# Size of variable arrays: sizeAlgebraic = 45 sizeStates = 16 sizeConstants = 50 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[45] = "RTONF in component membrane (millivolt)" legend_constants[3] = "C in component membrane (microF)" legend_constants[4] = "i_pulse in component membrane (nanoA)" legend_algebraic[25] = "i_f in component hyperpolarising_activated_current (nanoA)" legend_algebraic[27] = "i_K in component time_dependent_potassium_current (nanoA)" legend_algebraic[28] = "i_K1 in component time_independent_potassium_current (nanoA)" legend_algebraic[29] = "i_to in component transient_outward_current (nanoA)" legend_algebraic[30] = "i_Na_b in component sodium_background_current (nanoA)" legend_algebraic[32] = "i_Ca_b in component calcium_background_current (nanoA)" legend_algebraic[33] = "i_p in component sodium_potassium_pump (nanoA)" legend_algebraic[34] = "i_NaCa in component Na_Ca_exchanger (nanoA)" legend_algebraic[36] = "i_Na in component fast_sodium_current (nanoA)" legend_algebraic[43] = "i_si in component second_inward_current (nanoA)" legend_algebraic[23] = "i_fNa in component hyperpolarising_activated_current (nanoA)" legend_algebraic[0] = "E_Na in component hyperpolarising_activated_current (millivolt)" legend_algebraic[10] = "E_K in component hyperpolarising_activated_current (millivolt)" legend_algebraic[24] = "i_fK in component hyperpolarising_activated_current (nanoA)" legend_constants[5] = "g_f_Na in component hyperpolarising_activated_current (microS)" legend_constants[6] = "g_f_K in component hyperpolarising_activated_current (microS)" legend_constants[7] = "Km_f in component hyperpolarising_activated_current (millimolar)" legend_states[1] = "Kc in component extracellular_potassium_concentration (millimolar)" legend_states[2] = "Ki in component intracellular_potassium_concentration (millimolar)" legend_states[3] = "Nai in component intracellular_sodium_concentration (millimolar)" legend_constants[8] = "Nao in component extracellular_sodium_concentration (millimolar)" legend_states[4] = "y in component hyperpolarising_activated_current_y_gate (dimensionless)" legend_algebraic[1] = "alpha_y in component hyperpolarising_activated_current_y_gate (per_second)" legend_algebraic[19] = "beta_y in component hyperpolarising_activated_current_y_gate (per_second)" legend_constants[9] = "delta_y in component hyperpolarising_activated_current_y_gate (millivolt)" legend_algebraic[11] = "E0_y in component hyperpolarising_activated_current_y_gate (millivolt)" legend_algebraic[26] = "I_K in component time_dependent_potassium_current (nanoA)" legend_constants[10] = "i_K_max in component time_dependent_potassium_current (nanoA)" legend_states[5] = "x in component time_dependent_potassium_current_x_gate (dimensionless)" legend_algebraic[2] = "alpha_x in component time_dependent_potassium_current_x_gate (per_second)" legend_algebraic[12] = "beta_x in component time_dependent_potassium_current_x_gate (per_second)" legend_constants[11] = "g_K1 in component time_independent_potassium_current (microS)" legend_constants[12] = "Km_K1 in component time_independent_potassium_current (millimolar)" legend_constants[13] = "Km_to in component transient_outward_current (millimolar)" legend_constants[14] = "Km_Ca in component transient_outward_current (millimolar)" legend_constants[15] = "g_to in component transient_outward_current (microS_per_millimolar)" legend_states[6] = "Cai in component intracellular_calcium_concentration (millimolar)" legend_states[7] = "s in component transient_outward_current_s_gate (dimensionless)" legend_algebraic[3] = "alpha_s in component transient_outward_current_s_gate (per_second)" legend_algebraic[13] = "beta_s in component transient_outward_current_s_gate (per_second)" legend_constants[16] = "g_Nab in component sodium_background_current (microS)" legend_algebraic[31] = "E_Ca in component calcium_background_current (millivolt)" legend_constants[17] = "g_Cab in component calcium_background_current (microS)" legend_constants[18] = "Cao in component extracellular_calcium_concentration (millimolar)" legend_constants[19] = "I_p in component sodium_potassium_pump (nanoA)" legend_constants[20] = "K_mK in component sodium_potassium_pump (millimolar)" legend_constants[21] = "K_mNa in component sodium_potassium_pump (millimolar)" legend_constants[22] = "n_NaCa in component Na_Ca_exchanger (dimensionless)" legend_constants[23] = "K_NaCa in component Na_Ca_exchanger (nanoA)" legend_constants[24] = "d_NaCa in component Na_Ca_exchanger (dimensionless)" legend_constants[25] = "gamma in component Na_Ca_exchanger (dimensionless)" legend_constants[26] = "g_Na in component fast_sodium_current (microS)" legend_algebraic[35] = "E_mh in component fast_sodium_current (millivolt)" legend_states[8] = "m in component fast_sodium_current_m_gate (dimensionless)" legend_states[9] = "h in component fast_sodium_current_h_gate (dimensionless)" legend_algebraic[14] = "alpha_m in component fast_sodium_current_m_gate (per_second)" legend_algebraic[20] = "beta_m in component fast_sodium_current_m_gate (per_second)" legend_constants[27] = "delta_m in component fast_sodium_current_m_gate (millivolt)" legend_algebraic[4] = "E0_m in component fast_sodium_current_m_gate (millivolt)" legend_algebraic[5] = "alpha_h in component fast_sodium_current_h_gate (per_second)" legend_algebraic[15] = "beta_h in component fast_sodium_current_h_gate (per_second)" legend_algebraic[37] = "i_siCa in component second_inward_current (nanoA)" legend_algebraic[38] = "i_siK in component second_inward_current (nanoA)" legend_algebraic[40] = "i_siNa in component second_inward_current (nanoA)" legend_constants[28] = "P_si in component second_inward_current (nanoA_per_millimolar)" legend_states[10] = "d in component second_inward_current_d_gate (dimensionless)" legend_states[11] = "f in component second_inward_current_f_gate (dimensionless)" legend_states[12] = "f2 in component second_inward_current_f2_gate (dimensionless)" legend_algebraic[16] = "alpha_d in component second_inward_current_d_gate (per_second)" legend_algebraic[21] = "beta_d in component second_inward_current_d_gate (per_second)" legend_constants[29] = "delta_d in component second_inward_current_d_gate (millivolt)" legend_algebraic[6] = "E0_d in component second_inward_current_d_gate (millivolt)" legend_algebraic[17] = "alpha_f in component second_inward_current_f_gate (per_second)" legend_algebraic[22] = "beta_f in component second_inward_current_f_gate (per_second)" legend_constants[30] = "delta_f in component second_inward_current_f_gate (millivolt)" legend_algebraic[7] = "E0_f in component second_inward_current_f_gate (millivolt)" legend_constants[31] = "alpha_f2 in component second_inward_current_f2_gate (per_second)" legend_algebraic[8] = "beta_f2 in component second_inward_current_f2_gate (per_second)" legend_constants[32] = "K_mf2 in component second_inward_current_f2_gate (millimolar)" legend_constants[33] = "radius in component intracellular_sodium_concentration (micrometre)" legend_constants[34] = "length in component intracellular_sodium_concentration (micrometre)" legend_constants[35] = "V_e_ratio in component intracellular_sodium_concentration (dimensionless)" legend_constants[46] = "V_Cell in component intracellular_sodium_concentration (micrometre3)" legend_constants[47] = "Vi in component intracellular_sodium_concentration (micrometre3)" legend_constants[48] = "V_up in component intracellular_calcium_concentration (micrometre3)" legend_constants[49] = "V_rel in component intracellular_calcium_concentration (micrometre3)" legend_algebraic[39] = "i_up in component intracellular_calcium_concentration (nanoA)" legend_algebraic[41] = "i_tr in component intracellular_calcium_concentration (nanoA)" legend_algebraic[44] = "i_rel in component intracellular_calcium_concentration (nanoA)" legend_states[13] = "Ca_up in component intracellular_calcium_concentration (millimolar)" legend_states[14] = "Ca_rel in component intracellular_calcium_concentration (millimolar)" legend_constants[36] = "Ca_up_max in component intracellular_calcium_concentration (millimolar)" legend_constants[37] = "K_mCa in component intracellular_calcium_concentration (millimolar)" legend_states[15] = "p in component intracellular_calcium_concentration (dimensionless)" legend_algebraic[9] = "alpha_p in component intracellular_calcium_concentration (per_second)" legend_algebraic[18] = "beta_p in component intracellular_calcium_concentration (per_second)" legend_constants[38] = "tau_up in component intracellular_calcium_concentration (second)" legend_constants[39] = "tau_rep in component intracellular_calcium_concentration (second)" legend_constants[40] = "tau_rel in component intracellular_calcium_concentration (second)" legend_constants[41] = "rCa in component intracellular_calcium_concentration (dimensionless)" legend_constants[42] = "Ve in component extracellular_potassium_concentration (micrometre3)" legend_constants[43] = "Kb in component extracellular_potassium_concentration (millimolar)" legend_algebraic[42] = "i_mK in component extracellular_potassium_concentration (nanoA)" legend_constants[44] = "pf in component extracellular_potassium_concentration (per_second)" legend_rates[0] = "d/dt V in component membrane (millivolt)" legend_rates[4] = "d/dt y in component hyperpolarising_activated_current_y_gate (dimensionless)" legend_rates[5] = "d/dt x in component time_dependent_potassium_current_x_gate (dimensionless)" legend_rates[7] = "d/dt s in component transient_outward_current_s_gate (dimensionless)" legend_rates[8] = "d/dt m in component fast_sodium_current_m_gate (dimensionless)" legend_rates[9] = "d/dt h in component fast_sodium_current_h_gate (dimensionless)" legend_rates[10] = "d/dt d in component second_inward_current_d_gate (dimensionless)" legend_rates[11] = "d/dt f in component second_inward_current_f_gate (dimensionless)" legend_rates[12] = "d/dt f2 in component second_inward_current_f2_gate (dimensionless)" legend_rates[3] = "d/dt Nai in component intracellular_sodium_concentration (millimolar)" legend_rates[15] = "d/dt p in component intracellular_calcium_concentration (dimensionless)" legend_rates[13] = "d/dt Ca_up in component intracellular_calcium_concentration (millimolar)" legend_rates[14] = "d/dt Ca_rel in component intracellular_calcium_concentration (millimolar)" legend_rates[6] = "d/dt Cai in component intracellular_calcium_concentration (millimolar)" legend_rates[1] = "d/dt Kc in component extracellular_potassium_concentration (millimolar)" legend_rates[2] = "d/dt Ki in component intracellular_potassium_concentration (millimolar)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = -87 constants[0] = 8314.472 constants[1] = 310 constants[2] = 96485.3415 constants[3] = 0.075 constants[4] = 0 constants[5] = 3 constants[6] = 3 constants[7] = 45 states[1] = 4 states[2] = 140 states[3] = 8 constants[8] = 140 states[4] = 0.2 constants[9] = 1e-5 constants[10] = 180 states[5] = 0.01 constants[11] = 920 constants[12] = 210 constants[13] = 10 constants[14] = 0.0005 constants[15] = 0.28 states[6] = 5e-5 states[7] = 1 constants[16] = 0.18 constants[17] = 0.02 constants[18] = 2 constants[19] = 125 constants[20] = 1 constants[21] = 40 constants[22] = 3 constants[23] = 0.02 constants[24] = 0.001 constants[25] = 0.5 constants[26] = 750 states[8] = 0.01 states[9] = 0.8 constants[27] = 1e-5 constants[28] = 15 states[10] = 0.005 states[11] = 1 states[12] = 1 constants[29] = 0.0001 constants[30] = 0.0001 constants[31] = 5 constants[32] = 0.001 constants[33] = 0.05 constants[34] = 2 constants[35] = 0.1 states[13] = 2 states[14] = 1 constants[36] = 5 constants[37] = 0.001 states[15] = 1 constants[38] = 0.025 constants[39] = 2 constants[40] = 0.05 constants[41] = 2 constants[42] = 0.00157 constants[43] = 4 constants[44] = 0.7 constants[45] = (constants[0]*constants[1])/constants[2] constants[46] = 3.14159*(power(constants[33], 2.00000))*constants[34] constants[47] = constants[46]*(1.00000-constants[35]) constants[48] = constants[47]*0.0500000 constants[49] = constants[47]*0.0200000 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[8] = (states[6]*constants[31])/constants[32] rates[12] = constants[31]-states[12]*(constants[31]+algebraic[8]) algebraic[2] = (0.500000*exp(0.0826000*(states[0]+50.0000)))/(1.00000+exp(0.0570000*(states[0]+50.0000))) algebraic[12] = (1.30000*exp(-0.0600000*(states[0]+20.0000)))/(1.00000+exp(-0.0400000*(states[0]+20.0000))) rates[5] = algebraic[2]*(1.00000-states[5])-algebraic[12]*states[5] algebraic[3] = 0.0330000*exp(-states[0]/17.0000) algebraic[13] = 33.0000/(1.00000+exp(-(states[0]+10.0000)/8.00000)) rates[7] = algebraic[3]*(1.00000-states[7])-algebraic[13]*states[7] algebraic[5] = 20.0000*exp(-0.125000*(states[0]+75.0000)) algebraic[15] = 2000.00/(320.000*exp(-0.100000*(states[0]+75.0000))+1.00000) rates[9] = algebraic[5]*(1.00000-states[9])-algebraic[15]*states[9] algebraic[9] = (0.625000*(states[0]+34.0000))/(exp((states[0]+34.0000)/4.00000)-1.00000) algebraic[18] = 5.00000/(1.00000+exp((-1.00000*(states[0]+34.0000))/4.00000)) rates[15] = algebraic[9]*(1.00000-states[15])-algebraic[18]*states[15] algebraic[1] = 0.0500000*exp(-0.0670000*((states[0]+52.0000)-10.0000)) algebraic[11] = (states[0]+52.0000)-10.0000 algebraic[19] = custom_piecewise([less(fabs(algebraic[11]) , constants[9]), 2.50000 , True, (1.00000*algebraic[11])/(1.00000-exp(-0.200000*algebraic[11]))]) rates[4] = algebraic[1]*(1.00000-states[4])-algebraic[19]*states[4] algebraic[4] = states[0]+41.0000 algebraic[14] = custom_piecewise([less(fabs(algebraic[4]) , constants[27]), 2000.00 , True, (200.000*algebraic[4])/(1.00000-exp(-0.100000*algebraic[4]))]) algebraic[20] = 8000.00*exp(-0.0560000*(states[0]+66.0000)) rates[8] = algebraic[14]*(1.00000-states[8])-algebraic[20]*states[8] algebraic[6] = (states[0]+24.0000)-5.00000 algebraic[16] = custom_piecewise([less(fabs(algebraic[6]) , constants[29]), 120.000 , True, (30.0000*algebraic[6])/(1.00000-exp((-1.00000*algebraic[6])/4.00000))]) algebraic[21] = custom_piecewise([less(fabs(algebraic[6]) , constants[29]), 120.000 , True, (12.0000*algebraic[6])/(exp(algebraic[6]/10.0000)-1.00000)]) rates[10] = algebraic[16]*(1.00000-states[10])-algebraic[21]*states[10] algebraic[7] = states[0]+34.0000 algebraic[17] = custom_piecewise([less(fabs(algebraic[7]) , constants[30]), 25.0000 , True, (6.25000*algebraic[7])/(exp(algebraic[7]/4.00000)-1.00000)]) algebraic[22] = 50.0000/(1.00000+exp((-1.00000*(states[0]+34.0000))/4.00000)) rates[11] = algebraic[17]*(1.00000-states[11])-algebraic[22]*states[11] algebraic[0] = constants[45]*log(constants[8]/states[3]) algebraic[30] = constants[16]*(states[0]-algebraic[0]) algebraic[33] = (((constants[19]*states[1])/(constants[20]+states[1]))*states[3])/(constants[21]+states[3]) algebraic[34] = (constants[23]*(exp((constants[25]*(constants[22]-2.00000)*states[0])/constants[45])*(power(states[3], constants[22]))*constants[18]-exp(((constants[25]-1.00000)*(constants[22]-2.00000)*states[0])/constants[45])*(power(constants[8], constants[22]))*states[6]))/((1.00000+constants[24]*(states[6]*(power(constants[8], constants[22]))+constants[18]*(power(states[3], constants[22]))))*(1.00000+states[6]/0.00690000)) algebraic[35] = constants[45]*log((constants[8]+0.120000*states[1])/(states[3]+0.120000*states[2])) algebraic[36] = constants[26]*(power(states[8], 3.00000))*states[9]*(states[0]-algebraic[35]) algebraic[23] = ((states[4]*states[1])/(states[1]+constants[7]))*constants[5]*(states[0]-algebraic[0]) algebraic[40] = ((0.0100000*constants[28]*(states[0]-50.0000))/(constants[45]*(1.00000-exp((-1.00000*(states[0]-50.0000))/constants[45]))))*(states[3]*exp(50.0000/constants[45])-constants[8]*exp((-1.00000*(states[0]-50.0000))/constants[45]))*states[10]*states[11]*states[12] rates[3] = (-1.00000*(algebraic[36]+algebraic[30]+algebraic[23]+algebraic[40]+algebraic[33]*3.00000+(algebraic[34]*constants[22])/(constants[22]-2.00000)))/(1.00000*constants[47]*constants[2]) algebraic[39] = ((2.00000*1.00000*constants[47]*constants[2])/(1.00000*constants[38]*constants[36]))*states[6]*(constants[36]-states[13]) algebraic[41] = ((2.00000*1.00000*constants[49]*constants[2])/(1.00000*constants[39]))*states[15]*(states[13]-states[14]) rates[13] = (1.00000*(algebraic[39]-algebraic[41]))/(2.00000*1.00000*constants[48]*constants[2]) algebraic[26] = (constants[10]*(states[2]-states[1]*exp(-states[0]/constants[45])))/140.000 algebraic[27] = states[5]*algebraic[26] algebraic[10] = constants[45]*log(states[1]/states[2]) algebraic[28] = (((constants[11]*states[1])/(states[1]+constants[12]))*(states[0]-algebraic[10]))/(1.00000+exp((((states[0]+10.0000)-algebraic[10])*2.00000)/constants[45])) algebraic[29] = ((((states[7]*constants[15]*(0.200000+states[1]/(constants[13]+states[1]))*states[6])/(constants[14]+states[6]))*(states[0]+10.0000))/(1.00000-exp(-0.200000*(states[0]+10.0000))))*(states[2]*exp((0.500000*states[0])/constants[45])-states[1]*exp((-0.500000*states[0])/constants[45])) algebraic[24] = ((states[4]*states[1])/(states[1]+constants[7]))*constants[6]*(states[0]-algebraic[10]) algebraic[38] = ((0.0100000*constants[28]*(states[0]-50.0000))/(constants[45]*(1.00000-exp((-1.00000*(states[0]-50.0000))/constants[45]))))*(states[2]*exp(50.0000/constants[45])-states[1]*exp((-1.00000*(states[0]-50.0000))/constants[45]))*states[10]*states[11]*states[12] algebraic[42] = (algebraic[28]+algebraic[27]+algebraic[24]+algebraic[38]+algebraic[29])-2.00000*algebraic[33] rates[1] = -constants[44]*(states[1]-constants[43])+(1.00000*algebraic[42])/(1.00000*constants[42]*constants[2]) rates[2] = (-1.00000*algebraic[42])/(1.00000*constants[47]*constants[2]) algebraic[25] = algebraic[23]+algebraic[24] algebraic[31] = 0.500000*constants[45]*log(constants[18]/states[6]) algebraic[32] = constants[17]*(states[0]-algebraic[31]) algebraic[37] = ((4.00000*constants[28]*(states[0]-50.0000))/(constants[45]*(1.00000-exp((-1.00000*(states[0]-50.0000)*2.00000)/constants[45]))))*(states[6]*exp(100.000/constants[45])-constants[18]*exp((-2.00000*(states[0]-50.0000))/constants[45]))*states[10]*states[11]*states[12] algebraic[43] = algebraic[37]+algebraic[38]+algebraic[40] rates[0] = -(algebraic[25]+algebraic[27]+algebraic[28]+algebraic[29]+algebraic[30]+algebraic[32]+algebraic[33]+algebraic[34]+algebraic[36]+algebraic[43]+constants[4])/constants[3] algebraic[44] = (((2.00000*1.00000*constants[49]*constants[2])/(1.00000*constants[40]))*states[14]*(power(states[6], constants[41])))/(power(states[6], constants[41])+power(constants[37], constants[41])) rates[14] = (1.00000*(algebraic[41]-algebraic[44]))/(2.00000*1.00000*constants[49]*constants[2]) rates[6] = (-1.00000*((((algebraic[37]+algebraic[32])-(2.00000*algebraic[34])/(constants[22]-2.00000))-algebraic[44])+algebraic[39]))/(2.00000*1.00000*constants[47]*constants[2]) return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[8] = (states[6]*constants[31])/constants[32] algebraic[2] = (0.500000*exp(0.0826000*(states[0]+50.0000)))/(1.00000+exp(0.0570000*(states[0]+50.0000))) algebraic[12] = (1.30000*exp(-0.0600000*(states[0]+20.0000)))/(1.00000+exp(-0.0400000*(states[0]+20.0000))) algebraic[3] = 0.0330000*exp(-states[0]/17.0000) algebraic[13] = 33.0000/(1.00000+exp(-(states[0]+10.0000)/8.00000)) algebraic[5] = 20.0000*exp(-0.125000*(states[0]+75.0000)) algebraic[15] = 2000.00/(320.000*exp(-0.100000*(states[0]+75.0000))+1.00000) algebraic[9] = (0.625000*(states[0]+34.0000))/(exp((states[0]+34.0000)/4.00000)-1.00000) algebraic[18] = 5.00000/(1.00000+exp((-1.00000*(states[0]+34.0000))/4.00000)) algebraic[1] = 0.0500000*exp(-0.0670000*((states[0]+52.0000)-10.0000)) algebraic[11] = (states[0]+52.0000)-10.0000 algebraic[19] = custom_piecewise([less(fabs(algebraic[11]) , constants[9]), 2.50000 , True, (1.00000*algebraic[11])/(1.00000-exp(-0.200000*algebraic[11]))]) algebraic[4] = states[0]+41.0000 algebraic[14] = custom_piecewise([less(fabs(algebraic[4]) , constants[27]), 2000.00 , True, (200.000*algebraic[4])/(1.00000-exp(-0.100000*algebraic[4]))]) algebraic[20] = 8000.00*exp(-0.0560000*(states[0]+66.0000)) algebraic[6] = (states[0]+24.0000)-5.00000 algebraic[16] = custom_piecewise([less(fabs(algebraic[6]) , constants[29]), 120.000 , True, (30.0000*algebraic[6])/(1.00000-exp((-1.00000*algebraic[6])/4.00000))]) algebraic[21] = custom_piecewise([less(fabs(algebraic[6]) , constants[29]), 120.000 , True, (12.0000*algebraic[6])/(exp(algebraic[6]/10.0000)-1.00000)]) algebraic[7] = states[0]+34.0000 algebraic[17] = custom_piecewise([less(fabs(algebraic[7]) , constants[30]), 25.0000 , True, (6.25000*algebraic[7])/(exp(algebraic[7]/4.00000)-1.00000)]) algebraic[22] = 50.0000/(1.00000+exp((-1.00000*(states[0]+34.0000))/4.00000)) algebraic[0] = constants[45]*log(constants[8]/states[3]) algebraic[30] = constants[16]*(states[0]-algebraic[0]) algebraic[33] = (((constants[19]*states[1])/(constants[20]+states[1]))*states[3])/(constants[21]+states[3]) algebraic[34] = (constants[23]*(exp((constants[25]*(constants[22]-2.00000)*states[0])/constants[45])*(power(states[3], constants[22]))*constants[18]-exp(((constants[25]-1.00000)*(constants[22]-2.00000)*states[0])/constants[45])*(power(constants[8], constants[22]))*states[6]))/((1.00000+constants[24]*(states[6]*(power(constants[8], constants[22]))+constants[18]*(power(states[3], constants[22]))))*(1.00000+states[6]/0.00690000)) algebraic[35] = constants[45]*log((constants[8]+0.120000*states[1])/(states[3]+0.120000*states[2])) algebraic[36] = constants[26]*(power(states[8], 3.00000))*states[9]*(states[0]-algebraic[35]) algebraic[23] = ((states[4]*states[1])/(states[1]+constants[7]))*constants[5]*(states[0]-algebraic[0]) algebraic[40] = ((0.0100000*constants[28]*(states[0]-50.0000))/(constants[45]*(1.00000-exp((-1.00000*(states[0]-50.0000))/constants[45]))))*(states[3]*exp(50.0000/constants[45])-constants[8]*exp((-1.00000*(states[0]-50.0000))/constants[45]))*states[10]*states[11]*states[12] algebraic[39] = ((2.00000*1.00000*constants[47]*constants[2])/(1.00000*constants[38]*constants[36]))*states[6]*(constants[36]-states[13]) algebraic[41] = ((2.00000*1.00000*constants[49]*constants[2])/(1.00000*constants[39]))*states[15]*(states[13]-states[14]) algebraic[26] = (constants[10]*(states[2]-states[1]*exp(-states[0]/constants[45])))/140.000 algebraic[27] = states[5]*algebraic[26] algebraic[10] = constants[45]*log(states[1]/states[2]) algebraic[28] = (((constants[11]*states[1])/(states[1]+constants[12]))*(states[0]-algebraic[10]))/(1.00000+exp((((states[0]+10.0000)-algebraic[10])*2.00000)/constants[45])) algebraic[29] = ((((states[7]*constants[15]*(0.200000+states[1]/(constants[13]+states[1]))*states[6])/(constants[14]+states[6]))*(states[0]+10.0000))/(1.00000-exp(-0.200000*(states[0]+10.0000))))*(states[2]*exp((0.500000*states[0])/constants[45])-states[1]*exp((-0.500000*states[0])/constants[45])) algebraic[24] = ((states[4]*states[1])/(states[1]+constants[7]))*constants[6]*(states[0]-algebraic[10]) algebraic[38] = ((0.0100000*constants[28]*(states[0]-50.0000))/(constants[45]*(1.00000-exp((-1.00000*(states[0]-50.0000))/constants[45]))))*(states[2]*exp(50.0000/constants[45])-states[1]*exp((-1.00000*(states[0]-50.0000))/constants[45]))*states[10]*states[11]*states[12] algebraic[42] = (algebraic[28]+algebraic[27]+algebraic[24]+algebraic[38]+algebraic[29])-2.00000*algebraic[33] algebraic[25] = algebraic[23]+algebraic[24] algebraic[31] = 0.500000*constants[45]*log(constants[18]/states[6]) algebraic[32] = constants[17]*(states[0]-algebraic[31]) algebraic[37] = ((4.00000*constants[28]*(states[0]-50.0000))/(constants[45]*(1.00000-exp((-1.00000*(states[0]-50.0000)*2.00000)/constants[45]))))*(states[6]*exp(100.000/constants[45])-constants[18]*exp((-2.00000*(states[0]-50.0000))/constants[45]))*states[10]*states[11]*states[12] algebraic[43] = algebraic[37]+algebraic[38]+algebraic[40] algebraic[44] = (((2.00000*1.00000*constants[49]*constants[2])/(1.00000*constants[40]))*states[14]*(power(states[6], constants[41])))/(power(states[6], constants[41])+power(constants[37], constants[41])) 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)