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 = 92
sizeStates = 29
sizeConstants = 69
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 (ms)"
legend_constants[0] = "F in component Environment (C_per_mole)"
legend_constants[1] = "K_o in component Environment (mM)"
legend_constants[2] = "Ca_o in component Environment (mM)"
legend_constants[3] = "Na_o in component Environment (mM)"
legend_constants[4] = "Cl_o in component Environment (mM)"
legend_constants[5] = "FonRT in component Environment (per_mV)"
legend_constants[6] = "tissue in component Environment (dimensionless)"
legend_states[0] = "V in component cell (mV)"
legend_algebraic[62] = "INa in component INa (uA_per_uF)"
legend_algebraic[31] = "ICaL in component ICaL (uA_per_uF)"
legend_algebraic[77] = "IK1 in component IK1 (uA_per_uF)"
legend_algebraic[83] = "IKp in component IKp (uA_per_uF)"
legend_algebraic[85] = "IKs in component IKs (uA_per_uF)"
legend_algebraic[81] = "IKr in component IKr (uA_per_uF)"
legend_algebraic[49] = "IpCa in component IpCa (uA_per_uF)"
legend_algebraic[50] = "ICab in component ICab (uA_per_uF)"
legend_algebraic[48] = "INaCa in component INaCa (uA_per_uF)"
legend_algebraic[41] = "INaK in component INaK (uA_per_uF)"
legend_algebraic[82] = "Ito in component Ito (uA_per_uF)"
legend_algebraic[55] = "Ito2 in component Ito2 (uA_per_uF)"
legend_algebraic[88] = "IClb in component IClb (uA_per_uF)"
legend_algebraic[65] = "INal in component INal (uA_per_uF)"
legend_algebraic[51] = "caiont in component cell (uA_per_uF)"
legend_algebraic[68] = "naiont in component cell (uA_per_uF)"
legend_algebraic[86] = "kiont in component cell (uA_per_uF)"
legend_algebraic[89] = "clont in component cell (uA_per_uF)"
legend_constants[7] = "l in component cell (cm)"
legend_constants[8] = "a in component cell (cm)"
legend_constants[56] = "vcell in component cell (uL)"
legend_constants[60] = "ageo in component cell (cm2)"
legend_constants[63] = "Acap in component cell (uF)"
legend_constants[64] = "vmyo in component cell (uL)"
legend_constants[61] = "vmito in component cell (uL)"
legend_constants[62] = "vsr in component cell (uL)"
legend_constants[65] = "vnsr in component cell (uL)"
legend_constants[66] = "vjsr in component cell (uL)"
legend_constants[67] = "vss in component cell (uL)"
legend_constants[68] = "AF in component cell (uF_mole_per_C)"
legend_constants[9] = "stim_offset in component cell (ms)"
legend_constants[10] = "stim_period in component cell (ms)"
legend_constants[11] = "stim_duration in component cell (ms)"
legend_constants[12] = "stim_amplitude in component cell (uA_per_uF)"
legend_algebraic[16] = "i_Stim in component cell (uA_per_uF)"
legend_algebraic[0] = "past in component cell (ms)"
legend_algebraic[59] = "ENa in component reversal_potentials (mV)"
legend_constants[57] = "GNa in component INa (mS_per_uF)"
legend_algebraic[29] = "gNa in component INa (mS_per_uF)"
legend_states[1] = "H in component INa (dimensionless)"
legend_states[2] = "m in component INa (dimensionless)"
legend_states[3] = "J in component INa (dimensionless)"
legend_algebraic[1] = "am in component INa (per_ms)"
legend_algebraic[17] = "bm in component INa (per_ms)"
legend_algebraic[2] = "ah in component INa (per_ms)"
legend_algebraic[18] = "bh in component INa (per_ms)"
legend_algebraic[3] = "aj in component INa (per_ms)"
legend_algebraic[19] = "bj in component INa (per_ms)"
legend_states[4] = "Ca_ss in component Ca (mM)"
legend_states[5] = "d in component ICaL (dimensionless)"
legend_states[6] = "dp in component ICaL (dimensionless)"
legend_states[7] = "f in component ICaL (dimensionless)"
legend_states[8] = "fca in component ICaL (dimensionless)"
legend_states[9] = "fca2 in component ICaL (dimensionless)"
legend_states[10] = "f2 in component ICaL (dimensionless)"
legend_constants[13] = "pca in component ICaL (L_per_F_ms)"
legend_constants[14] = "gacai in component ICaL (dimensionless)"
legend_constants[15] = "gacao in component ICaL (dimensionless)"
legend_algebraic[54] = "CaMKactive in component Irel (dimensionless)"
legend_algebraic[30] = "ibarca in component ICaL (uA_per_uF)"
legend_algebraic[4] = "dss in component ICaL (dimensionless)"
legend_algebraic[20] = "taud in component ICaL (ms)"
legend_algebraic[5] = "fss in component ICaL (dimensionless)"
legend_algebraic[6] = "f2ss in component ICaL (dimensionless)"
legend_algebraic[21] = "tauf in component ICaL (ms)"
legend_algebraic[22] = "tauf2 in component ICaL (ms)"
legend_algebraic[7] = "dpss in component ICaL (dimensionless)"
legend_algebraic[32] = "fcass in component ICaL (dimensionless)"
legend_algebraic[33] = "fca2ss in component ICaL (dimensionless)"
legend_algebraic[56] = "taufca in component ICaL (ms)"
legend_algebraic[35] = "taufca2 in component ICaL (ms)"
legend_algebraic[70] = "EK in component reversal_potentials (mV)"
legend_algebraic[72] = "ak1 in component IK1 (per_ms)"
legend_algebraic[74] = "bk1 in component IK1 (per_ms)"
legend_constants[58] = "gkr in component IKr (mS_per_uF)"
legend_algebraic[37] = "r in component IKr (dimensionless)"
legend_states[11] = "xr in component IKr (dimensionless)"
legend_algebraic[8] = "xrss in component IKr (dimensionless)"
legend_algebraic[23] = "tauxr in component IKr (ms)"
legend_states[12] = "Ca_i in component Ca (mM)"
legend_algebraic[38] = "gks in component IKs (mS_per_uF)"
legend_algebraic[84] = "EKs in component reversal_potentials (mV)"
legend_algebraic[9] = "xss in component IKs (dimensionless)"
legend_algebraic[24] = "tauxs in component IKs (ms)"
legend_states[13] = "xs1 in component IKs (dimensionless)"
legend_states[14] = "xs2 in component IKs (dimensionless)"
legend_constants[16] = "gitodv in component Ito (mS_per_uF)"
legend_algebraic[39] = "rv in component Ito (dimensionless)"
legend_algebraic[10] = "ay in component Ito (per_ms)"
legend_algebraic[25] = "by in component Ito (per_ms)"
legend_algebraic[11] = "ay2 in component Ito (per_ms)"
legend_algebraic[26] = "by2 in component Ito (per_ms)"
legend_algebraic[12] = "ay3 in component Ito (per_ms)"
legend_algebraic[27] = "by3 in component Ito (per_ms)"
legend_states[15] = "ydv in component Ito (dimensionless)"
legend_states[16] = "ydv2 in component Ito (dimensionless)"
legend_states[17] = "zdv in component Ito (dimensionless)"
legend_states[18] = "Na_i in component Na (mM)"
legend_constants[17] = "kmnai in component INaK (mM)"
legend_constants[18] = "kmko in component INaK (mM)"
legend_constants[19] = "ibarnak in component INaK (uA_per_uF)"
legend_constants[59] = "sigma in component INaK (dimensionless)"
legend_algebraic[40] = "fnak in component INaK (dimensionless)"
legend_algebraic[42] = "ca_i_NaCa in component INaCa (mM)"
legend_constants[20] = "KmCa in component INaCa (mM)"
legend_algebraic[43] = "allo in component INaCa (dimensionless)"
legend_constants[21] = "NCXmax in component INaCa (uA_per_uF)"
legend_constants[22] = "ksat in component INaCa (dimensionless)"
legend_constants[23] = "eta in component INaCa (dimensionless)"
legend_constants[24] = "KmNai in component INaCa (mM)"
legend_constants[25] = "KmNao in component INaCa (mM)"
legend_constants[26] = "KmCai in component INaCa (mM)"
legend_constants[27] = "KmCao in component INaCa (mM)"
legend_algebraic[44] = "num in component INaCa (mM4)"
legend_algebraic[45] = "denom1 in component INaCa (dimensionless)"
legend_algebraic[46] = "denom2 in component INaCa (mM4)"
legend_algebraic[47] = "denom3 in component INaCa (mM4)"
legend_constants[28] = "ibarpca in component IpCa (uA_per_uF)"
legend_constants[29] = "kmpca in component IpCa (mM)"
legend_states[19] = "Cl_i in component Cl (mM)"
legend_constants[30] = "PCl in component Ito2 (L_per_F_ms)"
legend_states[20] = "AA in component Ito2 (dimensionless)"
legend_algebraic[53] = "Ito2_max in component Ito2 (uA_per_uF)"
legend_algebraic[13] = "AAss in component Ito2 (dimensionless)"
legend_constants[31] = "Kmto2 in component Ito2 (mM)"
legend_algebraic[87] = "ECl in component reversal_potentials (mV)"
legend_constants[32] = "GClb in component IClb (mS_per_uF)"
legend_constants[33] = "GNaL in component INal (mS_per_uF)"
legend_states[21] = "mL in component INal (dimensionless)"
legend_states[22] = "hL in component INal (dimensionless)"
legend_algebraic[14] = "amL in component INal (per_ms)"
legend_algebraic[28] = "bmL in component INal (per_ms)"
legend_algebraic[15] = "hLss in component INal (dimensionless)"
legend_states[23] = "K_i in component K (mM)"
legend_constants[34] = "prnak in component reversal_potentials (dimensionless)"
legend_states[24] = "Ca_jsr in component Ca (mM)"
legend_algebraic[61] = "Grel in component Irel (per_ms)"
legend_algebraic[34] = "dro_inf in component Irel (dimensionless)"
legend_constants[35] = "dtau_rel_max in component Irel (ms)"
legend_algebraic[60] = "dtau_rel in component Irel (ms)"
legend_algebraic[36] = "ross in component Irel (dimensionless)"
legend_algebraic[63] = "riss in component Irel (dimensionless)"
legend_algebraic[66] = "tauri in component Irel (ms)"
legend_algebraic[64] = "irelcicr in component Irel (mM_per_ms)"
legend_constants[36] = "CaMK0 in component Irel (dimensionless)"
legend_constants[37] = "Km in component Irel (mM)"
legend_constants[38] = "KmCaMK in component Irel (dimensionless)"
legend_algebraic[52] = "CaMKbound in component Irel (dimensionless)"
legend_states[25] = "CaMKtrap in component Irel (dimensionless)"
legend_states[26] = "ro in component Irel (dimensionless)"
legend_states[27] = "ri in component Irel (dimensionless)"
legend_algebraic[58] = "vg in component Irel (dimensionless)"
legend_algebraic[57] = "cafac in component Irel (dimensionless)"
legend_constants[39] = "dKmPLBmax in component Iup_Ileak (mM)"
legend_constants[40] = "dJupmax in component Iup_Ileak (dimensionless)"
legend_algebraic[67] = "dKmPLB in component Iup_Ileak (mM)"
legend_algebraic[69] = "dJup in component Iup_Ileak (dimensionless)"
legend_constants[41] = "iupmax in component Iup_Ileak (mM_per_ms)"
legend_constants[42] = "Kmup in component Iup_Ileak (mM)"
legend_constants[43] = "nsrmax in component Iup_Ileak (mM)"
legend_algebraic[71] = "iup in component Iup_Ileak (mM_per_ms)"
legend_algebraic[73] = "ileak in component Iup_Ileak (mM_per_ms)"
legend_states[28] = "Ca_nsr in component Ca (mM)"
legend_algebraic[76] = "idiff in component Idiff_Itr (mM_per_ms)"
legend_algebraic[75] = "itr in component Idiff_Itr (mM_per_ms)"
legend_algebraic[90] = "CTNaCl in component Na (mM_per_ms)"
legend_constants[44] = "CTNaClmax in component Na (mM_per_ms)"
legend_algebraic[91] = "CTKCl in component K (mM_per_ms)"
legend_constants[45] = "CTKClmax in component K (mM_per_ms)"
legend_constants[46] = "kmt in component Ca (mM)"
legend_constants[47] = "kmc in component Ca (mM)"
legend_constants[48] = "tbar in component Ca (mM)"
legend_constants[49] = "cbar in component Ca (mM)"
legend_constants[50] = "kmcsqn in component Ca (mM)"
legend_constants[51] = "csqnbar in component Ca (mM)"
legend_algebraic[78] = "bcsqn in component Ca (dimensionless)"
legend_algebraic[79] = "bmyo in component Ca (dimensionless)"
legend_constants[52] = "BSRmax in component Ca (mM)"
legend_constants[53] = "KmBSR in component Ca (mM)"
legend_constants[54] = "BSLmax in component Ca (mM)"
legend_constants[55] = "KmBSL in component Ca (mM)"
legend_algebraic[80] = "bss in component Ca (dimensionless)"
legend_rates[0] = "d/dt V in component cell (mV)"
legend_rates[1] = "d/dt H in component INa (dimensionless)"
legend_rates[2] = "d/dt m in component INa (dimensionless)"
legend_rates[3] = "d/dt J in component INa (dimensionless)"
legend_rates[5] = "d/dt d in component ICaL (dimensionless)"
legend_rates[6] = "d/dt dp in component ICaL (dimensionless)"
legend_rates[7] = "d/dt f in component ICaL (dimensionless)"
legend_rates[10] = "d/dt f2 in component ICaL (dimensionless)"
legend_rates[8] = "d/dt fca in component ICaL (dimensionless)"
legend_rates[9] = "d/dt fca2 in component ICaL (dimensionless)"
legend_rates[11] = "d/dt xr in component IKr (dimensionless)"
legend_rates[13] = "d/dt xs1 in component IKs (dimensionless)"
legend_rates[14] = "d/dt xs2 in component IKs (dimensionless)"
legend_rates[15] = "d/dt ydv in component Ito (dimensionless)"
legend_rates[16] = "d/dt ydv2 in component Ito (dimensionless)"
legend_rates[17] = "d/dt zdv in component Ito (dimensionless)"
legend_rates[20] = "d/dt AA in component Ito2 (dimensionless)"
legend_rates[21] = "d/dt mL in component INal (dimensionless)"
legend_rates[22] = "d/dt hL in component INal (dimensionless)"
legend_rates[26] = "d/dt ro in component Irel (dimensionless)"
legend_rates[27] = "d/dt ri in component Irel (dimensionless)"
legend_rates[25] = "d/dt CaMKtrap in component Irel (dimensionless)"
legend_rates[18] = "d/dt Na_i in component Na (mM)"
legend_rates[23] = "d/dt K_i in component K (mM)"
legend_rates[19] = "d/dt Cl_i in component Cl (mM)"
legend_rates[12] = "d/dt Ca_i in component Ca (mM)"
legend_rates[4] = "d/dt Ca_ss in component Ca (mM)"
legend_rates[28] = "d/dt Ca_nsr in component Ca (mM)"
legend_rates[24] = "d/dt Ca_jsr in component Ca (mM)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 96485
constants[1] = 5.4
constants[2] = 1.8
constants[3] = 140
constants[4] = 100
constants[5] = 0.0374358835078
constants[6] = 0
states[0] = -85.781844107117
constants[7] = 0.01
constants[8] = 0.0011
constants[9] = 0
constants[10] = 1e3
constants[11] = 3
constants[12] = -20
states[1] = 0.987317750543
states[2] = 0.001356538159
states[3] = 0.991924983076
states[4] = 0.00012271265
states[5] = 0.00000164013
states[6] = 8.98230672628
states[7] = 0.999961508634
states[8] = 0.97836624923
states[9] = 0.893052931249
states[10] = 0.992234519148
constants[13] = 2.43e-4
constants[14] = 1
constants[15] = 0.341
states[11] = 0.00000724074
states[12] = 0.00012131666
states[13] = 0.019883138161
states[14] = 0.019890650554
constants[16] = 0.095
states[15] = 0.013970786703
states[16] = 0.99996472752
states[17] = 0.829206149767
states[18] = 12.972433387269
constants[17] = 10
constants[18] = 1.5
constants[19] = 0.61875
constants[20] = 1.25e-4
constants[21] = 4.05
constants[22] = 0.27
constants[23] = 0.35
constants[24] = 12.3
constants[25] = 87.5
constants[26] = 0.0036
constants[27] = 1.3
constants[28] = 0.0575
constants[29] = 0.5e-3
states[19] = 15.59207157178
constants[30] = 4e-7
states[20] = 0.000816605172
constants[31] = 0.1502
constants[32] = 2.25e-4
constants[33] = 65e-4
states[21] = 0.001356538159
states[22] = 0.26130711759
states[23] = 135.469546216758
constants[34] = 0.01833
states[24] = 1.737580994071
constants[35] = 10
constants[36] = 0.05
constants[37] = 0.0015
constants[38] = 0.15
states[25] = 0.021123704774
states[26] = 0
states[27] = 0.862666650318
constants[39] = 0.00017
constants[40] = 0.75
constants[41] = 0.004375
constants[42] = 0.00092
constants[43] = 15
states[28] = 1.832822335168
constants[44] = 9.8443e-6
constants[45] = 7.0756e-6
constants[46] = 0.5e-3
constants[47] = 2.38e-3
constants[48] = 70e-3
constants[49] = 50e-3
constants[50] = 0.8
constants[51] = 10
constants[52] = 0.047
constants[53] = 0.00087
constants[54] = 1.124
constants[55] = 0.0087
constants[56] = 1000.00* pi*constants[8]*constants[8]*constants[7]
constants[57] = custom_piecewise([equal(constants[6] , 0.00000), 11.5000 , True, 4.00000*11.5000])
constants[58] = 0.0138542*(power(constants[1]/5.40000, 1.0/2))
constants[59] = (exp(constants[3]/67.3000)-1.00000)/7.00000
constants[60] = 2.00000* pi*constants[8]*constants[8]+2.00000* pi*constants[8]*constants[7]
constants[61] = constants[56]*0.260000
constants[62] = constants[56]*0.0600000
constants[63] = constants[60]*2.00000
constants[64] = constants[56]*0.680000
constants[65] = constants[56]*0.0552000
constants[66] = constants[56]*0.00480000
constants[67] = constants[56]*0.0200000
constants[68] = constants[63]/constants[0]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[7] = 9.00000-8.00000/(1.00000+exp(-(states[0]+65.0000)/3.40000))
rates[6] = (algebraic[7]-states[6])/10.0000
algebraic[13] = 1.00000/(1.00000+constants[31]/states[4])
rates[20] = (algebraic[13]-states[20])/1.00000
algebraic[15] = 1.00000/(1.00000+exp((states[0]+91.0000)/6.10000))
rates[22] = (algebraic[15]-states[22])/600.000
algebraic[2] = custom_piecewise([greater_equal(states[0] , -40.0000), 0.00000 , True, 0.135000*exp((80.0000+states[0])/-6.80000)])
algebraic[18] = custom_piecewise([greater_equal(states[0] , -40.0000), 1.00000/(0.130000*(1.00000+exp((states[0]+10.6600)/-11.1000))) , True, 3.56000*exp(0.0790000*states[0])+310000.*exp(0.350000*states[0])])
rates[1] = algebraic[2]*(1.00000-states[1])-algebraic[18]*states[1]
algebraic[1] = (0.320000*1.00000*(states[0]+47.1300))/(1.00000-exp(-0.100000*(states[0]+47.1300)))
algebraic[17] = 0.0800000*exp(-states[0]/11.0000)
rates[2] = algebraic[1]*(1.00000-states[2])-algebraic[17]*states[2]
algebraic[3] = custom_piecewise([greater_equal(states[0] , -40.0000), 0.00000 , True, ((-127140.*exp(0.244400*states[0])-3.47400e-05*exp(-0.0439100*states[0]))*1.00000*(states[0]+37.7800))/(1.00000+exp(0.311000*(states[0]+79.2300)))])
algebraic[19] = custom_piecewise([greater_equal(states[0] , -40.0000), (0.300000*exp(-2.53500e-07*states[0]))/(1.00000+exp(-0.100000*(states[0]+32.0000))) , True, (0.121200*exp(-0.0105200*states[0]))/(1.00000+exp(-0.137800*(states[0]+40.1400)))])
rates[3] = algebraic[3]*(1.00000-states[3])-algebraic[19]*states[3]
algebraic[4] = 1.00000/(1.00000+exp(-(states[0]-4.00000)/6.74000))
algebraic[20] = 0.590000+(0.800000*exp(0.0520000*(states[0]+13.0000)))/(1.00000+exp(0.132000*(states[0]+13.0000)))
rates[5] = (algebraic[4]-states[5])/algebraic[20]
algebraic[5] = 0.700000/(1.00000+exp((states[0]+17.1200)/7.00000))+0.300000
algebraic[21] = 1.00000/(0.241100*exp(-(power(0.0450000*(states[0]-9.69140), 2.00000)))+0.0529000)
rates[7] = (algebraic[5]-states[7])/algebraic[21]
algebraic[6] = 0.770000/(1.00000+exp((states[0]+17.1200)/7.00000))+0.230000
algebraic[22] = 1.00000/(0.0423000*exp(-(power(0.0590000*(states[0]-18.5726), 2.00000)))+0.00540000)
rates[10] = (algebraic[6]-states[10])/algebraic[22]
algebraic[8] = 1.00000/(1.00000+exp(-(states[0]+10.0850)/4.25000))
algebraic[23] = 1.00000/((0.000600000*(states[0]-1.73840))/(1.00000-exp(-0.136000*(states[0]-1.73840)))+(0.000300000*(states[0]+38.3608))/(exp(0.152200*(states[0]+38.3608))-1.00000))
rates[11] = (algebraic[8]-states[11])/algebraic[23]
algebraic[9] = 1.00000/(1.00000+exp(-(states[0]-10.5000)/24.7000))
algebraic[24] = 1.00000/((7.61000e-05*(states[0]+44.6000))/(1.00000-exp(-9.97000*(states[0]+44.6000)))+(0.000360000*(states[0]-0.550000))/(exp(0.128000*(states[0]-0.550000))-1.00000))
rates[13] = (algebraic[9]-states[13])/algebraic[24]
rates[14] = ((algebraic[9]-states[14])/algebraic[24])/2.00000
algebraic[10] = (25.0000*exp((states[0]-40.0000)/25.0000))/(1.00000+exp((states[0]-40.0000)/25.0000))
algebraic[25] = (25.0000*exp(-(states[0]+90.0000)/25.0000))/(1.00000+exp(-(states[0]+90.0000)/25.0000))
rates[15] = algebraic[10]*(1.00000-states[15])-algebraic[25]*states[15]
algebraic[11] = 0.0300000/(1.00000+exp((states[0]+60.0000)/5.00000))
algebraic[26] = (0.200000*exp((states[0]+25.0000)/5.00000))/(1.00000+exp((states[0]+25.0000)/5.00000))
rates[16] = algebraic[11]*(1.00000-states[16])-algebraic[26]*states[16]
algebraic[12] = 0.00260000/(1.00000+exp((states[0]+61.0000)/5.00000))
algebraic[27] = (0.100000*exp((states[0]+25.0000)/5.00000))/(1.00000+exp((states[0]+25.0000)/5.00000))
rates[17] = algebraic[12]*(1.00000-states[17])-algebraic[27]*states[17]
algebraic[14] = (0.320000*1.00000*(states[0]+47.1300))/(1.00000-exp(-0.100000*(states[0]+47.1300)))
algebraic[28] = 0.0800000*exp(-states[0]/11.0000)
rates[21] = algebraic[14]*(1.00000-states[21])-algebraic[28]*states[21]
algebraic[30] = (constants[13]*4.00000*(states[0]-15.0000)*constants[0]*constants[5]*(constants[14]*states[4]*exp(2.00000*(states[0]-15.0000)*constants[5])-constants[15]*constants[2]))/(exp(2.00000*(states[0]-15.0000)*constants[5])-1.00000)
algebraic[31] = custom_piecewise([equal(constants[6] , 0.00000), (power(states[5], states[6]))*states[7]*states[10]*states[8]*states[9]*algebraic[30] , True, states[5]*states[7]*states[10]*states[8]*states[9]*algebraic[30]])
algebraic[33] = 1.00000/(1.00000-algebraic[31]/0.0100000)
algebraic[35] = 300.000/(1.00000+exp((-algebraic[31]-0.175000)/0.0400000))+125.000
rates[9] = (algebraic[33]-states[9])/algebraic[35]
algebraic[34] = (power(states[24], 1.90000))/(power(states[24], 1.90000)+power((49.2800*states[4])/(states[4]+0.00280000), 1.90000))
algebraic[36] = algebraic[34]/(power(1.00000/algebraic[31], 2.00000)+1.00000)
rates[26] = (algebraic[36]-states[26])/3.00000
algebraic[52] = (constants[36]*(1.00000-states[25]))/(1.00000+constants[37]/states[4])
algebraic[54] = algebraic[52]+states[25]
rates[25] = 0.0500000*algebraic[54]*(algebraic[54]-states[25])-0.000680000*states[25]
algebraic[32] = 0.300000/(1.00000-algebraic[31]/0.0500000)+0.550000/(1.00000+states[4]/0.00300000)+0.150000
algebraic[56] = (10.0000*algebraic[54])/(0.150000+algebraic[54])+1.00000/(1.00000+states[4]/0.00300000)+0.500000
rates[8] = (algebraic[32]-states[8])/algebraic[56]
algebraic[57] = 1.00000/(1.00000+exp((algebraic[31]+0.0500000)/0.0150000))
algebraic[63] = 1.00000/(1.00000+exp(((states[4]-0.000400000)+0.00200000*algebraic[57])/2.50000e-05))
algebraic[60] = (constants[35]*algebraic[54])/(constants[38]+algebraic[54])
algebraic[66] = 3.00000+algebraic[60]+(350.000-algebraic[60])/(1.00000+exp(((states[4]-0.00300000)+0.00300000*algebraic[57])/0.000200000))
rates[27] = (algebraic[63]-states[27])/algebraic[66]
algebraic[67] = (constants[39]*algebraic[54])/(constants[38]+algebraic[54])
algebraic[69] = (constants[40]*algebraic[54])/(constants[38]+algebraic[54])
algebraic[71] = ((algebraic[69]+1.00000)*constants[41]*states[12])/((states[12]+constants[42])-algebraic[67])
algebraic[73] = (constants[41]*states[28])/constants[43]
algebraic[75] = (states[28]-states[24])/120.000
rates[28] = (algebraic[71]-(algebraic[75]*constants[66])/constants[65])-algebraic[73]
algebraic[49] = (constants[28]*states[12])/(constants[29]+states[12])
algebraic[50] = (1.99508e-07*4.00000*states[0]*constants[0]*constants[5]*(states[12]*exp(2.00000*states[0]*constants[5])-0.341000*constants[2]))/(exp(2.00000*states[0]*constants[5])-1.00000)
algebraic[42] = 1.50000*states[12]
algebraic[43] = 1.00000/(1.00000+power(constants[20]/algebraic[42], 2.00000))
algebraic[44] = (power(states[18], 3.00000))*constants[2]*exp(constants[23]*states[0]*constants[5])-(power(constants[3], 3.00000))*algebraic[42]*exp((constants[23]-1.00000)*states[0]*constants[5])
algebraic[45] = 1.00000+constants[22]*exp((constants[23]-1.00000)*states[0]*constants[5])
algebraic[46] = constants[27]*(power(states[18], 3.00000))+(power(constants[25], 3.00000))*algebraic[42]+(power(constants[24], 3.00000))*constants[2]*(1.00000+algebraic[42]/constants[26])
algebraic[47] = constants[26]*(power(constants[3], 3.00000))*(1.00000+power(states[18]/constants[24], 3.00000))+(power(states[18], 3.00000))*constants[2]+(power(constants[3], 3.00000))*algebraic[42]
algebraic[48] = (constants[21]*algebraic[43]*algebraic[44])/(algebraic[45]*(algebraic[46]+algebraic[47]))
algebraic[76] = (states[4]-states[12])/0.200000
algebraic[79] = 1.00000/(1.00000+(constants[49]*constants[47])/(power(states[12]+constants[47], 2.00000))+(constants[46]*constants[48])/(power(states[12]+constants[46], 2.00000)))
rates[12] = algebraic[79]*((-((algebraic[50]+algebraic[49])-2.00000*algebraic[48])*constants[68])/(constants[64]*2.00000)+((algebraic[73]-algebraic[71])*constants[65])/constants[64]+(algebraic[76]*constants[67])/constants[64])
algebraic[58] = custom_piecewise([equal(constants[6] , 0.00000), 1.00000/(1.00000+exp((algebraic[30]+13.0000)/5.00000)) , True, 1.00000])
algebraic[61] = 3000.00*algebraic[58]
algebraic[64] = algebraic[61]*states[26]*states[27]*(states[24]-states[4])
algebraic[80] = 1.00000/(1.00000+(constants[52]*constants[53])/(power(constants[53]+states[4], 2.00000))+(constants[54]*constants[55])/(power(constants[55]+states[4], 2.00000)))
rates[4] = algebraic[80]*(((-algebraic[31]*constants[68])/(constants[67]*2.00000)+(algebraic[64]*constants[66])/constants[67])-algebraic[76])
algebraic[78] = 1.00000/(1.00000+(constants[50]*constants[51])/(power(states[24]+constants[50], 2.00000)))
rates[24] = algebraic[78]*(algebraic[75]-algebraic[64])
algebraic[51] = (algebraic[31]+algebraic[50]+algebraic[49])-2.00000*algebraic[48]
algebraic[59] = log(constants[3]/states[18])/constants[5]
algebraic[29] = constants[57]*states[2]*states[2]*states[2]*states[1]*states[3]
algebraic[62] = algebraic[29]*(states[0]-algebraic[59])
algebraic[40] = 1.00000/(1.00000+0.124500*exp(-0.100000*states[0]*constants[5])+0.0365000*constants[59]*exp(-states[0]*constants[5]))
algebraic[41] = (((constants[19]*algebraic[40]*1.00000)/(1.00000+power(constants[17]/states[18], 2.00000)))*constants[1])/(constants[1]+constants[18])
algebraic[65] = constants[33]*(power(states[21], 3.00000))*states[22]*(states[0]-algebraic[59])
algebraic[68] = algebraic[62]+3.00000*algebraic[48]+3.00000*algebraic[41]+algebraic[65]
algebraic[70] = log(constants[1]/states[23])/constants[5]
algebraic[72] = 1.02000/(1.00000+exp(0.238500*((states[0]-algebraic[70])-59.2150)))
algebraic[74] = (0.491240*exp(0.0803200*((states[0]-algebraic[70])+5.47600))+1.00000*exp(0.0617500*((states[0]-algebraic[70])-594.310)))/(1.00000+exp(-0.514300*((states[0]-algebraic[70])+4.75300)))
algebraic[77] = ((0.500000*(power(constants[1]/5.40000, 1.0/2))*algebraic[72])/(algebraic[72]+algebraic[74]))*(states[0]-algebraic[70])
algebraic[83] = (0.00276000*(states[0]-algebraic[70]))/(1.00000+exp((7.48800-states[0])/5.98000))
algebraic[38] = 0.0224077*(1.00000+0.600000/(1.00000+power(3.80000e-05/states[12], 1.40000)))
algebraic[84] = log((constants[1]+constants[34]*constants[3])/(states[23]+constants[34]*states[18]))/constants[5]
algebraic[85] = algebraic[38]*states[13]*states[14]*(states[0]-algebraic[84])
algebraic[37] = 1.00000/(1.00000+exp((states[0]+10.0000)/15.4000))
algebraic[81] = constants[58]*states[11]*algebraic[37]*(states[0]-algebraic[70])
algebraic[39] = exp(states[0]/300.000)
algebraic[82] = constants[16]*(power(states[15], 3.00000))*states[16]*states[17]*algebraic[39]*(states[0]-algebraic[70])
algebraic[0] = floor(voi/constants[10])*constants[10]
algebraic[16] = custom_piecewise([greater_equal(voi-algebraic[0] , constants[9]) & less_equal(voi-algebraic[0] , constants[9]+constants[11]), constants[12] , True, 0.00000])
algebraic[86] = ((algebraic[81]+algebraic[85]+algebraic[77]+algebraic[83])-2.00000*algebraic[41])+algebraic[82]+0.500000*algebraic[16]
algebraic[53] = (constants[30]*states[0]*constants[0]*constants[5]*(states[19]-constants[4]*exp(states[0]*constants[5])))/(1.00000-exp(states[0]*constants[5]))
algebraic[55] = algebraic[53]*states[20]
algebraic[87] = -log(constants[4]/states[19])/constants[5]
algebraic[88] = constants[32]*(states[0]-algebraic[87])
algebraic[89] = algebraic[88]+algebraic[55]+0.500000*algebraic[16]
rates[0] = -(algebraic[68]+algebraic[86]+algebraic[51]+algebraic[89])
algebraic[90] = (constants[44]*(power(algebraic[59]-algebraic[87], 4.00000)))/(power(algebraic[59]-algebraic[87], 4.00000)+power(87.8251, 4.00000))
rates[18] = (-algebraic[68]*constants[68])/constants[64]+algebraic[90]
algebraic[91] = (constants[45]*(algebraic[70]-algebraic[87]))/((algebraic[70]-algebraic[87])+87.8251)
rates[23] = (-algebraic[86]*constants[68])/constants[64]+algebraic[91]
rates[19] = (algebraic[89]*constants[68])/constants[64]+algebraic[90]+algebraic[91]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[7] = 9.00000-8.00000/(1.00000+exp(-(states[0]+65.0000)/3.40000))
algebraic[13] = 1.00000/(1.00000+constants[31]/states[4])
algebraic[15] = 1.00000/(1.00000+exp((states[0]+91.0000)/6.10000))
algebraic[2] = custom_piecewise([greater_equal(states[0] , -40.0000), 0.00000 , True, 0.135000*exp((80.0000+states[0])/-6.80000)])
algebraic[18] = custom_piecewise([greater_equal(states[0] , -40.0000), 1.00000/(0.130000*(1.00000+exp((states[0]+10.6600)/-11.1000))) , True, 3.56000*exp(0.0790000*states[0])+310000.*exp(0.350000*states[0])])
algebraic[1] = (0.320000*1.00000*(states[0]+47.1300))/(1.00000-exp(-0.100000*(states[0]+47.1300)))
algebraic[17] = 0.0800000*exp(-states[0]/11.0000)
algebraic[3] = custom_piecewise([greater_equal(states[0] , -40.0000), 0.00000 , True, ((-127140.*exp(0.244400*states[0])-3.47400e-05*exp(-0.0439100*states[0]))*1.00000*(states[0]+37.7800))/(1.00000+exp(0.311000*(states[0]+79.2300)))])
algebraic[19] = custom_piecewise([greater_equal(states[0] , -40.0000), (0.300000*exp(-2.53500e-07*states[0]))/(1.00000+exp(-0.100000*(states[0]+32.0000))) , True, (0.121200*exp(-0.0105200*states[0]))/(1.00000+exp(-0.137800*(states[0]+40.1400)))])
algebraic[4] = 1.00000/(1.00000+exp(-(states[0]-4.00000)/6.74000))
algebraic[20] = 0.590000+(0.800000*exp(0.0520000*(states[0]+13.0000)))/(1.00000+exp(0.132000*(states[0]+13.0000)))
algebraic[5] = 0.700000/(1.00000+exp((states[0]+17.1200)/7.00000))+0.300000
algebraic[21] = 1.00000/(0.241100*exp(-(power(0.0450000*(states[0]-9.69140), 2.00000)))+0.0529000)
algebraic[6] = 0.770000/(1.00000+exp((states[0]+17.1200)/7.00000))+0.230000
algebraic[22] = 1.00000/(0.0423000*exp(-(power(0.0590000*(states[0]-18.5726), 2.00000)))+0.00540000)
algebraic[8] = 1.00000/(1.00000+exp(-(states[0]+10.0850)/4.25000))
algebraic[23] = 1.00000/((0.000600000*(states[0]-1.73840))/(1.00000-exp(-0.136000*(states[0]-1.73840)))+(0.000300000*(states[0]+38.3608))/(exp(0.152200*(states[0]+38.3608))-1.00000))
algebraic[9] = 1.00000/(1.00000+exp(-(states[0]-10.5000)/24.7000))
algebraic[24] = 1.00000/((7.61000e-05*(states[0]+44.6000))/(1.00000-exp(-9.97000*(states[0]+44.6000)))+(0.000360000*(states[0]-0.550000))/(exp(0.128000*(states[0]-0.550000))-1.00000))
algebraic[10] = (25.0000*exp((states[0]-40.0000)/25.0000))/(1.00000+exp((states[0]-40.0000)/25.0000))
algebraic[25] = (25.0000*exp(-(states[0]+90.0000)/25.0000))/(1.00000+exp(-(states[0]+90.0000)/25.0000))
algebraic[11] = 0.0300000/(1.00000+exp((states[0]+60.0000)/5.00000))
algebraic[26] = (0.200000*exp((states[0]+25.0000)/5.00000))/(1.00000+exp((states[0]+25.0000)/5.00000))
algebraic[12] = 0.00260000/(1.00000+exp((states[0]+61.0000)/5.00000))
algebraic[27] = (0.100000*exp((states[0]+25.0000)/5.00000))/(1.00000+exp((states[0]+25.0000)/5.00000))
algebraic[14] = (0.320000*1.00000*(states[0]+47.1300))/(1.00000-exp(-0.100000*(states[0]+47.1300)))
algebraic[28] = 0.0800000*exp(-states[0]/11.0000)
algebraic[30] = (constants[13]*4.00000*(states[0]-15.0000)*constants[0]*constants[5]*(constants[14]*states[4]*exp(2.00000*(states[0]-15.0000)*constants[5])-constants[15]*constants[2]))/(exp(2.00000*(states[0]-15.0000)*constants[5])-1.00000)
algebraic[31] = custom_piecewise([equal(constants[6] , 0.00000), (power(states[5], states[6]))*states[7]*states[10]*states[8]*states[9]*algebraic[30] , True, states[5]*states[7]*states[10]*states[8]*states[9]*algebraic[30]])
algebraic[33] = 1.00000/(1.00000-algebraic[31]/0.0100000)
algebraic[35] = 300.000/(1.00000+exp((-algebraic[31]-0.175000)/0.0400000))+125.000
algebraic[34] = (power(states[24], 1.90000))/(power(states[24], 1.90000)+power((49.2800*states[4])/(states[4]+0.00280000), 1.90000))
algebraic[36] = algebraic[34]/(power(1.00000/algebraic[31], 2.00000)+1.00000)
algebraic[52] = (constants[36]*(1.00000-states[25]))/(1.00000+constants[37]/states[4])
algebraic[54] = algebraic[52]+states[25]
algebraic[32] = 0.300000/(1.00000-algebraic[31]/0.0500000)+0.550000/(1.00000+states[4]/0.00300000)+0.150000
algebraic[56] = (10.0000*algebraic[54])/(0.150000+algebraic[54])+1.00000/(1.00000+states[4]/0.00300000)+0.500000
algebraic[57] = 1.00000/(1.00000+exp((algebraic[31]+0.0500000)/0.0150000))
algebraic[63] = 1.00000/(1.00000+exp(((states[4]-0.000400000)+0.00200000*algebraic[57])/2.50000e-05))
algebraic[60] = (constants[35]*algebraic[54])/(constants[38]+algebraic[54])
algebraic[66] = 3.00000+algebraic[60]+(350.000-algebraic[60])/(1.00000+exp(((states[4]-0.00300000)+0.00300000*algebraic[57])/0.000200000))
algebraic[67] = (constants[39]*algebraic[54])/(constants[38]+algebraic[54])
algebraic[69] = (constants[40]*algebraic[54])/(constants[38]+algebraic[54])
algebraic[71] = ((algebraic[69]+1.00000)*constants[41]*states[12])/((states[12]+constants[42])-algebraic[67])
algebraic[73] = (constants[41]*states[28])/constants[43]
algebraic[75] = (states[28]-states[24])/120.000
algebraic[49] = (constants[28]*states[12])/(constants[29]+states[12])
algebraic[50] = (1.99508e-07*4.00000*states[0]*constants[0]*constants[5]*(states[12]*exp(2.00000*states[0]*constants[5])-0.341000*constants[2]))/(exp(2.00000*states[0]*constants[5])-1.00000)
algebraic[42] = 1.50000*states[12]
algebraic[43] = 1.00000/(1.00000+power(constants[20]/algebraic[42], 2.00000))
algebraic[44] = (power(states[18], 3.00000))*constants[2]*exp(constants[23]*states[0]*constants[5])-(power(constants[3], 3.00000))*algebraic[42]*exp((constants[23]-1.00000)*states[0]*constants[5])
algebraic[45] = 1.00000+constants[22]*exp((constants[23]-1.00000)*states[0]*constants[5])
algebraic[46] = constants[27]*(power(states[18], 3.00000))+(power(constants[25], 3.00000))*algebraic[42]+(power(constants[24], 3.00000))*constants[2]*(1.00000+algebraic[42]/constants[26])
algebraic[47] = constants[26]*(power(constants[3], 3.00000))*(1.00000+power(states[18]/constants[24], 3.00000))+(power(states[18], 3.00000))*constants[2]+(power(constants[3], 3.00000))*algebraic[42]
algebraic[48] = (constants[21]*algebraic[43]*algebraic[44])/(algebraic[45]*(algebraic[46]+algebraic[47]))
algebraic[76] = (states[4]-states[12])/0.200000
algebraic[79] = 1.00000/(1.00000+(constants[49]*constants[47])/(power(states[12]+constants[47], 2.00000))+(constants[46]*constants[48])/(power(states[12]+constants[46], 2.00000)))
algebraic[58] = custom_piecewise([equal(constants[6] , 0.00000), 1.00000/(1.00000+exp((algebraic[30]+13.0000)/5.00000)) , True, 1.00000])
algebraic[61] = 3000.00*algebraic[58]
algebraic[64] = algebraic[61]*states[26]*states[27]*(states[24]-states[4])
algebraic[80] = 1.00000/(1.00000+(constants[52]*constants[53])/(power(constants[53]+states[4], 2.00000))+(constants[54]*constants[55])/(power(constants[55]+states[4], 2.00000)))
algebraic[78] = 1.00000/(1.00000+(constants[50]*constants[51])/(power(states[24]+constants[50], 2.00000)))
algebraic[51] = (algebraic[31]+algebraic[50]+algebraic[49])-2.00000*algebraic[48]
algebraic[59] = log(constants[3]/states[18])/constants[5]
algebraic[29] = constants[57]*states[2]*states[2]*states[2]*states[1]*states[3]
algebraic[62] = algebraic[29]*(states[0]-algebraic[59])
algebraic[40] = 1.00000/(1.00000+0.124500*exp(-0.100000*states[0]*constants[5])+0.0365000*constants[59]*exp(-states[0]*constants[5]))
algebraic[41] = (((constants[19]*algebraic[40]*1.00000)/(1.00000+power(constants[17]/states[18], 2.00000)))*constants[1])/(constants[1]+constants[18])
algebraic[65] = constants[33]*(power(states[21], 3.00000))*states[22]*(states[0]-algebraic[59])
algebraic[68] = algebraic[62]+3.00000*algebraic[48]+3.00000*algebraic[41]+algebraic[65]
algebraic[70] = log(constants[1]/states[23])/constants[5]
algebraic[72] = 1.02000/(1.00000+exp(0.238500*((states[0]-algebraic[70])-59.2150)))
algebraic[74] = (0.491240*exp(0.0803200*((states[0]-algebraic[70])+5.47600))+1.00000*exp(0.0617500*((states[0]-algebraic[70])-594.310)))/(1.00000+exp(-0.514300*((states[0]-algebraic[70])+4.75300)))
algebraic[77] = ((0.500000*(power(constants[1]/5.40000, 1.0/2))*algebraic[72])/(algebraic[72]+algebraic[74]))*(states[0]-algebraic[70])
algebraic[83] = (0.00276000*(states[0]-algebraic[70]))/(1.00000+exp((7.48800-states[0])/5.98000))
algebraic[38] = 0.0224077*(1.00000+0.600000/(1.00000+power(3.80000e-05/states[12], 1.40000)))
algebraic[84] = log((constants[1]+constants[34]*constants[3])/(states[23]+constants[34]*states[18]))/constants[5]
algebraic[85] = algebraic[38]*states[13]*states[14]*(states[0]-algebraic[84])
algebraic[37] = 1.00000/(1.00000+exp((states[0]+10.0000)/15.4000))
algebraic[81] = constants[58]*states[11]*algebraic[37]*(states[0]-algebraic[70])
algebraic[39] = exp(states[0]/300.000)
algebraic[82] = constants[16]*(power(states[15], 3.00000))*states[16]*states[17]*algebraic[39]*(states[0]-algebraic[70])
algebraic[0] = floor(voi/constants[10])*constants[10]
algebraic[16] = custom_piecewise([greater_equal(voi-algebraic[0] , constants[9]) & less_equal(voi-algebraic[0] , constants[9]+constants[11]), constants[12] , True, 0.00000])
algebraic[86] = ((algebraic[81]+algebraic[85]+algebraic[77]+algebraic[83])-2.00000*algebraic[41])+algebraic[82]+0.500000*algebraic[16]
algebraic[53] = (constants[30]*states[0]*constants[0]*constants[5]*(states[19]-constants[4]*exp(states[0]*constants[5])))/(1.00000-exp(states[0]*constants[5]))
algebraic[55] = algebraic[53]*states[20]
algebraic[87] = -log(constants[4]/states[19])/constants[5]
algebraic[88] = constants[32]*(states[0]-algebraic[87])
algebraic[89] = algebraic[88]+algebraic[55]+0.500000*algebraic[16]
algebraic[90] = (constants[44]*(power(algebraic[59]-algebraic[87], 4.00000)))/(power(algebraic[59]-algebraic[87], 4.00000)+power(87.8251, 4.00000))
algebraic[91] = (constants[45]*(algebraic[70]-algebraic[87]))/((algebraic[70]-algebraic[87])+87.8251)
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)