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 = 24
sizeStates = 33
sizeConstants = 97
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 (hour)"
legend_states[0] = "ATbl in component ATbl (nanomole)"
legend_constants[0] = "k2T in component ATbl (nmol_hr)"
legend_algebraic[17] = "Qb in component model_parameters (l_hr)"
legend_algebraic[15] = "Qp in component Qp (l_hr)"
legend_constants[1] = "Ql in component model_parameters (l_hr)"
legend_constants[2] = "Qt in component model_parameters (l_hr)"
legend_constants[94] = "CTbf in component model_parameters (nM)"
legend_algebraic[0] = "CTblf in component CTblf (nM)"
legend_algebraic[10] = "CTpf in component CTpf (nM)"
legend_constants[3] = "CTbl in component model_parameters (nM)"
legend_constants[90] = "CTlf in component CTlf (nM)"
legend_constants[93] = "CTtv in component CTtv (nM)"
legend_constants[4] = "ts in component model_parameters (dimensionless)"
legend_states[1] = "ADbl in component ADbl (nanomole)"
legend_algebraic[18] = "Qbt in component model_parameters (l_hr)"
legend_constants[95] = "CDbf in component model_parameters (nM)"
legend_algebraic[4] = "CDblf in component CDblf (nM)"
legend_algebraic[12] = "CDpf in component CDpf (nM)"
legend_constants[92] = "CDlf in component CDlf (nM)"
legend_constants[5] = "CDbl in component model_parameters (nM)"
legend_states[2] = "CT_A in component CT_A (nM)"
legend_constants[6] = "kTA_on in component CT_A (second_order_rate_constant)"
legend_constants[7] = "kTA_off in component CT_A (first_order_rate_constant)"
legend_algebraic[8] = "CAf in component CAf (nM)"
legend_states[3] = "CD_A in component CD_A (nM)"
legend_constants[8] = "kDA_on in component CD_A (second_order_rate_constant)"
legend_constants[9] = "kDA_off in component CD_A (first_order_rate_constant)"
legend_constants[10] = "CA in component model_parameters (nM)"
legend_states[4] = "ATl in component ATl (nanomole)"
legend_constants[11] = "k1T in component model_parameters (first_order_rate_constant)"
legend_constants[12] = "km5alpha in component model_parameters (nM)"
legend_constants[13] = "Vmax1 in component model_parameters (nmol_hr)"
legend_constants[14] = "PTl in component model_parameters (dimensionless)"
legend_states[5] = "ADl in component ADl (nanomole)"
legend_constants[15] = "k1D in component model_parameters (first_order_rate_constant)"
legend_constants[16] = "PDl in component model_parameters (dimensionless)"
legend_constants[17] = "CTl in component model_parameters (nM)"
legend_constants[18] = "CDl in component model_parameters (nM)"
legend_states[6] = "ATif in component ATif (nanomole)"
legend_constants[19] = "mu in component model_parameters (l_hr)"
legend_constants[20] = "PTif in component model_parameters (dimensionless)"
legend_constants[21] = "CTif in component model_parameters (nM)"
legend_constants[22] = "CTst in component model_parameters (nM)"
legend_constants[23] = "CLH in component model_parameters (nanomole)"
legend_constants[24] = "PTst in component model_parameters (dimensionless)"
legend_states[7] = "ATst in component ATst (nanomole)"
legend_states[8] = "ATp in component ATp (nanomole)"
legend_constants[25] = "Vmax0 in component model_parameters (nmol_hr)"
legend_states[9] = "ADp in component ADp (nanomole)"
legend_states[10] = "CT_R in component CT_R (nM)"
legend_constants[26] = "kTR_on in component CT_R (second_order_rate_constant)"
legend_constants[27] = "kTR_off in component CT_R (first_order_rate_constant)"
legend_algebraic[23] = "CRf in component CRf (nM)"
legend_states[11] = "CD_R in component CD_R (nM)"
legend_constants[28] = "kDR_on in component CD_R (second_order_rate_constant)"
legend_constants[29] = "kDR_off in component CD_R (first_order_rate_constant)"
legend_states[12] = "CDT in component CDT (nM)"
legend_constants[30] = "kDT_on in component CDT (second_order_rate_constant)"
legend_constants[31] = "kDT_off in component CDT (first_order_rate_constant)"
legend_states[13] = "CDD in component CDD (nM)"
legend_constants[32] = "kDD_on in component CDD (second_order_rate_constant)"
legend_constants[33] = "kDD_off in component CDD (first_order_rate_constant)"
legend_states[14] = "CTT in component CTT (nM)"
legend_constants[34] = "kTT_on in component CTT (second_order_rate_constant)"
legend_constants[35] = "kTT_off in component CTT (first_order_rate_constant)"
legend_states[15] = "CDD5a in component CDD5a (nM)"
legend_constants[36] = "kDNA_onDD5a in component CDD5a (second_order_rate_constant)"
legend_constants[37] = "kDNA_offDD5a in component CDD5a (first_order_rate_constant)"
legend_algebraic[19] = "CDNA5af in component CDNA5af (nM)"
legend_states[16] = "CDDcd in component CDDcd (nM)"
legend_constants[38] = "kDNA_onDDcd in component CDDcd (second_order_rate_constant)"
legend_constants[39] = "kDNA_offDDcd in component CDDcd (first_order_rate_constant)"
legend_algebraic[14] = "CDNAcdf in component CDNAcdf (nM)"
legend_states[17] = "CDDsec in component CDDsec (nM)"
legend_constants[40] = "kDNA_onDDsec in component CDDsec (second_order_rate_constant)"
legend_constants[41] = "kDNA_offDDsec in component CDDsec (first_order_rate_constant)"
legend_algebraic[16] = "CDNAsecf in component CDNAsecf (nM)"
legend_states[18] = "CDDcp in component CDDcp (nM)"
legend_constants[42] = "kDNA_onDDcp in component CDDcp (second_order_rate_constant)"
legend_constants[43] = "kDNA_offDDcp in component CDDcp (first_order_rate_constant)"
legend_algebraic[20] = "CDNAcpf in component CDNAcpf (nM)"
legend_states[19] = "CDT5a in component CDT5a (nM)"
legend_constants[44] = "kDNA_onDT5a in component CDT5a (second_order_rate_constant)"
legend_constants[45] = "kDNA_offDT5a in component CDT5a (first_order_rate_constant)"
legend_states[20] = "CDTcd in component CDTcd (nM)"
legend_constants[46] = "kDNA_onDTcd in component CDTcd (second_order_rate_constant)"
legend_constants[47] = "kDNA_offDTcd in component CDTcd (first_order_rate_constant)"
legend_states[21] = "CDTsec in component CDTsec (nM)"
legend_constants[48] = "kDNA_onDTsec in component CDTsec (second_order_rate_constant)"
legend_constants[49] = "kDNA_offDTsec in component CDTsec (first_order_rate_constant)"
legend_states[22] = "CDTcp in component CDTcp (nM)"
legend_constants[50] = "kDNA_onDTcp in component CDTcp (second_order_rate_constant)"
legend_constants[51] = "kDNA_offDTcp in component CDTcp (first_order_rate_constant)"
legend_states[23] = "CTT5a in component CTT5a (nM)"
legend_constants[52] = "kDNA_onTT5a in component CTT5a (second_order_rate_constant)"
legend_constants[53] = "kDNA_offTT5a in component CTT5a (first_order_rate_constant)"
legend_states[24] = "CTTcd in component CTTcd (nM)"
legend_constants[54] = "kDNA_onTTcd in component CTTcd (second_order_rate_constant)"
legend_constants[55] = "kDNA_offTTcd in component CTTcd (first_order_rate_constant)"
legend_states[25] = "CTTsec in component CTTsec (nM)"
legend_constants[56] = "kDNA_onTTsec in component CTTsec (second_order_rate_constant)"
legend_constants[57] = "kDNA_offTTsec in component CTTsec (first_order_rate_constant)"
legend_states[26] = "CTTcp in component CTTcp (nM)"
legend_constants[58] = "kDNA_onTTcp in component CTTcp (second_order_rate_constant)"
legend_constants[59] = "kDNA_offTTcp in component CTTcp (first_order_rate_constant)"
legend_algebraic[7] = "T in component CTpf (nM)"
legend_constants[60] = "NTp in component CTpf (dimensionless)"
legend_constants[61] = "CTp in component model_parameters (nM)"
legend_algebraic[11] = "D in component CDpf (nM)"
legend_constants[62] = "NDp in component CDpf (dimensionless)"
legend_constants[63] = "CDp in component model_parameters (nM)"
legend_algebraic[22] = "CR in component CR (nM)"
legend_constants[64] = "CDNAcd in component model_parameters (nM)"
legend_constants[65] = "CDNAsec in component model_parameters (nM)"
legend_constants[66] = "CDNA5a in component model_parameters (nM)"
legend_constants[67] = "CDNAcp in component model_parameters (nM)"
legend_algebraic[1] = "DNAocp in component DNAocp (dimensionless)"
legend_algebraic[2] = "DNAosec in component DNAosec (dimensionless)"
legend_algebraic[5] = "DNAocd in component DNAocd (dimensionless)"
legend_algebraic[3] = "DNAo5a in component DNAo5a (dimensionless)"
legend_states[27] = "ATb in component ATb (nanomole)"
legend_constants[68] = "CTb in component model_parameters (nM)"
legend_constants[69] = "PTb in component model_parameters (dimensionless)"
legend_states[28] = "ADb in component ADb (nanomole)"
legend_constants[70] = "CDb in component model_parameters (nM)"
legend_constants[71] = "PDb in component model_parameters (dimensionless)"
legend_states[29] = "ALH in component ALH (nanomole)"
legend_constants[72] = "kLH1 in component ALH (l_hr)"
legend_constants[73] = "kLH2 in component ALH (nmol_hr)"
legend_constants[74] = "kLH3 in component ALH (nmol_hr)"
legend_constants[75] = "kLH4 in component ALH (first_order_rate_constant)"
legend_constants[76] = "alpha_T in component ALH (dimensionless)"
legend_constants[77] = "alpha_D in component ALH (dimensionless)"
legend_algebraic[9] = "A in component ALH (nmol_hr)"
legend_constants[91] = "B in component ALH (nmol_hr)"
legend_states[30] = "AR in component AR (nanomole)"
legend_constants[78] = "k1R in component AR (nmol_hr)"
legend_constants[79] = "keR in component AR (l_hr)"
legend_algebraic[21] = "Vp in component Vp (litre)"
legend_constants[80] = "kQp in component Qp (first_order_rate_constant)"
legend_algebraic[13] = "Vpc in component Qp (litre)"
legend_states[31] = "VPC1 in component VPC1 (litre)"
legend_constants[81] = "VPC2 in component model_parameters (litre)"
legend_algebraic[6] = "Vmax in component Vmax (nmol_hr)"
legend_constants[82] = "k5a in component Vmax (nmol_hr)"
legend_constants[83] = "kcpl in component VPC1 (kg_hr)"
legend_constants[84] = "kcd1 in component VPC1 (first_order_rate_constant)"
legend_constants[85] = "VPC1b in component model_parameters (kg)"
legend_states[32] = "VPL1 in component VPL1 (litre)"
legend_constants[86] = "ksec in component VPL1 (kg_hr)"
legend_constants[87] = "kflo in component VPL1 (first_order_rate_constant)"
legend_constants[88] = "VPL2 in component model_parameters (litre)"
legend_constants[89] = "Qc in component model_parameters (l_hr)"
legend_rates[0] = "d/dt ATbl in component ATbl (nanomole)"
legend_rates[1] = "d/dt ADbl in component ADbl (nanomole)"
legend_rates[2] = "d/dt CT_A in component CT_A (nM)"
legend_rates[3] = "d/dt CD_A in component CD_A (nM)"
legend_rates[4] = "d/dt ATl in component ATl (nanomole)"
legend_rates[5] = "d/dt ADl in component ADl (nanomole)"
legend_rates[6] = "d/dt ATif in component ATif (nanomole)"
legend_rates[7] = "d/dt ATst in component ATst (nanomole)"
legend_rates[8] = "d/dt ATp in component ATp (nanomole)"
legend_rates[9] = "d/dt ADp in component ADp (nanomole)"
legend_rates[10] = "d/dt CT_R in component CT_R (nM)"
legend_rates[11] = "d/dt CD_R in component CD_R (nM)"
legend_rates[12] = "d/dt CDT in component CDT (nM)"
legend_rates[13] = "d/dt CDD in component CDD (nM)"
legend_rates[14] = "d/dt CTT in component CTT (nM)"
legend_rates[15] = "d/dt CDD5a in component CDD5a (nM)"
legend_rates[16] = "d/dt CDDcd in component CDDcd (nM)"
legend_rates[17] = "d/dt CDDsec in component CDDsec (nM)"
legend_rates[18] = "d/dt CDDcp in component CDDcp (nM)"
legend_rates[19] = "d/dt CDT5a in component CDT5a (nM)"
legend_rates[20] = "d/dt CDTcd in component CDTcd (nM)"
legend_rates[21] = "d/dt CDTsec in component CDTsec (nM)"
legend_rates[22] = "d/dt CDTcp in component CDTcp (nM)"
legend_rates[23] = "d/dt CTT5a in component CTT5a (nM)"
legend_rates[24] = "d/dt CTTcd in component CTTcd (nM)"
legend_rates[25] = "d/dt CTTsec in component CTTsec (nM)"
legend_rates[26] = "d/dt CTTcp in component CTTcp (nM)"
legend_rates[27] = "d/dt ATb in component ATb (nanomole)"
legend_rates[28] = "d/dt ADb in component ADb (nanomole)"
legend_rates[29] = "d/dt ALH in component ALH (nanomole)"
legend_rates[30] = "d/dt AR in component AR (nanomole)"
legend_rates[31] = "d/dt VPC1 in component VPC1 (litre)"
legend_rates[32] = "d/dt VPL1 in component VPL1 (litre)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 0.0
constants[0] = 0.17
constants[1] = 1.06
constants[2] = 0.061
constants[3] = 7.60
constants[4] = 0.56
states[1] = 0.0
constants[5] = 0.59
states[2] = 0.0
constants[6] = 0.18
constants[7] = 8131.0
states[3] = 0.0
constants[8] = 0.15
constants[9] = 5407.0
constants[10] = 5.00E5
states[4] = 0.0
constants[11] = 87.93
constants[12] = 40.00
constants[13] = 3.65
constants[14] = 2.75
states[5] = 0.0
constants[15] = 77.20
constants[16] = 2.00
constants[17] = 9.92
constants[18] = 0.92
states[6] = 0.0
constants[19] = 1000.0
constants[20] = 1.96
constants[21] = 307.29
constants[22] = 307.29
constants[23] = 0.104
constants[24] = 1.00
states[7] = 0.0
states[8] = 0.0
constants[25] = 2.89
states[9] = 0.0
states[10] = 0.0
constants[26] = 0.14
constants[27] = 0.069
states[11] = 0.0
constants[28] = 0.053
constants[29] = 0.018
states[12] = 0.0
constants[30] = 0.14
constants[31] = 3.13
states[13] = 0.0
constants[32] = 0.14
constants[33] = 3.13
states[14] = 0.0
constants[34] = 0.14
constants[35] = 3.13
states[15] = 0.0
constants[36] = 0.14
constants[37] = 0.07
states[16] = 0.0
constants[38] = 0.14
constants[39] = 0.1
states[17] = 0.0
constants[40] = 0.14
constants[41] = 0.2
states[18] = 0.0
constants[42] = 0.14
constants[43] = 0.7
states[19] = 0.0
constants[44] = 0.14
constants[45] = 0.56
states[20] = 0.0
constants[46] = 0.14
constants[47] = 0.8
states[21] = 0.0
constants[48] = 0.14
constants[49] = 1.6
states[22] = 0.0
constants[50] = 0.14
constants[51] = 5.6
states[23] = 0.0
constants[52] = 0.14
constants[53] = 0.84
states[24] = 0.0
constants[54] = 0.14
constants[55] = 1.2
states[25] = 0.0
constants[56] = 0.14
constants[57] = 2.4
states[26] = 0.0
constants[58] = 0.14
constants[59] = 8.4
constants[60] = 0.79
constants[61] = 11.38
constants[62] = 1.00
constants[63] = 52.46
constants[64] = 0.075
constants[65] = 0.075
constants[66] = 0.075
constants[67] = 0.075
states[27] = 0.0
constants[68] = 0.6275
constants[69] = 1.00
states[28] = 0.0
constants[70] = 0.019884
constants[71] = 0.62
states[29] = 0.0
constants[72] = 0.13
constants[73] = 0.026
constants[74] = 1.68E-4
constants[75] = 0.80
constants[76] = 0.25
constants[77] = 0.75
states[30] = 0.0
constants[78] = 68.15
constants[79] = 71.90
constants[80] = 73.84
states[31] = 0.0
constants[81] = 5.08E-5
constants[82] = 3.02
constants[83] = 1.17E-7
constants[84] = 0.014
constants[85] = 1E-4
states[32] = 0.0
constants[86] = 8.44E-6
constants[87] = 0.043
constants[88] = 3.08E-6
constants[89] = 6.08
constants[90] = constants[17]/constants[14]
constants[91] = constants[74]
constants[96] = constants[19]*(constants[21]-constants[22]/constants[24])
constants[92] = constants[18]/constants[16]
constants[93] = constants[21]/constants[20]
constants[94] = constants[68]/constants[69]
constants[95] = constants[70]/constants[71]
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[7] = constants[96]
rates[4] = constants[1]*(constants[3]-constants[90])-((constants[13]*constants[90])/(constants[12]+constants[90])+constants[11]*(states[4]/constants[14]))
rates[5] = constants[1]*(constants[5]-constants[92])-((constants[13]*constants[90])/(constants[12]+constants[90])+constants[15]*(states[5]/constants[16]))
rates[12] = constants[30]*states[11]*states[10]-constants[31]*states[12]
rates[13] = constants[32]*(power(states[11], 2.00000))-constants[33]*states[13]
rates[14] = constants[34]*(power(states[10], 2.00000))-constants[35]*states[14]
algebraic[0] = constants[3]-states[2]
rates[6] = constants[2]*(1.00000-constants[4])*(algebraic[0]-constants[21]/constants[20])+constants[19]*(constants[22]/constants[24]-constants[21])+constants[11]*constants[23]
algebraic[2] = (states[25]+states[17]+states[21])/constants[65]
rates[32] = (states[31]/constants[85])*constants[86]*algebraic[2]-constants[87]*states[32]
algebraic[1] = (states[26]+states[18]+states[22])/constants[67]
algebraic[5] = (states[24]+states[16]+states[20])/constants[64]
rates[31] = (states[31]/constants[85])*constants[83]*algebraic[1]-constants[84]*(1.00000-algebraic[5])*states[31]
algebraic[8] = constants[10]-(states[2]+states[3])
rates[2] = constants[6]*algebraic[0]*algebraic[8]-constants[7]*states[2]
algebraic[4] = constants[5]-states[3]
rates[3] = constants[8]*algebraic[4]*algebraic[8]-constants[9]*states[3]
algebraic[9] = -constants[72]*(constants[76]*algebraic[0]+constants[77]*algebraic[4])+constants[73]
rates[29] = custom_piecewise([greater(algebraic[9] , constants[91]), algebraic[9]-constants[75]*states[29] , True, constants[91]-constants[75]*states[29]])
algebraic[14] = constants[64]-(states[24]+states[16]+states[20])
rates[16] = constants[38]*states[13]*algebraic[14]-constants[39]*states[16]
rates[20] = constants[46]*states[12]*algebraic[14]-constants[47]*states[20]
rates[24] = constants[54]*states[14]*algebraic[14]-constants[55]*states[24]
algebraic[13] = states[31]+constants[81]
algebraic[15] = constants[80]*algebraic[13]
algebraic[7] = states[25]+states[21]+states[23]+states[19]+states[24]+states[20]+states[26]+states[22]
algebraic[10] = (constants[61]-(states[10]+2.00000*states[14]+states[12]+algebraic[7]))/(1.00000+constants[60])
rates[8] = algebraic[15]*(constants[3]-algebraic[10])-(constants[25]*algebraic[10])/(constants[12]+algebraic[10])
algebraic[11] = states[17]+states[21]+states[15]+states[19]+states[16]+states[20]+states[18]+states[22]
algebraic[12] = (constants[63]-(states[11]+2.00000*states[13]+states[12]+algebraic[11]))/(1.00000+constants[62])
rates[9] = algebraic[15]*(constants[5]-algebraic[12])-(constants[25]*algebraic[10])/(constants[12]+algebraic[10])
algebraic[16] = constants[65]-(states[25]+states[17]+states[21])
rates[17] = constants[40]*states[13]*algebraic[16]-constants[41]*states[17]
rates[21] = constants[48]*states[12]*algebraic[16]-constants[49]*states[21]
rates[25] = constants[56]*states[14]*algebraic[16]-constants[57]*states[25]
algebraic[17] = constants[89]-(algebraic[15]+constants[2]+constants[1])
rates[0] = algebraic[17]*(constants[94]-algebraic[0])+algebraic[15]*(algebraic[10]-constants[3])+constants[1]*(constants[90]-constants[3])+constants[2]*(1.00000-constants[4])*(constants[93]-algebraic[0])+constants[0]
algebraic[18] = constants[89]-(algebraic[15]+constants[1])
rates[1] = algebraic[18]*(constants[95]-algebraic[4])+algebraic[15]*(algebraic[12]-algebraic[4])+constants[1]*(constants[92]-constants[5])
algebraic[19] = constants[66]-(states[23]+states[15]+states[19])
rates[15] = constants[36]*states[13]*algebraic[19]-constants[37]*states[15]
rates[19] = constants[44]*states[12]*algebraic[19]-constants[45]*states[19]
rates[23] = constants[52]*states[14]*algebraic[19]-constants[53]*states[23]
rates[27] = algebraic[17]*(algebraic[0]-constants[68]/constants[69])
rates[28] = algebraic[18]*(algebraic[4]-constants[70]/constants[71])
algebraic[20] = constants[67]-(states[26]+states[18]+states[22])
rates[18] = constants[42]*states[13]*algebraic[20]-constants[43]*states[18]
rates[22] = constants[50]*states[12]*algebraic[20]-constants[51]*states[22]
rates[26] = constants[58]*states[14]*algebraic[20]-constants[59]*states[26]
algebraic[21] = states[31]+constants[81]+states[32]+constants[88]
algebraic[22] = states[30]/algebraic[21]
algebraic[23] = algebraic[22]-(states[10]+states[11]+2.00000*(states[14]+states[13]+states[12])+2.00000*(algebraic[14]+algebraic[16]+algebraic[20]+algebraic[19]))
rates[10] = constants[26]*algebraic[10]*algebraic[23]-constants[27]*states[10]
rates[11] = constants[28]*algebraic[12]*algebraic[23]-constants[29]*states[11]
rates[30] = constants[78]-constants[79]*algebraic[23]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = constants[3]-states[2]
algebraic[2] = (states[25]+states[17]+states[21])/constants[65]
algebraic[1] = (states[26]+states[18]+states[22])/constants[67]
algebraic[5] = (states[24]+states[16]+states[20])/constants[64]
algebraic[8] = constants[10]-(states[2]+states[3])
algebraic[4] = constants[5]-states[3]
algebraic[9] = -constants[72]*(constants[76]*algebraic[0]+constants[77]*algebraic[4])+constants[73]
algebraic[14] = constants[64]-(states[24]+states[16]+states[20])
algebraic[13] = states[31]+constants[81]
algebraic[15] = constants[80]*algebraic[13]
algebraic[7] = states[25]+states[21]+states[23]+states[19]+states[24]+states[20]+states[26]+states[22]
algebraic[10] = (constants[61]-(states[10]+2.00000*states[14]+states[12]+algebraic[7]))/(1.00000+constants[60])
algebraic[11] = states[17]+states[21]+states[15]+states[19]+states[16]+states[20]+states[18]+states[22]
algebraic[12] = (constants[63]-(states[11]+2.00000*states[13]+states[12]+algebraic[11]))/(1.00000+constants[62])
algebraic[16] = constants[65]-(states[25]+states[17]+states[21])
algebraic[17] = constants[89]-(algebraic[15]+constants[2]+constants[1])
algebraic[18] = constants[89]-(algebraic[15]+constants[1])
algebraic[19] = constants[66]-(states[23]+states[15]+states[19])
algebraic[20] = constants[67]-(states[26]+states[18]+states[22])
algebraic[21] = states[31]+constants[81]+states[32]+constants[88]
algebraic[22] = states[30]/algebraic[21]
algebraic[23] = algebraic[22]-(states[10]+states[11]+2.00000*(states[14]+states[13]+states[12])+2.00000*(algebraic[14]+algebraic[16]+algebraic[20]+algebraic[19]))
algebraic[3] = (states[23]+states[15]+states[19])/constants[66]
algebraic[6] = constants[82]*algebraic[3]
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)