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 = 30
sizeStates = 14
sizeConstants = 93
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 (minute)"
legend_states[0] = "CycA in component CycA (dimensionless)"
legend_constants[0] = "k_assa in component kinetic_parameters (first_order_rate_constant)"
legend_constants[1] = "k_dissa in component kinetic_parameters (first_order_rate_constant)"
legend_algebraic[20] = "V_di in component V_di (first_order_rate_constant)"
legend_algebraic[21] = "V_sa in component V_sa (first_order_rate_constant)"
legend_algebraic[14] = "V_da in component V_da (first_order_rate_constant)"
legend_states[1] = "Tri_A in component Tri_A (dimensionless)"
legend_states[2] = "CKI in component CKI (dimensionless)"
legend_states[3] = "CycB in component CycB (dimensionless)"
legend_constants[2] = "k_assb in component kinetic_parameters (first_order_rate_constant)"
legend_constants[3] = "k_dissb in component kinetic_parameters (first_order_rate_constant)"
legend_algebraic[24] = "V_sb in component V_sb (first_order_rate_constant)"
legend_algebraic[25] = "V_db in component V_db (first_order_rate_constant)"
legend_algebraic[29] = "V_25 in component V_25 (first_order_rate_constant)"
legend_algebraic[27] = "V_wee in component V_wee (first_order_rate_constant)"
legend_states[4] = "pB in component pB (dimensionless)"
legend_states[5] = "BCKI in component BCKI (dimensionless)"
legend_states[6] = "CycE in component CycE (dimensionless)"
legend_constants[4] = "k_disse in component kinetic_parameters (first_order_rate_constant)"
legend_constants[5] = "k_asse in component kinetic_parameters (first_order_rate_constant)"
legend_algebraic[23] = "V_se in component V_se (first_order_rate_constant)"
legend_algebraic[13] = "V_de in component V_de (first_order_rate_constant)"
legend_states[7] = "Tri_E in component Tri_E (dimensionless)"
legend_algebraic[1] = "CycD in component CycD (dimensionless)"
legend_constants[6] = "CycD_0 in component CycD (dimensionless)"
legend_states[8] = "mass in component mass (dimensionless)"
legend_states[9] = "Cdc20_A in component Cdc20_A (dimensionless)"
legend_constants[7] = "k_a20 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[8] = "k_i20 in component kinetic_parameters (first_order_rate_constant)"
legend_constants[9] = "k_d20 in component kinetic_parameters (first_order_rate_constant)"
legend_states[10] = "APCP in component APCP (dimensionless)"
legend_states[11] = "Cdc20_i in component Cdc20_i (dimensionless)"
legend_constants[10] = "J_a20 in component Cdc20_A (dimensionless)"
legend_constants[11] = "J_i20 in component Cdc20_A (dimensionless)"
legend_constants[12] = "k_s20p in component kinetic_parameters (first_order_rate_constant)"
legend_constants[13] = "k_s20pp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[14] = "n20 in component Cdc20_i (dimensionless)"
legend_constants[15] = "J_20 in component Cdc20_i (dimensionless)"
legend_constants[16] = "J_a20 in component Cdc20_i (dimensionless)"
legend_constants[17] = "J_i20 in component Cdc20_i (dimensionless)"
legend_algebraic[0] = "APC in component APC (dimensionless)"
legend_constants[18] = "APC_T in component APC (dimensionless)"
legend_constants[19] = "k_aie in component kinetic_parameters (first_order_rate_constant)"
legend_constants[20] = "k_iie in component kinetic_parameters (first_order_rate_constant)"
legend_constants[21] = "J_aie in component APCP (dimensionless)"
legend_constants[22] = "J_iie in component APCP (dimensionless)"
legend_states[12] = "pBCKI in component pBCKI (dimensionless)"
legend_algebraic[18] = "V_si in component V_si (first_order_rate_constant)"
legend_algebraic[9] = "Cdh1_i in component Cdh1_i (dimensionless)"
legend_constants[23] = "Cdh1_T in component Cdh1_i (dimensionless)"
legend_states[13] = "Cdh1 in component Cdh1 (dimensionless)"
legend_algebraic[17] = "V_ah1 in component V_ah1 (first_order_rate_constant)"
legend_algebraic[19] = "V_ih1 in component V_ih1 (first_order_rate_constant)"
legend_constants[24] = "J_ah1 in component Cdh1 (dimensionless)"
legend_constants[25] = "J_ih1 in component Cdh1 (dimensionless)"
legend_constants[26] = "mu in component mass (first_order_rate_constant)"
legend_constants[27] = "maxmass in component mass (dimensionless)"
legend_algebraic[10] = "V_atf in component V_atf (first_order_rate_constant)"
legend_constants[28] = "k_atfp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[29] = "k_atfapp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[30] = "k_atfepp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[31] = "k_atfdpp in component kinetic_parameters (first_order_rate_constant)"
legend_algebraic[11] = "V_itf in component V_itf (first_order_rate_constant)"
legend_constants[32] = "k_itfp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[33] = "k_itfapp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[34] = "k_itfbpp in component kinetic_parameters (first_order_rate_constant)"
legend_algebraic[12] = "TF_E in component TF_E (dimensionless)"
legend_constants[35] = "J_itf in component TF_E (dimensionless)"
legend_constants[36] = "J_atf in component TF_E (dimensionless)"
legend_constants[37] = "k_dep in component kinetic_parameters (first_order_rate_constant)"
legend_constants[38] = "k_deepp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[39] = "k_deapp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[40] = "k_debpp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[41] = "k_dap in component kinetic_parameters (first_order_rate_constant)"
legend_constants[42] = "k_dapp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[43] = "k_dappp in component kinetic_parameters (first_order_rate_constant)"
legend_algebraic[16] = "TF_I in component TF_I (dimensionless)"
legend_constants[44] = "k_afi in component kinetic_parameters (first_order_rate_constant)"
legend_constants[45] = "k_ifip in component kinetic_parameters (first_order_rate_constant)"
legend_constants[46] = "k_ifibpp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[47] = "J_ifi in component TF_I (dimensionless)"
legend_constants[48] = "J_afi in component TF_I (dimensionless)"
legend_algebraic[15] = "Cdc14 in component TF_I (dimensionless)"
legend_constants[49] = "k_ah1p in component kinetic_parameters (first_order_rate_constant)"
legend_constants[50] = "k_ah1pp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[51] = "k_ih1p in component kinetic_parameters (first_order_rate_constant)"
legend_constants[52] = "k_ih1app in component kinetic_parameters (first_order_rate_constant)"
legend_constants[53] = "k_ih1bpp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[54] = "k_ih1epp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[55] = "k_ih1dpp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[56] = "k_sip in component kinetic_parameters (first_order_rate_constant)"
legend_constants[57] = "k_sipp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[58] = "k_dip in component kinetic_parameters (first_order_rate_constant)"
legend_constants[59] = "k_diapp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[60] = "k_diepp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[61] = "k_didpp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[62] = "k_dibpp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[63] = "k_14di in component kinetic_parameters (dimensionless)"
legend_algebraic[2] = "preMPF in component preMPF (dimensionless)"
legend_algebraic[3] = "CycBT in component CycBT (dimensionless)"
legend_algebraic[4] = "CycAT in component CycAT (dimensionless)"
legend_algebraic[5] = "CycET in component CycET (dimensionless)"
legend_algebraic[6] = "Tri_B in component Tri_B (dimensionless)"
legend_algebraic[7] = "CKIT in component CKIT (dimensionless)"
legend_algebraic[8] = "Cdc20_T in component Cdc20_T (dimensionless)"
legend_algebraic[22] = "TF_B in component TF_B (dimensionless)"
legend_constants[64] = "k_afb in component kinetic_parameters (first_order_rate_constant)"
legend_constants[65] = "k_ifb in component kinetic_parameters (first_order_rate_constant)"
legend_constants[66] = "J_ifb in component TF_B (dimensionless)"
legend_constants[67] = "J_afb in component TF_B (dimensionless)"
legend_constants[68] = "k_sbp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[69] = "k_sbpp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[70] = "k_sap in component kinetic_parameters (first_order_rate_constant)"
legend_constants[71] = "k_sapp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[72] = "k_sep in component kinetic_parameters (first_order_rate_constant)"
legend_constants[73] = "k_sepp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[74] = "k_dbp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[75] = "k_dbhpp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[76] = "k_dbcpp in component kinetic_parameters (first_order_rate_constant)"
legend_algebraic[26] = "Wee1 in component Wee1 (dimensionless)"
legend_constants[77] = "k_aweep in component kinetic_parameters (first_order_rate_constant)"
legend_constants[78] = "k_aweepp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[79] = "k_iweep in component kinetic_parameters (first_order_rate_constant)"
legend_constants[80] = "k_iweepp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[81] = "J_iwee in component Wee1 (dimensionless)"
legend_constants[82] = "J_awee in component Wee1 (dimensionless)"
legend_constants[83] = "k_weep in component kinetic_parameters (first_order_rate_constant)"
legend_constants[84] = "k_weepp in component kinetic_parameters (first_order_rate_constant)"
legend_algebraic[28] = "Cdc25 in component Cdc25 (dimensionless)"
legend_constants[85] = "k_a25p in component kinetic_parameters (first_order_rate_constant)"
legend_constants[86] = "k_a25pp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[87] = "k_i25p in component kinetic_parameters (first_order_rate_constant)"
legend_constants[88] = "k_i25pp in component kinetic_parameters (first_order_rate_constant)"
legend_constants[89] = "J_i25 in component Cdc25 (dimensionless)"
legend_constants[90] = "J_a25 in component Cdc25 (dimensionless)"
legend_constants[91] = "k_25p in component kinetic_parameters (first_order_rate_constant)"
legend_constants[92] = "k_25pp in component kinetic_parameters (first_order_rate_constant)"
legend_rates[0] = "d/dt CycA in component CycA (dimensionless)"
legend_rates[3] = "d/dt CycB in component CycB (dimensionless)"
legend_rates[6] = "d/dt CycE in component CycE (dimensionless)"
legend_rates[9] = "d/dt Cdc20_A in component Cdc20_A (dimensionless)"
legend_rates[11] = "d/dt Cdc20_i in component Cdc20_i (dimensionless)"
legend_rates[10] = "d/dt APCP in component APCP (dimensionless)"
legend_rates[4] = "d/dt pB in component pB (dimensionless)"
legend_rates[5] = "d/dt BCKI in component BCKI (dimensionless)"
legend_rates[12] = "d/dt pBCKI in component pBCKI (dimensionless)"
legend_rates[1] = "d/dt Tri_A in component Tri_A (dimensionless)"
legend_rates[7] = "d/dt Tri_E in component Tri_E (dimensionless)"
legend_rates[2] = "d/dt CKI in component CKI (dimensionless)"
legend_rates[13] = "d/dt Cdh1 in component Cdh1 (dimensionless)"
legend_rates[8] = "d/dt mass in component mass (dimensionless)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 0.009940445423126221
constants[0] = 25
constants[1] = 1
states[1] = 0.01715379953384399
states[2] = 0.2954076826572418
states[3] = 0.1668413728475571
constants[2] = 0
constants[3] = 0
states[4] = 0.009814870543777943
states[5] = 0
states[6] = 0.07760512828826904
constants[4] = 1
constants[5] = 50
states[7] = 0.3117263317108154
constants[6] = 0.05
states[8] = 1.174216866493225
states[9] = 0.6605867147445679
constants[7] = 0.5
constants[8] = 0.25
constants[9] = 0.15
states[10] = 0.6716265678405762
states[11] = 0.01855352707207203
constants[10] = 0.005
constants[11] = 0.005
constants[12] = 0
constants[13] = 0.15
constants[14] = 1
constants[15] = 1
constants[16] = 0.005
constants[17] = 0.005
constants[18] = 1
constants[19] = 0.07
constants[20] = 0.18
constants[21] = 0.01
constants[22] = 0.01
states[12] = 0
constants[23] = 1
states[13] = 0.9992357492446899
constants[24] = 0.01
constants[25] = 0.01
constants[26] = 0.004951
constants[27] = 10000
constants[28] = 0
constants[29] = 0.2
constants[30] = 0.5
constants[31] = 3
constants[32] = 0.25
constants[33] = 0.1
constants[34] = 0.1
constants[35] = 0.01
constants[36] = 0.01
constants[37] = 0.01
constants[38] = 0.1
constants[39] = 0.5
constants[40] = 0.5
constants[41] = 0.02
constants[42] = 2
constants[43] = 0
constants[44] = 88
constants[45] = 88
constants[46] = 88
constants[47] = 88
constants[48] = 88
constants[49] = 0.18
constants[50] = 3.5
constants[51] = 0
constants[52] = 0.2
constants[53] = 1
constants[54] = 0.1
constants[55] = 0
constants[56] = 1.8
constants[57] = 0
constants[58] = 0.8
constants[59] = 5
constants[60] = 5
constants[61] = 0
constants[62] = 5
constants[63] = 0
constants[64] = 1
constants[65] = 0.1
constants[66] = 0.1
constants[67] = 0.1
constants[68] = 0.01
constants[69] = 0.03
constants[70] = 0
constants[71] = 0.025
constants[72] = 0.01
constants[73] = 0.18
constants[74] = 0.005
constants[75] = 2
constants[76] = 0.1
constants[77] = 0.3
constants[78] = 0
constants[79] = 0
constants[80] = 1
constants[81] = 0.05
constants[82] = 0.05
constants[83] = 0.02
constants[84] = 0.2
constants[85] = 0
constants[86] = 1
constants[87] = 0.3
constants[88] = 0
constants[89] = 0.1
constants[90] = 0.1
constants[91] = 0.01
constants[92] = 5
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
rates[9] = ((constants[7]*states[10]*states[11])/(constants[10]+states[11])-(states[9]*constants[8])/(constants[11]+states[9]))-states[9]*constants[9]
rates[11] = (((constants[12]+constants[13]*(power(states[3], constants[14])))/(power(constants[15], constants[14])+power(states[3], constants[14]))+(states[9]*constants[8])/(constants[17]+states[9]))-constants[9]*states[11])-(constants[7]*states[10]*states[11])/(constants[16]+states[11])
rates[8] = constants[26]*states[8]*(1.00000-states[8]/constants[27])
algebraic[0] = (constants[18]-states[10])/1.00000
rates[10] = (constants[19]*states[3]*algebraic[0])/(constants[21]+algebraic[0])-(constants[20]*states[10])/(constants[22]+states[10])
algebraic[9] = (constants[23]-states[13])/1.00000
algebraic[15] = states[9]
algebraic[17] = constants[49]+constants[50]*algebraic[15]
algebraic[1] = constants[6]*states[8]
algebraic[19] = constants[51]+constants[52]*states[0]+constants[53]*states[3]+constants[54]*states[6]+constants[55]*algebraic[1]
rates[13] = (algebraic[9]*algebraic[17])/(constants[24]+algebraic[9])-(states[13]*algebraic[19])/(constants[25]+states[13])
algebraic[20] = (constants[58]+constants[59]*states[0]+constants[62]*states[3]+constants[60]*states[6]+constants[61]*algebraic[1])/(1.00000+constants[63]*algebraic[15])
algebraic[14] = constants[41]+(constants[42]+constants[43])*states[9]+constants[43]*states[11]
rates[1] = ((constants[0]*states[2]*states[0]-constants[1]*states[1])-algebraic[20]*states[1])-algebraic[14]*states[1]
algebraic[13] = constants[37]+constants[38]*states[6]+constants[39]*states[0]+constants[40]*states[3]
rates[7] = ((constants[5]*states[2]*states[6]-constants[4]*states[7])-algebraic[20]*states[7])-algebraic[13]*states[7]
algebraic[10] = constants[28]+constants[29]*states[0]+constants[30]*states[6]+constants[31]*algebraic[1]
algebraic[11] = constants[32]+constants[33]*states[0]+constants[34]*states[3]
algebraic[12] = (2.00000*algebraic[10]*constants[35])/((algebraic[11]-algebraic[10])+constants[36]*algebraic[11]+constants[35]*algebraic[10]+power(power((algebraic[11]-algebraic[10])+constants[36]*algebraic[11]+constants[35]*algebraic[10], 2.00000)-4.00000*(algebraic[11]-algebraic[10])*constants[35]*algebraic[10], 1.0/2))
algebraic[21] = states[8]*(constants[70]+constants[71]*algebraic[12])
rates[0] = ((constants[1]*states[1]+algebraic[20]*states[1]+algebraic[21])-algebraic[14]*states[0])-constants[0]*states[2]*states[0]
algebraic[23] = states[8]*(constants[72]+constants[73]*algebraic[12])
rates[6] = ((constants[4]*states[7]+algebraic[20]*states[7]+algebraic[23])-algebraic[13]*states[6])-constants[5]*states[2]*states[6]
algebraic[25] = constants[74]+constants[75]*states[13]+constants[76]*states[9]
algebraic[16] = (2.00000*constants[44]*algebraic[15]*constants[47])/(((constants[45]+constants[46]*states[3])-constants[44]*algebraic[15])+constants[48]*(constants[45]+constants[46]*states[3])+constants[47]*constants[44]*algebraic[15]+power(power(((constants[45]+constants[46]*states[3])-constants[44]*algebraic[15])+constants[48]*(constants[45]+constants[46]*states[3])+constants[47]*constants[44]*algebraic[15], 2.00000)-4.00000*((constants[45]+constants[46]*states[3])-constants[44]*algebraic[15])*constants[47]*constants[44]*algebraic[15], 1.0/2))
algebraic[18] = constants[56]+constants[57]*algebraic[16]
rates[2] = (((((((-constants[2]*states[3]*states[2]+constants[3]*states[5])-constants[2]*states[4]*states[2])+constants[3]*states[12]+algebraic[25]*states[5]+algebraic[25]*states[12]+algebraic[18])-algebraic[20]*states[2])-constants[0]*states[2]*states[0])+constants[1]*states[1]+algebraic[14]*states[1])-constants[5]*states[2]*states[6])+constants[4]*states[7]+algebraic[13]*states[7]
algebraic[22] = (2.00000*constants[64]*states[3]*constants[66])/((constants[65]-constants[64]*states[3])+constants[67]*constants[65]+constants[66]*constants[64]*states[3]+power(power((constants[65]-constants[64]*states[3])+constants[67]*constants[65]+constants[66]*constants[64]*states[3], 2.00000)-4.00000*(constants[65]-constants[64]*states[3])*constants[64]*states[3]*constants[66], 1.0/2))
algebraic[24] = states[8]*(constants[68]+constants[69]*algebraic[22])
algebraic[28] = (2.00000*(constants[85]+constants[86]*states[3])*constants[89])/(((constants[87]+constants[88]*algebraic[15])-(constants[85]+constants[86]*states[3]))+constants[90]*(constants[87]+constants[88]*algebraic[15])+(constants[85]+constants[86]*states[3])*constants[89]+power(power(((constants[87]+constants[88]*algebraic[15])-(constants[85]+constants[86]*states[3]))+constants[90]*(constants[87]+constants[88]*algebraic[15])+(constants[85]+constants[86]*states[3])*constants[89], 2.00000)-4.00000*((constants[87]+constants[88]*algebraic[15])-(constants[85]+constants[86]*states[3]))*(constants[85]+constants[86]*states[3])*constants[89], 1.0/2))
algebraic[29] = constants[91]+constants[92]*algebraic[28]
algebraic[26] = (2.00000*(constants[77]+constants[78]*algebraic[15])*constants[81])/(((constants[79]+constants[80]*states[3])-(constants[77]+constants[78]*algebraic[15]))+constants[82]*(constants[79]+constants[80]*states[3])+constants[81]*(constants[77]+constants[78]*algebraic[15])+power(power(((constants[79]+constants[80]*states[3])-(constants[77]+constants[78]*algebraic[15]))+constants[82]*(constants[79]+constants[80]*states[3])+constants[81]*(constants[77]+constants[78]*algebraic[15]), 2.00000)-4.00000*((constants[79]+constants[80]*states[3])-(constants[77]+constants[78]*algebraic[15]))*(constants[77]+constants[78]*algebraic[15])*constants[81], 1.0/2))
algebraic[27] = constants[83]+constants[84]*algebraic[26]
rates[3] = ((((algebraic[24]-algebraic[25]*states[3])+algebraic[29]*states[4])-algebraic[27]*states[3])-constants[2]*states[3]*states[2])+constants[3]*states[5]+algebraic[20]*states[5]
rates[4] = (((algebraic[27]*states[3]-algebraic[25]*states[4])-constants[2]*states[4]*states[2])+constants[3]*states[12]+algebraic[20]*states[12])-algebraic[29]*states[4]
rates[5] = ((((constants[2]*states[3]*states[2]-constants[3]*states[5])+algebraic[29]*states[12])-algebraic[27]*states[5])-algebraic[25]*states[5])-algebraic[20]*states[5]
rates[12] = ((((constants[2]*states[4]*states[2]-constants[3]*states[12])-algebraic[29]*states[12])+algebraic[27]*states[5])-algebraic[25]*states[12])-algebraic[20]*states[12]
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[0] = (constants[18]-states[10])/1.00000
algebraic[9] = (constants[23]-states[13])/1.00000
algebraic[15] = states[9]
algebraic[17] = constants[49]+constants[50]*algebraic[15]
algebraic[1] = constants[6]*states[8]
algebraic[19] = constants[51]+constants[52]*states[0]+constants[53]*states[3]+constants[54]*states[6]+constants[55]*algebraic[1]
algebraic[20] = (constants[58]+constants[59]*states[0]+constants[62]*states[3]+constants[60]*states[6]+constants[61]*algebraic[1])/(1.00000+constants[63]*algebraic[15])
algebraic[14] = constants[41]+(constants[42]+constants[43])*states[9]+constants[43]*states[11]
algebraic[13] = constants[37]+constants[38]*states[6]+constants[39]*states[0]+constants[40]*states[3]
algebraic[10] = constants[28]+constants[29]*states[0]+constants[30]*states[6]+constants[31]*algebraic[1]
algebraic[11] = constants[32]+constants[33]*states[0]+constants[34]*states[3]
algebraic[12] = (2.00000*algebraic[10]*constants[35])/((algebraic[11]-algebraic[10])+constants[36]*algebraic[11]+constants[35]*algebraic[10]+power(power((algebraic[11]-algebraic[10])+constants[36]*algebraic[11]+constants[35]*algebraic[10], 2.00000)-4.00000*(algebraic[11]-algebraic[10])*constants[35]*algebraic[10], 1.0/2))
algebraic[21] = states[8]*(constants[70]+constants[71]*algebraic[12])
algebraic[23] = states[8]*(constants[72]+constants[73]*algebraic[12])
algebraic[25] = constants[74]+constants[75]*states[13]+constants[76]*states[9]
algebraic[16] = (2.00000*constants[44]*algebraic[15]*constants[47])/(((constants[45]+constants[46]*states[3])-constants[44]*algebraic[15])+constants[48]*(constants[45]+constants[46]*states[3])+constants[47]*constants[44]*algebraic[15]+power(power(((constants[45]+constants[46]*states[3])-constants[44]*algebraic[15])+constants[48]*(constants[45]+constants[46]*states[3])+constants[47]*constants[44]*algebraic[15], 2.00000)-4.00000*((constants[45]+constants[46]*states[3])-constants[44]*algebraic[15])*constants[47]*constants[44]*algebraic[15], 1.0/2))
algebraic[18] = constants[56]+constants[57]*algebraic[16]
algebraic[22] = (2.00000*constants[64]*states[3]*constants[66])/((constants[65]-constants[64]*states[3])+constants[67]*constants[65]+constants[66]*constants[64]*states[3]+power(power((constants[65]-constants[64]*states[3])+constants[67]*constants[65]+constants[66]*constants[64]*states[3], 2.00000)-4.00000*(constants[65]-constants[64]*states[3])*constants[64]*states[3]*constants[66], 1.0/2))
algebraic[24] = states[8]*(constants[68]+constants[69]*algebraic[22])
algebraic[28] = (2.00000*(constants[85]+constants[86]*states[3])*constants[89])/(((constants[87]+constants[88]*algebraic[15])-(constants[85]+constants[86]*states[3]))+constants[90]*(constants[87]+constants[88]*algebraic[15])+(constants[85]+constants[86]*states[3])*constants[89]+power(power(((constants[87]+constants[88]*algebraic[15])-(constants[85]+constants[86]*states[3]))+constants[90]*(constants[87]+constants[88]*algebraic[15])+(constants[85]+constants[86]*states[3])*constants[89], 2.00000)-4.00000*((constants[87]+constants[88]*algebraic[15])-(constants[85]+constants[86]*states[3]))*(constants[85]+constants[86]*states[3])*constants[89], 1.0/2))
algebraic[29] = constants[91]+constants[92]*algebraic[28]
algebraic[26] = (2.00000*(constants[77]+constants[78]*algebraic[15])*constants[81])/(((constants[79]+constants[80]*states[3])-(constants[77]+constants[78]*algebraic[15]))+constants[82]*(constants[79]+constants[80]*states[3])+constants[81]*(constants[77]+constants[78]*algebraic[15])+power(power(((constants[79]+constants[80]*states[3])-(constants[77]+constants[78]*algebraic[15]))+constants[82]*(constants[79]+constants[80]*states[3])+constants[81]*(constants[77]+constants[78]*algebraic[15]), 2.00000)-4.00000*((constants[79]+constants[80]*states[3])-(constants[77]+constants[78]*algebraic[15]))*(constants[77]+constants[78]*algebraic[15])*constants[81], 1.0/2))
algebraic[27] = constants[83]+constants[84]*algebraic[26]
algebraic[2] = states[4]+states[5]
algebraic[3] = states[3]+states[4]+states[5]+states[12]
algebraic[4] = states[0]+states[1]
algebraic[5] = states[6]+states[7]
algebraic[6] = states[5]+states[12]
algebraic[7] = states[2]+states[5]+states[12]+states[1]+states[7]
algebraic[8] = states[11]+states[9]
return algebraic
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)