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 = 75
sizeStates = 9
sizeConstants = 54
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 (millisecond)"
legend_states[0] = "Gi in component Gi (millimolar)"
legend_algebraic[6] = "Jglut in component Jglut (millimolar_per_millisecond)"
legend_algebraic[7] = "Jgk in component Jgk (millimolar_per_millisecond)"
legend_algebraic[3] = "Ge in component Ge (millimolar)"
legend_constants[0] = "gluper in component Ge (dimensionless)"
legend_constants[1] = "gluamp in component Ge (millimolar)"
legend_constants[2] = "glubasa1 in component Ge (millimolar)"
legend_constants[3] = "glustep in component Ge (dimensionless)"
legend_constants[4] = "steptime in component Ge (millisecond)"
legend_algebraic[0] = "GeStep in component Ge (millimolar)"
legend_states[1] = "G6P in component G6P (millimolar)"
legend_constants[5] = "kappa in component model_parameters (dimensionless)"
legend_algebraic[74] = "JPFK in component JPFK (micromolar_per_millisecond)"
legend_states[2] = "FBP in component FBP (micromolar)"
legend_algebraic[8] = "JGPDH in component JGPDH (micromolar_per_millisecond)"
legend_algebraic[5] = "F6P in component F6P (millimolar)"
legend_constants[6] = "Kglut in component Jglut (millimolar)"
legend_constants[7] = "Vglut in component Jglut (millimolar_per_millisecond)"
legend_constants[8] = "Kgk in component Jgk (millimolar)"
legend_constants[9] = "Vgk in component Jgk (millimolar_per_millisecond)"
legend_constants[10] = "ngk in component Jgk (dimensionless)"
legend_constants[11] = "pfkbas in component JPFK (dimensionless)"
legend_constants[12] = "cat in component JPFK (micromolar_per_millisecond)"
legend_algebraic[60] = "topb in component w (dimensionless)"
legend_algebraic[72] = "topa16 in component w (dimensionless)"
legend_algebraic[73] = "bottom16 in component w (dimensionless)"
legend_constants[51] = "weight1 in component w (dimensionless)"
legend_algebraic[51] = "weight9 in component w (dimensionless)"
legend_algebraic[9] = "weight5 in component w (dimensionless)"
legend_algebraic[10] = "weight3 in component w (dimensionless)"
legend_algebraic[15] = "weight2 in component w (dimensionless)"
legend_algebraic[53] = "weight13 in component w (dimensionless)"
legend_algebraic[54] = "weight11 in component w (dimensionless)"
legend_algebraic[56] = "weight10 in component w (dimensionless)"
legend_algebraic[23] = "weight6 in component w (dimensionless)"
legend_algebraic[26] = "weight4 in component w (dimensionless)"
legend_algebraic[59] = "weight15 in component w (dimensionless)"
legend_algebraic[45] = "weight8 in component w (dimensionless)"
legend_algebraic[61] = "weight12 in component w (dimensionless)"
legend_algebraic[66] = "weight14 in component w (dimensionless)"
legend_algebraic[71] = "weight16 in component w (dimensionless)"
legend_algebraic[12] = "weight7 in component w (dimensionless)"
legend_constants[50] = "topa1 in component w (dimensionless)"
legend_constants[53] = "topa2 in component w (dimensionless)"
legend_algebraic[11] = "topa3 in component w (dimensionless)"
legend_algebraic[29] = "topa4 in component w (dimensionless)"
legend_algebraic[32] = "topa5 in component w (dimensionless)"
legend_algebraic[35] = "topa6 in component w (dimensionless)"
legend_algebraic[43] = "topa7 in component w (dimensionless)"
legend_algebraic[46] = "topa8 in component w (dimensionless)"
legend_algebraic[47] = "topa9 in component w (dimensionless)"
legend_algebraic[48] = "topa10 in component w (dimensionless)"
legend_algebraic[55] = "topa11 in component w (dimensionless)"
legend_algebraic[62] = "topa12 in component w (dimensionless)"
legend_algebraic[63] = "topa13 in component w (dimensionless)"
legend_algebraic[67] = "topa14 in component w (dimensionless)"
legend_algebraic[68] = "topa15 in component w (dimensionless)"
legend_constants[52] = "bottom1 in component w (dimensionless)"
legend_algebraic[18] = "bottom2 in component w (dimensionless)"
legend_algebraic[21] = "bottom3 in component w (dimensionless)"
legend_algebraic[37] = "bottom4 in component w (dimensionless)"
legend_algebraic[39] = "bottom5 in component w (dimensionless)"
legend_algebraic[41] = "bottom6 in component w (dimensionless)"
legend_algebraic[44] = "bottom7 in component w (dimensionless)"
legend_algebraic[49] = "bottom8 in component w (dimensionless)"
legend_algebraic[52] = "bottom9 in component w (dimensionless)"
legend_algebraic[57] = "bottom10 in component w (dimensionless)"
legend_algebraic[58] = "bottom11 in component w (dimensionless)"
legend_algebraic[64] = "bottom12 in component w (dimensionless)"
legend_algebraic[65] = "bottom13 in component w (dimensionless)"
legend_algebraic[69] = "bottom14 in component w (dimensionless)"
legend_algebraic[70] = "bottom15 in component w (dimensionless)"
legend_constants[13] = "famp in component w (dimensionless)"
legend_constants[14] = "ffbp in component w (dimensionless)"
legend_constants[15] = "fmt in component w (dimensionless)"
legend_constants[16] = "fbt in component w (dimensionless)"
legend_constants[17] = "fatp in component w (dimensionless)"
legend_constants[18] = "K1 in component w (micromolar)"
legend_constants[19] = "K2 in component w (micromolar)"
legend_constants[20] = "K3 in component w (micromolar)"
legend_constants[21] = "K4 in component w (micromolar)"
legend_algebraic[50] = "AMP in component AMP (micromolar)"
legend_algebraic[14] = "ATP in component ATP (micromolar)"
legend_constants[22] = "Atot in component ATP (micromolar)"
legend_algebraic[13] = "rad in component ATP (micromolar)"
legend_states[3] = "ADP in component ADP (micromolar)"
legend_algebraic[16] = "y in component ADP (dimensionless)"
legend_constants[23] = "tau_a in component ADP (millisecond)"
legend_constants[24] = "r in component ADP (dimensionless)"
legend_constants[25] = "r1 in component ADP (micromolar)"
legend_constants[26] = "autoadp in component ADP (dimensionless)"
legend_constants[27] = "adpknot in component ADP (micromolar)"
legend_algebraic[19] = "fback in component ADP (dimensionless)"
legend_constants[28] = "ky in component ADP (dimensionless)"
legend_constants[29] = "kg in component ADP (micromolar_per_millisecond)"
legend_states[4] = "Ca in component Ca (micromolar)"
legend_states[5] = "v in component membrane (millivolt)"
legend_constants[30] = "cm in component membrane (femtofarad)"
legend_algebraic[22] = "I_Ca in component I_Ca (femtoampere)"
legend_algebraic[17] = "I_K in component I_K (femtoampere)"
legend_algebraic[24] = "I_K_Ca in component I_K_Ca (femtoampere)"
legend_algebraic[42] = "I_K_ATP in component I_K_ATP (femtoampere)"
legend_constants[31] = "gK in component I_K (picosiemens)"
legend_constants[32] = "vK in component model_parameters (millivolt)"
legend_states[6] = "n in component n (dimensionless)"
legend_algebraic[4] = "n_infinity in component n (dimensionless)"
legend_algebraic[1] = "tau_n in component n (millisecond)"
legend_constants[33] = "gCa in component I_Ca (picosiemens)"
legend_constants[34] = "vCa in component model_parameters (millivolt)"
legend_algebraic[20] = "m_infinity in component m (dimensionless)"
legend_constants[35] = "gkCa in component I_K_Ca (picosiemens)"
legend_constants[36] = "KD in component I_K_Ca (micromolar)"
legend_constants[37] = "nh in component I_K_Ca (dimensionless)"
legend_constants[38] = "gkATP_bar in component I_K_ATP (picosiemens)"
legend_algebraic[40] = "katpo in component I_K_ATP (dimensionless)"
legend_algebraic[30] = "topo in component I_K_ATP (dimensionless)"
legend_algebraic[38] = "bottomo in component I_K_ATP (dimensionless)"
legend_algebraic[27] = "MgADP in component I_K_ATP (micromolar)"
legend_algebraic[33] = "ADP3 in component I_K_ATP (micromolar)"
legend_algebraic[36] = "ATP4 in component I_K_ATP (micromolar)"
legend_constants[39] = "fcyt in component Ca (dimensionless)"
legend_algebraic[25] = "Jmem in component Jmem (micromolar_per_millisecond)"
legend_algebraic[34] = "Jer in component Jer (micromolar_per_millisecond)"
legend_states[7] = "Caer in component Caer (micromolar)"
legend_constants[40] = "fer in component Caer (dimensionless)"
legend_constants[41] = "sigmav in component Caer (dimensionless)"
legend_constants[42] = "kPMCA in component Jmem (first_order_rate_constant)"
legend_constants[43] = "alpha in component Jmem (micromolar_per_millisecond)"
legend_algebraic[31] = "Jleak in component Jleak (micromolar_per_millisecond)"
legend_algebraic[28] = "JSERCA in component JSERCA (micromolar_per_millisecond)"
legend_constants[44] = "kSERCA in component JSERCA (first_order_rate_constant)"
legend_constants[45] = "pleak in component Jleak (first_order_rate_constant)"
legend_states[8] = "I in component I (dimensionless)"
legend_algebraic[2] = "I_infinity in component I (dimensionless)"
legend_constants[46] = "tau_I in component I (millisecond)"
legend_constants[47] = "I_max in component I (dimensionless)"
legend_constants[48] = "delta in component I (dimensionless)"
legend_constants[49] = "ki in component I (micromolar)"
legend_rates[0] = "d/dt Gi in component Gi (millimolar)"
legend_rates[1] = "d/dt G6P in component G6P (millimolar)"
legend_rates[2] = "d/dt FBP in component FBP (micromolar)"
legend_rates[3] = "d/dt ADP in component ADP (micromolar)"
legend_rates[5] = "d/dt v in component membrane (millivolt)"
legend_rates[6] = "d/dt n in component n (dimensionless)"
legend_rates[4] = "d/dt Ca in component Ca (micromolar)"
legend_rates[7] = "d/dt Caer in component Caer (micromolar)"
legend_rates[8] = "d/dt I in component I (dimensionless)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 6.0637
constants[0] = 7.0
constants[1] = 0.0
constants[2] = 7.0
constants[3] = 0.0
constants[4] = 480000
states[1] = 525.97
constants[5] = 0.005
states[2] = 0.2088
constants[6] = 7
constants[7] = 8
constants[8] = 7
constants[9] = 0.8
constants[10] = 4
constants[11] = 0.06
constants[12] = 2
constants[13] = 0.02
constants[14] = 0.2
constants[15] = 20
constants[16] = 20
constants[17] = 20
constants[18] = 30
constants[19] = 1
constants[20] = 50000
constants[21] = 1000
constants[22] = 3000
states[3] = 537.6
constants[23] = 300000
constants[24] = 0.5
constants[25] = 0.35
constants[26] = 1.0
constants[27] = 800.0
constants[28] = 2.2
constants[29] = 0.1
states[4] = 0.05626
states[5] = -66.7
constants[30] = 5300
constants[31] = 2700
constants[32] = -75
states[6] = 0.00012
constants[33] = 1000
constants[34] = 25
constants[35] = 400
constants[36] = 0.5
constants[37] = 2.0
constants[38] = 2000
constants[39] = 0.01
states[7] = 121.8
constants[40] = 0.01
constants[41] = 31
constants[42] = 0.18
constants[43] = 4.5e-6
constants[44] = 0.4
constants[45] = 0.0002
states[8] = 0.316
constants[46] = 10000
constants[47] = 20
constants[48] = 8.0
constants[49] = 0.1
constants[50] = 0.00000
constants[51] = 1.00000
constants[52] = 1.00000
constants[53] = constants[50]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[2] = constants[47]*((power(states[4], constants[48]))/(power(constants[49], constants[48])+power(states[4], constants[48])))
rates[8] = (algebraic[2]-states[8])/constants[46]
algebraic[4] = 0.500000*(1.00000+tanh((states[5]--16.0000)/11.2000))
algebraic[1] = 1.00000/(0.0350000*cosh((states[5]--16.0000)/22.4000))
rates[6] = (algebraic[4]-states[6])/algebraic[1]
algebraic[0] = custom_piecewise([greater((voi-constants[4])/1000.00 , 1.00000), constants[3]*constants[1] , greater((voi-constants[4])/1000.00 , 0.00000) & less((voi-constants[4])/1000.00 , 1.00000), ((voi-constants[4])/1000.00)*constants[3]*constants[1] , less((voi-constants[4])/1000.00 , 0.00000), 0.00000 , True, float('nan')])
algebraic[3] = constants[2]+constants[1]*(1.00000-constants[3])*cos((voi*2.00000* pi)/(60000.0*constants[0]))+algebraic[0]
algebraic[6] = constants[7]*(((algebraic[3]-states[0])*constants[6])/((constants[6]+algebraic[3])*(constants[6]+states[0])))
algebraic[7] = (constants[9]*(power(states[0], constants[10])))/(power(constants[8], constants[10])+power(states[0], constants[10]))
rates[0] = algebraic[6]-algebraic[7]
algebraic[13] = power(power(states[3]-constants[22], 2.00000)-4.00000*(power(states[3], 2.00000)), 1.0/2)
algebraic[14] = 0.500000*((constants[22]+algebraic[13])-states[3])
algebraic[8] = 0.200000*(power(states[2]/1.00000, 1.0/2))
algebraic[16] = (constants[28]*algebraic[8])/(constants[29]+algebraic[8])
algebraic[19] = constants[24]+algebraic[16]
rates[3] = constants[26]*((algebraic[14]-states[3]*exp(algebraic[19]*((1.00000-states[4])/constants[25])))/constants[23])+1.00000*(1.00000-constants[26])*(constants[27]-states[3])
algebraic[20] = 0.500000*(1.00000+tanh((states[5]--20.0000)/24.0000))
algebraic[22] = constants[33]*algebraic[20]*(states[5]-constants[34])
algebraic[25] = -(constants[43]*1.00000*algebraic[22]+constants[42]*states[4])
algebraic[31] = constants[45]*(states[7]-states[4])
algebraic[28] = constants[44]*states[4]
algebraic[34] = algebraic[31]-algebraic[28]
rates[4] = constants[39]*(algebraic[25]+algebraic[34])
rates[7] = -constants[40]*constants[41]*algebraic[34]
algebraic[17] = constants[31]*states[6]*(states[5]-constants[32])
algebraic[24] = (constants[35]/(1.00000+power(constants[36]/states[4], constants[37])))*(states[5]-constants[32])
algebraic[27] = 0.165000*states[3]
algebraic[30] = 0.0800000*(1.00000+(2.00000*algebraic[27])/17.0000)+0.890000*(power(algebraic[27]/17.0000, 2.00000))
algebraic[33] = 0.135000*states[3]
algebraic[36] = 0.0500000*algebraic[14]
algebraic[38] = (power(1.00000+algebraic[27]/17.0000, 2.00000))*(1.00000+algebraic[33]/26.0000+algebraic[36]/1.00000)
algebraic[40] = 20.0000*(algebraic[30]/algebraic[38])
algebraic[42] = constants[38]*algebraic[40]*(states[5]-constants[32])
rates[5] = -(algebraic[17]+algebraic[22]+algebraic[24]+algebraic[42])/constants[30]
algebraic[5] = 0.300000*states[1]
algebraic[50] = (power(states[3], 2.00000))/algebraic[14]
algebraic[59] = (algebraic[50]*states[2]*(power(algebraic[5], 2.00000)))/(1.00000*constants[18]*constants[19]*constants[20]*constants[14]*constants[13])
algebraic[60] = algebraic[59]
algebraic[71] = (algebraic[50]*states[2]*(power(algebraic[5], 2.00000))*(power(algebraic[14], 2.00000)))/(1.00000*constants[18]*constants[19]*constants[20]*constants[21]*constants[14]*constants[13]*constants[16]*constants[15]*constants[17])
algebraic[61] = (algebraic[50]*(power(algebraic[5], 2.00000))*(power(algebraic[14], 2.00000)))/(1.00000*constants[18]*constants[20]*constants[21]*constants[13]*constants[15]*constants[17])
algebraic[54] = (algebraic[50]*(power(algebraic[5], 2.00000)))/(1.00000*constants[18]*constants[20]*constants[13])
algebraic[45] = (states[2]*(power(algebraic[5], 2.00000))*(power(algebraic[14], 2.00000)))/(1.00000*constants[19]*constants[20]*constants[21]*constants[14]*constants[16]*constants[17])
algebraic[12] = (states[2]*(power(algebraic[5], 2.00000)))/(1.00000*constants[19]*constants[20]*constants[14])
algebraic[26] = (power(algebraic[5]*algebraic[14], 2.00000))/(1.00000*constants[17]*constants[20]*constants[21])
algebraic[10] = (power(algebraic[5], 2.00000))/(1.00000*constants[20])
algebraic[11] = constants[53]+algebraic[10]
algebraic[29] = algebraic[11]+algebraic[26]
algebraic[32] = algebraic[29]
algebraic[35] = algebraic[32]
algebraic[43] = algebraic[35]+algebraic[12]
algebraic[46] = algebraic[43]+algebraic[45]
algebraic[47] = algebraic[46]
algebraic[48] = algebraic[47]
algebraic[55] = algebraic[48]+algebraic[54]
algebraic[62] = algebraic[55]+algebraic[61]
algebraic[63] = algebraic[62]
algebraic[67] = algebraic[63]
algebraic[68] = algebraic[67]
algebraic[72] = algebraic[68]+algebraic[71]
algebraic[66] = (algebraic[50]*states[2]*(power(algebraic[14], 2.00000)))/(1.00000*constants[18]*constants[19]*constants[21]*constants[16]*constants[15])
algebraic[53] = (algebraic[50]*states[2])/(constants[18]*constants[19])
algebraic[56] = (algebraic[50]*(power(algebraic[14], 2.00000)))/(1.00000*constants[18]*constants[21]*constants[15])
algebraic[51] = algebraic[50]/constants[18]
algebraic[23] = (states[2]*(power(algebraic[14], 2.00000)))/(1.00000*constants[19]*constants[21]*constants[16])
algebraic[9] = states[2]/constants[19]
algebraic[15] = (power(algebraic[14], 2.00000))/(1.00000*constants[21])
algebraic[18] = constants[52]+algebraic[15]
algebraic[21] = algebraic[18]+algebraic[10]
algebraic[37] = algebraic[21]+algebraic[26]
algebraic[39] = algebraic[37]+algebraic[9]
algebraic[41] = algebraic[39]+algebraic[23]
algebraic[44] = algebraic[41]+algebraic[12]
algebraic[49] = algebraic[44]+algebraic[45]
algebraic[52] = algebraic[49]+algebraic[51]
algebraic[57] = algebraic[52]+algebraic[56]
algebraic[58] = algebraic[57]+algebraic[54]
algebraic[64] = algebraic[58]+algebraic[61]
algebraic[65] = algebraic[64]+algebraic[53]
algebraic[69] = algebraic[65]+algebraic[66]
algebraic[70] = algebraic[69]+algebraic[59]
algebraic[73] = algebraic[70]+algebraic[71]
algebraic[74] = (constants[11]*constants[12]*algebraic[72]+constants[12]*algebraic[60])/algebraic[73]
rates[1] = constants[5]*(algebraic[7]-algebraic[74])
rates[2] = constants[5]*(algebraic[74]-0.500000*algebraic[8])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[2] = constants[47]*((power(states[4], constants[48]))/(power(constants[49], constants[48])+power(states[4], constants[48])))
algebraic[4] = 0.500000*(1.00000+tanh((states[5]--16.0000)/11.2000))
algebraic[1] = 1.00000/(0.0350000*cosh((states[5]--16.0000)/22.4000))
algebraic[0] = custom_piecewise([greater((voi-constants[4])/1000.00 , 1.00000), constants[3]*constants[1] , greater((voi-constants[4])/1000.00 , 0.00000) & less((voi-constants[4])/1000.00 , 1.00000), ((voi-constants[4])/1000.00)*constants[3]*constants[1] , less((voi-constants[4])/1000.00 , 0.00000), 0.00000 , True, float('nan')])
algebraic[3] = constants[2]+constants[1]*(1.00000-constants[3])*cos((voi*2.00000* pi)/(60000.0*constants[0]))+algebraic[0]
algebraic[6] = constants[7]*(((algebraic[3]-states[0])*constants[6])/((constants[6]+algebraic[3])*(constants[6]+states[0])))
algebraic[7] = (constants[9]*(power(states[0], constants[10])))/(power(constants[8], constants[10])+power(states[0], constants[10]))
algebraic[13] = power(power(states[3]-constants[22], 2.00000)-4.00000*(power(states[3], 2.00000)), 1.0/2)
algebraic[14] = 0.500000*((constants[22]+algebraic[13])-states[3])
algebraic[8] = 0.200000*(power(states[2]/1.00000, 1.0/2))
algebraic[16] = (constants[28]*algebraic[8])/(constants[29]+algebraic[8])
algebraic[19] = constants[24]+algebraic[16]
algebraic[20] = 0.500000*(1.00000+tanh((states[5]--20.0000)/24.0000))
algebraic[22] = constants[33]*algebraic[20]*(states[5]-constants[34])
algebraic[25] = -(constants[43]*1.00000*algebraic[22]+constants[42]*states[4])
algebraic[31] = constants[45]*(states[7]-states[4])
algebraic[28] = constants[44]*states[4]
algebraic[34] = algebraic[31]-algebraic[28]
algebraic[17] = constants[31]*states[6]*(states[5]-constants[32])
algebraic[24] = (constants[35]/(1.00000+power(constants[36]/states[4], constants[37])))*(states[5]-constants[32])
algebraic[27] = 0.165000*states[3]
algebraic[30] = 0.0800000*(1.00000+(2.00000*algebraic[27])/17.0000)+0.890000*(power(algebraic[27]/17.0000, 2.00000))
algebraic[33] = 0.135000*states[3]
algebraic[36] = 0.0500000*algebraic[14]
algebraic[38] = (power(1.00000+algebraic[27]/17.0000, 2.00000))*(1.00000+algebraic[33]/26.0000+algebraic[36]/1.00000)
algebraic[40] = 20.0000*(algebraic[30]/algebraic[38])
algebraic[42] = constants[38]*algebraic[40]*(states[5]-constants[32])
algebraic[5] = 0.300000*states[1]
algebraic[50] = (power(states[3], 2.00000))/algebraic[14]
algebraic[59] = (algebraic[50]*states[2]*(power(algebraic[5], 2.00000)))/(1.00000*constants[18]*constants[19]*constants[20]*constants[14]*constants[13])
algebraic[60] = algebraic[59]
algebraic[71] = (algebraic[50]*states[2]*(power(algebraic[5], 2.00000))*(power(algebraic[14], 2.00000)))/(1.00000*constants[18]*constants[19]*constants[20]*constants[21]*constants[14]*constants[13]*constants[16]*constants[15]*constants[17])
algebraic[61] = (algebraic[50]*(power(algebraic[5], 2.00000))*(power(algebraic[14], 2.00000)))/(1.00000*constants[18]*constants[20]*constants[21]*constants[13]*constants[15]*constants[17])
algebraic[54] = (algebraic[50]*(power(algebraic[5], 2.00000)))/(1.00000*constants[18]*constants[20]*constants[13])
algebraic[45] = (states[2]*(power(algebraic[5], 2.00000))*(power(algebraic[14], 2.00000)))/(1.00000*constants[19]*constants[20]*constants[21]*constants[14]*constants[16]*constants[17])
algebraic[12] = (states[2]*(power(algebraic[5], 2.00000)))/(1.00000*constants[19]*constants[20]*constants[14])
algebraic[26] = (power(algebraic[5]*algebraic[14], 2.00000))/(1.00000*constants[17]*constants[20]*constants[21])
algebraic[10] = (power(algebraic[5], 2.00000))/(1.00000*constants[20])
algebraic[11] = constants[53]+algebraic[10]
algebraic[29] = algebraic[11]+algebraic[26]
algebraic[32] = algebraic[29]
algebraic[35] = algebraic[32]
algebraic[43] = algebraic[35]+algebraic[12]
algebraic[46] = algebraic[43]+algebraic[45]
algebraic[47] = algebraic[46]
algebraic[48] = algebraic[47]
algebraic[55] = algebraic[48]+algebraic[54]
algebraic[62] = algebraic[55]+algebraic[61]
algebraic[63] = algebraic[62]
algebraic[67] = algebraic[63]
algebraic[68] = algebraic[67]
algebraic[72] = algebraic[68]+algebraic[71]
algebraic[66] = (algebraic[50]*states[2]*(power(algebraic[14], 2.00000)))/(1.00000*constants[18]*constants[19]*constants[21]*constants[16]*constants[15])
algebraic[53] = (algebraic[50]*states[2])/(constants[18]*constants[19])
algebraic[56] = (algebraic[50]*(power(algebraic[14], 2.00000)))/(1.00000*constants[18]*constants[21]*constants[15])
algebraic[51] = algebraic[50]/constants[18]
algebraic[23] = (states[2]*(power(algebraic[14], 2.00000)))/(1.00000*constants[19]*constants[21]*constants[16])
algebraic[9] = states[2]/constants[19]
algebraic[15] = (power(algebraic[14], 2.00000))/(1.00000*constants[21])
algebraic[18] = constants[52]+algebraic[15]
algebraic[21] = algebraic[18]+algebraic[10]
algebraic[37] = algebraic[21]+algebraic[26]
algebraic[39] = algebraic[37]+algebraic[9]
algebraic[41] = algebraic[39]+algebraic[23]
algebraic[44] = algebraic[41]+algebraic[12]
algebraic[49] = algebraic[44]+algebraic[45]
algebraic[52] = algebraic[49]+algebraic[51]
algebraic[57] = algebraic[52]+algebraic[56]
algebraic[58] = algebraic[57]+algebraic[54]
algebraic[64] = algebraic[58]+algebraic[61]
algebraic[65] = algebraic[64]+algebraic[53]
algebraic[69] = algebraic[65]+algebraic[66]
algebraic[70] = algebraic[69]+algebraic[59]
algebraic[73] = algebraic[70]+algebraic[71]
algebraic[74] = (constants[11]*constants[12]*algebraic[72]+constants[12]*algebraic[60])/algebraic[73]
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)