per_fmol)"
legend_constants[12] = "q_init_2 in component params_BG (fmol)"
legend_constants[13] = "K_3 in component params_BG (per_fmol)"
legend_constants[14] = "q_init_3 in component params_BG (fmol)"
legend_constants[15] = "K_4 in component params_BG (per_fmol)"
legend_constants[16] = "q_init_4 in component params_BG (fmol)"
legend_constants[17] = "K_5 in component params_BG (per_fmol)"
legend_constants[18] = "q_init_5 in component params_BG (fmol)"
legend_constants[19] = "K_6 in component params_BG (per_fmol)"
legend_constants[20] = "q_init_6 in component params_BG (fmol)"
legend_constants[21] = "K_7 in component params_BG (per_fmol)"
legend_constants[22] = "q_init_7 in component params_BG (fmol)"
legend_constants[23] = "K_8 in component params_BG (per_fmol)"
legend_constants[24] = "q_init_8 in component params_BG (fmol)"
legend_constants[25] = "kappa_r1 in component params_BG (fmol_per_s)"
legend_constants[26] = "kappa_r2 in component params_BG (fmol_per_s)"
legend_constants[27] = "kappa_r3 in component params_BG (fmol_per_s)"
legend_constants[28] = "kappa_r4 in component params_BG (fmol_per_s)"
legend_constants[29] = "kappa_r5 in component params_BG (fmol_per_s)"
legend_constants[30] = "kappa_r6 in component params_BG (fmol_per_s)"
legend_constants[31] = "kappa_r7 in component params_BG (fmol_per_s)"
legend_constants[32] = "kappa_r8 in component params_BG (fmol_per_s)"
legend_constants[33] = "kappa_r9 in component params_BG (fmol_per_s)"
legend_constants[34] = "kappa_r10 in component params_BG (fmol_per_s)"
legend_constants[46] = "mu_Nai in component BG_NDCBE (J_per_mol)"
legend_constants[48] = "mu_Nao in component BG_NDCBE (J_per_mol)"
legend_constants[50] = "mu_Cli in component BG_NDCBE (J_per_mol)"
legend_constants[52] = "mu_Clo in component BG_NDCBE (J_per_mol)"
legend_constants[54] = "mu_HCO3i in component BG_NDCBE (J_per_mol)"
legend_constants[56] = "mu_HCO3o in component BG_NDCBE (J_per_mol)"
legend_algebraic[0] = "mu_1 in component BG_NDCBE (J_per_mol)"
legend_algebraic[46] = "v_1 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[2] = "mu_2 in component BG_NDCBE (J_per_mol)"
legend_algebraic[40] = "v_2 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[4] = "mu_3 in component BG_NDCBE (J_per_mol)"
legend_algebraic[33] = "v_3 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[5] = "mu_4 in component BG_NDCBE (J_per_mol)"
legend_algebraic[36] = "v_4 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[6] = "mu_5 in component BG_NDCBE (J_per_mol)"
legend_algebraic[41] = "v_5 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[7] = "mu_6 in component BG_NDCBE (J_per_mol)"
legend_algebraic[47] = "v_6 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[8] = "mu_7 in component BG_NDCBE (J_per_mol)"
legend_algebraic[43] = "v_7 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[9] = "mu_8 in component BG_NDCBE (J_per_mol)"
legend_algebraic[45] = "v_8 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[3] = "V_Vm in component BG_NDCBE (volt)"
legend_algebraic[1] = "V0_Vm in component params_BG (volt)"
legend_algebraic[10] = "A_f_r1 in component BG_NDCBE (J_per_mol)"
legend_algebraic[30] = "v_r1 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[11] = "A_r_r1 in component BG_NDCBE (J_per_mol)"
legend_algebraic[12] = "A_f_r2 in component BG_NDCBE (J_per_mol)"
legend_algebraic[31] = "v_r2 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[13] = "A_r_r2 in component BG_NDCBE (J_per_mol)"
legend_algebraic[14] = "A_f_r3 in component BG_NDCBE (J_per_mol)"
legend_algebraic[32] = "v_r3 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[15] = "A_r_r3 in component BG_NDCBE (J_per_mol)"
legend_algebraic[16] = "A_f_r4 in component BG_NDCBE (J_per_mol)"
legend_algebraic[34] = "v_r4 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[17] = "A_r_r4 in component BG_NDCBE (J_per_mol)"
legend_algebraic[18] = "A_f_r5 in component BG_NDCBE (J_per_mol)"
legend_algebraic[35] = "v_r5 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[19] = "A_r_r5 in component BG_NDCBE (J_per_mol)"
legend_algebraic[20] = "A_f_r6 in component BG_NDCBE (J_per_mol)"
legend_algebraic[37] = "v_r6 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[21] = "A_r_r6 in component BG_NDCBE (J_per_mol)"
legend_algebraic[22] = "A_f_r7 in component BG_NDCBE (J_per_mol)"
legend_algebraic[39] = "v_r7 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[23] = "A_r_r7 in component BG_NDCBE (J_per_mol)"
legend_algebraic[24] = "A_f_r8 in component BG_NDCBE (J_per_mol)"
legend_algebraic[42] = "v_r8 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[25] = "A_r_r8 in component BG_NDCBE (J_per_mol)"
legend_algebraic[26] = "A_f_r9 in component BG_NDCBE (J_per_mol)"
legend_algebraic[44] = "v_r9 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[27] = "A_r_r9 in component BG_NDCBE (J_per_mol)"
legend_algebraic[28] = "A_f_r10 in component BG_NDCBE (J_per_mol)"
legend_algebraic[38] = "v_r10 in component BG_NDCBE (fmol_per_s)"
legend_algebraic[29] = "A_r_r10 in component BG_NDCBE (J_per_mol)"
legend_states[0] = "q_1 in component BG_NDCBE (fmol)"
legend_states[1] = "q_2 in component BG_NDCBE (fmol)"
legend_states[2] = "q_3 in component BG_NDCBE (fmol)"
legend_states[3] = "q_4 in component BG_NDCBE (fmol)"
legend_states[4] = "q_5 in component BG_NDCBE (fmol)"
legend_states[5] = "q_6 in component BG_NDCBE (fmol)"
legend_states[6] = "q_7 in component BG_NDCBE (fmol)"
legend_states[7] = "q_8 in component BG_NDCBE (fmol)"
legend_constants[35] = "nHCO3 in component BG_NDCBE (dimensionless)"
legend_constants[36] = "Nai in component params_BG (mM)"
legend_constants[37] = "Nao in component params_BG (mM)"
legend_constants[38] = "Cli in component params_BG (mM)"
legend_constants[39] = "Clo in component params_BG (mM)"
legend_constants[40] = "HCO3i in component params_BG (mM)"
legend_constants[41] = "HCO3o in component params_BG (mM)"
legend_constants[42] = "V_i in component params_BG (pL)"
legend_constants[43] = "V_o in component params_BG (pL)"
legend_states[8] = "V_E in component params_BG (volt)"
legend_constants[44] = "dt in component params_BG (second)"
legend_rates[0] = "d/dt q_1 in component BG_NDCBE (fmol)"
legend_rates[1] = "d/dt q_2 in component BG_NDCBE (fmol)"
legend_rates[2] = "d/dt q_3 in component BG_NDCBE (fmol)"
legend_rates[3] = "d/dt q_4 in component BG_NDCBE (fmol)"
legend_rates[4] = "d/dt q_5 in component BG_NDCBE (fmol)"
legend_rates[5] = "d/dt q_6 in component BG_NDCBE (fmol)"
legend_rates[6] = "d/dt q_7 in component BG_NDCBE (fmol)"
legend_rates[7] = "d/dt q_8 in component BG_NDCBE (fmol)"
legend_rates[8] = "d/dt V_E in component params_BG (volt)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 8.31
constants[1] = 293
constants[2] = 96485
constants[3] = 1e-08
constants[4] = 1e-08
constants[5] = 1e-08
constants[6] = 1e-08
constants[7] = 1e-06
constants[8] = 1e-06
constants[9] = 1
constants[10] = 1
constants[11] = 1
constants[12] = 1
constants[13] = 1
constants[14] = 1
constants[15] = 1
constants[16] = 1
constants[17] = 1
constants[18] = 1
constants[19] = 1
constants[20] = 1
constants[21] = 1
constants[22] = 1
constants[23] = 1
constants[24] = 1
constants[25] = 1
constants[26] = 1
constants[27] = 1
constants[28] = 1
constants[29] = 1
constants[30] = 1
constants[31] = 1
constants[32] = 1
constants[33] = 1
constants[34] = 1
constants[35] = 2
constants[36] = 20
constants[37] = 100
constants[38] = 20
constants[39] = 100
constants[40] = 10e-3
constants[41] = 1e-12
constants[42] = 8.5e5
constants[43] = 8.5e5
states[8] = -0.05
constants[44] = 1e-3
constants[45] = constants[36]*constants[42]
constants[57] = 0.00000
constants[46] = constants[0]*constants[1]*log(constants[3]*constants[45])
constants[47] = constants[37]*constants[43]
constants[48] = constants[0]*constants[1]*log(constants[4]*constants[47])
constants[49] = constants[38]*constants[42]
constants[50] = constants[0]*constants[1]*log(constants[5]*constants[49])
constants[51] = constants[39]*constants[43]
constants[52] = constants[0]*constants[1]*log(constants[6]*constants[51])
constants[53] = constants[40]*constants[42]
constants[54] = constants[0]*constants[1]*log(constants[7]*constants[53])
constants[55] = constants[41]*constants[43]
constants[56] = constants[0]*constants[1]*log(constants[8]*constants[55])
states[0] = constants[10]
states[1] = constants[12]
states[2] = constants[14]
states[3] = constants[16]
states[4] = constants[18]
states[5] = constants[20]
states[6] = constants[20]
states[7] = constants[20]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[8] = constants[57]
algebraic[2] = constants[0]*constants[1]*log(constants[11]*states[1])
algebraic[12] = constants[35]*constants[56]+algebraic[2]
algebraic[4] = constants[0]*constants[1]*log(constants[13]*states[2])
algebraic[13] = algebraic[4]
algebraic[31] = constants[26]*(exp(algebraic[12]/(constants[0]*constants[1]))-exp(algebraic[13]/(constants[0]*constants[1])))
algebraic[14] = algebraic[4]
algebraic[5] = constants[0]*constants[1]*log(constants[15]*states[3])
algebraic[15] = algebraic[5]
algebraic[32] = constants[27]*(exp(algebraic[14]/(constants[0]*constants[1]))-exp(algebraic[15]/(constants[0]*constants[1])))
algebraic[33] = algebraic[31]-algebraic[32]
rates[2] = algebraic[33]
algebraic[16] = algebraic[5]
algebraic[6] = constants[0]*constants[1]*log(constants[17]*states[4])
algebraic[17] = algebraic[6]+constants[35]*constants[54]
algebraic[34] = constants[28]*(exp(algebraic[16]/(constants[0]*constants[1]))-exp(algebraic[17]/(constants[0]*constants[1])))
algebraic[36] = algebraic[32]-algebraic[34]
rates[3] = algebraic[36]
algebraic[0] = constants[0]*constants[1]*log(constants[9]*states[0])
algebraic[10] = constants[48]+algebraic[0]
algebraic[11] = algebraic[2]
algebraic[30] = constants[25]*(exp(algebraic[10]/(constants[0]*constants[1]))-exp(algebraic[11]/(constants[0]*constants[1])))
algebraic[28] = algebraic[2]
algebraic[29] = algebraic[6]
algebraic[38] = constants[34]*(exp(algebraic[28]/(constants[0]*constants[1]))-exp(algebraic[29]/(constants[0]*constants[1])))
algebraic[40] = (algebraic[30]-algebraic[31])-algebraic[38]
rates[1] = algebraic[40]
algebraic[18] = algebraic[6]
algebraic[7] = constants[0]*constants[1]*log(constants[19]*states[5])
algebraic[19] = constants[46]+algebraic[7]
algebraic[35] = constants[29]*(exp(algebraic[18]/(constants[0]*constants[1]))-exp(algebraic[19]/(constants[0]*constants[1])))
algebraic[41] = (algebraic[34]+algebraic[38])-algebraic[35]
rates[4] = algebraic[41]
algebraic[20] = constants[50]+algebraic[7]
algebraic[8] = constants[0]*constants[1]*log(constants[21]*states[6])
algebraic[21] = algebraic[8]
algebraic[37] = constants[30]*(exp(algebraic[20]/(constants[0]*constants[1]))-exp(algebraic[21]/(constants[0]*constants[1])))
algebraic[22] = algebraic[8]
algebraic[9] = constants[0]*constants[1]*log(constants[23]*states[7])
algebraic[23] = algebraic[9]
algebraic[39] = constants[31]*(exp(algebraic[22]/(constants[0]*constants[1]))-exp(algebraic[23]/(constants[0]*constants[1])))
algebraic[43] = algebraic[37]-algebraic[39]
rates[6] = algebraic[43]
algebraic[24] = algebraic[9]
algebraic[25] = constants[52]+algebraic[0]
algebraic[42] = constants[32]*(exp(algebraic[24]/(constants[0]*constants[1]))-exp(algebraic[25]/(constants[0]*constants[1])))
algebraic[45] = algebraic[39]-algebraic[42]
rates[7] = algebraic[45]
algebraic[26] = algebraic[0]
algebraic[27] = algebraic[7]
algebraic[44] = constants[33]*(exp(algebraic[26]/(constants[0]*constants[1]))-exp(algebraic[27]/(constants[0]*constants[1])))
algebraic[46] = (algebraic[42]-algebraic[30])-algebraic[44]
rates[0] = algebraic[46]
algebraic[47] = (algebraic[35]+algebraic[44])-algebraic[37]
rates[5] = algebraic[47]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[2] = constants[0]*constants[1]*log(constants[11]*states[1])
algebraic[12] = constants[35]*constants[56]+algebraic[2]
algebraic[4] = constants[0]*constants[1]*log(constants[13]*states[2])
algebraic[13] = algebraic[4]
algebraic[31] = constants[26]*(exp(algebraic[12]/(constants[0]*constants[1]))-exp(algebraic[13]/(constants[0]*constants[1])))
algebraic[14] = algebraic[4]
algebraic[5] = constants[0]*constants[1]*log(constants[15]*states[3])
algebraic[15] = algebraic[5]
algebraic[32] = constants[27]*(exp(algebraic[14]/(constants[0]*constants[1]))-exp(algebraic[15]/(constants[0]*constants[1])))
algebraic[33] = algebraic[31]-algebraic[32]
algebraic[16] = algebraic[5]
algebraic[6] = constants[0]*constants[1]*log(constants[17]*states[4])
algebraic[17] = algebraic[6]+constants[35]*constants[54]
algebraic[34] = constants[28]*(exp(algebraic[16]/(constants[0]*constants[1]))-exp(algebraic[17]/(constants[0]*constants[1])))
algebraic[36] = algebraic[32]-algebraic[34]
algebraic[0] = constants[0]*constants[1]*log(constants[9]*states[0])
algebraic[10] = constants[48]+algebraic[0]
algebraic[11] = algebraic[2]
algebraic[30] = constants[25]*(exp(algebraic[10]/(constants[0]*constants[1]))-exp(algebraic[11]/(constants[0]*constants[1])))
algebraic[28] = algebraic[2]
algebraic[29] = algebraic[6]
algebraic[38] = constants[34]*(exp(algebraic[28]/(constants[0]*constants[1]))-exp(algebraic[29]/(constants[0]*constants[1])))
algebraic[40] = (algebraic[30]-algebraic[31])-algebraic[38]
algebraic[18] = algebraic[6]
algebraic[7] = constants[0]*constants[1]*log(constants[19]*states[5])
algebraic[19] = constants[46]+algebraic[7]
algebraic[35] = constants[29]*(exp(algebraic[18]/(constants[0]*constants[1]))-exp(algebraic[19]/(constants[0]*constants[1])))
algebraic[41] = (algebraic[34]+algebraic[38])-algebraic[35]
algebraic[20] = constants[50]+algebraic[7]
algebraic[8] = constants[0]*constants[1]*log(constants[21]*states[6])
algebraic[21] = algebraic[8]
algebraic[37] = constants[30]*(exp(algebraic[20]/(constants[0]*constants[1]))-exp(algebraic[21]/(constants[0]*constants[1])))
algebraic[22] = algebraic[8]
algebraic[9] = constants[0]*constants[1]*log(constants[23]*states[7])
algebraic[23] = algebraic[9]
algebraic[39] = constants[31]*(exp(algebraic[22]/(constants[0]*constants[1]))-exp(algebraic[23]/(constants[0]*constants[1])))
algebraic[43] = algebraic[37]-algebraic[39]
algebraic[24] = algebraic[9]
algebraic[25] = constants[52]+algebraic[0]
algebraic[42] = constants[32]*(exp(algebraic[24]/(constants[0]*constants[1]))-exp(algebraic[25]/(constants[0]*constants[1])))
algebraic[45] = algebraic[39]-algebraic[42]
algebraic[26] = algebraic[0]
algebraic[27] = algebraic[7]
algebraic[44] = constants[33]*(exp(algebraic[26]/(constants[0]*constants[1]))-exp(algebraic[27]/(constants[0]*constants[1])))
algebraic[46] = (algebraic[42]-algebraic[30])-algebraic[44]
algebraic[47] = (algebraic[35]+algebraic[44])-algebraic[37]
algebraic[1] = states[8]
algebraic[3] = algebraic[1]
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)