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 = 82
sizeStates = 22
sizeConstants = 83
from math import *
from numpy import *
def createLegends():
legend_states = [""] * sizeStates
legend_rates = [""] * sizeStates
legend_algebraic = [""] * sizeAlgebraic
legend_voi = ""
legend_constants = [""] * sizeConstants
legend_constants[0] = "I_hold in component interface (pA_per_pF)"
legend_constants[1] = "I_test in component interface (pA_per_pF)"
legend_constants[2] = "test_start in component interface (msec)"
legend_constants[3] = "test_end in component interface (msec)"
legend_algebraic[0] = "Ist in component interface (pA_per_pF)"
legend_voi = "time in component environment (msec)"
legend_algebraic[79] = "I_tot in component membrane_potential (pA_per_pF)"
legend_algebraic[61] = "I_Ca_tot in component membrane_potential (pA_per_pF)"
legend_states[0] = "v in component membrane_potential (mV)"
legend_constants[67] = "Cm in component parameters (uF_per_cm2)"
legend_algebraic[42] = "ina in component I_Na (pA_per_pF)"
legend_algebraic[49] = "ical in component I_CaL (pA_per_pF)"
legend_algebraic[51] = "icat in component I_CaT (pA_per_pF)"
legend_algebraic[52] = "ib in component I_b (pA_per_pF)"
legend_algebraic[53] = "ik1 in component I_K1 (pA_per_pF)"
legend_algebraic[54] = "ik2 in component I_K2 (pA_per_pF)"
legend_algebraic[55] = "ika in component I_Ka (pA_per_pF)"
legend_algebraic[56] = "iBKa in component I_BKa (pA_per_pF)"
legend_algebraic[57] = "iBKab in component I_BKab (pA_per_pF)"
legend_algebraic[58] = "ih in component I_h (pA_per_pF)"
legend_algebraic[59] = "icl in component I_Cl (pA_per_pF)"
legend_algebraic[63] = "insna in component I_ns (pA_per_pF)"
legend_algebraic[60] = "insca in component I_ns (pA_per_pF)"
legend_algebraic[65] = "insk in component I_ns (pA_per_pF)"
legend_algebraic[67] = "inak in component I_NaK (pA_per_pF)"
legend_algebraic[76] = "inaca in component I_NaCa (pA_per_pF)"
legend_algebraic[80] = "J_tot in component Ca_Concentrations (mM_per_msec)"
legend_algebraic[62] = "J_Ca_mem in component Ca_Concentrations (mM_per_msec)"
legend_states[1] = "cai in component Ca_Concentrations (mM)"
legend_algebraic[75] = "jnaca in component J_NaCa (mM_per_msec)"
legend_algebraic[77] = "jpmca in component J_PMCA (mM_per_msec)"
legend_constants[62] = "buff in component parameters (dimensionless)"
legend_constants[63] = "AV in component parameters (cm2_per_uL)"
legend_constants[64] = "zca in component parameters (dimensionless)"
legend_constants[66] = "frdy in component parameters (coulomb_per_mole)"
legend_algebraic[64] = "jcamem_plot in component Ca_Concentrations (M_per_msec)"
legend_algebraic[81] = "jpmca_plot in component Ca_Concentrations (M_per_msec)"
legend_algebraic[78] = "jnaca_plot in component Ca_Concentrations (M_per_msec)"
legend_constants[4] = "conversion in component Ca_Concentrations (mM_to_M)"
legend_constants[11] = "ki in component parameters (mM)"
legend_constants[53] = "nai in component parameters (mM)"
legend_constants[56] = "cli in component parameters (mM)"
legend_constants[57] = "ko in component parameters (mM)"
legend_constants[12] = "cao in component parameters (mM)"
legend_constants[58] = "nao in component parameters (mM)"
legend_constants[60] = "clo in component parameters (mM)"
legend_constants[13] = "mgo in component parameters (mM)"
legend_constants[14] = "zna in component parameters (dimensionless)"
legend_constants[15] = "zk in component parameters (dimensionless)"
legend_constants[65] = "R in component parameters (joule_per_kelvin_per_kilomole)"
legend_constants[68] = "temp in component parameters (kelvin)"
legend_constants[16] = "gna in component parameters (nS_per_pF)"
legend_constants[17] = "gcal in component parameters (nS_per_pF)"
legend_constants[18] = "ecal in component parameters (mV)"
legend_constants[19] = "kmca in component parameters (mM)"
legend_constants[20] = "gcat in component parameters (nS_per_pF)"
legend_constants[21] = "ecat in component parameters (mV)"
legend_constants[22] = "gkca in component parameters (nS_per_pF)"
legend_constants[23] = "gb in component parameters (nS_per_pF)"
legend_constants[24] = "gk1 in component parameters (nS_per_pF)"
legend_constants[25] = "gk2 in component parameters (nS_per_pF)"
legend_constants[26] = "gbka in component parameters (dimensionless)"
legend_constants[27] = "gbkab in component parameters (dimensionless)"
legend_constants[28] = "gka in component parameters (nS_per_pF)"
legend_constants[29] = "gcl in component parameters (nS_per_pF)"
legend_constants[30] = "gh in component parameters (nS_per_pF)"
legend_constants[31] = "gns in component parameters (nS_per_pF)"
legend_constants[32] = "PnsK in component parameters (dimensionless)"
legend_constants[33] = "PnsNa in component parameters (dimensionless)"
legend_constants[34] = "PnsCa in component parameters (dimensionless)"
legend_constants[35] = "PnsCs in component parameters (dimensionless)"
legend_constants[36] = "gnsCa in component parameters (dimensionless)"
legend_constants[37] = "gnsNa in component parameters (dimensionless)"
legend_constants[38] = "gnsK in component parameters (dimensionless)"
legend_constants[39] = "gnsCs in component parameters (dimensionless)"
legend_constants[69] = "ginak in component parameters (pA_per_pF)"
legend_constants[74] = "nakKmko in component parameters (mM)"
legend_constants[76] = "nakKmnai in component parameters (mM)"
legend_constants[70] = "PK in component parameters (dimensionless)"
legend_constants[75] = "PNa in component parameters (dimensionless)"
legend_constants[40] = "Jpmca in component parameters (mM_per_msec)"
legend_constants[41] = "Kmpmca in component parameters (mM)"
legend_constants[42] = "npmca in component parameters (dimensionless)"
legend_constants[78] = "Jnaca in component parameters (mM_per_msec)"
legend_constants[43] = "Kmallo in component parameters (mM)"
legend_constants[44] = "nallo in component parameters (dimensionless)"
legend_constants[79] = "ksat in component parameters (dimensionless)"
legend_constants[80] = "xgamma in component parameters (dimensionless)"
legend_constants[45] = "Kmnai in component parameters (mM)"
legend_constants[46] = "Kmcai in component parameters (mM)"
legend_constants[47] = "Kmnao in component parameters (mM)"
legend_constants[48] = "Kmcao in component parameters (mM)"
legend_constants[49] = "Fmax in component parameters (uN)"
legend_constants[50] = "FKm in component parameters (nM)"
legend_constants[51] = "Fn in component parameters (dimensionless)"
legend_algebraic[18] = "vFRT in component parameters (dimensionless)"
legend_constants[71] = "ena in component parameters (mV)"
legend_constants[72] = "ek in component parameters (mV)"
legend_constants[77] = "eh in component parameters (mV)"
legend_constants[73] = "ecl in component parameters (mV)"
legend_algebraic[37] = "enscc in component parameters (mV)"
legend_algebraic[1] = "wss in component Ca_dependent_Force (dimensionless)"
legend_algebraic[19] = "wtc in component Ca_dependent_Force (msec)"
legend_constants[5] = "conversion in component Ca_dependent_Force (nM_to_mM)"
legend_algebraic[2] = "Force in component Ca_dependent_Force (uN)"
legend_states[2] = "w in component Ca_dependent_Force (dimensionless)"
legend_algebraic[3] = "mss in component I_Na (dimensionless)"
legend_algebraic[4] = "hss in component I_Na (dimensionless)"
legend_algebraic[20] = "mtc in component I_Na (msec)"
legend_algebraic[21] = "htc in component I_Na (msec)"
legend_states[3] = "m in component I_Na (dimensionless)"
legend_states[4] = "h in component I_Na (dimensionless)"
legend_algebraic[5] = "dss in component I_CaL (dimensionless)"
legend_algebraic[6] = "fss in component I_CaL (dimensionless)"
legend_algebraic[47] = "fca in component I_CaL (dimensionless)"
legend_algebraic[22] = "dtc in component I_CaL (msec)"
legend_constants[52] = "f1tc in component I_CaL (msec)"
legend_algebraic[23] = "f2tc in component I_CaL (msec)"
legend_states[5] = "d in component I_CaL (dimensionless)"
legend_states[6] = "f1 in component I_CaL (dimensionless)"
legend_states[7] = "f2 in component I_CaL (dimensionless)"
legend_algebraic[7] = "bss in component I_CaT (dimensionless)"
legend_algebraic[8] = "gss in component I_CaT (dimensionless)"
legend_algebraic[24] = "btc in component I_CaT (msec)"
legend_algebraic[25] = "gtc in component I_CaT (msec)"
legend_states[8] = "b in component I_CaT (dimensionless)"
legend_states[9] = "g in component I_CaT (dimensionless)"
legend_algebraic[9] = "qss in component I_K1 (dimensionless)"
legend_algebraic[10] = "rss in component I_K1 (dimensionless)"
legend_algebraic[26] = "qtc in component I_K1 (msec)"
legend_algebraic[27] = "r1tc in component I_K1 (msec)"
legend_algebraic[28] = "r2tc in component I_K1 (msec)"
legend_states[10] = "q in component I_K1 (dimensionless)"
legend_states[11] = "r1 in component I_K1 (dimensionless)"
legend_states[12] = "r2 in component I_K1 (dimensionless)"
legend_algebraic[11] = "pss in component I_K2 (dimensionless)"
legend_algebraic[12] = "kss in component I_K2 (dimensionless)"
legend_algebraic[29] = "ptc in component I_K2 (msec)"
legend_algebraic[30] = "k1tc in component I_K2 (msec)"
legend_algebraic[31] = "k2tc in component I_K2 (msec)"
legend_states[13] = "p in component I_K2 (dimensionless)"
legend_states[14] = "k1 in component I_K2 (dimensionless)"
legend_states[15] = "k2 in component I_K2 (dimensionless)"
legend_algebraic[13] = "sss in component I_Ka (dimensionless)"
legend_algebraic[14] = "xss in component I_Ka (dimensionless)"
legend_algebraic[32] = "stc in component I_Ka (msec)"
legend_algebraic[33] = "xtc in component I_Ka (msec)"
legend_states[16] = "s in component I_Ka (dimensionless)"
legend_states[17] = "x in component I_Ka (dimensionless)"
legend_algebraic[15] = "xass_z in component I_BKa (dimensionless)"
legend_algebraic[34] = "xass_vh in component I_BKa (mV)"
legend_constants[6] = "conversion in component I_BKa (mM_to_M)"
legend_algebraic[38] = "xass in component I_BKa (dimensionless)"
legend_algebraic[43] = "xatc in component I_BKa (msec)"
legend_states[18] = "xa in component I_BKa (dimensionless)"
legend_algebraic[16] = "xabss_z in component I_BKab (dimensionless)"
legend_algebraic[35] = "xabss_vh in component I_BKab (mV)"
legend_constants[7] = "conversion in component I_BKab (mM_to_M)"
legend_algebraic[39] = "xabss in component I_BKab (dimensionless)"
legend_algebraic[44] = "xabtc in component I_BKab (msec)"
legend_states[19] = "xab in component I_BKab (dimensionless)"
legend_algebraic[17] = "yss in component I_h (dimensionless)"
legend_algebraic[45] = "ytc in component I_h (msec)"
legend_algebraic[36] = "ya in component I_h (per_msec)"
legend_algebraic[40] = "yb in component I_h (per_msec)"
legend_states[20] = "y in component I_h (dimensionless)"
legend_algebraic[48] = "css in component I_Cl (dimensionless)"
legend_algebraic[50] = "ctc in component I_Cl (msec)"
legend_algebraic[41] = "K1cl in component I_Cl (mM)"
legend_algebraic[46] = "K2cl in component I_Cl (dimensionless)"
legend_states[21] = "c in component I_Cl (dimensionless)"
legend_constants[54] = "fmg in component I_ns (dimensionless)"
legend_constants[61] = "gs_nao in component I_ns (dimensionless)"
legend_constants[55] = "gs_cao in component I_ns (dimensionless)"
legend_constants[59] = "gs_ko in component I_ns (dimensionless)"
legend_constants[8] = "tinyamount in component I_ns (mM)"
legend_algebraic[66] = "fnak in component I_NaK (dimensionless)"
legend_constants[81] = "knak in component I_NaK (dimensionless)"
legend_constants[82] = "nnak in component I_NaK (dimensionless)"
legend_constants[9] = "inaca_sign in component I_NaCa (dimensionless)"
legend_algebraic[68] = "f1naca in component J_NaCa (dimensionless)"
legend_algebraic[69] = "f2naca in component J_NaCa (dimensionless)"
legend_algebraic[70] = "fallo in component J_NaCa (dimensionless)"
legend_algebraic[71] = "naca_Eup in component J_NaCa (mM4)"
legend_algebraic[72] = "naca_Ed1 in component J_NaCa (dimensionless)"
legend_algebraic[73] = "naca_Ed2 in component J_NaCa (mM4)"
legend_algebraic[74] = "naca_Ed3 in component J_NaCa (mM4)"
legend_constants[10] = "jnaca_sign in component J_NaCa (dimensionless)"
legend_rates[0] = "d/dt v in component membrane_potential (mV)"
legend_rates[1] = "d/dt cai in component Ca_Concentrations (mM)"
legend_rates[2] = "d/dt w in component Ca_dependent_Force (dimensionless)"
legend_rates[3] = "d/dt m in component I_Na (dimensionless)"
legend_rates[4] = "d/dt h in component I_Na (dimensionless)"
legend_rates[5] = "d/dt d in component I_CaL (dimensionless)"
legend_rates[6] = "d/dt f1 in component I_CaL (dimensionless)"
legend_rates[7] = "d/dt f2 in component I_CaL (dimensionless)"
legend_rates[8] = "d/dt b in component I_CaT (dimensionless)"
legend_rates[9] = "d/dt g in component I_CaT (dimensionless)"
legend_rates[10] = "d/dt q in component I_K1 (dimensionless)"
legend_rates[11] = "d/dt r1 in component I_K1 (dimensionless)"
legend_rates[12] = "d/dt r2 in component I_K1 (dimensionless)"
legend_rates[13] = "d/dt p in component I_K2 (dimensionless)"
legend_rates[14] = "d/dt k1 in component I_K2 (dimensionless)"
legend_rates[15] = "d/dt k2 in component I_K2 (dimensionless)"
legend_rates[16] = "d/dt s in component I_Ka (dimensionless)"
legend_rates[17] = "d/dt x in component I_Ka (dimensionless)"
legend_rates[18] = "d/dt xa in component I_BKa (dimensionless)"
legend_rates[19] = "d/dt xab in component I_BKab (dimensionless)"
legend_rates[20] = "d/dt y in component I_h (dimensionless)"
legend_rates[21] = "d/dt c in component I_Cl (dimensionless)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 0
constants[1] = -0.5
constants[2] = 1000
constants[3] = 3000
states[0] = -53.90915441282156
states[1] = 0.0001161881607214449
constants[4] = 1000
constants[5] = 1e-6
states[2] = 0.2345238135343783
states[3] = 0.1253518889572223
states[4] = 0.404599170710196
states[5] = 0.01036961357784695
states[6] = 0.9065941499695301
states[7] = 0.9065967263076083
states[8] = 0.508117603077852
states[9] = 0.03582573962705717
states[10] = 0.2060363247740295
states[11] = 0.1922244113609531
states[12] = 0.1932803618375963
states[13] = 0.1174074734567931
states[14] = 0.9968385770271651
states[15] = 0.9968408069904307
states[16] = 0.0307583106982354
states[17] = 0.08785242843398365
constants[6] = 1000.0
states[18] = 0.0003569126518797985
constants[7] = 1000.0
states[19] = 0.002220456569762898
states[20] = 0.002604864867063448
states[21] = 0.0003764413740731269
constants[8] = 1e-8
constants[9] = -1
constants[10] = -1
constants[11] = 140.000
constants[12] = 2.50000
constants[13] = 0.500000
constants[14] = 1.00000
constants[15] = 1.00000
constants[16] = 0.00000
constants[17] = 0.600000
constants[18] = 45.0000
constants[19] = 0.00100000
constants[20] = 0.0580000
constants[21] = 42.0000
constants[22] = 0.800000
constants[23] = 0.00400000
constants[24] = 0.520000
constants[25] = 0.0320000
constants[26] = 0.200000
constants[27] = 0.100000
constants[28] = 0.160000
constants[29] = 0.187500
constants[30] = 0.0542000
constants[31] = 0.0123000
constants[32] = 1.30000
constants[33] = 0.900000
constants[34] = 0.890000
constants[35] = 1.00000
constants[36] = 0.500000
constants[37] = 1.00000
constants[38] = 1.19000
constants[39] = 1.60000
constants[40] = 3.50000e-07
constants[41] = 0.000500000
constants[42] = 2.00000
constants[43] = 0.000300000
constants[44] = 4.00000
constants[45] = 30.0000
constants[46] = 0.00700000
constants[47] = 87.5000
constants[48] = 1.30000
constants[49] = 3.00000
constants[50] = 161.301
constants[51] = 3.60205
constants[52] = 12.0000
constants[53] = 4.00000
constants[54] = 0.108043+0.903902/(1.00000+power(constants[13]/0.281007, 1.29834))
constants[55] = ((1.00000/0.000525000)*0.0300000)/(1.00000+power(150.000/(constants[12]+constants[8]), 2.00000))
constants[56] = 46.0000
constants[57] = 6.00000
constants[58] = 130.000
constants[59] = ((1.00000/0.0123000)*0.0300000)/(1.00000+power(150.000/(constants[57]+constants[8]), 2.00000))
constants[60] = 130.000
constants[61] = ((1.00000/0.0123000)*0.0300000)/(1.00000+power(150.000/(constants[58]+constants[8]), 2.00000))
constants[62] = 0.0150000
constants[63] = 4.00000
constants[64] = 2.00000
constants[65] = 8314.00
constants[66] = 96485.0
constants[67] = 1.00000
constants[68] = 308.000
constants[69] = 1.70000
constants[70] = 1.00000
constants[71] = ((constants[65]*constants[68])/constants[66])*log(constants[58]/constants[53])
constants[72] = ((constants[65]*constants[68])/constants[66])*log(constants[57]/constants[11])
constants[73] = ((constants[65]*constants[68])/constants[66])*log(constants[56]/constants[60])
constants[74] = 2.00000
constants[75] = 0.350000
constants[76] = 22.0000
constants[77] = ((constants[65]*constants[68])/constants[66])*log((constants[57]+(constants[75]/constants[70])*constants[58])/(constants[11]+(constants[75]/constants[70])*constants[53]))
constants[78] = 3.50000e-06
constants[79] = 0.270000
constants[80] = 0.350000
constants[81] = 1.00000/(1.00000+power(constants[74]/constants[57], 1.50000))
constants[82] = 1.00000/(1.00000+power(constants[76]/constants[53], 2.00000))
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[6] = 1.00000/(1.00000+exp((states[0]+38.0000)/7.00000))
rates[6] = (algebraic[6]-states[6])/constants[52]
algebraic[1] = 1.00000/(1.00000+power((constants[50]*constants[5])/states[1], constants[51]))
algebraic[19] = 4000.00*(0.234845+(1.00000-0.234845)/(1.00000+power(states[1]/(constants[50]*constants[5]), constants[51])))
rates[2] = (algebraic[1]-states[2])/algebraic[19]
algebraic[3] = 1.00000/(1.00000+exp(-(states[0]+35.9584)/9.24013))
algebraic[20] = 0.250000+7.00000/(1.00000+exp((states[0]+38.0000)/10.0000))
rates[3] = (algebraic[3]-states[3])/algebraic[20]
algebraic[4] = 1.00000/(1.00000+exp((states[0]+57.0000)/8.00000))
algebraic[21] = 0.900000+1002.85/(1.00000+power((states[0]+47.5000)/1.50000, 2.00000))
rates[4] = (algebraic[4]-states[4])/algebraic[21]
algebraic[5] = 1.00000/(1.00000+exp(-(states[0]+22.0000)/7.00000))
algebraic[22] = 2.29000+5.70000/(1.00000+power((states[0]+29.9700)/9.00000, 2.00000))
rates[5] = (algebraic[5]-states[5])/algebraic[22]
algebraic[23] = 90.9699*(1.00000-1.00000/((1.00000+exp((states[0]+13.9629)/45.3782))*(1.00000+exp(-(states[0]+9.49866)/3.39450))))
rates[7] = (algebraic[6]-states[7])/algebraic[23]
algebraic[7] = 1.00000/(1.00000+exp(-(states[0]+54.2300)/9.88000))
algebraic[24] = 0.450000+3.90000/(1.00000+power((states[0]+66.0000)/26.0000, 2.00000))
rates[8] = (algebraic[7]-states[8])/algebraic[24]
algebraic[8] = 0.0200000+0.980000/(1.00000+exp((states[0]+72.9780)/4.64000))
algebraic[25] = 150.000*(1.00000-1.00000/((1.00000+exp((states[0]-417.430)/203.180))*(1.00000+exp(-(states[0]+61.1100)/8.07000))))
rates[9] = (algebraic[8]-states[9])/algebraic[25]
algebraic[9] = 0.978613/(1.00000+exp(-(states[0]+18.6736)/26.6606))
algebraic[26] = 500.000/(1.00000+power((states[0]+60.7100)/15.7900, 2.00000))
rates[10] = (algebraic[9]-states[10])/algebraic[26]
algebraic[10] = 1.00000/(1.00000+exp((states[0]+63.0000)/6.30000))
algebraic[27] = 5000.00/(1.00000+power((states[0]+62.7133)/35.8611, 2.00000))
rates[11] = (algebraic[10]-states[11])/algebraic[27]
algebraic[28] = 30000.0+220000./(1.00000+exp((states[0]+22.0000)/4.00000))
rates[12] = (algebraic[10]-states[12])/algebraic[28]
algebraic[11] = 0.948000/(1.00000+exp(-(states[0]+17.9100)/18.4000))
algebraic[29] = 100.000/(1.00000+power((states[0]+64.1000)/28.6700, 2.00000))
rates[13] = (algebraic[11]-states[13])/algebraic[29]
algebraic[12] = 1.00000/(1.00000+exp((states[0]+21.2000)/5.70000))
algebraic[30] = 1.00000e+06*(1.00000-1.00000/((1.00000+exp((states[0]-315.000)/50.0000))*(1.00000+exp(-(states[0]+74.9000)/8.00000))))
rates[14] = (algebraic[12]-states[14])/algebraic[30]
algebraic[31] = 2.50000e+06*(1.00000-1.00000/((1.00000+exp((states[0]-132.868)/25.3992))*(1.00000+exp(-(states[0]+24.9203)/2.67915))))
rates[15] = (algebraic[12]-states[15])/algebraic[31]
algebraic[13] = 1.00000/(1.00000+exp(-(states[0]+27.7900)/7.57000))
algebraic[32] = 17.0000/(1.00000+power((states[0]+20.5232)/35.0000, 2.00000))
rates[16] = (algebraic[13]-states[16])/algebraic[32]
algebraic[14] = 0.0200000+0.980000/(1.00000+exp((states[0]+69.5000)/6.00000))
algebraic[33] = 7.50000+10.0000/(1.00000+power((states[0]+34.1765)/120.000, 2.00000))
rates[17] = (algebraic[14]-states[17])/algebraic[33]
algebraic[15] = -0.749234/(1.00000+power((states[1]*constants[6]-0.0630535)/0.161942, 2.00000))+8.38384/(1.00000+power((states[1]*constants[6]+1538.29)/739.057, 2.00000))
algebraic[34] = 5011.47/(1.00000+power((states[1]*constants[6]+0.237503)/0.000239278, 0.422910))-37.5137
algebraic[38] = 1.00000/(1.00000+exp((-algebraic[15]*constants[66]*(states[0]-algebraic[34]))/(constants[65]*constants[68])))
algebraic[43] = 2.40914/(1.00000+power((states[0]-158.779)/-52.1497, 2.00000))
rates[18] = (algebraic[38]-states[18])/algebraic[43]
algebraic[16] = -0.681249/(1.00000+power((states[1]*constants[7]-0.218988)/0.428335, 2.00000))+1.40001/(1.00000+power((states[1]*constants[7]+228.710)/684.946, 2.00000))
algebraic[35] = 8540.23/(1.00000+power((states[1]*constants[7]+0.401189)/0.00399115, 0.668054))-109.275
algebraic[39] = 1.00000/(1.00000+exp((-algebraic[16]*constants[66]*(states[0]-algebraic[35]))/(constants[65]*constants[68])))
algebraic[44] = 13.8049/(1.00000+power((states[0]-153.019)/66.4952, 2.00000))
rates[19] = (algebraic[39]-states[19])/algebraic[44]
algebraic[17] = 1.00000/(1.00000+exp((states[0]+105.390)/8.65530))
algebraic[36] = 3.50000e-06*exp(-0.0497000*states[0])
algebraic[40] = 0.0400300*exp(0.0521100*states[0])
algebraic[45] = 1.00000/(algebraic[36]+algebraic[40])
rates[20] = (algebraic[17]-states[20])/algebraic[45]
algebraic[18] = (states[0]*constants[66])/(constants[65]*constants[68])
algebraic[41] = 0.000600000*exp(2.53000*algebraic[18])
algebraic[46] = 0.100000*exp(-5.00000*algebraic[18])
algebraic[48] = 1.00000/(1.00000+algebraic[46]*(power(algebraic[41]/states[1], 2.00000)+algebraic[41]/states[1]+1.00000))
algebraic[50] = -160.000+210.000/(1.00000+exp((states[0]+4.56000)/11.6200))+170.000/(1.00000+exp(-(states[0]+25.5000)/11.6200))
rates[21] = (algebraic[48]-states[21])/algebraic[50]
algebraic[0] = custom_piecewise([greater(voi , constants[2]) & less(voi , constants[3]), constants[1] , True, constants[0]])
algebraic[42] = constants[16]*states[3]*states[3]*states[3]*states[4]*(states[0]-constants[71])
algebraic[47] = 1.00000/(1.00000+power(states[1]/constants[19], 4.00000))
algebraic[49] = constants[17]*algebraic[47]*states[5]*states[5]*(0.800000*states[6]+0.200000*states[7])*(states[0]-constants[18])
algebraic[51] = constants[20]*states[8]*states[8]*states[9]*(states[0]-constants[21])
algebraic[52] = constants[23]*(states[0]-constants[72])
algebraic[53] = constants[24]*states[10]*states[10]*(0.380000*states[11]+0.630000*states[12])*(states[0]-constants[72])
algebraic[54] = constants[25]*states[13]*states[13]*(0.750000*states[14]+0.250000*states[15])*(states[0]-constants[72])
algebraic[55] = constants[28]*states[16]*states[17]*(states[0]-constants[72])
algebraic[56] = constants[22]*constants[26]*states[18]*(states[0]-constants[72])
algebraic[57] = constants[22]*constants[27]*states[19]*(states[0]-constants[72])
algebraic[58] = constants[30]*states[20]*(states[0]-constants[77])
algebraic[59] = constants[29]*states[21]*(states[0]-constants[73])
algebraic[37] = ((constants[65]*constants[68])/constants[66])*log((constants[32]*constants[57]+constants[33]*constants[58]+(4.00000*constants[34]*constants[12])/(1.00000+exp(algebraic[18])))/(constants[32]*constants[11]+constants[33]*constants[53]+(4.00000*constants[34]*states[1])/(1.00000+exp(algebraic[18]))))
algebraic[63] = constants[54]*constants[61]*constants[37]*constants[31]*(states[0]-algebraic[37])
algebraic[60] = constants[54]*constants[55]*constants[36]*constants[31]*(states[0]-algebraic[37])
algebraic[65] = constants[54]*constants[59]*constants[38]*constants[31]*(states[0]-algebraic[37])
algebraic[66] = 1.00000/(1.00000+0.124500*exp(-0.100000*algebraic[18])+0.00219000*exp(constants[58]/49.7100)*exp(-1.90000*algebraic[18]))
algebraic[67] = constants[69]*constants[81]*constants[82]*algebraic[66]
algebraic[70] = 1.00000/(1.00000+power(constants[43]/states[1], constants[44]))
algebraic[68] = exp((constants[80]-1.00000)*algebraic[18])
algebraic[69] = exp(constants[80]*algebraic[18])
algebraic[71] = (power(constants[53], 3.00000))*constants[12]*algebraic[69]-(power(constants[58], 3.00000))*states[1]*algebraic[68]
algebraic[72] = 1.00000+constants[79]*algebraic[68]
algebraic[73] = constants[48]*(power(constants[53], 3.00000))+(power(constants[47], 3.00000))*states[1]+(power(constants[45], 3.00000))*constants[12]*(1.00000+states[1]/constants[46])
algebraic[74] = constants[12]*(power(constants[53], 3.00000))+(power(constants[58], 3.00000))*states[1]+(power(constants[58], 3.00000))*constants[46]*(1.00000+power(constants[53]/constants[45], 3.00000))
algebraic[75] = (constants[10]*constants[78]*algebraic[70]*algebraic[71])/(algebraic[72]*(algebraic[73]+algebraic[74]))
algebraic[76] = ((0.500000*constants[64]*constants[66])/(constants[63]*constants[67]*constants[62]))*constants[9]*algebraic[75]
algebraic[79] = algebraic[42]+algebraic[58]+algebraic[76]+algebraic[67]+algebraic[49]+algebraic[51]+algebraic[59]+algebraic[53]+algebraic[54]+algebraic[55]+algebraic[56]+algebraic[57]+algebraic[63]+algebraic[65]+algebraic[60]+algebraic[52]
rates[0] = -(algebraic[79]+algebraic[0])
algebraic[61] = algebraic[49]+algebraic[51]+algebraic[60]
algebraic[62] = ((constants[63]*constants[67]*constants[62])/(constants[64]*constants[66]))*algebraic[61]
algebraic[77] = constants[40]/(1.00000+power(constants[41]/states[1], constants[42]))
algebraic[80] = algebraic[62]+algebraic[75]+algebraic[77]
rates[1] = -algebraic[80]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[6] = 1.00000/(1.00000+exp((states[0]+38.0000)/7.00000))
algebraic[1] = 1.00000/(1.00000+power((constants[50]*constants[5])/states[1], constants[51]))
algebraic[19] = 4000.00*(0.234845+(1.00000-0.234845)/(1.00000+power(states[1]/(constants[50]*constants[5]), constants[51])))
algebraic[3] = 1.00000/(1.00000+exp(-(states[0]+35.9584)/9.24013))
algebraic[20] = 0.250000+7.00000/(1.00000+exp((states[0]+38.0000)/10.0000))
algebraic[4] = 1.00000/(1.00000+exp((states[0]+57.0000)/8.00000))
algebraic[21] = 0.900000+1002.85/(1.00000+power((states[0]+47.5000)/1.50000, 2.00000))
algebraic[5] = 1.00000/(1.00000+exp(-(states[0]+22.0000)/7.00000))
algebraic[22] = 2.29000+5.70000/(1.00000+power((states[0]+29.9700)/9.00000, 2.00000))
algebraic[23] = 90.9699*(1.00000-1.00000/((1.00000+exp((states[0]+13.9629)/45.3782))*(1.00000+exp(-(states[0]+9.49866)/3.39450))))
algebraic[7] = 1.00000/(1.00000+exp(-(states[0]+54.2300)/9.88000))
algebraic[24] = 0.450000+3.90000/(1.00000+power((states[0]+66.0000)/26.0000, 2.00000))
algebraic[8] = 0.0200000+0.980000/(1.00000+exp((states[0]+72.9780)/4.64000))
algebraic[25] = 150.000*(1.00000-1.00000/((1.00000+exp((states[0]-417.430)/203.180))*(1.00000+exp(-(states[0]+61.1100)/8.07000))))
algebraic[9] = 0.978613/(1.00000+exp(-(states[0]+18.6736)/26.6606))
algebraic[26] = 500.000/(1.00000+power((states[0]+60.7100)/15.7900, 2.00000))
algebraic[10] = 1.00000/(1.00000+exp((states[0]+63.0000)/6.30000))
algebraic[27] = 5000.00/(1.00000+power((states[0]+62.7133)/35.8611, 2.00000))
algebraic[28] = 30000.0+220000./(1.00000+exp((states[0]+22.0000)/4.00000))
algebraic[11] = 0.948000/(1.00000+exp(-(states[0]+17.9100)/18.4000))
algebraic[29] = 100.000/(1.00000+power((states[0]+64.1000)/28.6700, 2.00000))
algebraic[12] = 1.00000/(1.00000+exp((states[0]+21.2000)/5.70000))
algebraic[30] = 1.00000e+06*(1.00000-1.00000/((1.00000+exp((states[0]-315.000)/50.0000))*(1.00000+exp(-(states[0]+74.9000)/8.00000))))
algebraic[31] = 2.50000e+06*(1.00000-1.00000/((1.00000+exp((states[0]-132.868)/25.3992))*(1.00000+exp(-(states[0]+24.9203)/2.67915))))
algebraic[13] = 1.00000/(1.00000+exp(-(states[0]+27.7900)/7.57000))
algebraic[32] = 17.0000/(1.00000+power((states[0]+20.5232)/35.0000, 2.00000))
algebraic[14] = 0.0200000+0.980000/(1.00000+exp((states[0]+69.5000)/6.00000))
algebraic[33] = 7.50000+10.0000/(1.00000+power((states[0]+34.1765)/120.000, 2.00000))
algebraic[15] = -0.749234/(1.00000+power((states[1]*constants[6]-0.0630535)/0.161942, 2.00000))+8.38384/(1.00000+power((states[1]*constants[6]+1538.29)/739.057, 2.00000))
algebraic[34] = 5011.47/(1.00000+power((states[1]*constants[6]+0.237503)/0.000239278, 0.422910))-37.5137
algebraic[38] = 1.00000/(1.00000+exp((-algebraic[15]*constants[66]*(states[0]-algebraic[34]))/(constants[65]*constants[68])))
algebraic[43] = 2.40914/(1.00000+power((states[0]-158.779)/-52.1497, 2.00000))
algebraic[16] = -0.681249/(1.00000+power((states[1]*constants[7]-0.218988)/0.428335, 2.00000))+1.40001/(1.00000+power((states[1]*constants[7]+228.710)/684.946, 2.00000))
algebraic[35] = 8540.23/(1.00000+power((states[1]*constants[7]+0.401189)/0.00399115, 0.668054))-109.275
algebraic[39] = 1.00000/(1.00000+exp((-algebraic[16]*constants[66]*(states[0]-algebraic[35]))/(constants[65]*constants[68])))
algebraic[44] = 13.8049/(1.00000+power((states[0]-153.019)/66.4952, 2.00000))
algebraic[17] = 1.00000/(1.00000+exp((states[0]+105.390)/8.65530))
algebraic[36] = 3.50000e-06*exp(-0.0497000*states[0])
algebraic[40] = 0.0400300*exp(0.0521100*states[0])
algebraic[45] = 1.00000/(algebraic[36]+algebraic[40])
algebraic[18] = (states[0]*constants[66])/(constants[65]*constants[68])
algebraic[41] = 0.000600000*exp(2.53000*algebraic[18])
algebraic[46] = 0.100000*exp(-5.00000*algebraic[18])
algebraic[48] = 1.00000/(1.00000+algebraic[46]*(power(algebraic[41]/states[1], 2.00000)+algebraic[41]/states[1]+1.00000))
algebraic[50] = -160.000+210.000/(1.00000+exp((states[0]+4.56000)/11.6200))+170.000/(1.00000+exp(-(states[0]+25.5000)/11.6200))
algebraic[0] = custom_piecewise([greater(voi , constants[2]) & less(voi , constants[3]), constants[1] , True, constants[0]])
algebraic[42] = constants[16]*states[3]*states[3]*states[3]*states[4]*(states[0]-constants[71])
algebraic[47] = 1.00000/(1.00000+power(states[1]/constants[19], 4.00000))
algebraic[49] = constants[17]*algebraic[47]*states[5]*states[5]*(0.800000*states[6]+0.200000*states[7])*(states[0]-constants[18])
algebraic[51] = constants[20]*states[8]*states[8]*states[9]*(states[0]-constants[21])
algebraic[52] = constants[23]*(states[0]-constants[72])
algebraic[53] = constants[24]*states[10]*states[10]*(0.380000*states[11]+0.630000*states[12])*(states[0]-constants[72])
algebraic[54] = constants[25]*states[13]*states[13]*(0.750000*states[14]+0.250000*states[15])*(states[0]-constants[72])
algebraic[55] = constants[28]*states[16]*states[17]*(states[0]-constants[72])
algebraic[56] = constants[22]*constants[26]*states[18]*(states[0]-constants[72])
algebraic[57] = constants[22]*constants[27]*states[19]*(states[0]-constants[72])
algebraic[58] = constants[30]*states[20]*(states[0]-constants[77])
algebraic[59] = constants[29]*states[21]*(states[0]-constants[73])
algebraic[37] = ((constants[65]*constants[68])/constants[66])*log((constants[32]*constants[57]+constants[33]*constants[58]+(4.00000*constants[34]*constants[12])/(1.00000+exp(algebraic[18])))/(constants[32]*constants[11]+constants[33]*constants[53]+(4.00000*constants[34]*states[1])/(1.00000+exp(algebraic[18]))))
algebraic[63] = constants[54]*constants[61]*constants[37]*constants[31]*(states[0]-algebraic[37])
algebraic[60] = constants[54]*constants[55]*constants[36]*constants[31]*(states[0]-algebraic[37])
algebraic[65] = constants[54]*constants[59]*constants[38]*constants[31]*(states[0]-algebraic[37])
algebraic[66] = 1.00000/(1.00000+0.124500*exp(-0.100000*algebraic[18])+0.00219000*exp(constants[58]/49.7100)*exp(-1.90000*algebraic[18]))
algebraic[67] = constants[69]*constants[81]*constants[82]*algebraic[66]
algebraic[70] = 1.00000/(1.00000+power(constants[43]/states[1], constants[44]))
algebraic[68] = exp((constants[80]-1.00000)*algebraic[18])
algebraic[69] = exp(constants[80]*algebraic[18])
algebraic[71] = (power(constants[53], 3.00000))*constants[12]*algebraic[69]-(power(constants[58], 3.00000))*states[1]*algebraic[68]
algebraic[72] = 1.00000+constants[79]*algebraic[68]
algebraic[73] = constants[48]*(power(constants[53], 3.00000))+(power(constants[47], 3.00000))*states[1]+(power(constants[45], 3.00000))*constants[12]*(1.00000+states[1]/constants[46])
algebraic[74] = constants[12]*(power(constants[53], 3.00000))+(power(constants[58], 3.00000))*states[1]+(power(constants[58], 3.00000))*constants[46]*(1.00000+power(constants[53]/constants[45], 3.00000))
algebraic[75] = (constants[10]*constants[78]*algebraic[70]*algebraic[71])/(algebraic[72]*(algebraic[73]+algebraic[74]))
algebraic[76] = ((0.500000*constants[64]*constants[66])/(constants[63]*constants[67]*constants[62]))*constants[9]*algebraic[75]
algebraic[79] = algebraic[42]+algebraic[58]+algebraic[76]+algebraic[67]+algebraic[49]+algebraic[51]+algebraic[59]+algebraic[53]+algebraic[54]+algebraic[55]+algebraic[56]+algebraic[57]+algebraic[63]+algebraic[65]+algebraic[60]+algebraic[52]
algebraic[61] = algebraic[49]+algebraic[51]+algebraic[60]
algebraic[62] = ((constants[63]*constants[67]*constants[62])/(constants[64]*constants[66]))*algebraic[61]
algebraic[77] = constants[40]/(1.00000+power(constants[41]/states[1], constants[42]))
algebraic[80] = algebraic[62]+algebraic[75]+algebraic[77]
algebraic[2] = constants[49]*(states[2]-0.234500)
algebraic[64] = algebraic[62]*constants[4]
algebraic[78] = algebraic[75]*constants[4]
algebraic[81] = algebraic[77]*constants[4]
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)