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 = 55
sizeStates = 19
sizeConstants = 59
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_constants[0] = "q_RB1_inactive_init in component environment (fmol)"
legend_constants[1] = "q_L_RB1_inactive_init in component environment (fmol)"
legend_algebraic[0] = "q_LB1_init in component environment (fmol)"
legend_constants[2] = "q_RB1_init in component environment (fmol)"
legend_constants[3] = "q_Gs_init in component environment (fmol)"
legend_constants[4] = "q_RB1_Gs_init in component environment (fmol)"
legend_constants[5] = "q_L_RB1_init in component environment (fmol)"
legend_constants[6] = "q_L_RB1_Gs_init in component environment (fmol)"
legend_constants[7] = "q_Gsa_GTP_init in component environment (fmol)"
legend_constants[8] = "q_Gsbetagamma_init in component environment (fmol)"
legend_constants[9] = "q_Gsa_GDP_init in component environment (fmol)"
legend_constants[10] = "q_GTP_init in component environment (fmol)"
legend_constants[11] = "q_GDP_init in component environment (fmol)"
legend_constants[12] = "q_Pi_init in component environment (fmol)"
legend_constants[13] = "q_RB1_tag_init in component environment (fmol)"
legend_constants[14] = "q_L_RB1_tag_init in component environment (fmol)"
legend_constants[15] = "q_RB1_GRKArr_init in component environment (fmol)"
legend_constants[16] = "q_L_RB1_GRKArr_init in component environment (fmol)"
legend_constants[17] = "q_GRKArr_init in component environment (fmol)"
legend_constants[18] = "stimSt in component environment (second)"
legend_constants[19] = "stimDur in component environment (second)"
legend_constants[20] = "tR in component environment (second)"
legend_constants[21] = "stimMag in component environment (fmol)"
legend_constants[22] = "stimHolding in component environment (fmol)"
legend_constants[57] = "m in component environment (fmol_per_sec)"
legend_algebraic[1] = "q_RB1_inactive in component environment (fmol)"
legend_algebraic[2] = "q_L_RB1_inactive in component environment (fmol)"
legend_algebraic[3] = "q_LB1 in component environment (fmol)"
legend_algebraic[4] = "q_RB1 in component environment (fmol)"
legend_algebraic[5] = "q_Gs in component environment (fmol)"
legend_algebraic[6] = "q_RB1_Gs in component environment (fmol)"
legend_algebraic[7] = "q_L_RB1 in component environment (fmol)"
legend_algebraic[8] = "q_L_RB1_Gs in component environment (fmol)"
legend_algebraic[9] = "q_Gsa_GTP in component environment (fmol)"
legend_algebraic[10] = "q_Gsbetagamma in component environment (fmol)"
legend_algebraic[11] = "q_Gsa_GDP in component environment (fmol)"
legend_algebraic[13] = "q_GTP in component environment (fmol)"
legend_algebraic[14] = "q_GDP in component environment (fmol)"
legend_algebraic[15] = "q_Pi in component environment (fmol)"
legend_algebraic[16] = "q_RB1_tag in component environment (fmol)"
legend_algebraic[17] = "q_L_RB1_tag in component environment (fmol)"
legend_algebraic[18] = "q_RB1_GRKArr in component environment (fmol)"
legend_algebraic[19] = "q_L_RB1_GRKArr in component environment (fmol)"
legend_algebraic[22] = "q_GRKArr in component environment (fmol)"
legend_states[0] = "q_RB1_inactive in component GPCR_B1AR_reduced (fmol)"
legend_states[1] = "q_L_RB1_inactive in component GPCR_B1AR_reduced (fmol)"
legend_states[2] = "q_LB1 in component GPCR_B1AR_reduced (fmol)"
legend_states[3] = "q_RB1 in component GPCR_B1AR_reduced (fmol)"
legend_states[4] = "q_Gs in component GPCR_B1AR_reduced (fmol)"
legend_states[5] = "q_RB1_Gs in component GPCR_B1AR_reduced (fmol)"
legend_states[6] = "q_L_RB1 in component GPCR_B1AR_reduced (fmol)"
legend_states[7] = "q_L_RB1_Gs in component GPCR_B1AR_reduced (fmol)"
legend_states[8] = "q_Gsa_GTP in component GPCR_B1AR_reduced (fmol)"
legend_states[9] = "q_Gsbetagamma in component GPCR_B1AR_reduced (fmol)"
legend_states[10] = "q_Gsa_GDP in component GPCR_B1AR_reduced (fmol)"
legend_states[11] = "q_GTP in component GPCR_B1AR_reduced (fmol)"
legend_states[12] = "q_GDP in component GPCR_B1AR_reduced (fmol)"
legend_states[13] = "q_Pi in component GPCR_B1AR_reduced (fmol)"
legend_states[14] = "q_RB1_tag in component GPCR_B1AR_reduced (fmol)"
legend_states[15] = "q_L_RB1_tag in component GPCR_B1AR_reduced (fmol)"
legend_states[16] = "q_RB1_GRKArr in component GPCR_B1AR_reduced (fmol)"
legend_states[17] = "q_L_RB1_GRKArr in component GPCR_B1AR_reduced (fmol)"
legend_states[18] = "q_GRKArr in component GPCR_B1AR_reduced (fmol)"
legend_algebraic[20] = "conserv_R_T in component environment (fmol)"
legend_algebraic[21] = "conserv_L_T in component environment (fmol)"
legend_algebraic[12] = "conserv_G_T in component environment (fmol)"
legend_constants[58] = "total_R_init in component environment (fmol)"
legend_constants[23] = "kappa_Rswitch_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)"
legend_constants[24] = "kappa_LRswitch_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)"
legend_constants[25] = "kappa_C_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)"
legend_constants[26] = "kappa_R_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)"
legend_constants[27] = "kappa_L_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)"
legend_constants[28] = "kappa_L_actR in component GPCR_B1AR_reduced_parameters (fmol_per_sec)"
legend_constants[29] = "kappa_Act1_Gs in component GPCR_B1AR_reduced_parameters (fmol_per_sec)"
legend_constants[30] = "kappa_Act2_Gs in component GPCR_B1AR_reduced_parameters (fmol_per_sec)"
legend_constants[31] = "kappa_Hyd_Gs in component GPCR_B1AR_reduced_parameters (fmol_per_sec)"
legend_constants[32] = "kappa_Reassoc_Gs in component GPCR_B1AR_reduced_parameters (fmol_per_sec)"
legend_constants[33] = "kappa_InternR_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)"
legend_constants[34] = "kappa_InternLR_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)"
legend_constants[35] = "K_RB1_inactive in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[36] = "K_L_RB1_inactive in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[37] = "K_LB1 in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[38] = "K_RB1 in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[39] = "K_Gs in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[40] = "K_RB1_Gs in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[41] = "K_L_RB1 in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[42] = "K_L_RB1_Gs in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[43] = "K_Gsa_GTP in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[44] = "K_Gsbetagamma in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[45] = "K_Gsa_GDP in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[46] = "K_GTP in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[47] = "K_GDP in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[48] = "K_Pi in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[49] = "K_RB1_tag in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[50] = "K_L_RB1_tag in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[51] = "K_RB1_GRKArr in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[52] = "K_L_RB1_GRKArr in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[53] = "K_GRKArr in component GPCR_B1AR_reduced_parameters (per_fmol)"
legend_constants[54] = "R in component constants (J_per_K_per_mol)"
legend_constants[55] = "T in component constants (kelvin)"
legend_algebraic[23] = "mu_RB1_inactive in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[24] = "mu_L_RB1_inactive in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[25] = "mu_LB1 in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[26] = "mu_RB1 in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[27] = "mu_Gs in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[28] = "mu_RB1_Gs in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[29] = "mu_L_RB1 in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[30] = "mu_L_RB1_Gs in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[31] = "mu_Gsa_GTP in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[32] = "mu_Gsbetagamma in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[33] = "mu_Gsa_GDP in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[34] = "mu_GTP in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[35] = "mu_GDP in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[36] = "mu_Pi in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[37] = "mu_RB1_tag in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[38] = "mu_L_RB1_tag in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[39] = "mu_RB1_GRKArr in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[40] = "mu_L_RB1_GRKArr in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[41] = "mu_GRKArr in component GPCR_B1AR_reduced (J_per_mol)"
legend_algebraic[42] = "v_Rswitch_B1 in component GPCR_B1AR_reduced (fmol_per_sec)"
legend_algebraic[43] = "v_LRswitch_B1 in component GPCR_B1AR_reduced (fmol_per_sec)"
legend_algebraic[44] = "v_C_B1 in component GPCR_B1AR_reduced (fmol_per_sec)"
legend_algebraic[45] = "v_R_B1 in component GPCR_B1AR_reduced (fmol_per_sec)"
legend_algebraic[46] = "v_L_B1 in component GPCR_B1AR_reduced (fmol_per_sec)"
legend_algebraic[48] = "v_L_actR in component GPCR_B1AR_reduced (fmol_per_sec)"
legend_algebraic[47] = "v_Act1_Gs in component GPCR_B1AR_reduced (fmol_per_sec)"
legend_algebraic[49] = "v_Act2_Gs in component GPCR_B1AR_reduced (fmol_per_sec)"
legend_algebraic[50] = "v_Hyd_Gs in component GPCR_B1AR_reduced (fmol_per_sec)"
legend_algebraic[53] = "v_Reassoc_Gs in component GPCR_B1AR_reduced (fmol_per_sec)"
legend_algebraic[51] = "v_InternR_B1 in component GPCR_B1AR_reduced (fmol_per_sec)"
legend_algebraic[54] = "v_InternLR_B1 in component GPCR_B1AR_reduced (fmol_per_sec)"
legend_algebraic[52] = "v_Rsynthesis in component GPCR_B1AR_reduced (fmol_per_sec)"
legend_constants[56] = "F in component constants (C_per_mol)"
legend_rates[0] = "d/dt q_RB1_inactive in component GPCR_B1AR_reduced (fmol)"
legend_rates[1] = "d/dt q_L_RB1_inactive in component GPCR_B1AR_reduced (fmol)"
legend_rates[2] = "d/dt q_LB1 in component GPCR_B1AR_reduced (fmol)"
legend_rates[3] = "d/dt q_RB1 in component GPCR_B1AR_reduced (fmol)"
legend_rates[4] = "d/dt q_Gs in component GPCR_B1AR_reduced (fmol)"
legend_rates[5] = "d/dt q_RB1_Gs in component GPCR_B1AR_reduced (fmol)"
legend_rates[6] = "d/dt q_L_RB1 in component GPCR_B1AR_reduced (fmol)"
legend_rates[7] = "d/dt q_L_RB1_Gs in component GPCR_B1AR_reduced (fmol)"
legend_rates[8] = "d/dt q_Gsa_GTP in component GPCR_B1AR_reduced (fmol)"
legend_rates[9] = "d/dt q_Gsbetagamma in component GPCR_B1AR_reduced (fmol)"
legend_rates[10] = "d/dt q_Gsa_GDP in component GPCR_B1AR_reduced (fmol)"
legend_rates[11] = "d/dt q_GTP in component GPCR_B1AR_reduced (fmol)"
legend_rates[12] = "d/dt q_GDP in component GPCR_B1AR_reduced (fmol)"
legend_rates[13] = "d/dt q_Pi in component GPCR_B1AR_reduced (fmol)"
legend_rates[14] = "d/dt q_RB1_tag in component GPCR_B1AR_reduced (fmol)"
legend_rates[15] = "d/dt q_L_RB1_tag in component GPCR_B1AR_reduced (fmol)"
legend_rates[16] = "d/dt q_RB1_GRKArr in component GPCR_B1AR_reduced (fmol)"
legend_rates[17] = "d/dt q_L_RB1_GRKArr in component GPCR_B1AR_reduced (fmol)"
legend_rates[18] = "d/dt q_GRKArr in component GPCR_B1AR_reduced (fmol)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
constants[0] = 0.0004579000e0
constants[1] = 1e-18
constants[2] = 1e-18
constants[3] = 0.1455400000
constants[4] = 1e-18
constants[5] = 1e-18
constants[6] = 1e-18
constants[7] = 0.01
constants[8] = 0.02
constants[9] = 0.01
constants[10] = 2.2
constants[11] = 1.1
constants[12] = 570
constants[13] = 1e-18
constants[14] = 1e-18
constants[15] = 1e-18
constants[16] = 1e-18
constants[17] = 1e-3
constants[18] = 2.5
constants[19] = 5e-1
constants[20] = 5e0
constants[21] = 1e1
constants[22] = 1e-8
states[0] = 1e-16
states[1] = 1e-16
states[2] = 1e-16
states[3] = 1e-16
states[4] = 1e-16
states[5] = 1e-16
states[6] = 1e-16
states[7] = 1e-16
states[8] = 1e-16
states[9] = 1e-16
states[10] = 1e-16
states[11] = 1e-16
states[12] = 1e-16
states[13] = 1e-16
states[14] = 1e-16
states[15] = 1e-16
states[16] = 1e-16
states[17] = 1e-16
states[18] = 1e-16
constants[23] = 1036.38
constants[24] = 1.83921e-07
constants[25] = 891573
constants[26] = 1.58222e+06
constants[27] = 0
constants[28] = 52417.5
constants[29] = 0.000610519
constants[30] = 0.576677
constants[31] = 0.0661821
constants[32] = 8.60273e-06
constants[33] = 0.00230556
constants[34] = 2.17775
constants[35] = 28.0492
constants[36] = 1.58056e+11
constants[37] = 0.0574759
constants[38] = 0.280492
constants[39] = 0.00337913
constants[40] = 1.07597
constants[41] = 0.158056
constants[42] = 0.00113911
constants[43] = 0.00878478
constants[44] = 736.699
constants[45] = 161.34
constants[46] = 823.314
constants[47] = 3.61368e-10
constants[48] = 7.91408e-11
constants[49] = 0.500146
constants[50] = 0.000529497
constants[51] = 1.26086e-05
constants[52] = 1.33485e-08
constants[53] = 732843
constants[54] = 8.31
constants[55] = 310
constants[56] = 96485
constants[57] = constants[21]/constants[20]
constants[58] = constants[0]+constants[1]+constants[2]+constants[4]+constants[5]+constants[6]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[2] = states[1]+constants[1]
algebraic[24] = constants[54]*constants[55]*log(constants[36]*algebraic[2])
algebraic[7] = states[6]+constants[5]
algebraic[29] = constants[54]*constants[55]*log(constants[41]*algebraic[7])
algebraic[43] = constants[24]*(exp(algebraic[24]/(constants[54]*constants[55]))-exp(algebraic[29]/(constants[54]*constants[55])))
algebraic[1] = states[0]+constants[0]
algebraic[23] = constants[54]*constants[55]*log(constants[35]*algebraic[1])
algebraic[0] = custom_piecewise([less(voi , constants[18]) & greater(voi , constants[18]-constants[20]), constants[22]+constants[57]*((voi-constants[18])+constants[20]) , greater_equal(voi , constants[18]) & less(voi , constants[18]+constants[19]), constants[21]+constants[22] , less_equal(voi , constants[18]+constants[20]+constants[19]) & greater_equal(voi , constants[18]+constants[19]), constants[22]+-constants[57]*(((voi-constants[18])-constants[20])-constants[19]) , True, constants[22]])
algebraic[3] = states[2]+algebraic[0]
algebraic[25] = constants[54]*constants[55]*log(constants[37]*algebraic[3])
algebraic[46] = constants[27]*(exp((algebraic[23]+algebraic[25])/(constants[54]*constants[55]))-exp(algebraic[24]/(constants[54]*constants[55])))
rates[1] = -algebraic[43]+algebraic[46]
algebraic[4] = states[3]+constants[2]
algebraic[26] = constants[54]*constants[55]*log(constants[38]*algebraic[4])
algebraic[5] = states[4]+constants[3]
algebraic[27] = constants[54]*constants[55]*log(constants[39]*algebraic[5])
algebraic[6] = states[5]+constants[4]
algebraic[28] = constants[54]*constants[55]*log(constants[40]*algebraic[6])
algebraic[44] = constants[25]*(exp((algebraic[26]+algebraic[27])/(constants[54]*constants[55]))-exp(algebraic[28]/(constants[54]*constants[55])))
algebraic[9] = states[8]+constants[7]
algebraic[31] = constants[54]*constants[55]*log(constants[43]*algebraic[9])
algebraic[10] = states[9]+constants[8]
algebraic[32] = constants[54]*constants[55]*log(constants[44]*algebraic[10])
algebraic[13] = states[11]+constants[10]
algebraic[34] = constants[54]*constants[55]*log(constants[46]*algebraic[13])
algebraic[14] = states[12]+constants[11]
algebraic[35] = constants[54]*constants[55]*log(constants[47]*algebraic[14])
algebraic[16] = states[14]+constants[13]
algebraic[37] = constants[54]*constants[55]*log(constants[49]*algebraic[16])
algebraic[47] = constants[29]*(exp((algebraic[28]+algebraic[34])/(constants[54]*constants[55]))-exp((algebraic[31]+algebraic[32]+algebraic[37]+algebraic[35])/(constants[54]*constants[55])))
rates[5] = algebraic[44]-algebraic[47]
algebraic[48] = constants[28]*(exp((algebraic[26]+algebraic[25])/(constants[54]*constants[55]))-exp(algebraic[29]/(constants[54]*constants[55])))
rates[2] = -algebraic[46]-algebraic[48]
algebraic[42] = constants[23]*(exp(algebraic[23]/(constants[54]*constants[55]))-exp(algebraic[26]/(constants[54]*constants[55])))
rates[3] = (algebraic[42]-algebraic[44])-algebraic[48]
algebraic[8] = states[7]+constants[6]
algebraic[30] = constants[54]*constants[55]*log(constants[42]*algebraic[8])
algebraic[45] = constants[26]*(exp((algebraic[29]+algebraic[27])/(constants[54]*constants[55]))-exp(algebraic[30]/(constants[54]*constants[55])))
rates[6] = (algebraic[43]-algebraic[45])+algebraic[48]
algebraic[17] = states[15]+constants[14]
algebraic[38] = constants[54]*constants[55]*log(constants[50]*algebraic[17])
algebraic[49] = constants[30]*(exp((algebraic[30]+algebraic[34])/(constants[54]*constants[55]))-exp((algebraic[31]+algebraic[32]+algebraic[38]+algebraic[35])/(constants[54]*constants[55])))
rates[7] = algebraic[45]-algebraic[49]
rates[11] = -algebraic[47]-algebraic[49]
rates[12] = algebraic[47]+algebraic[49]
algebraic[52] = algebraic[42]+algebraic[48]
rates[0] = (-algebraic[42]-algebraic[46])+0.00000*algebraic[52]
algebraic[11] = states[10]+constants[9]
algebraic[33] = constants[54]*constants[55]*log(constants[45]*algebraic[11])
algebraic[15] = states[13]+constants[12]
algebraic[36] = constants[54]*constants[55]*log(constants[48]*algebraic[15])
algebraic[50] = constants[31]*(exp(algebraic[31]/(constants[54]*constants[55]))-exp((algebraic[33]+algebraic[36])/(constants[54]*constants[55])))
rates[8] = (algebraic[47]+algebraic[49])-algebraic[50]
rates[13] = algebraic[50]
algebraic[18] = states[16]+constants[15]
algebraic[39] = constants[54]*constants[55]*log(constants[51]*algebraic[18])
algebraic[22] = states[18]+constants[17]
algebraic[41] = constants[54]*constants[55]*log(constants[53]*algebraic[22])
algebraic[51] = constants[33]*(exp((algebraic[37]+algebraic[41])/(constants[54]*constants[55]))-exp(algebraic[39]/(constants[54]*constants[55])))
rates[14] = algebraic[47]-algebraic[51]
rates[16] = algebraic[51]
algebraic[53] = constants[32]*(exp((algebraic[33]+algebraic[32])/(constants[54]*constants[55]))-exp(algebraic[27]/(constants[54]*constants[55])))
rates[4] = (-algebraic[44]-algebraic[45])+algebraic[53]
rates[9] = (algebraic[47]+algebraic[49])-algebraic[53]
rates[10] = algebraic[50]-algebraic[53]
algebraic[19] = states[17]+constants[16]
algebraic[40] = constants[54]*constants[55]*log(constants[52]*algebraic[19])
algebraic[54] = constants[34]*(exp((algebraic[38]+algebraic[41])/(constants[54]*constants[55]))-exp(algebraic[40]/(constants[54]*constants[55])))
rates[15] = algebraic[49]-algebraic[54]
rates[17] = algebraic[54]
rates[18] = -algebraic[51]-algebraic[54]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[2] = states[1]+constants[1]
algebraic[24] = constants[54]*constants[55]*log(constants[36]*algebraic[2])
algebraic[7] = states[6]+constants[5]
algebraic[29] = constants[54]*constants[55]*log(constants[41]*algebraic[7])
algebraic[43] = constants[24]*(exp(algebraic[24]/(constants[54]*constants[55]))-exp(algebraic[29]/(constants[54]*constants[55])))
algebraic[1] = states[0]+constants[0]
algebraic[23] = constants[54]*constants[55]*log(constants[35]*algebraic[1])
algebraic[0] = custom_piecewise([less(voi , constants[18]) & greater(voi , constants[18]-constants[20]), constants[22]+constants[57]*((voi-constants[18])+constants[20]) , greater_equal(voi , constants[18]) & less(voi , constants[18]+constants[19]), constants[21]+constants[22] , less_equal(voi , constants[18]+constants[20]+constants[19]) & greater_equal(voi , constants[18]+constants[19]), constants[22]+-constants[57]*(((voi-constants[18])-constants[20])-constants[19]) , True, constants[22]])
algebraic[3] = states[2]+algebraic[0]
algebraic[25] = constants[54]*constants[55]*log(constants[37]*algebraic[3])
algebraic[46] = constants[27]*(exp((algebraic[23]+algebraic[25])/(constants[54]*constants[55]))-exp(algebraic[24]/(constants[54]*constants[55])))
algebraic[4] = states[3]+constants[2]
algebraic[26] = constants[54]*constants[55]*log(constants[38]*algebraic[4])
algebraic[5] = states[4]+constants[3]
algebraic[27] = constants[54]*constants[55]*log(constants[39]*algebraic[5])
algebraic[6] = states[5]+constants[4]
algebraic[28] = constants[54]*constants[55]*log(constants[40]*algebraic[6])
algebraic[44] = constants[25]*(exp((algebraic[26]+algebraic[27])/(constants[54]*constants[55]))-exp(algebraic[28]/(constants[54]*constants[55])))
algebraic[9] = states[8]+constants[7]
algebraic[31] = constants[54]*constants[55]*log(constants[43]*algebraic[9])
algebraic[10] = states[9]+constants[8]
algebraic[32] = constants[54]*constants[55]*log(constants[44]*algebraic[10])
algebraic[13] = states[11]+constants[10]
algebraic[34] = constants[54]*constants[55]*log(constants[46]*algebraic[13])
algebraic[14] = states[12]+constants[11]
algebraic[35] = constants[54]*constants[55]*log(constants[47]*algebraic[14])
algebraic[16] = states[14]+constants[13]
algebraic[37] = constants[54]*constants[55]*log(constants[49]*algebraic[16])
algebraic[47] = constants[29]*(exp((algebraic[28]+algebraic[34])/(constants[54]*constants[55]))-exp((algebraic[31]+algebraic[32]+algebraic[37]+algebraic[35])/(constants[54]*constants[55])))
algebraic[48] = constants[28]*(exp((algebraic[26]+algebraic[25])/(constants[54]*constants[55]))-exp(algebraic[29]/(constants[54]*constants[55])))
algebraic[42] = constants[23]*(exp(algebraic[23]/(constants[54]*constants[55]))-exp(algebraic[26]/(constants[54]*constants[55])))
algebraic[8] = states[7]+constants[6]
algebraic[30] = constants[54]*constants[55]*log(constants[42]*algebraic[8])
algebraic[45] = constants[26]*(exp((algebraic[29]+algebraic[27])/(constants[54]*constants[55]))-exp(algebraic[30]/(constants[54]*constants[55])))
algebraic[17] = states[15]+constants[14]
algebraic[38] = constants[54]*constants[55]*log(constants[50]*algebraic[17])
algebraic[49] = constants[30]*(exp((algebraic[30]+algebraic[34])/(constants[54]*constants[55]))-exp((algebraic[31]+algebraic[32]+algebraic[38]+algebraic[35])/(constants[54]*constants[55])))
algebraic[52] = algebraic[42]+algebraic[48]
algebraic[11] = states[10]+constants[9]
algebraic[33] = constants[54]*constants[55]*log(constants[45]*algebraic[11])
algebraic[15] = states[13]+constants[12]
algebraic[36] = constants[54]*constants[55]*log(constants[48]*algebraic[15])
algebraic[50] = constants[31]*(exp(algebraic[31]/(constants[54]*constants[55]))-exp((algebraic[33]+algebraic[36])/(constants[54]*constants[55])))
algebraic[18] = states[16]+constants[15]
algebraic[39] = constants[54]*constants[55]*log(constants[51]*algebraic[18])
algebraic[22] = states[18]+constants[17]
algebraic[41] = constants[54]*constants[55]*log(constants[53]*algebraic[22])
algebraic[51] = constants[33]*(exp((algebraic[37]+algebraic[41])/(constants[54]*constants[55]))-exp(algebraic[39]/(constants[54]*constants[55])))
algebraic[53] = constants[32]*(exp((algebraic[33]+algebraic[32])/(constants[54]*constants[55]))-exp(algebraic[27]/(constants[54]*constants[55])))
algebraic[19] = states[17]+constants[16]
algebraic[40] = constants[54]*constants[55]*log(constants[52]*algebraic[19])
algebraic[54] = constants[34]*(exp((algebraic[38]+algebraic[41])/(constants[54]*constants[55]))-exp(algebraic[40]/(constants[54]*constants[55])))
algebraic[12] = algebraic[5]+algebraic[6]+algebraic[8]+algebraic[9]+algebraic[11]
algebraic[20] = algebraic[1]+algebraic[2]+algebraic[4]+algebraic[6]+algebraic[7]+algebraic[8]+algebraic[16]+algebraic[17]+algebraic[18]+algebraic[19]
algebraic[21] = algebraic[2]+algebraic[3]+algebraic[7]+algebraic[8]+algebraic[17]+algebraic[19]
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)