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 = 34
sizeStates = 19
sizeConstants = 60
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 Environment (second)"
legend_constants[0] = "Mg_tot in component Environment (molar)"
legend_constants[1] = "Pi_e in component Environment (molar)"
legend_constants[2] = "ADP_e in component Environment (molar)"
legend_constants[3] = "RT in component Fixed_parameters (kilojoule_per_mole)"
legend_constants[4] = "F in component Fixed_parameters (kilojoule_per_mole_per_millivolt)"
legend_constants[5] = "n_A in component Fixed_parameters (dimensionless)"
legend_constants[6] = "dG_C1o in component Fixed_parameters (kilojoule_per_mole)"
legend_constants[7] = "dG_C3o in component Fixed_parameters (kilojoule_per_mole)"
legend_constants[8] = "dG_C4o in component Fixed_parameters (kilojoule_per_mole)"
legend_constants[9] = "dG_F1o in component Fixed_parameters (kilojoule_per_mole)"
legend_constants[10] = "pH_e in component Fixed_parameters (dimensionless)"
legend_constants[47] = "H_e in component Fixed_parameters (molar)"
legend_constants[11] = "K_e in component Fixed_parameters (molar)"
legend_constants[12] = "ATP_e in component Fixed_parameters (molar)"
legend_constants[13] = "AMP_e in component Fixed_parameters (molar)"
legend_constants[48] = "k_dHPi in component Fixed_parameters (molar)"
legend_constants[49] = "k_dHatp in component Fixed_parameters (molar)"
legend_constants[50] = "k_dHadp in component Fixed_parameters (molar)"
legend_constants[14] = "K_DT in component Fixed_parameters (molar)"
legend_constants[15] = "K_DD in component Fixed_parameters (molar)"
legend_constants[16] = "K_AK in component Fixed_parameters (dimensionless)"
legend_constants[17] = "W_m in component Fixed_parameters (l_water_per_l_mito)"
legend_constants[52] = "W_x in component Fixed_parameters (l_water_per_l_mito)"
legend_constants[55] = "W_i in component Fixed_parameters (l_water_per_l_mito)"
legend_constants[18] = "gamma in component Fixed_parameters (per_micron)"
legend_constants[19] = "Ctot in component Fixed_parameters (molar)"
legend_constants[20] = "Qtot in component Fixed_parameters (molar)"
legend_constants[21] = "NADtot in component Fixed_parameters (molar)"
legend_constants[54] = "H_i in component Fixed_parameters (molar)"
legend_constants[51] = "K_i in component Fixed_parameters (molar)"
legend_constants[22] = "k_Pi1 in component Adjustable_parameters (molar)"
legend_constants[23] = "k_Pi2 in component Adjustable_parameters (molar)"
legend_constants[24] = "k_Pi3 in component Adjustable_parameters (molar)"
legend_constants[25] = "k_Pi4 in component Adjustable_parameters (molar)"
legend_constants[26] = "k_PiH in component Adjustable_parameters (molar)"
legend_constants[27] = "r in component Adjustable_parameters (dimensionless)"
legend_constants[28] = "x_DH in component Adjustable_parameters (mole_per_second_per_l_mito_per_molar)"
legend_constants[29] = "x_C1 in component Adjustable_parameters (mole_per_second_per_l_mito_per_molar)"
legend_constants[30] = "x_C3 in component Adjustable_parameters (mole_per_second_per_l_mito_per_molar)"
legend_constants[31] = "x_C4 in component Adjustable_parameters (mole_per_second_per_l_mito_per_molar)"
legend_constants[32] = "x_F1 in component Adjustable_parameters (mole_per_second_per_l_mito_per_molar_per_molar)"
legend_constants[33] = "x_ANT in component Adjustable_parameters (mole_per_second_per_l_mito)"
legend_constants[34] = "x_Pi1 in component Adjustable_parameters (mole_per_second_per_l_mito_per_molar)"
legend_constants[35] = "x_KH in component Adjustable_parameters (mole_per_second_per_l_mito_per_molar_per_molar)"
legend_constants[36] = "x_Hle in component Adjustable_parameters (mole_per_second_per_l_mito_per_molar_per_millivolt)"
legend_constants[37] = "x_K in component Adjustable_parameters (mole_per_second_per_l_mito_per_molar_per_millivolt)"
legend_constants[38] = "k_mADP in component Adjustable_parameters (molar)"
legend_constants[39] = "x_AK in component Adjustable_parameters (mole_per_second_per_l_mito_per_molar_per_molar)"
legend_constants[40] = "p_A in component Adjustable_parameters (micron_per_second)"
legend_constants[41] = "k_O2 in component Adjustable_parameters (molar)"
legend_constants[42] = "x_buff in component Adjustable_parameters (per_molar)"
legend_constants[43] = "x_MgA in component Adjustable_parameters (mole_per_second_per_l_mito_per_molar_per_molar)"
legend_constants[44] = "x_Pi2 in component Adjustable_parameters (micron_per_second)"
legend_algebraic[0] = "dG_H in component Proton_motive_force (kilojoule_per_mole)"
legend_states[0] = "dPsi in component dPsi_dt (millivolt)"
legend_states[1] = "H_x in component dH_x_dt (molar)"
legend_algebraic[26] = "J_DH in component Dehydrogenase_flux (mole_per_second_per_l_mito)"
legend_algebraic[25] = "NAD_x in component NAD_x_concentration (molar)"
legend_states[2] = "NADH_x in component dNADH_x_dt (molar)"
legend_states[3] = "Pi_x in component dPi_x_dt (molar)"
legend_algebraic[29] = "J_C1 in component Electron_flux_complex_I (mole_per_second_per_l_mito)"
legend_algebraic[28] = "dG_C1op in component Electron_flux_complex_I (kilojoule_per_mole)"
legend_algebraic[27] = "Q in component Q_concentration (molar)"
legend_states[4] = "QH2 in component dQH2_dt (molar)"
legend_algebraic[32] = "J_C3 in component Electron_flux_complex_III (mole_per_second_per_l_mito)"
legend_algebraic[30] = "dG_C3op in component Electron_flux_complex_III (kilojoule_per_mole)"
legend_algebraic[31] = "Cox in component Cox_concentration (molar)"
legend_states[5] = "Cred in component dCred_dt (molar)"
legend_algebraic[33] = "J_C4 in component Electron_flux_complex_IV (mole_per_second_per_l_mito)"
legend_algebraic[1] = "dG_C4op in component Electron_flux_complex_IV (kilojoule_per_mole)"
legend_states[6] = "O2 in component dO2_dt (molar)"
legend_algebraic[2] = "J_F1 in component ATP_synthesis_flux (mole_per_second_per_l_mito)"
legend_states[7] = "ADP_mx in component dADP_mx_dt (molar)"
legend_states[8] = "ATP_mx in component dATP_mx_dt (molar)"
legend_algebraic[12] = "J_ANT in component ANT_flux (mole_per_second_per_l_mito)"
legend_algebraic[3] = "Psi_x in component ANT_flux (millivolt)"
legend_algebraic[4] = "Psi_i in component ANT_flux (millivolt)"
legend_algebraic[10] = "ADP_fi in component MgADPi_binding_flux (molar)"
legend_algebraic[8] = "ATP_fi in component MgATPi_binding_flux (molar)"
legend_algebraic[7] = "ADP_fx in component MgADPx_binding_flux (molar)"
legend_algebraic[5] = "ATP_fx in component MgATPx_binding_flux (molar)"
legend_constants[45] = "mincond in component ANT_flux (molar)"
legend_algebraic[6] = "J_MgATPx in component MgATPx_binding_flux (mole_per_second_per_l_mito)"
legend_states[9] = "ATP_x in component dATP_x_dt (molar)"
legend_states[10] = "Mg_x in component dMg_x_dt (molar)"
legend_algebraic[9] = "J_MgADPx in component MgADPx_binding_flux (mole_per_second_per_l_mito)"
legend_states[11] = "ADP_x in component dADP_x_dt (molar)"
legend_algebraic[11] = "J_MgATPi in component MgATPi_binding_flux (mole_per_second_per_l_mito)"
legend_states[12] = "ATP_i in component dATP_i_dt (molar)"
legend_states[13] = "ATP_mi in component dATP_mi_dt (molar)"
legend_constants[58] = "Mg_i in component Mg_binding (molar)"
legend_algebraic[13] = "J_MgADPi in component MgADPi_binding_flux (mole_per_second_per_l_mito)"
legend_states[14] = "ADP_i in component dADP_i_dt (molar)"
legend_states[15] = "ADP_mi in component dADP_mi_dt (molar)"
legend_algebraic[15] = "J_ATP in component ATP_substrate_flux (mole_per_second_per_l_mito)"
legend_algebraic[17] = "J_ADP in component ADP_substrate_flux (mole_per_second_per_l_mito)"
legend_algebraic[19] = "J_AMP in component AMP_substrate_flux (mole_per_second_per_l_mito)"
legend_states[16] = "AMP_i in component dAMP_i_dt (molar)"
legend_algebraic[14] = "J_Pi2 in component Pi_substrate_flux (mole_per_second_per_l_mito)"
legend_states[17] = "Pi_i in component dPi_i_dt (molar)"
legend_algebraic[20] = "J_Pi1 in component Phosphate_hydrogen_cotransporter_flux (mole_per_second_per_l_mito)"
legend_algebraic[16] = "H2PIi in component Phosphate_hydrogen_cotransporter_flux (molar)"
legend_algebraic[18] = "H2PIx in component Phosphate_hydrogen_cotransporter_flux (molar)"
legend_algebraic[21] = "J_AKi in component Adenylate_kinase_flux (mole_per_second_per_l_mito)"
legend_algebraic[22] = "J_Hle in component Hydrogen_leak_flux (mole_per_second_per_l_mito)"
legend_algebraic[23] = "J_K in component Passive_potassium_flux (mole_per_second_per_l_mito)"
legend_states[18] = "K_x in component dK_x_dt (molar)"
legend_algebraic[24] = "J_KH in component Potassium_hydrogen_flux (mole_per_second_per_l_mito)"
legend_constants[53] = "ADP_me in component ADP_binding (molar)"
legend_constants[56] = "ADP_fe in component ADP_binding (molar)"
legend_constants[57] = "Mg_e in component Mg_binding (molar)"
legend_constants[46] = "C_im in component dPsi_dt (mole_per_l_mito_per_millivolt)"
legend_rates[1] = "d/dt H_x in component dH_x_dt (molar)"
legend_rates[18] = "d/dt K_x in component dK_x_dt (molar)"
legend_rates[10] = "d/dt Mg_x in component dMg_x_dt (molar)"
legend_rates[2] = "d/dt NADH_x in component dNADH_x_dt (molar)"
legend_rates[4] = "d/dt QH2 in component dQH2_dt (molar)"
legend_rates[5] = "d/dt Cred in component dCred_dt (molar)"
legend_rates[9] = "d/dt ATP_x in component dATP_x_dt (molar)"
legend_rates[11] = "d/dt ADP_x in component dADP_x_dt (molar)"
legend_rates[8] = "d/dt ATP_mx in component dATP_mx_dt (molar)"
legend_rates[7] = "d/dt ADP_mx in component dADP_mx_dt (molar)"
legend_rates[3] = "d/dt Pi_x in component dPi_x_dt (molar)"
legend_rates[12] = "d/dt ATP_i in component dATP_i_dt (molar)"
legend_rates[14] = "d/dt ADP_i in component dADP_i_dt (molar)"
legend_rates[16] = "d/dt AMP_i in component dAMP_i_dt (molar)"
legend_rates[13] = "d/dt ATP_mi in component dATP_mi_dt (molar)"
legend_rates[15] = "d/dt ADP_mi in component dADP_mi_dt (molar)"
legend_rates[17] = "d/dt Pi_i in component dPi_i_dt (molar)"
legend_rates[0] = "d/dt dPsi in component dPsi_dt (millivolt)"
legend_rates[6] = "d/dt O2 in component dO2_dt (molar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 0.005
constants[1] = 0.000125
constants[2] = 0
constants[3] = 2.4734
constants[4] = 0.096484
constants[5] = 3
constants[6] = -69.37
constants[7] = -32.53
constants[8] = -122.94
constants[9] = 36.03
constants[10] = 7.1
constants[11] = 0.15
constants[12] = 0
constants[13] = 0
constants[14] = 2.4e-5
constants[15] = 3.47e-4
constants[16] = 0.4331
constants[17] = 0.72376
constants[18] = 5.99
constants[19] = 0.0027
constants[20] = 0.00135
constants[21] = 0.00297
constants[22] = 1.3413e-4
constants[23] = 6.7668e-4
constants[24] = 1.9172e-4
constants[25] = 0.02531
constants[26] = 4.5082e-4
constants[27] = 4.5807
constants[28] = 0.09183
constants[29] = 0.36923
constants[30] = 0.091737
constants[31] = 3.2562e-5
constants[32] = 150.93
constants[33] = 0.0079204
constants[34] = 339430
constants[35] = 2.9802e7
constants[36] = 250
constants[37] = 0
constants[38] = 3.5e-6
constants[39] = 0
constants[40] = 85
constants[41] = 1.2e-4
constants[42] = 100
constants[43] = 1000000
constants[44] = 327
states[0] = 160
states[1] = 6.30957344480193e-8
states[2] = 0.0015
states[3] = 0.001
states[4] = 8e-4
states[5] = 0.001
states[6] = 2.6e-5
states[7] = 0
states[8] = 0
constants[45] = 1e-12
states[9] = 0
states[10] = 0.005
states[11] = 0.01
states[12] = 0
states[13] = 0
states[14] = 0
states[15] = 0
states[16] = 0
states[17] = 0.001
states[18] = 0.14
constants[46] = 6.756756756756757e-6
constants[47] = 1.00000*(power(10.0000, -constants[10]))
constants[48] = 1.00000*(power(10.0000, -6.75000))
constants[49] = 1.00000*(power(10.0000, -6.48000))
constants[50] = 1.00000*(power(10.0000, -6.29000))
constants[51] = constants[11]
constants[52] = 0.900000*constants[17]
constants[53] = ((constants[15]+constants[2]+constants[0])-power(power(constants[15]+constants[2]+constants[0], 2.00000)-4.00000*constants[0]*constants[2], 1.0/2))/2.00000
constants[59] = 0.00000
constants[54] = constants[47]
constants[55] = 0.100000*constants[17]
constants[56] = constants[2]-constants[53]
constants[57] = constants[0]-constants[53]
constants[58] = constants[57]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[6] = constants[59]
algebraic[5] = states[9]-states[8]
algebraic[6] = constants[43]*(algebraic[5]*states[10]-constants[14]*states[8])
rates[8] = algebraic[6]/constants[52]
algebraic[7] = states[11]-states[7]
algebraic[9] = constants[43]*(algebraic[7]*states[10]-constants[15]*states[7])
rates[10] = (-algebraic[6]-algebraic[9])/constants[52]
rates[7] = algebraic[9]/constants[52]
algebraic[8] = states[12]-states[13]
algebraic[11] = constants[43]*(algebraic[8]*constants[58]-constants[14]*states[13])
rates[13] = algebraic[11]/constants[55]
algebraic[0] = constants[4]*states[0]+constants[3]*log(constants[54]/states[1])
algebraic[2] = constants[32]*(((exp(-(constants[9]-constants[5]*algebraic[0])/constants[3])*constants[15])/constants[14])*states[7]*states[3]-states[8]*1.00000)
algebraic[3] = -0.650000*states[0]
algebraic[4] = 0.350000*states[0]
algebraic[10] = states[14]-states[15]
algebraic[12] = custom_piecewise([greater(algebraic[10] , constants[45]) | greater(algebraic[8] , constants[45]), (constants[33]*(algebraic[10]/(algebraic[10]+algebraic[8]*exp((-constants[4]*algebraic[4])/constants[3]))-algebraic[7]/(algebraic[7]+algebraic[5]*exp((-constants[4]*algebraic[3])/constants[3])))*algebraic[10])/(constants[38]+algebraic[10]) , True, 0.00000])
rates[9] = (algebraic[2]-algebraic[12])/constants[52]
rates[11] = (-algebraic[2]+algebraic[12])/constants[52]
algebraic[13] = constants[43]*(algebraic[10]*constants[58]-constants[15]*states[15])
rates[15] = algebraic[13]/constants[55]
algebraic[16] = (states[17]*constants[54])/(constants[54]+constants[48])
algebraic[18] = (states[3]*states[1])/(states[1]+constants[48])
algebraic[20] = (constants[34]*(states[1]*algebraic[16]-constants[54]*algebraic[18]))/(algebraic[16]+constants[26])
rates[3] = (-algebraic[2]+algebraic[20])/constants[52]
algebraic[15] = constants[18]*constants[40]*(constants[12]-states[12])
algebraic[21] = constants[39]*(constants[16]*states[14]*states[14]-states[16]*states[12])
rates[12] = (algebraic[15]+algebraic[12]+algebraic[21])/constants[55]
algebraic[17] = constants[18]*constants[40]*(constants[2]-states[14])
rates[14] = ((algebraic[17]-algebraic[12])-2.00000*algebraic[21])/constants[55]
algebraic[19] = constants[18]*constants[40]*(constants[13]-states[16])
rates[16] = (algebraic[19]+algebraic[21])/constants[55]
algebraic[14] = constants[18]*constants[44]*(constants[1]-states[17])
rates[17] = (-algebraic[20]+algebraic[14])/constants[55]
algebraic[23] = (constants[37]*states[0]*(constants[51]*exp((constants[4]*states[0])/constants[3])-states[18]))/(exp((constants[4]*states[0])/constants[3])-1.00000)
algebraic[24] = constants[35]*(constants[51]*states[1]-states[18]*constants[54])
rates[18] = (algebraic[24]+algebraic[23])/constants[52]
algebraic[25] = constants[21]-states[2]
algebraic[26] = (constants[28]*(constants[27]*algebraic[25]-states[2])*(1.00000+states[3]/constants[22]))/(1.00000+states[3]/constants[23])
algebraic[27] = constants[20]-states[4]
algebraic[28] = (constants[6]-constants[3]*log(states[1]/1.00000e-07))-constants[3]*log(algebraic[27]/states[4])
algebraic[29] = constants[29]*(exp(-(algebraic[28]+4.00000*algebraic[0])/constants[3])*states[2]-algebraic[25])
rates[2] = (algebraic[26]-algebraic[29])/constants[52]
algebraic[30] = (constants[7]+2.00000*constants[3]*log(states[1]/1.00000e-07))-constants[3]*log(states[4]/algebraic[27])
algebraic[31] = constants[19]-states[5]
algebraic[32] = ((constants[30]*(1.00000+states[3]/constants[24]))/(1.00000+states[3]/constants[25]))*(exp(-((algebraic[30]+4.00000*algebraic[0])-2.00000*constants[4]*states[0])/(2.00000*constants[3]))*algebraic[31]-states[5])
rates[4] = (algebraic[29]-algebraic[32])/constants[52]
algebraic[1] = (constants[8]-2.00000*constants[3]*log(states[1]/1.00000e-07))-(constants[3]/2.00000)*log(states[6]/1.00000)
algebraic[33] = ((((constants[31]*1.00000)/(1.00000+constants[41]/states[6]))*states[5])/constants[19])*(exp(-(algebraic[1]+2.00000*algebraic[0])/(2.00000*constants[3]))*states[5]-algebraic[31]*exp((constants[4]*states[0])/constants[3]))
algebraic[22] = (constants[36]*states[0]*(constants[54]*exp((constants[4]*states[0])/constants[3])-states[1]))/(exp((constants[4]*states[0])/constants[3])-1.00000)
rates[1] = (constants[42]*states[1]*(((((algebraic[26]-5.00000*algebraic[29])-2.00000*algebraic[32])-4.00000*algebraic[33])+(constants[5]-1.00000)*algebraic[2]+2.00000*algebraic[20]+algebraic[22])-algebraic[24]))/constants[52]
rates[5] = (2.00000*algebraic[32]-2.00000*algebraic[33])/constants[55]
rates[0] = (((((4.00000*algebraic[29]+2.00000*algebraic[32]+4.00000*algebraic[33])-constants[5]*algebraic[2])-algebraic[12])-algebraic[22])-algebraic[23])/constants[46]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[5] = states[9]-states[8]
algebraic[6] = constants[43]*(algebraic[5]*states[10]-constants[14]*states[8])
algebraic[7] = states[11]-states[7]
algebraic[9] = constants[43]*(algebraic[7]*states[10]-constants[15]*states[7])
algebraic[8] = states[12]-states[13]
algebraic[11] = constants[43]*(algebraic[8]*constants[58]-constants[14]*states[13])
algebraic[0] = constants[4]*states[0]+constants[3]*log(constants[54]/states[1])
algebraic[2] = constants[32]*(((exp(-(constants[9]-constants[5]*algebraic[0])/constants[3])*constants[15])/constants[14])*states[7]*states[3]-states[8]*1.00000)
algebraic[3] = -0.650000*states[0]
algebraic[4] = 0.350000*states[0]
algebraic[10] = states[14]-states[15]
algebraic[12] = custom_piecewise([greater(algebraic[10] , constants[45]) | greater(algebraic[8] , constants[45]), (constants[33]*(algebraic[10]/(algebraic[10]+algebraic[8]*exp((-constants[4]*algebraic[4])/constants[3]))-algebraic[7]/(algebraic[7]+algebraic[5]*exp((-constants[4]*algebraic[3])/constants[3])))*algebraic[10])/(constants[38]+algebraic[10]) , True, 0.00000])
algebraic[13] = constants[43]*(algebraic[10]*constants[58]-constants[15]*states[15])
algebraic[16] = (states[17]*constants[54])/(constants[54]+constants[48])
algebraic[18] = (states[3]*states[1])/(states[1]+constants[48])
algebraic[20] = (constants[34]*(states[1]*algebraic[16]-constants[54]*algebraic[18]))/(algebraic[16]+constants[26])
algebraic[15] = constants[18]*constants[40]*(constants[12]-states[12])
algebraic[21] = constants[39]*(constants[16]*states[14]*states[14]-states[16]*states[12])
algebraic[17] = constants[18]*constants[40]*(constants[2]-states[14])
algebraic[19] = constants[18]*constants[40]*(constants[13]-states[16])
algebraic[14] = constants[18]*constants[44]*(constants[1]-states[17])
algebraic[23] = (constants[37]*states[0]*(constants[51]*exp((constants[4]*states[0])/constants[3])-states[18]))/(exp((constants[4]*states[0])/constants[3])-1.00000)
algebraic[24] = constants[35]*(constants[51]*states[1]-states[18]*constants[54])
algebraic[25] = constants[21]-states[2]
algebraic[26] = (constants[28]*(constants[27]*algebraic[25]-states[2])*(1.00000+states[3]/constants[22]))/(1.00000+states[3]/constants[23])
algebraic[27] = constants[20]-states[4]
algebraic[28] = (constants[6]-constants[3]*log(states[1]/1.00000e-07))-constants[3]*log(algebraic[27]/states[4])
algebraic[29] = constants[29]*(exp(-(algebraic[28]+4.00000*algebraic[0])/constants[3])*states[2]-algebraic[25])
algebraic[30] = (constants[7]+2.00000*constants[3]*log(states[1]/1.00000e-07))-constants[3]*log(states[4]/algebraic[27])
algebraic[31] = constants[19]-states[5]
algebraic[32] = ((constants[30]*(1.00000+states[3]/constants[24]))/(1.00000+states[3]/constants[25]))*(exp(-((algebraic[30]+4.00000*algebraic[0])-2.00000*constants[4]*states[0])/(2.00000*constants[3]))*algebraic[31]-states[5])
algebraic[1] = (constants[8]-2.00000*constants[3]*log(states[1]/1.00000e-07))-(constants[3]/2.00000)*log(states[6]/1.00000)
algebraic[33] = ((((constants[31]*1.00000)/(1.00000+constants[41]/states[6]))*states[5])/constants[19])*(exp(-(algebraic[1]+2.00000*algebraic[0])/(2.00000*constants[3]))*states[5]-algebraic[31]*exp((constants[4]*states[0])/constants[3]))
algebraic[22] = (constants[36]*states[0]*(constants[54]*exp((constants[4]*states[0])/constants[3])-states[1]))/(exp((constants[4]*states[0])/constants[3])-1.00000)
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)