# Size of variable arrays: sizeAlgebraic = 60 sizeStates = 20 sizeConstants = 66 from math import * from numpy import * def createLegends(): legend_states = [""] * sizeStates legend_rates = [""] * sizeStates legend_algebraic = [""] * sizeAlgebraic legend_voi = "" legend_constants = [""] * sizeConstants legend_voi = "time in component environment (second)" legend_states[0] = "V in component membrane (millivolt)" legend_constants[0] = "R in component membrane (joule_per_kilomole_kelvin)" legend_constants[1] = "T in component membrane (kelvin)" legend_constants[2] = "F in component membrane (coulomb_per_mole)" legend_constants[3] = "Cm in component membrane (microF)" legend_algebraic[28] = "i_K1 in component time_independent_potassium_current (nanoA)" legend_algebraic[51] = "i_to in component transient_outward_current (nanoA)" legend_algebraic[30] = "i_Kr in component rapid_delayed_rectifier_potassium_current (nanoA)" legend_algebraic[32] = "i_Ks in component slow_delayed_rectifier_potassium_current (nanoA)" legend_algebraic[42] = "i_Ca_L_K_cyt in component L_type_Ca_channel (nanoA)" legend_algebraic[47] = "i_Ca_L_K_ds in component L_type_Ca_channel (nanoA)" legend_algebraic[52] = "i_NaK in component sodium_potassium_pump (nanoA)" legend_algebraic[33] = "i_Na in component fast_sodium_current (nanoA)" legend_algebraic[35] = "i_b_Na in component sodium_background_current (nanoA)" legend_algebraic[34] = "i_p_Na in component persistent_sodium_current (nanoA)" legend_algebraic[43] = "i_Ca_L_Na_cyt in component L_type_Ca_channel (nanoA)" legend_algebraic[48] = "i_Ca_L_Na_ds in component L_type_Ca_channel (nanoA)" legend_algebraic[53] = "i_NaCa_cyt in component sodium_calcium_exchanger (nanoA)" legend_algebraic[54] = "i_NaCa_ds in component sodium_calcium_exchanger (nanoA)" legend_algebraic[41] = "i_Ca_L_Ca_cyt in component L_type_Ca_channel (nanoA)" legend_algebraic[46] = "i_Ca_L_Ca_ds in component L_type_Ca_channel (nanoA)" legend_algebraic[50] = "i_b_Ca in component calcium_background_current (nanoA)" legend_algebraic[6] = "i_Stim in component membrane (nanoA)" legend_constants[4] = "stim_duration in component membrane (second)" legend_constants[5] = "stim_amplitude in component membrane (nanoA)" legend_algebraic[15] = "E_Na in component reversal_potentials (millivolt)" legend_algebraic[20] = "E_K in component reversal_potentials (millivolt)" legend_algebraic[22] = "E_Ks in component reversal_potentials (millivolt)" legend_algebraic[24] = "E_Ca in component reversal_potentials (millivolt)" legend_algebraic[26] = "E_mh in component reversal_potentials (millivolt)" legend_constants[6] = "P_kna in component reversal_potentials (dimensionless)" legend_constants[7] = "K_o in component extracellular_potassium_concentration (millimolar)" legend_constants[8] = "Na_o in component extracellular_sodium_concentration (millimolar)" legend_states[1] = "K_i in component intracellular_potassium_concentration (millimolar)" legend_states[2] = "Na_i in component intracellular_sodium_concentration (millimolar)" legend_constants[9] = "Ca_o in component extracellular_calcium_concentration (millimolar)" legend_states[3] = "Ca_i in component intracellular_calcium_concentration (millimolar)" legend_constants[10] = "K_mk1 in component time_independent_potassium_current (millimolar)" legend_constants[11] = "g_K1 in component time_independent_potassium_current (microS)" legend_constants[12] = "g_Kr1 in component rapid_delayed_rectifier_potassium_current (microS)" legend_constants[13] = "g_Kr2 in component rapid_delayed_rectifier_potassium_current (microS)" legend_states[4] = "xr1 in component rapid_delayed_rectifier_potassium_current_xr1_gate (dimensionless)" legend_states[5] = "xr2 in component rapid_delayed_rectifier_potassium_current_xr2_gate (dimensionless)" legend_algebraic[0] = "alpha_xr1 in component rapid_delayed_rectifier_potassium_current_xr1_gate (per_second)" legend_algebraic[9] = "beta_xr1 in component rapid_delayed_rectifier_potassium_current_xr1_gate (per_second)" legend_algebraic[1] = "alpha_xr2 in component rapid_delayed_rectifier_potassium_current_xr2_gate (per_second)" legend_algebraic[10] = "beta_xr2 in component rapid_delayed_rectifier_potassium_current_xr2_gate (per_second)" legend_constants[14] = "g_Ks in component slow_delayed_rectifier_potassium_current (microS)" legend_states[6] = "xs in component slow_delayed_rectifier_potassium_current_xs_gate (dimensionless)" legend_algebraic[2] = "alpha_xs in component slow_delayed_rectifier_potassium_current_xs_gate (per_second)" legend_algebraic[11] = "beta_xs in component slow_delayed_rectifier_potassium_current_xs_gate (per_second)" legend_constants[15] = "g_Na in component fast_sodium_current (microS)" legend_states[7] = "m in component fast_sodium_current_m_gate (dimensionless)" legend_states[8] = "h in component fast_sodium_current_h_gate (dimensionless)" legend_algebraic[12] = "alpha_m in component fast_sodium_current_m_gate (per_second)" legend_algebraic[18] = "beta_m in component fast_sodium_current_m_gate (per_second)" legend_constants[16] = "delta_m in component fast_sodium_current_m_gate (millivolt)" legend_algebraic[3] = "E0_m in component fast_sodium_current_m_gate (millivolt)" legend_algebraic[4] = "alpha_h in component fast_sodium_current_h_gate (per_second)" legend_algebraic[13] = "beta_h in component fast_sodium_current_h_gate (per_second)" legend_constants[17] = "shift_h in component fast_sodium_current_h_gate (millivolt)" legend_constants[18] = "g_pna in component persistent_sodium_current (microS)" legend_constants[19] = "g_bna in component sodium_background_current (microS)" legend_algebraic[49] = "i_Ca_L in component L_type_Ca_channel (nanoA)" legend_constants[20] = "P_Ca_L in component L_type_Ca_channel (nanoA_per_millimolar)" legend_constants[21] = "P_CaK in component L_type_Ca_channel (dimensionless)" legend_constants[22] = "P_CaNa in component L_type_Ca_channel (dimensionless)" legend_states[9] = "Ca_ds in component intracellular_calcium_concentration (millimolar)" legend_states[10] = "d in component L_type_Ca_channel_d_gate (dimensionless)" legend_algebraic[40] = "CaChoncyt in component L_type_Ca_channel_f_gate (dimensionless)" legend_algebraic[45] = "CaChonds in component L_type_Ca_channel_f_gate (dimensionless)" legend_constants[23] = "KCaChoff in component L_type_Ca_channel (millimolar)" legend_constants[24] = "Kmdsinact in component L_type_Ca_channel (millimolar)" legend_constants[25] = "FrICa in component L_type_Ca_channel (dimensionless)" legend_algebraic[14] = "alpha_d in component L_type_Ca_channel_d_gate (per_second)" legend_algebraic[19] = "beta_d in component L_type_Ca_channel_d_gate (per_second)" legend_algebraic[5] = "E0_d in component L_type_Ca_channel_d_gate (millivolt)" legend_constants[26] = "speed_d in component L_type_Ca_channel_d_gate (dimensionless)" legend_states[11] = "f in component L_type_Ca_channel_f_gate (dimensionless)" legend_algebraic[39] = "CaChoffcyt in component L_type_Ca_channel_f_gate (dimensionless)" legend_algebraic[44] = "CaChoffds in component L_type_Ca_channel_f_gate (dimensionless)" legend_algebraic[37] = "alpha_f in component L_type_Ca_channel_f_gate (per_second)" legend_algebraic[38] = "beta_f in component L_type_Ca_channel_f_gate (per_second)" legend_constants[27] = "speed_f in component L_type_Ca_channel_f_gate (dimensionless)" legend_constants[28] = "delta_f in component L_type_Ca_channel_f_gate (millivolt)" legend_algebraic[36] = "E0_f in component L_type_Ca_channel_f_gate (millivolt)" legend_constants[29] = "g_bca in component calcium_background_current (microS)" legend_constants[30] = "g_to in component transient_outward_current (microS)" legend_constants[31] = "g_tos in component transient_outward_current (dimensionless)" legend_states[12] = "s in component transient_outward_current_s_gate (dimensionless)" legend_states[13] = "r in component transient_outward_current_r_gate (dimensionless)" legend_algebraic[7] = "alpha_s in component transient_outward_current_s_gate (per_second)" legend_algebraic[16] = "beta_s in component transient_outward_current_s_gate (per_second)" legend_constants[32] = "i_NaK_max in component sodium_potassium_pump (nanoA)" legend_constants[33] = "K_mK in component sodium_potassium_pump (millimolar)" legend_constants[34] = "K_mNa in component sodium_potassium_pump (millimolar)" legend_algebraic[55] = "i_NaCa in component sodium_calcium_exchanger (nanoA)" legend_constants[35] = "k_NaCa in component sodium_calcium_exchanger (nanoA)" legend_constants[36] = "n_NaCa in component sodium_calcium_exchanger (dimensionless)" legend_constants[37] = "d_NaCa in component sodium_calcium_exchanger (dimensionless)" legend_constants[38] = "gamma in component sodium_calcium_exchanger (dimensionless)" legend_constants[39] = "FRiNaCa in component sodium_calcium_exchanger (dimensionless)" legend_algebraic[57] = "i_up in component sarcoplasmic_reticulum_calcium_pump (millimolar_per_second)" legend_constants[63] = "K_1 in component sarcoplasmic_reticulum_calcium_pump (dimensionless)" legend_algebraic[56] = "K_2 in component sarcoplasmic_reticulum_calcium_pump (millimolar)" legend_constants[40] = "K_cyca in component sarcoplasmic_reticulum_calcium_pump (millimolar)" legend_constants[41] = "K_xcs in component sarcoplasmic_reticulum_calcium_pump (dimensionless)" legend_constants[42] = "K_srca in component sarcoplasmic_reticulum_calcium_pump (millimolar)" legend_constants[43] = "alpha_up in component sarcoplasmic_reticulum_calcium_pump (millimolar_per_second)" legend_constants[44] = "beta_up in component sarcoplasmic_reticulum_calcium_pump (millimolar_per_second)" legend_states[14] = "Ca_up in component intracellular_calcium_concentration (millimolar)" legend_algebraic[58] = "i_trans in component calcium_translocation (millimolar_per_second)" legend_states[15] = "Ca_rel in component intracellular_calcium_concentration (millimolar)" legend_algebraic[59] = "i_rel in component calcium_release (millimolar_per_second)" legend_algebraic[8] = "VoltDep in component calcium_release (dimensionless)" legend_algebraic[23] = "RegBindSite in component calcium_release (dimensionless)" legend_algebraic[17] = "CaiReg in component calcium_release (dimensionless)" legend_algebraic[21] = "CadsReg in component calcium_release (dimensionless)" legend_algebraic[25] = "ActRate in component calcium_release (per_second)" legend_algebraic[27] = "InactRate in component calcium_release (per_second)" legend_constants[45] = "K_leak_rate in component calcium_release (per_second)" legend_constants[46] = "K_m_rel in component calcium_release (per_second)" legend_constants[47] = "K_m_Ca_cyt in component calcium_release (millimolar)" legend_constants[48] = "K_m_Ca_ds in component calcium_release (millimolar)" legend_algebraic[31] = "PrecFrac in component calcium_release (dimensionless)" legend_states[16] = "ActFrac in component calcium_release (dimensionless)" legend_states[17] = "ProdFrac in component calcium_release (dimensionless)" legend_algebraic[29] = "SpeedRel in component calcium_release (dimensionless)" legend_constants[65] = "V_i in component intracellular_calcium_concentration (micrometre3)" legend_states[18] = "Ca_Calmod in component intracellular_calcium_concentration (millimolar)" legend_states[19] = "Ca_Trop in component intracellular_calcium_concentration (millimolar)" legend_constants[49] = "Calmod in component intracellular_calcium_concentration (millimolar)" legend_constants[50] = "Trop in component intracellular_calcium_concentration (millimolar)" legend_constants[51] = "alpha_Calmod in component intracellular_calcium_concentration (per_millimolar_second)" legend_constants[52] = "beta_Calmod in component intracellular_calcium_concentration (per_second)" legend_constants[53] = "alpha_Trop in component intracellular_calcium_concentration (per_millimolar_second)" legend_constants[54] = "beta_Trop in component intracellular_calcium_concentration (per_second)" legend_constants[55] = "radius in component intracellular_calcium_concentration (micrometre)" legend_constants[56] = "length in component intracellular_calcium_concentration (micrometre)" legend_constants[62] = "V_Cell in component intracellular_calcium_concentration (micrometre3)" legend_constants[64] = "V_i_ratio in component intracellular_calcium_concentration (dimensionless)" legend_constants[57] = "V_ds_ratio in component intracellular_calcium_concentration (dimensionless)" legend_constants[58] = "V_rel_ratio in component intracellular_calcium_concentration (dimensionless)" legend_constants[59] = "V_e_ratio in component intracellular_calcium_concentration (dimensionless)" legend_constants[60] = "V_up_ratio in component intracellular_calcium_concentration (dimensionless)" legend_constants[61] = "Kdecay in component intracellular_calcium_concentration (per_second)" legend_rates[0] = "d/dt V in component membrane (millivolt)" legend_rates[4] = "d/dt xr1 in component rapid_delayed_rectifier_potassium_current_xr1_gate (dimensionless)" legend_rates[5] = "d/dt xr2 in component rapid_delayed_rectifier_potassium_current_xr2_gate (dimensionless)" legend_rates[6] = "d/dt xs in component slow_delayed_rectifier_potassium_current_xs_gate (dimensionless)" legend_rates[7] = "d/dt m in component fast_sodium_current_m_gate (dimensionless)" legend_rates[8] = "d/dt h in component fast_sodium_current_h_gate (dimensionless)" legend_rates[10] = "d/dt d in component L_type_Ca_channel_d_gate (dimensionless)" legend_rates[11] = "d/dt f in component L_type_Ca_channel_f_gate (dimensionless)" legend_rates[12] = "d/dt s in component transient_outward_current_s_gate (dimensionless)" legend_rates[13] = "d/dt r in component transient_outward_current_r_gate (dimensionless)" legend_rates[16] = "d/dt ActFrac in component calcium_release (dimensionless)" legend_rates[17] = "d/dt ProdFrac in component calcium_release (dimensionless)" legend_rates[2] = "d/dt Na_i in component intracellular_sodium_concentration (millimolar)" legend_rates[1] = "d/dt K_i in component intracellular_potassium_concentration (millimolar)" legend_rates[3] = "d/dt Ca_i in component intracellular_calcium_concentration (millimolar)" legend_rates[18] = "d/dt Ca_Calmod in component intracellular_calcium_concentration (millimolar)" legend_rates[19] = "d/dt Ca_Trop in component intracellular_calcium_concentration (millimolar)" legend_rates[9] = "d/dt Ca_ds in component intracellular_calcium_concentration (millimolar)" legend_rates[14] = "d/dt Ca_up in component intracellular_calcium_concentration (millimolar)" legend_rates[15] = "d/dt Ca_rel in component intracellular_calcium_concentration (millimolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = -92.8915042 constants[0] = 8314.472 constants[1] = 310 constants[2] = 96485.3415 constants[3] = 9.5e-5 constants[4] = 0.002 constants[5] = -6 constants[6] = 0.03 constants[7] = 4 constants[8] = 140 states[1] = 136.1745362 states[2] = 7.6713487 constants[9] = 2 states[3] = 1.49e-5 constants[10] = 10 constants[11] = 0.5 constants[12] = 0.0028 constants[13] = 0.0017 states[4] = 1.02e-5 states[5] = 2e-7 constants[14] = 0.0016 states[6] = 0.0006469 constants[15] = 0.5 states[7] = 0.0016111 states[8] = 0.9944559 constants[16] = 1e-5 constants[17] = 0 constants[18] = 0.0027 constants[19] = 0.0006 constants[20] = 1 constants[21] = 0.002 constants[22] = 0.01 states[9] = 2.7e-6 states[10] = 0 constants[23] = 0.01 constants[24] = 0.001 constants[25] = 0.7 constants[26] = 3 states[11] = 0 constants[27] = 0.3 constants[28] = 0.0001 constants[29] = 0.00025 constants[30] = 0.005 constants[31] = 0 states[12] = 0.9948645 states[13] = 0 constants[32] = 0.7 constants[33] = 1 constants[34] = 40 constants[35] = 0.0005 constants[36] = 3 constants[37] = 0 constants[38] = 0.2 constants[39] = 0.001 constants[40] = 0.0003 constants[41] = 0.4 constants[42] = 0.5 constants[43] = 0.4 constants[44] = 0.03 states[14] = 0.36963 states[15] = 0.6460487 constants[45] = 0.05 constants[46] = 250 constants[47] = 0.0005 constants[48] = 0.01 states[16] = 0.0049039 states[17] = 0.6950649 states[18] = 0.0005841 states[19] = 0.0003732 constants[49] = 0.02 constants[50] = 0.05 constants[51] = 100000 constants[52] = 50 constants[53] = 100000 constants[54] = 200 constants[55] = 12 constants[56] = 74 constants[57] = 0.1 constants[58] = 0.1 constants[59] = 0.4 constants[60] = 0.01 constants[61] = 10 constants[62] = (3.14159*(power(constants[55]/1000.00, 2.00000))*constants[56])/1000.00 constants[63] = (constants[40]*constants[41])/constants[42] constants[64] = ((1.00000-constants[59])-constants[60])-constants[58] constants[65] = constants[62]*constants[64] return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[13] = 333.000*(1.00000/(1.00000+exp(-(states[0]+4.00000)/5.00000))-states[13]) algebraic[0] = 50.0000/(1.00000+exp(-(states[0]-5.00000)/9.00000)) algebraic[9] = 0.0500000*exp(-(states[0]-20.0000)/15.0000) rates[4] = algebraic[0]*(1.00000-states[4])-algebraic[9]*states[4] algebraic[1] = 50.0000/(1.00000+exp(-(states[0]-5.00000)/9.00000)) algebraic[10] = 0.400000*exp(-(power((states[0]+30.0000)/30.0000, 3.00000))) rates[5] = algebraic[1]*(1.00000-states[5])-algebraic[10]*states[5] algebraic[2] = 14.0000/(1.00000+exp(-(states[0]-40.0000)/9.00000)) algebraic[11] = 1.00000*exp(-states[0]/45.0000) rates[6] = algebraic[2]*(1.00000-states[6])-algebraic[11]*states[6] algebraic[4] = 20.0000*exp(-0.125000*((states[0]+75.0000)-constants[17])) algebraic[13] = 2000.00/(1.00000+320.000*exp(-0.100000*((states[0]+75.0000)-constants[17]))) rates[8] = algebraic[4]*(1.00000-states[8])-algebraic[13]*states[8] algebraic[7] = 0.0330000*exp(-states[0]/17.0000) algebraic[16] = 33.0000/(1.00000+exp(-0.125000*(states[0]+10.0000))) rates[12] = algebraic[7]*(1.00000-states[12])-algebraic[16]*states[12] algebraic[3] = states[0]+41.0000 algebraic[12] = custom_piecewise([less(fabs(algebraic[3]) , constants[16]), 2000.00 , True, (200.000*algebraic[3])/(1.00000-exp(-0.100000*algebraic[3]))]) algebraic[18] = 8000.00*exp(-0.0560000*(states[0]+66.0000)) rates[7] = algebraic[12]*(1.00000-states[7])-algebraic[18]*states[7] algebraic[5] = (states[0]+24.0000)-5.00000 algebraic[14] = custom_piecewise([less(fabs(algebraic[5]) , 0.000100000), 120.000 , True, (30.0000*algebraic[5])/(1.00000-exp(-algebraic[5]/4.00000))]) algebraic[19] = custom_piecewise([less(fabs(algebraic[5]) , 0.000100000), 120.000 , True, (12.0000*algebraic[5])/(exp(algebraic[5]/10.0000)-1.00000)]) rates[10] = constants[26]*(algebraic[14]*(1.00000-states[10])-algebraic[19]*states[10]) algebraic[17] = states[3]/(states[3]+constants[47]) algebraic[21] = states[9]/(states[9]+constants[48]) algebraic[23] = algebraic[17]+(1.00000-algebraic[17])*algebraic[21] algebraic[27] = 60.0000+500.000*(power(algebraic[23], 2.00000)) algebraic[29] = custom_piecewise([less(states[0] , -50.0000), 5.00000 , True, 1.00000]) rates[17] = states[16]*algebraic[29]*algebraic[27]-algebraic[29]*1.00000*states[17] algebraic[8] = exp(0.0800000*(states[0]-40.0000)) algebraic[25] = 0.00000*algebraic[8]+90.0000*(power(algebraic[23], 2.00000)) algebraic[31] = (1.00000-states[16])-states[17] rates[16] = algebraic[31]*algebraic[29]*algebraic[25]-states[16]*algebraic[29]*algebraic[27] algebraic[39] = states[3]/(constants[23]+states[3]) algebraic[36] = states[0]+34.0000 algebraic[37] = custom_piecewise([less(fabs(algebraic[36]) , constants[28]), 25.0000 , True, (6.25000*algebraic[36])/(exp(algebraic[36]/4.00000)-1.00000)]) algebraic[38] = 12.0000/(1.00000+exp((-1.00000*(states[0]+34.0000))/4.00000)) rates[11] = (120.000*(1.00000-states[11])*algebraic[39]+(1.00000-states[11])*(1.00000-algebraic[39]))*constants[27]*algebraic[38]-algebraic[37]*states[11] algebraic[44] = states[9]/(constants[24]+states[9]) algebraic[45] = (1.00000-states[11])*(1.00000-algebraic[44]) algebraic[46] = (((constants[25]*4.00000*constants[20]*states[10]*algebraic[45]*(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))/(1.00000-exp((-(states[0]-50.0000)*constants[2]*2.00000)/(constants[0]*constants[1]))))*(states[3]*exp((100.000*constants[2])/(constants[0]*constants[1]))-constants[9]*exp((-(states[0]-50.0000)*constants[2]*2.00000)/(constants[0]*constants[1]))) rates[9] = (-1.00000*algebraic[46])/(2.00000*1.00000*constants[57]*constants[65]*constants[2])-states[9]*constants[61] algebraic[20] = ((constants[0]*constants[1])/constants[2])*log(constants[7]/states[1]) algebraic[28] = (((constants[11]*constants[7])/(constants[7]+constants[10]))*(states[0]-algebraic[20]))/(1.00000+exp((((states[0]-algebraic[20])-10.0000)*constants[2]*1.25000)/(constants[0]*constants[1]))) algebraic[51] = constants[30]*(constants[31]+states[12]*(1.00000-constants[31]))*states[13]*(states[0]-algebraic[20]) algebraic[30] = (((constants[12]*states[4]+constants[13]*states[5])*1.00000)/(1.00000+exp((states[0]+9.00000)/22.4000)))*(states[0]-algebraic[20]) algebraic[22] = ((constants[0]*constants[1])/constants[2])*log((constants[7]+constants[6]*constants[8])/(states[1]+constants[6]*states[2])) algebraic[32] = constants[14]*(power(states[6], 2.00000))*(states[0]-algebraic[22]) algebraic[40] = (1.00000-states[11])*(1.00000-algebraic[39]) algebraic[42] = ((((1.00000-constants[25])*constants[21]*constants[20]*states[10]*algebraic[40]*(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))/(1.00000-exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))))*(states[1]*exp((50.0000*constants[2])/(constants[0]*constants[1]))-constants[7]*exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))) algebraic[47] = (((constants[25]*constants[21]*constants[20]*states[10]*algebraic[45]*(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))/(1.00000-exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))))*(states[1]*exp((50.0000*constants[2])/(constants[0]*constants[1]))-constants[7]*exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))) algebraic[52] = (((constants[32]*constants[7])/(constants[33]+constants[7]))*states[2])/(constants[34]+states[2]) rates[1] = (-1.00000/(1.00000*constants[65]*constants[2]))*((algebraic[28]+algebraic[30]+algebraic[32]+algebraic[42]+algebraic[47]+algebraic[51])-2.00000*algebraic[52]) algebraic[26] = ((constants[0]*constants[1])/constants[2])*log((constants[8]+0.120000*constants[7])/(states[2]+0.120000*states[1])) algebraic[33] = constants[15]*(power(states[7], 3.00000))*states[8]*(states[0]-algebraic[26]) algebraic[15] = ((constants[0]*constants[1])/constants[2])*log(constants[8]/states[2]) algebraic[35] = constants[19]*(states[0]-algebraic[15]) algebraic[34] = ((constants[18]*1.00000)/(1.00000+exp(-(states[0]+52.0000)/8.00000)))*(states[0]-algebraic[15]) algebraic[43] = ((((1.00000-constants[25])*constants[22]*constants[20]*states[10]*algebraic[40]*(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))/(1.00000-exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))))*(states[2]*exp((50.0000*constants[2])/(constants[0]*constants[1]))-constants[8]*exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))) algebraic[48] = (((constants[25]*constants[22]*constants[20]*states[10]*algebraic[45]*(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))/(1.00000-exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))))*(states[2]*exp((50.0000*constants[2])/(constants[0]*constants[1]))-constants[8]*exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))) algebraic[53] = ((1.00000-constants[39])*constants[35]*(exp((constants[38]*(constants[36]-2.00000)*states[0]*constants[2])/(constants[0]*constants[1]))*(power(states[2], constants[36]))*constants[9]-exp(((constants[38]-1.00000)*(constants[36]-2.00000)*states[0]*constants[2])/(constants[0]*constants[1]))*(power(constants[8], constants[36]))*states[3]))/((1.00000+constants[37]*(states[3]*(power(constants[8], constants[36]))+constants[9]*(power(states[2], constants[36]))))*(1.00000+states[3]/0.00690000)) rates[2] = (-1.00000/(1.00000*constants[65]*constants[2]))*(algebraic[33]+algebraic[34]+algebraic[35]+3.00000*algebraic[52]+3.00000*algebraic[53]+algebraic[43]+algebraic[48]) algebraic[54] = (constants[39]*constants[35]*(exp((constants[38]*(constants[36]-2.00000)*states[0]*constants[2])/(constants[0]*constants[1]))*(power(states[2], constants[36]))*constants[9]-exp(((constants[38]-1.00000)*(constants[36]-2.00000)*states[0]*constants[2])/(constants[0]*constants[1]))*(power(constants[8], constants[36]))*states[9]))/((1.00000+constants[37]*(states[9]*(power(constants[8], constants[36]))+constants[9]*(power(states[2], constants[36]))))*(1.00000+states[9]/0.00690000)) algebraic[41] = ((((1.00000-constants[25])*4.00000*constants[20]*states[10]*algebraic[40]*(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))/(1.00000-exp((-(states[0]-50.0000)*constants[2]*2.00000)/(constants[0]*constants[1]))))*(states[3]*exp((100.000*constants[2])/(constants[0]*constants[1]))-constants[9]*exp((-(states[0]-50.0000)*constants[2]*2.00000)/(constants[0]*constants[1]))) algebraic[24] = ((0.500000*constants[0]*constants[1])/constants[2])*log(constants[9]/states[3]) algebraic[50] = constants[29]*(states[0]-algebraic[24]) algebraic[6] = custom_piecewise([greater_equal(voi , 0.0500000) & less_equal(voi , 0.0500000+constants[4]), constants[5] , True, 0.00000]) rates[0] = (-1.00000/constants[3])*(algebraic[6]+algebraic[28]+algebraic[51]+algebraic[30]+algebraic[32]+algebraic[52]+algebraic[33]+algebraic[35]+algebraic[34]+algebraic[43]+algebraic[48]+algebraic[53]+algebraic[54]+algebraic[41]+algebraic[46]+algebraic[42]+algebraic[47]+algebraic[50]) algebraic[56] = states[3]+states[14]*constants[63]+constants[40]*constants[41]+constants[40] algebraic[57] = (states[3]/algebraic[56])*constants[43]-((states[14]*constants[63])/algebraic[56])*constants[44] algebraic[58] = 50.0000*(states[14]-states[15]) rates[14] = (constants[64]/constants[60])*algebraic[57]-algebraic[58] rates[18] = constants[51]*states[3]*(constants[49]-states[18])-constants[52]*states[18] algebraic[59] = ((power(states[16]/(states[16]+0.250000), 2.00000))*constants[46]+constants[45])*states[15] rates[15] = (constants[60]/constants[58])*algebraic[58]-algebraic[59] rates[19] = constants[53]*states[3]*(constants[50]-states[19])-constants[54]*states[19] rates[3] = ((((-1.00000/(2.00000*1.00000*constants[65]*constants[2]))*(((algebraic[41]+algebraic[50])-2.00000*algebraic[53])-2.00000*algebraic[54])+states[9]*constants[57]*constants[61]+(algebraic[59]*constants[58])/constants[64])-rates[18])-rates[19])-algebraic[57] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = 50.0000/(1.00000+exp(-(states[0]-5.00000)/9.00000)) algebraic[9] = 0.0500000*exp(-(states[0]-20.0000)/15.0000) algebraic[1] = 50.0000/(1.00000+exp(-(states[0]-5.00000)/9.00000)) algebraic[10] = 0.400000*exp(-(power((states[0]+30.0000)/30.0000, 3.00000))) algebraic[2] = 14.0000/(1.00000+exp(-(states[0]-40.0000)/9.00000)) algebraic[11] = 1.00000*exp(-states[0]/45.0000) algebraic[4] = 20.0000*exp(-0.125000*((states[0]+75.0000)-constants[17])) algebraic[13] = 2000.00/(1.00000+320.000*exp(-0.100000*((states[0]+75.0000)-constants[17]))) algebraic[7] = 0.0330000*exp(-states[0]/17.0000) algebraic[16] = 33.0000/(1.00000+exp(-0.125000*(states[0]+10.0000))) algebraic[3] = states[0]+41.0000 algebraic[12] = custom_piecewise([less(fabs(algebraic[3]) , constants[16]), 2000.00 , True, (200.000*algebraic[3])/(1.00000-exp(-0.100000*algebraic[3]))]) algebraic[18] = 8000.00*exp(-0.0560000*(states[0]+66.0000)) algebraic[5] = (states[0]+24.0000)-5.00000 algebraic[14] = custom_piecewise([less(fabs(algebraic[5]) , 0.000100000), 120.000 , True, (30.0000*algebraic[5])/(1.00000-exp(-algebraic[5]/4.00000))]) algebraic[19] = custom_piecewise([less(fabs(algebraic[5]) , 0.000100000), 120.000 , True, (12.0000*algebraic[5])/(exp(algebraic[5]/10.0000)-1.00000)]) algebraic[17] = states[3]/(states[3]+constants[47]) algebraic[21] = states[9]/(states[9]+constants[48]) algebraic[23] = algebraic[17]+(1.00000-algebraic[17])*algebraic[21] algebraic[27] = 60.0000+500.000*(power(algebraic[23], 2.00000)) algebraic[29] = custom_piecewise([less(states[0] , -50.0000), 5.00000 , True, 1.00000]) algebraic[8] = exp(0.0800000*(states[0]-40.0000)) algebraic[25] = 0.00000*algebraic[8]+90.0000*(power(algebraic[23], 2.00000)) algebraic[31] = (1.00000-states[16])-states[17] algebraic[39] = states[3]/(constants[23]+states[3]) algebraic[36] = states[0]+34.0000 algebraic[37] = custom_piecewise([less(fabs(algebraic[36]) , constants[28]), 25.0000 , True, (6.25000*algebraic[36])/(exp(algebraic[36]/4.00000)-1.00000)]) algebraic[38] = 12.0000/(1.00000+exp((-1.00000*(states[0]+34.0000))/4.00000)) algebraic[44] = states[9]/(constants[24]+states[9]) algebraic[45] = (1.00000-states[11])*(1.00000-algebraic[44]) algebraic[46] = (((constants[25]*4.00000*constants[20]*states[10]*algebraic[45]*(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))/(1.00000-exp((-(states[0]-50.0000)*constants[2]*2.00000)/(constants[0]*constants[1]))))*(states[3]*exp((100.000*constants[2])/(constants[0]*constants[1]))-constants[9]*exp((-(states[0]-50.0000)*constants[2]*2.00000)/(constants[0]*constants[1]))) algebraic[20] = ((constants[0]*constants[1])/constants[2])*log(constants[7]/states[1]) algebraic[28] = (((constants[11]*constants[7])/(constants[7]+constants[10]))*(states[0]-algebraic[20]))/(1.00000+exp((((states[0]-algebraic[20])-10.0000)*constants[2]*1.25000)/(constants[0]*constants[1]))) algebraic[51] = constants[30]*(constants[31]+states[12]*(1.00000-constants[31]))*states[13]*(states[0]-algebraic[20]) algebraic[30] = (((constants[12]*states[4]+constants[13]*states[5])*1.00000)/(1.00000+exp((states[0]+9.00000)/22.4000)))*(states[0]-algebraic[20]) algebraic[22] = ((constants[0]*constants[1])/constants[2])*log((constants[7]+constants[6]*constants[8])/(states[1]+constants[6]*states[2])) algebraic[32] = constants[14]*(power(states[6], 2.00000))*(states[0]-algebraic[22]) algebraic[40] = (1.00000-states[11])*(1.00000-algebraic[39]) algebraic[42] = ((((1.00000-constants[25])*constants[21]*constants[20]*states[10]*algebraic[40]*(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))/(1.00000-exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))))*(states[1]*exp((50.0000*constants[2])/(constants[0]*constants[1]))-constants[7]*exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))) algebraic[47] = (((constants[25]*constants[21]*constants[20]*states[10]*algebraic[45]*(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))/(1.00000-exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))))*(states[1]*exp((50.0000*constants[2])/(constants[0]*constants[1]))-constants[7]*exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))) algebraic[52] = (((constants[32]*constants[7])/(constants[33]+constants[7]))*states[2])/(constants[34]+states[2]) algebraic[26] = ((constants[0]*constants[1])/constants[2])*log((constants[8]+0.120000*constants[7])/(states[2]+0.120000*states[1])) algebraic[33] = constants[15]*(power(states[7], 3.00000))*states[8]*(states[0]-algebraic[26]) algebraic[15] = ((constants[0]*constants[1])/constants[2])*log(constants[8]/states[2]) algebraic[35] = constants[19]*(states[0]-algebraic[15]) algebraic[34] = ((constants[18]*1.00000)/(1.00000+exp(-(states[0]+52.0000)/8.00000)))*(states[0]-algebraic[15]) algebraic[43] = ((((1.00000-constants[25])*constants[22]*constants[20]*states[10]*algebraic[40]*(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))/(1.00000-exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))))*(states[2]*exp((50.0000*constants[2])/(constants[0]*constants[1]))-constants[8]*exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))) algebraic[48] = (((constants[25]*constants[22]*constants[20]*states[10]*algebraic[45]*(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))/(1.00000-exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))))*(states[2]*exp((50.0000*constants[2])/(constants[0]*constants[1]))-constants[8]*exp((-(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))) algebraic[53] = ((1.00000-constants[39])*constants[35]*(exp((constants[38]*(constants[36]-2.00000)*states[0]*constants[2])/(constants[0]*constants[1]))*(power(states[2], constants[36]))*constants[9]-exp(((constants[38]-1.00000)*(constants[36]-2.00000)*states[0]*constants[2])/(constants[0]*constants[1]))*(power(constants[8], constants[36]))*states[3]))/((1.00000+constants[37]*(states[3]*(power(constants[8], constants[36]))+constants[9]*(power(states[2], constants[36]))))*(1.00000+states[3]/0.00690000)) algebraic[54] = (constants[39]*constants[35]*(exp((constants[38]*(constants[36]-2.00000)*states[0]*constants[2])/(constants[0]*constants[1]))*(power(states[2], constants[36]))*constants[9]-exp(((constants[38]-1.00000)*(constants[36]-2.00000)*states[0]*constants[2])/(constants[0]*constants[1]))*(power(constants[8], constants[36]))*states[9]))/((1.00000+constants[37]*(states[9]*(power(constants[8], constants[36]))+constants[9]*(power(states[2], constants[36]))))*(1.00000+states[9]/0.00690000)) algebraic[41] = ((((1.00000-constants[25])*4.00000*constants[20]*states[10]*algebraic[40]*(states[0]-50.0000)*constants[2])/(constants[0]*constants[1]))/(1.00000-exp((-(states[0]-50.0000)*constants[2]*2.00000)/(constants[0]*constants[1]))))*(states[3]*exp((100.000*constants[2])/(constants[0]*constants[1]))-constants[9]*exp((-(states[0]-50.0000)*constants[2]*2.00000)/(constants[0]*constants[1]))) algebraic[24] = ((0.500000*constants[0]*constants[1])/constants[2])*log(constants[9]/states[3]) algebraic[50] = constants[29]*(states[0]-algebraic[24]) algebraic[6] = custom_piecewise([greater_equal(voi , 0.0500000) & less_equal(voi , 0.0500000+constants[4]), constants[5] , True, 0.00000]) algebraic[56] = states[3]+states[14]*constants[63]+constants[40]*constants[41]+constants[40] algebraic[57] = (states[3]/algebraic[56])*constants[43]-((states[14]*constants[63])/algebraic[56])*constants[44] algebraic[58] = 50.0000*(states[14]-states[15]) algebraic[59] = ((power(states[16]/(states[16]+0.250000), 2.00000))*constants[46]+constants[45])*states[15] algebraic[49] = algebraic[41]+algebraic[42]+algebraic[43]+algebraic[46]+algebraic[47]+algebraic[48] algebraic[55] = algebraic[53]+algebraic[54] 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)