INDISIM-Denitrification
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; INDISIM-Denitrification - NetLogo Implementation ; Araujo-Granda P.A., Gras A., Ginovart M. and Moulton V. - 2019 ;______________________________ Global Variables __________________________________________________________________________________ extensions [matrix] globals [ world ; culture medium continuos size [ litres ] steptime ; step time [h] time_now ; simulated time [hours] gbacteria gdioxide gbicarbonate gn2o gno2- gno gn2 gsuccinate gamonium gnitrate goxygen ; global variables for graphical and numerical outputs output_file ; global variables for outputs files DST DSTb DSTr DSTm ; Variables for General Standard Deviation succinatemedium amoniummedium oxygenmedium nitratemedium nitritemedium monoxidemedium dinitrogenmedium nitrogenmedium dioxidemedium bicarbonatemedium Suc Amo Oxy Nrt Nit N2O succinate-input amonium-input nitrate-input xsc xam xox xntr xnr xmn xdn xn2 xco2 xhco3 bacteriaout xbacteria d untri isuccinate iamonium ioxygen initrate initrite imonoxide idinitrogen initrogen idioxide ibicarbonate ibacteria icbacteria inbacteria fsuccinate famonium foxygen fnitrate fnitrite fmonoxide fdinitrogen fnitrogen fdioxide fbicarbonate fbacteria fcbacteria fnbacteria insuccinate inamonium innitrate outsuccinate outamonium outoxygen outnitrate outnitrite outmonoxide outdinitrogen outnitrogen outdioxide outbicarbonate outbacteria outcbacteria outnbacteria c-bacteria n-bacteria c-succinate n-amonium n-nitrate n-nitrite n-monoxide n-dinitrogen n-nitrogen c-co2 c-hco3 n-obtained n-delivered c-obtained c-delivered %_e_c %_e_n yc/c scm oxm ntrm q sc-mant2 sc-mant3 sc-mant4 ini_biomass rep_biomass fmol_small fmol_big deq_small deq_big molecular-weight e-eeq/mol dGpc A1 fs1 fe1 yc/c1 A2 fs2 fe2 yc/c2 A3 fs3 fe3 yc/c3 A4 fs4 fe4 yc/c4 A5 fs5 fe5 yc/c5 A6 fs6 fe6 yc/c6 donor acceptor1 acceptor2 acceptor3 acceptor4 acceptor5 acceptor6 b-biomass pathway1 pathway2 pathway3 pathway4 pathway5 pathway6 auto_consum_NO auto_consum_N2O auto_consum_NO2- rx_mant-aero rx_mant_anox1 rx_mant_anox2 rx_mant_anox3 rx_mant_anox4 gamma_cells u_succ u_nh4+ u_no3-a u_no3-x u_no2- u_no u_n2o u_o2 u u0 u1 u3 umax ; for Mahcine learning matrix procedure biomass_matrix GRI_biomass nitrate_matrix GRI_nitrate nitrite_matrix GRI_nitrite nitrous_oxide_matrix GRI_nitrous_oxide Fitness ] ; ____________________________ Microorganism variables ____________________________________________________________________________ breed [bacteria bacterium] ; microorganism definition bacteria-own [ biomass ; microorganism biomass [ mmol ] biomass-reproduction ; reproduction treshold biomass [ mmol ] ac_mn ac_dn R ; reproductions counter m_aero s_aero_1 s_aero_2 ; aerobic phase counter m_anox_1 m_anox_2 m_anox_3 m_anox_4 s_anox_1 s_anox_2 s_anox_3 s_anox_4 ; anaerobic reactions counters sc-useful am-useful ox-useful ntr-useful nr-useful mn-useful dn-useful ; usefuls nutrients variables bm ] ; ____________________________ Culture Medium variables ____________________________________________________________________________ patches-own [ succinate-medium ; culture medium variable for the electron donor and C-Source in aerobic and anaerobic phases [ mmol ] amonium-medium ; culture medium variable for the N-Source in aerobic and anaerobic phases [ mmol ] oxygen-medium ; culture medium variable for the electron aceptor in aerobic phase [ mmol ] nitrate-medium ; culture medium variable for the electron aceptor in anoxic reaction 1 [ mmol ] nitrite-medium ; culture medium variable for the electron aceptor in anoxic reaction 2 [ mmol ] monoxide-medium ; culture medium variable for the electron aceptor in anoxic reaction 3 [ mmol ] dinitrogen-medium ; culture medium variable for the electron aceptor in anoxic reaction 4 [ mmol ] dioxide nitrogen bicarbonate ; culture medium variables for the denitrification products [ mmol ] ] ; ____________________________ Virtual Bioreactor Setting ____________________________________________________________________________ to setup clear-all ; clear all variables, graphical and numerical outputs reset-ticks ; reset tick counter setup-thermodynamics ; setup thermodynamic coefficients accord to McCarty 2007, TEEM2 setup-model ; setup general model parameters to obtain the starting points accord to Felgate's (2012) experiment setup-time ; scaled time setting setup-medium ; formulation of the initial culture medium setup-bacteria ; formulation of initial bacterial inoculum setup-monitors ; monitors setting if Output_file? = true [ setup-output ; setup output file write-outputfile ; write initial values on output file ] setup-balance ; mass balance setup set u0 gbacteria set u3 0 setup-machine.learning end ;___________________________________ Initial data according to Felgate's Experiments _____________________________________________________ to setup-model set world (world-width * world-height) ; Differential adjustment of reactor volume set DSTb 0.15 ; Standard Deviation for initial biomass distribution set DSTr 0.15 ; Standard Deviation for biomass reproduction set DST 0.05 ; Standard Deviation for general model varaibles set DSTm 0.25 ; Strandard Deviation for culture medium availability set nsc 0.28 set nam 0.84 set nx 0.79 set nntr 0.63 set nnr 0.77 set nmn 1 set ndn 0.49 ; Setup of culture medium nutrients availability obtanied from Dab if Denitrifying_bacterium = "P._denitrificans" [ set deq_small abs random-normal (0.5) (DST * 0.5) ; define the minimun bacterium size Bergey's reference taking into account the spherical shape set deq_big abs random-normal (0.9) (DST * 0.9) ; define the maximun bacterium size Bergey's reference taking into account the spherical shape set fmol_small (((deq_small * 1e-4) ^ 3) * (pi / 6)) * 1.1 * 1e15 / molecular-weight ; small bacteria expresed in fmol set fmol_big (((deq_big * 1e-4) ^ 3) * (pi / 6)) * 1.1 * 1e15 / molecular-weight ; big bacteria expresed in fmol set ini_biomass 0.75 * fmol_big ; [fmol] initial biomass for each bacterium set rep_biomass 0.75 * fmol_big ; [fmol] reproduction treshold biomass for each bacterium if Experiment = "Succ_High/Nitrate_Low" ; setup for experiment C-source sufficient / electron-acceptor limited [ Set Succinate 20 Set Nitrate 4.99825 ; Succiante and Nitrate setup accord to Felgate's (2012) experiment (Succinate High/Nitrate low) let paracoccus abs random-normal (0.0033683) (DSTr * 0.0033683) ; Initial biomass concentration accord to Felgate's (2012) experiment (succinate High/Nitrate low) set Microrganism round ((paracoccus * 1000 * world) / (molecular-weight * ini_biomass)) ; Individual's initial number accord to Felgate's (2012) experiment. ] if Experiment = "Succ_Low/Nitrate_High" ; setup for experiment C-source limited / electron-accpetor suficient [ Set Succinate 5 set Nitrate 21.60951 ; Succiante and Nitrate setup accord to Felgate's (2012) experiment (Succinate Low/Nitrate high) let paracoccus abs random-normal (0.0668478) (DSTr * 0.0668478) ; Initial biomass concentration accord to Felgate's (2012) experiment (succinate low/Nitrate high) set Microrganism round ((paracoccus * 1000 * world) / (molecular-weight * ini_biomass)) ; Individual's initial number accord to Felgate's (2012) experiment. ] ] if Denitrifying_bacterium = "A._xylosoxidans" [ set deq_small abs random-normal (0.63) (DST * 0.63) ; define the minimun bacterium size Bergey's reference taking into account the spherical shape set deq_big abs random-normal (1.40) (DST * 1.40) ; define the maximun bacterium size Bergey's reference taking into account the spherical shape set fmol_small (((deq_small * 1e-4) ^ 3) * (pi / 6)) * 1.1 * 1e15 / molecular-weight ; small bacteria expresed in fmol set fmol_big (((deq_big * 1e-4) ^ 3) * (pi / 6)) * 1.1 * 1e15 / molecular-weight ; big bacteria expresed in fmol set ini_biomass 0.75 * fmol_big ; [fmol] initial biomass for each bacterium set rep_biomass 0.75 * fmol_big ; [fmol] reproduction treshold biomass for each bacteirum if Experiment = "Succ_High/Nitrate_Low" ; setup for experiment C-source sufficient / electron-acceptor limited [ Set Succinate 20 Set Nitrate 5.15375 ; Succiante and Nitrate setup accord to Felgate's (2012) experiment (Succinate High/Nitrate low) let achromobacter abs random-normal (0.07695) (DSTr * 0.07695) ; Initial biomass concentration accord to Felgate's (2012) experiment (succinate High/Nitrate low) set Microrganism round ((achromobacter * 1000 * world) / (molecular-weight * ini_biomass)) ; Individual's initial number accord to Felgate's (2012) experiment. ] if Experiment = "Succ_Low/Nitrate_High" ; setup for experiment C-source limited / electron-accpetor suficient [ Set Succinate 5 set Nitrate 21.74694 ; Succiante and Nitrate setup accord to Felgate's (2012) experiment (Succinate Low/Nitrate high) let achromobacter abs random-normal (0.05182) (DSTr * 0.05182) ; Initial biomass concentration accord to Felgate's (2012) experiment (succinate low/Nitrate high) set Microrganism round ((achromobacter * 1000 * world) / (molecular-weight * ini_biomass)) ; Individual's initial number accord to Felgate's (2012) experiment. ] ] end ; ___________________________________ Proceeding to Scaled time ____________________________________________________________________________ to setup-time set steptime (Min/steptime / 60) ; User define the number of minute for each step time using a slider labeled "Min_per_steptime" end ; ___________________________________ Proceeding to Formulation of Initial culture medium __________________________________________________ to setup-medium if Denitrifying_bacterium = "P._denitrificans" [ if Experiment = "Succ_High/Nitrate_Low" [ set Suc random-normal (Succinate) (DST * Succinate) ; Succinate initial concentration (user define using a slider labeled Succinate) [mM] set Amo random-normal (Amonium) (DST * Amonium) ; Amonium initial concentration (user define using a slider labeled Amonium) [mM] set Oxy random-normal (0.2360) (DST * 0.2360) ; Oxygen initial concentration (simulated saturated conditions) accord to Felgate's (2012) experiment [mM] set Nrt random-normal (Nitrate) (DST * Nitrate) ; Nitrate initial concentration (user define using a slider labeled Nitrate) [mM] set Nit random-normal (0.0255) (DST * 0.0255) ; Nitrite initial concentration accord to Felgate's (2012) experiment [mM] set N2O random-normal (0.003003178) (DST * 0.003003178) ; Nitrous oxide initial concentration accord to Felgate's (2012) experiment [mM] ] if Experiment = "Succ_Low/Nitrate_High" [ set Suc random-normal (Succinate) (DST * Succinate) ; Succinate initial concentration (user define using a slider labeled Succinate) [mM] set Amo random-normal (Amonium) (DST * Amonium) ; Amonium initial concentration (user define using a slider labeled Amonium) [mM] set Oxy random-normal (0.2360) (DST * 0.2360) ; Oxygen initial concentration (simulated saturated conditions) accord to Felgate's (2012) experiment [mM] set Nrt random-normal (Nitrate) (DST * Nitrate) ; Nitrate initial concentration (user define using a slider labeled Nitrate) [mM] set Nit random-normal (0.011163522) (DST * 0.011163522) ; Nitrite initial concentration accord to Felgate's (2012) experiment [mM] set N2O random-normal (0.000028413312) (DST * 0.000028413312) ; Nitrous oxide initial concentration accord to Felgate's (2012) experiment [mM] ] ] if Denitrifying_bacterium = "A._xylosoxidans" [ if Experiment = "Succ_High/Nitrate_Low" [ set Suc random-normal (Succinate) (DST * Succinate) ; Succinate initial concentration (user define using a slider labeled Succinate) [mM] set Amo random-normal (Amonium) (DST * Amonium) ; Amonium initial concentration (user define using a slider labeled Amonium) [mM] set Oxy random-normal (0.2360) (DST * 0.2360) ; Oxygen initial concentration (simulated saturated conditions) accord to Felgate's (2012) experiment [mM] set Nrt random-normal (Nitrate) (DST * Nitrate) ; Nitrate initial concentration (user define using a slider labeled Nitrate) [mM] set Nit random-normal (0.36863) (DST * 0.36863) ; Nitrite initial concentration accord to Felgate's (2012) experiment [mM] set N2O random-normal (0.00006263) (DST * 0.00006263) ; Nitrous oxide initial concentration accord to Felgate's (2012) experiment [mM] ] if Experiment = "Succ_Low/Nitrate_High" [ set Suc random-normal (Succinate) (DST * Succinate) ; Succinate initial concentration (user define using a slider labeled Succinate) [mM] set Amo random-normal (Amonium) (DST * Amonium) ; Amonium initial concentration (user define using a slider labeled Amonium) [mM] set Oxy random-normal (0.2360) (DST * 0.2360) ; Oxygen initial concentration (simulated saturated conditions) accord to Felgate's (2012) experiment [mM] set Nrt random-normal (Nitrate) (DST * Nitrate) ; Nitrate initial concentration (user define using a slider labeled Nitrate) [mM] set Nit random-normal (0.00765) (DST * 0.00765) ; Nitrite initial concentration accord to Felgate's (2012) experiment [mM] set N2O random-normal (0.00001818) (DST * 0.00001818) ; Nitrous oxide initial concentration accord to Felgate's (2012) experiment [mM] ] ] ask patches [ set succinate-medium abs random-normal (Suc) (DST * Suc) ; Assign the succinate concentration to each cell according to the model's standar deviation set amonium-medium abs random-normal (Amo) (DST * Amo) ; Assign the amonium concentration to each cell according to the model's standar deviation set oxygen-medium abs random-normal (Oxy) (DST * Oxy) ; Assign the oxygen concentration to each cell according to the model's standar deviation set nitrate-medium abs random-normal (Nrt) (DST * Nrt) ; Assign the nitrate concentration to each cell according to the model's standar deviation set nitrite-medium abs random-normal (Nit) (DST * Nit) ; Assign the nitrite concentration to each cell according to the model's standar deviation set dinitrogen-medium abs random-normal (N2O) (DST * N2O) ; Assign the nitrous oxide concentration to each cell according to the model's standar deviation set monoxide-medium 0 ; Nitric Oxide initial concentration accord to Felgate's (2012) experiment [mM] set nitrogen 0 ; Nitrogen gas (N2) initial concentration accord to Felgate's (2012) experiment [mM] set dioxide 0 ; Carbon Dioxide initial concentration accord to Felgate's (2012) experiment [mM] set bicarbonate 0 ; Bicarbonate initial concentration [mM] set pcolor scale-color blue succinate-medium 0 Succinate ] end ; ____________________________ Proceeding to Formulation the Initial bacterial inoculum __________________________________________________ to setup-bacteria create-bacteria Microrganism ; User define the amount of initial active bacteria using a slider labaled Microrganism [ if Denitrifying_bacterium = "A._xylosoxidans" [set shape "cylinder"] ; Achrobobacter xylosoxidans is a rod bacteria if Denitrifying_bacterium = "P._denitrificans" [set shape "circle"] ; Paracoccus denitrificans is a spherical bacteria set size 0.5 ; This size is for visual propouse only set color green ; This color is for visual propouse only setxy random-xcor random-ycor ; Random inicial position on culture medium set biomass abs random-normal (ini_biomass) (DSTb * ini_biomass) ; Initial biomass for each microorganism [fmol] according to model's standar deviation set biomass-reproduction abs random-normal (rep_biomass) (DSTr * rep_biomass) ; reproduction treshold biomass [fmol] accord to INDISIM general procedures. ] end ; ____________________________ Proceeding to monitors setting __________________________________________________________________________ to setup-monitors set time_now ticks * steptime ; Simulated time [ h ] set gbacteria ((sum [biomass] of bacteria / world) / 1000) * molecular-weight ; Biomass concentration [ mg/ml ] set gsuccinate (sum[succinate-medium]of patches / world) ; Succinate concentration [ mM ] set gamonium (sum [amonium-medium] of patches / world) ; Amonium concentration [ mM ] set goxygen (sum [oxygen-medium] of patches / world) ; Oxygen concentration [ mM ] set gnitrate (sum [nitrate-medium] of patches / world) ; Nitrate concentration [ mM ] set gno2- (sum [nitrite-medium] of patches / world) ; Nitrite concentration [ mM ] set gno (sum [monoxide-medium] of patches / world) ; Nitric Oxide concentration [ mM ] if Experiment = "Succ_Low/Nitrate_High"[set gn2o (sum [dinitrogen-medium] of patches / world) * 1000] ; Nitrous Oxide concentration [ uM ] if Experiment = "Succ_High/Nitrate_Low"[set gn2o (sum [dinitrogen-medium] of patches / world)] ; Nitrous Oxide concentration [ mM ] set gdioxide (sum [dioxide] of patches / world) ; Carbon dioxide concentration [ mM ] set gn2 (sum [nitrogen] of patches / world) ; Nitrogen concentration [ mM ] set gbicarbonate (sum [bicarbonate] of patches / world) ; Bicarbonate concentration [ mM ] reactor_balance end ; ____________________________ Proceeding to setup output file __________________________________________________________________________ to setup-output file-close if Experiment = "Succ_Low/Nitrate_High" [ if Denitrifying_bacterium = "P._denitrificans" [set output_file (word (word behaviorspace-run-number"_"molecular-weight)"_PD_I_Denitrification_V10_ScLw_NtHg_" ".txt")] ; Outputfile name with .txt extension and Behaviorspace numering if Denitrifying_bacterium = "A._xylosoxidans" [set output_file (word (word behaviorspace-run-number"_"molecular-weight)"_AX_I_Denitrification_V10_ScLw_NtHg_" ".txt")] ; Outputfile name with .txt extension and Behaviorspace numering ] if Experiment = "Succ_High/Nitrate_Low" [ if Denitrifying_bacterium = "P._denitrificans" [set output_file (word (word behaviorspace-run-number"_"molecular-weight)"_PD_I_Denitrification_V10_ScHg_NtLw_" ".txt")] ; Outputfile name with .txt extension and Behaviorspace numering if Denitrifying_bacterium = "A._xylosoxidans" [set output_file (word (word behaviorspace-run-number"_"molecular-weight)"_AX_I_Denitrification_V10_ScHg_NtLw_" ".txt")] ; Outputfile name with .txt extension and Behaviorspace numering ] carefully [file-delete output_file] [ ] file-open output_file file-type "Time_[h] " ; Simulation time labed in outputfile unit hours file-type "Succinate_[mM] " ; Succinate concentration labed in outputfile unit milimolar file-type "NH4+_[mM] " ; Amonium concentration labed in outputfile unit milimolar file-type "O2_[mg/l] " ; Oxygen concentration labed in outputfile unit mg/ml file-type "NO3-_[mM] " ; Nitrate concentration labed in outputfile unit milimolar file-type "NO2-_[mM] " ; Nitrite concentration labed in outputfile unit milimolar file-type "NO_[mM] " ; Nitric Oxide concentration labed in outputfile unit milimolar if Experiment = "Succ_Low/Nitrate_High" [file-type "N2O_[uM] "] ; Dinitrogen concentration labed in outputfile unit micromolar if Experiment = "Succ_High/Nitrate_Low" [file-type "N2O_[mM] "] ; Dinitrogen concentration labed in outputfile unit milimolar file-type "N2_[mM] " ; Nitrogen concentration labed in outputfile unit milimolar file-type "CO2_[mM] " ; Carbon dioxide concentration labed in outputfile unit milimolar file-type "Biomass_[mg/ml] " ; Biomass concentration labed in outputfile unit miligrams / mililiter file-type "Individuals " ; Individuals into bioreactor labed in outputfile file-type "d " ; Reactor dilution ratio labed in outputfile units (h^-1) file-type "Sc_In_[mmol] " ; Inflow Succinate labed in outputfile units milimoles file-type "NH4+_In_[mmol] " ; Inflow Amonium labed in outputfile units milimoles file-type "NO3-_In_[mmol] " ; Inflow Nitrate labed in outputfile units milimoles file-type "Sc_Out_[mmol] " ; Outflow Succinate labed in outputfile units milimoles file-type "NH4+_Out_[mmol] " ; Outflow amonium labed in outputfile units milimoles file-type "NO3-_Out_[mmol] " ; Outflow nitrate labed in outputfile units milimoles file-type "NO2-_Out_[mmol] " ; Outflow nitrite labed in outputfile units milimoles file-type "NO_Out_[mmol] " ; Outflow Nitric Oxide labed in outputfile units milimoles if Experiment = "Succ_Low/Nitrate_High" [file-type "N2O_Out_[umol] "] ; Outflow Nitrous Oxide labed in outputfile units micromoles if Experiment = "Succ_High/Nitrate_Low" [file-type "N2O_Out_[mmol] "] ; Outflow Nitrous oxide labed in outputfile units milimoles file-type "N2_Out_[mmol] " ; Outflow Nitrogen gas labed in outputfile units milimoles file-type "Ind_Out " ; Outflow Microorganims labed in outputfile file-type "HCO3_[mM] " ; Bicarbonate concentration labed in outputfile units milimolar file-type "HCO3_Out_[mmol] " ; Outflow Bicarbonate labed in outputfile units milimoles file-type "CO2_Out_[mmol] " ; Outflow Carbon dioxide labed in outputfile units milimoles file-print " " end ; ____________________________ Proceeding to write values on output file __________________________________________________________________________ to write-outputfile setup-monitors file-type time_now ; Outputfile Simulated time [h] file-type " " file-type gsuccinate ; Outputfile Bioreactor Succinate concentration [mM] file-type " " file-type gamonium ; Outputfile Bioreactor Amonium concentration [mM] file-type " " file-type goxygen * 32 ; Outputfile Bioreactor Oxygen concentration [mg/l] file-type " " file-type gnitrate ; Outputfile Bioreactor Nitrate concentration [mM] file-type " " file-type gno2- ; Outputfile Bioreactor Nitrite concentration [mM] file-type " " file-type gno ; Outputfile Bioreactor Nitric Oxide concentration [mM] file-type " " file-type gn2o ; Outputfile Bioreactor Nitrous Oxide concentration [mM][uM] file-type " " file-type gn2 ; Outputfile Bioreactor Nitrogen gas concentration [mM] file-type " " file-type gdioxide ; Outputfile Bioreactor Carbon Dioxide concentration [mM] file-type " " file-type gbacteria ; Outputfile Bioreactor Biomass concentration [mg/ml] file-type " " file-type count bacteria ; Outputfile Bioreactor microorganism count [individuals] file-type " " file-type d ; Outputfile Bioreactor Dilution ratio [h^1] file-type " " file-type succinate-input ; Outputfile Inflow Succinate quantity [mmol] file-type " " file-type amonium-input ; Outputfile Inflow Amonioum quantity [mmol] file-type " " file-type nitrate-input ; Outputfile Inflow Nitrate quantity [mmol] file-type " " file-type xsc ; Outputfile Outflow Succinate quantity [mmol] file-type " " file-type xam ; Outputfile Outflow Amonium quantity [mmol] file-type " " file-type xntr ; Outputfile Outflow Nitrate quantity [mmol] file-type " " file-type xnr ; Outputfile Outflow Nitrite quantity [mmol] file-type " " file-type xmn ; Outputfile Outflow Nitric oxide quantity [mmol] file-type " " if Experiment = "Succ_Low/Nitrate_High"[file-type xdn * 1000] ; Outputfile Outflow Nitrous oxide quantity [umol] if Experiment = "Succ_High/Nitrate_Low"[file-type xdn] ; Outputfile Outflow Nitrous oxide quantity [mmol] file-type " " file-type xn2 ; Outputfile Outflow Nitrogen gas quantity [mmol] file-type " " file-type bacteriaout ; Outputfile Outflow microrganism quantity [individuals] file-type " " file-type gbicarbonate ; Outputfile Bioreactor Bicarbonate concentration [mM] file-type " " file-type xhco3 ; Outputfile Outflow bicarbonate quantity [mmol] file-type " " file-type xco2 ; Outputfile Outflow Carbon Dioxide quantity [mmol] file-type " " file-print " " end ; ____________________________ General mass balance proceedings _____________________________________________________________________________ to setup-balance set ibacteria (sum [biomass] of bacteria) ; Initial Biomass [mmol] set isuccinate (sum[succinate-medium]of patches) ; Initial Succinate [mmol] set iamonium (sum [amonium-medium] of patches) ; Initial Amonium [mmol] set ioxygen (sum [oxygen-medium] of patches) ; Initial Oxygen [mmol] set initrate (sum [nitrate-medium] of patches) ; Initial Nitrate [mmol] set initrite (sum [nitrite-medium] of patches) ; Initial Nitrite [mmol] set imonoxide (sum [monoxide-medium] of patches) ; Initial Monoxide [mmol] set idinitrogen (sum [dinitrogen-medium] of patches) ; Initial Dinitrogen [mmol] set idioxide (sum [dioxide] of patches) ; Initial Carbon dioxide [mmol] set initrogen (sum [nitrogen] of patches) ; Initial Nitrogen [mmol] set ibicarbonate (sum [bicarbonate] of patches) ; Initial Bicarbonate [mmol] end to reactor_balance set fbacteria (gbacteria * 1000 * world / molecular-weight) ; Final Biomass [mmol] set fsuccinate (gsuccinate * world) ; Final Succinate [mmol] set famonium (gamonium * world) ; Final Amonium [mmol] set foxygen (goxygen * world) ; Final Oxygen [mmol] set fnitrate (gnitrate * world) ; Final Nitrate [mmol] set fnitrite (gno2- * world) ; Final Nitrite [mmol] set fmonoxide (gno * world) ; Final Monoxide [mmol] if Experiment = "Succ_Low/Nitrate_High"[set fdinitrogen ((gn2o * world) / 1000)] ; Final Dinitrogen [mmol] if Experiment = "Succ_High/Nitrate_Low"[set fdinitrogen (gn2o * world)] ; FInal Dinitrogen [mmol] set fdioxide (gdioxide * world) ; Final Carbon dioxide [mmol] set fnitrogen (gn2 * world) ; Final Nitrogen [mmol] set fbicarbonate (gbicarbonate * world) ; Final Bicarbonate [mmol] end to inflow_balance set insuccinate (insuccinate + succinate-input) ; Inflow Succinate [mmol] set inamonium (inamonium + amonium-input) ; Inflow Amonium [mmol] set innitrate (innitrate + nitrate-input) ; Inflow Nitrate [mmol] end to outflow_balance set outsuccinate (outsuccinate + xsc) ; OutFlow Succinate [mmol] set outamonium (outamonium + xam) ; OutFlow Amonium [mmol] set outoxygen (outoxygen + xox) ; OutFlow Oxygen [mmol] set outnitrate (outnitrate + xntr) ; Outflow Nitrtate [mmol] set outnitrite (outnitrite + xnr) ; Outflow Nitrite [mmol] set outmonoxide (outmonoxide + xmn) ; Outflow Monoxide [mmol] set outdinitrogen (outdinitrogen + xdn) ; Outflow N2O [mmol] set outnitrogen (outnitrogen + xn2) ; Outflow N2 [mmol] set outdioxide (outdioxide + xco2) ; Outflow CO2 [mmol] set outbicarbonate (outbicarbonate + xhco3) ; outflow HCO3 [mmol] set outbacteria (outbacteria + xbacteria) ; OutFlow Baacteria [mmol] end to general_mass_balance set icbacteria (ibacteria * carbon * 12.011) ; Initial C-Mic [mg] set inbacteria (ibacteria * b-nitrogen * 14) ; Initial N-Mic [mg] set fcbacteria (fbacteria * carbon * 12.011) ; Final C-Mic [mg] set fnbacteria (fbacteria * b-nitrogen * 14) ; Final N-Mic [mg] set outcbacteria (outbacteria * carbon * 12.011) ; OutFlow C-Mic [mg] set outnbacteria (outbacteria * b-nitrogen * 14) ; OutFlow N-Mic [mg] set c-bacteria (fcbacteria - icbacteria) - (0 - outcbacteria) ; Microorganism Carbon balance set n-bacteria (fnbacteria - inbacteria) - (0 - outnbacteria) ; Microorganims Nitrogen balance set c-succinate ((fsuccinate - isuccinate) - (insuccinate - outsuccinate)) * 4 * 12.011 ; Succinate carbon balance set n-amonium ((famonium - iamonium) - (inamonium - outamonium)) * 1 * 14 ; Amonium nitrogen balance set n-nitrate ((fnitrate - initrate) - (innitrate - outnitrate)) * 1 * 14 ; Nitrate nitrogen balance set n-nitrite ((fnitrite - initrite) - (0 - outnitrite)) * 1 * 14 ; Nitrite nitrogen balance set n-monoxide ((fmonoxide - imonoxide) - (0 - outmonoxide)) * 1 * 14 ; Nitric oxide nitrogen balance set n-dinitrogen ((fdinitrogen - idinitrogen) - (0 - outdinitrogen)) * 2 * 14 ; Nitrous oxide nitrogen balance set n-nitrogen ((fnitrogen - initrogen) - (0 - outnitrogen)) * 2 * 14 ; Nitrogen gas nitrogen balance set c-co2 ((fdioxide - idioxide) - (0 - outdioxide)) * 1 * 12.011 ; Carbon dixoide carbon balance set c-hco3 ((fbicarbonate - ibicarbonate) - (0 - outbicarbonate)) * 1 * 12.011 ; Bicarbonate carbon balance set n-obtained abs (n-nitrite + n-monoxide + n-dinitrogen + n-nitrogen + n-bacteria) ; Total nitrogen obtained set n-delivered abs (n-amonium + n-nitrate) ; Total nitrogen delivered set c-obtained abs (c-co2 + c-hco3 + c-bacteria) ; Total carbon obtained set c-delivered abs (c-succinate) ; Total carbon delivered set %_e_c abs ((c-delivered - c-obtained) / c-delivered ) * 100 ; Carbon general mass balance porcentual error set %_e_n abs ((n-delivered - n-obtained) / n-delivered ) * 100 ; Nitrogen general mass balance porcentual error set yc/c abs (c-bacteria / c-succinate) ; Population Yield growth end ; ____________________________ Run Proceeding to Virtual Bioreactor __________________________________________________________________________ to go tick ; Start tick counter stir ; Observer procedure to stablish quantities for outflow in batch and continuos culture. outflow ; Observer and patch procedure to make outflow from bioreactor in continuos culture with or without culture medium homogenization inflow ; Observer procedure to simulate input nutrients to bioreactor according to dilution ratio with or without culture medium homogenization maintenance-requirements ; Observer procedure to calculate maintenance requirements for aerobic and anaerobic phases. ask bacteria [ uptake ; Agent procedure, each time step the bacteria establish their uptake capacities of all nutrients ifelse oxygen-medium >= abs random-normal NOX (DSTr * NOX) ; Agent procedure, according to oxygen local concentration runs different metabolic pathways [mant-aerobic][mant-anoxic1] auto_consum metabolism_end ; Agent procedure, after cellular maintenance and biomass synthesis the uptaked nutrient quantities are updated bipartition ; Agent procedure, after execute metabolic pathways if the biomass reached the treshold valeu microorganism reproduce by bipartition ] ask bacteria [ move ] ; Agent procedure, effect produced by the bioreactor agitation do-plotting ; Observer procedure, to setup graphical outputs if Output_file? = true [ ; if ; time_now = 5 or ; time_now = 6 or ; time_now = 24 or ; time_now = 24.5 or ; time_now = 25 or ; time_now = 30 or ; time_now = 48 or ; time_now = 54 or ; time_now = 72 or ; time_now = 78 or ; time_now = 97 or ; time_now = 99 or ; time_now = 102 or ; time_now = 120 ; [ write-outputfile ] ; ] ; Observer procedure, write-out the all simulated data to output file. general_mass_balance to-umax get_data_machine.learning if time_now >= Simulation_Time [machine.learning file-close stop] ; Stop simulation if time is over and close output-file if (sum [succinate-medium] of patches / world) < 0 [machine.learning file-close stop] ; Stop simulation if the succinate global concentration is lower to zero and close output-file if (sum [amonium-medium] of patches / world) < 0 [machine.learning file-close stop] ; Stop simulation if the amonium global concentration is lower to zero and close output-file if (sum [oxygen-medium] of patches / world) < 0 [machine.learning file-close stop] ; Stop simulation if the oxygen global concentration is lower to zero and close output-file if (sum [nitrate-medium] of patches / world) < 0 [machine.learning file-close stop] ; Stop simulation if the nitrate global concentration is lower to zero and close output-file end ; ____________________________ Proceeding to simulate bioreactor agitation over the culture medium ____________________________________________________ to stir set succinatemedium (sum [succinate-medium] of patches) ; Total Succinate in culture medium [mmol] set amoniummedium (sum [amonium-medium] of patches) ; Total Amonium in culture medium [mmol] set oxygenmedium (sum [oxygen-medium] of patches) ; Total Oxygen in culture medium [mmol] set nitratemedium (sum [nitrate-medium] of patches) ; Total Nitrate in culture medium [mmol] set nitritemedium (sum [nitrite-medium] of patches) ; Total Nitrite in culture medium [mmol] set monoxidemedium (sum [monoxide-medium] of patches) ; Total Nitric oxide in culture medium [mmol] set dinitrogenmedium (sum [dinitrogen-medium] of patches) ; Total Nitrous oxide in culture medium [mmol] set nitrogenmedium (sum [nitrogen] of patches) ; Total nitrogen gas in culture medium [mmol] set dioxidemedium (sum [dioxide] of patches) ; Total carbon dioxide in culture medium [mmol] set bicarbonatemedium (sum [bicarbonate] of patches) ; Total bicarbonate in culture medium [mmol] ifelse time_now >= Time_Shutdown_O2 ; if simulated time is lower than time_shutdown_O2 [set d abs random-normal (di) (DST * di)] ; Bioreactor works in continuos culture according to dilution ratio [ set d 0 ; the bioreactor works in batch conditions if oxygenmedium > 0.2360 * world [set oxygenmedium 0.2360 * world] ; and the oxygen keep saturated conditions ] set xsc d * succinatemedium * steptime ; succinate outflow according to dilution ratio [mmol] set xam d * amoniummedium * steptime ; amonium outflow according to dilution ratio [mmol] set xox d * oxygenmedium * steptime ; oxygen outflow according to dilution ration [mmol] set xntr d * nitratemedium * steptime ; nitrate outflow according to dilution ration [mmol] set xnr d * nitritemedium * steptime ; nitrite outflow according to dilution ration [mmol] set xmn d * monoxidemedium * steptime ; nitric oxide outflow according to dilution ration [mmol] set xdn d * dinitrogenmedium * steptime ; nitrous oxide outflow according to dilution ration [mmol] set xn2 d * nitrogenmedium * steptime ; nitrogen gas outflow according to dilution ration [mmol] set xco2 d * dioxidemedium * steptime ; carbon dioxide outflow according to dilution ration [mmol] set xhco3 d * bicarbonatemedium * steptime ; bicarbonate outflow according to dilution ration [mmol] if xmn >= (3.27 * world) [set xmn (3.27 * world)] ; if nitric oxide quantity is higher than maximun saturated conditions outflow only the saturated conditions if xdn >= (58.27 * world) [set xdn (58.27 * world)] ; if nitrous oxide quantity is higher than maximun saturated conditions outflow only the saturated conditions if xn2 >= (104.91 * world) [set xn2 (104.91 * world)] ; if nitrogen gas quantity is higher than maximun saturated conditions outflow only the saturated conditions if xco2 >= (8009.05 * world) [set xco2 (8009.05 * world)] ; if carbon dioxide quantity is higher than maximun saturated conditions outflow only the saturated conditions let bactout (sum [biomass] of bacteria) ; Total biomass in culture medium [mmol] let xbact (d * bactout * steptime) ; biomass outflow according to dilution ratio [mmol] let prom (count bacteria / bactout) ; average individual per biomass in outflow [individual ml /mg] set bacteriaout round (xbact * prom) ; Microorganism quantity to outflow [individuals] let monp (bactout / count bacteria) ; average biomass per individual in outflow [mg / ml individual] set xbacteria (monp * bacteriaout) ; Microorganism biomass concentration to outflow [mmol] outflow_balance end ; ____________________________ Proceeding to simulate reactor OutFlow ________________________________________________________________________________________ to outflow set q random 2 ifelse q = 0 [ ask patches [ set succinate-medium (succinatemedium - xsc) / world ; The succinate outflow quantity is taken from global quantity and then homogenization occurs. set amonium-medium (amoniummedium - xam) / world ; The amonium outflow quantity is taken from global quantity and then homogenization occurs. set oxygen-medium (oxygenmedium) / world ; Agitation and homogenization of oxygen set nitrate-medium (nitratemedium - xntr) / world ; The nitrate outflow quantity is taken from global quantity and then homogenization occurs. set nitrite-medium (nitritemedium - xnr) / world ; The nitrite outflow quantity is taken from global quantity and then homogenization occurs. set monoxide-medium (monoxidemedium - xmn) / world ; The nitric oxide outflow quantity is taken from global quantity and then homogenization occurs. set dinitrogen-medium (dinitrogenmedium - xdn) / world ; The nitrous oxide outflow quantity is taken from global quantity and then homogenization occurs. set nitrogen (nitrogenmedium - xn2) / world ; The nitrogen gas outflow quantity is taken from global quantity and then homogenization occurs. set dioxide (dioxidemedium - xco2 ) / world ; The carbon dioxide outflow quantity is taken from global quantity and then homogenization occurs. set bicarbonate (bicarbonatemedium - xhco3) / world ; The bicarbonate outflow quantity is taken from global quantity and then homogenization occurs. set pcolor scale-color blue succinate-medium 0 Succinate ] ] [ ask patches [ set succinate-medium succinate-medium - (xsc / world) ; The succinate outflow concentration is taken from local quantity without homogenization. set amonium-medium amonium-medium - (xam / world) ; The amonium outflow concentration is taken from local quantity without homogenization. set oxygen-medium (oxygenmedium) / world ; Agitation and homogenization of oxygen set nitrate-medium nitrate-medium - (xntr / world) ; The nitrate outflow concentration is taken from local quantity without homogenization. set nitrite-medium nitrite-medium - (xnr / world) ; The nitrite outflow concentration is taken from local quantity without homogenization. set monoxide-medium monoxide-medium - (xmn / world) ; The nitric oxide outflow concentration is taken from local quantity without homogenization. set dinitrogen-medium dinitrogen-medium - (xdn / world) ; The nitrous oxide outflow concentration is taken from local quantity without homogenization. set nitrogen nitrogen - (xn2 / world) ; The nitrogen gas outflow concentration is taken from local quantity without homogenization. set dioxide dioxide - (xco2 / world) ; The carbon dioxide outflow concentration is taken from local quantity without homogenization. set bicarbonate bicarbonate - (xhco3 / world) ; The bicarbonate outflow concentration is taken from local quantity without homogenization. set pcolor scale-color blue succinate-medium 0 Succinate ] ] ask n-of bacteriaout bacteria [ die ] ; Choose random bacteria and outflow accord to reactor dilution ratio end ; __________________________________ Proceeding to simulate reactor Inflow ____________________________________________________________________________________ to inflow set succinate-input d * world * (isuccinate / world) * steptime ; Succinate inflow to continuos culture according to the slider labed succinate [mmol] set amonium-input d * world * (iamonium / world) * steptime ; Amonium inflow to continuos culture according to the slider labed amonium [mmol] set nitrate-input d * world * (initrate / world) * steptime ; Nitrate inflow to continuos culture according to the slider labed nitrate [mmol] set succinatemedium (sum [succinate-medium] of patches) + (succinate-input) ; Total Succinate in culture medium after inflow [mmol] set amoniummedium (sum [amonium-medium] of patches) + (amonium-input) ; Total Amonium in culture medium after inflow [mmol] set nitratemedium (sum [nitrate-medium] of patches) + (nitrate-input) ; Total Nitrate in culture medium after inflow [mmol] if time_now <= Time_Shutdown_O2 [set oxygenmedium 0.2360 * world] inflow_balance ifelse q = 0 [ ask patches [ set succinate-medium succinatemedium / world ; The succinate inflow quantity is added to global quantity and then homogenization occurs. set amonium-medium amoniummedium / world ; The amonium inflow quantity is added to global quantity and then homogenization occurs. set oxygen-medium oxygenmedium / world ; The oxygen inflow quantity is added to global quantity and then homogenization occurs. set nitrate-medium nitratemedium / world ; The nitrate inflow quantity is added to global quantity and then homogenization occurs. set pcolor scale-color blue succinate-medium 0 Succinate ] ] [ ask patches [ set succinate-medium succinate-medium + (succinate-input / world) ; The succinate inflow concentration is added to local quantity without homogenization. set amonium-medium amonium-medium + (amonium-input / world) ; The amonium inflow concentration is added to local quantity without homogenization. set oxygen-medium oxygenmedium / world set nitrate-medium nitrate-medium + (nitrate-input / world) ; The nitrate inflow concentration is added to local quantity without homogenization. set pcolor scale-color blue succinate-medium 0 Succinate ] ] end ; ____________________________ Maintenance Requirements for aerobic and anaerobic phases __________________________________________________________________________ to maintenance-requirements ifelse time_now <= Time_Shutdown_O2 [ ; 1/14 (C4H4O4)2- + 1/4 O2 -> 1/7 CO2 + 1/7 HCO3- + 1/14 H2O set scm (energy_maintenance * steptime * carbon / 4) ; [mol succinate / molBiomass] set oxm (scm * abs (matrix:get rx_mant-aero 0 0) / abs (matrix:get rx_mant-aero 0 8)) ; [mol oxygen / molBiomass ] ] [ ; 1/14 (C4H4O4)2- + 1/2 NO3- -> 1/7 CO2 + 1/7 HCO3- + 1/2 NO2- + 1/14 H2O set scm (energy_maintenance * steptime * carbon / 4) ; [mol succinate / molBiomass ] set ntrm (scm * abs (matrix:get rx_mant_anox1 0 0) / abs (matrix:get rx_mant_anox1 0 8)) ; [mol nitrate / molBiomass ] ] end ; ____________________________ Uptake proceeding according the core model INDISM __________________________________________________________________________ to uptake let uptsc (abs (random-normal (uSc) (DSTr * uSc)) * biomass * carbon * steptime) ; [mmo] succinate by biomass uptake accord to INDISIM let uptam (abs (random-normal (uam) (DSTr * uam)) * biomass * carbon * steptime) ; [mmol] amonium by biomass uptake accord to INDISIM let uptox (abs (random-normal (uox) (DSTr * uox)) * biomass * carbon * steptime) ; [mmol] oxygen by biomass uptake accord to INDISIM ifelse time_now <= Time_Shutdown_O2 [set untri uNO3-a][set untri uNO3-x] ; The microorganism takes different uptake coefficient for aerobic and anaerobic phase. let uptntr (abs (random-normal (untri) (DSTr * untri)) * biomass * carbon * steptime) ; [mmol] nitrate by biomass uptake accord to INDISIM let uptnr (abs (random-normal (uNO2-) (DSTr * uNO2-)) * biomass * carbon * steptime) ; [mmol] nitrite by biomass uptake accord to INDISIM let uptmn (abs (random-normal (uNO) (DSTr * uNO)) * biomass * carbon * steptime) ; [mmol] nitric oxide by biomass uptake accord to INDISIM let uptdn (abs (random-normal (uN2O) (DSTr * uN2O)) * biomass * carbon * steptime) ; [mmol] nitrous oxide by biomass uptake accord to INDISIM let sc-available (abs (random-normal (nsc) (DSTm * nsc)) * succinate-medium * k_avail) ; INDISIM lineal model to determine succinate availability in culture medium [mmol] let am-available (abs (random-normal (nam) (DSTm * nam)) * amonium-medium * k_avail) ; INDISIM lineal model to determine amonium availability in culture medium [mmol] let ox-available (abs (random-normal (nx) (DSTm * nx)) * oxygen-medium * k_avail) ; INDISIM lineal model to determine oxygen availability in culture medium [mmol] let ntr-available (abs (random-normal (nntr) (DSTm * nntr)) * nitrate-medium * k_avail) ; INDISIM lineal model to determine nitrate availability in culture medium [mmol] let nr-available (abs (random-normal (nnr) (DSTm * nnr)) * nitrite-medium * k_avail) ; INDISIM lineal model to determine nitrite availability in culture medium [mmol] let mn-available (abs (random-normal (nmn) (DSTm * nmn)) * monoxide-medium * k_avail) ; INDISIM lineal model to determine nitric oxide availability in culture medium [mmol] let dn-available (abs (random-normal (ndn) (DSTm * ndn)) * dinitrogen-medium * k_avail) ; INDISIM lineal model to determine nitrous oxide availability in culture medium [mmol] ifelse sc-available <= uptsc [set sc-useful sc-available] [set sc-useful uptsc] ; For succinate comparation between uptake by biomass and availability and takes the lowest value. ifelse am-available <= uptam [set am-useful am-available] [set am-useful uptam] ; For amonium comparation between uptake by biomass and availability and takes the lowest value. ifelse ox-available <= uptox [set ox-useful ox-available] [set ox-useful uptox] ; For oxygen comparation between uptake by biomass and availability and takes the lowest value. ifelse ntr-available <= uptntr [set ntr-useful ntr-available] [set ntr-useful uptntr] ; For nitrate comparation between uptake by biomass and availability and takes the lowest value. ifelse nr-available <= uptnr [set nr-useful nr-available] [set nr-useful uptnr] ; For nitrite comparation between uptake by biomass and availability and takes the lowest value. ifelse mn-available <= uptmn [set mn-useful mn-available] [set mn-useful uptmn] ; For nitric oxide comparation between uptake by biomass and availability and takes the lowest value. ifelse dn-available <= uptdn [set dn-useful dn-available] [set dn-useful uptdn] ; For nitrous oxide comparation between uptake by biomass and availability and takes the lowest value. set succinate-medium (succinate-medium - sc-useful) ; Update local quantity of succinate set amonium-medium (amonium-medium - am-useful) ; Update local quantity of amonium set oxygen-medium (oxygen-medium - ox-useful) ; Update local quantity of oxygen set nitrate-medium (nitrate-medium - ntr-useful) ; Update local quantity of nitrate set nitrite-medium (nitrite-medium - nr-useful) ; Update local quantity of nitrite set monoxide-medium (monoxide-medium - mn-useful) ; Update local quantity of nitric oxide set dinitrogen-medium (dinitrogen-medium - dn-useful) ; Update local quantity of nitrous oxide end ; ____________________________ Aerobic phase proceeding according to TEEM2 __________________________________________________________________________ ; ____________________________ Aerobic Maintenance __________________________________________________________________________________________________ to mant-aerobic let sc-mant (scm * biomass) ; Succinate celullar maintenance requirements by biomass [mmol] let ox-mant (oxm * biomass) ; Oxygen cellular maintenance requirements by biomass [mmol] let y min (list sc-mant sc-useful) ; takes the minimum value between maintenance requirements and uptake quantity for Succinate [mmol] let z min (list ox-mant ox-useful) ; takes the minimum value between maintenance requirements and uptake quantity for Oxygen [mmol] let y1 (y / abs (matrix:get rx_mant-aero 0 8)) ; succinate quantity by stoichometric coefficient let z1 (z / abs (matrix:get rx_mant-aero 0 0)) ; oxygen quantity by stoichiometric coefficient let w1 min (list y1 z1) ; limiting nutrient for aerobic maintenance let ndioxide (abs (matrix:get rx_mant-aero 0 3) * w1) ; Carbon dioxide generation by cellular maintenance [mmol] let nbicarbonate (abs (matrix:get rx_mant-aero 0 5) * w1) ; Bicarbonate generation by cellular maintenance [mmol] set dioxide (dioxide + ndioxide) ; Carbon dioxide local quantity update set bicarbonate (bicarbonate + nbicarbonate) ; Bicarbonate local quantity update set sc-useful (sc-useful - abs (matrix:get rx_mant-aero 0 8) * w1) ; Update of Succinate uptaked [mmol] set ox-useful (ox-useful - abs (matrix:get rx_mant-aero 0 0) * w1) ; Update of Oxygen uptaked [mmol] set m_aero m_aero + 1 ; counter to maintenance reaction on aerobic phase if (sc-useful > 0) and (am-useful > 0) and (ox-useful > 0) [aerobic1] ; if uptaken updated quantities are higher than zero the microorganism could execute first aerobic parthway if (sc-useful > 0) and (am-useful > 0) and (ntr-useful > 0) [aerobic2] ; if uptaken updated quantities are higher than zero the microorganism could execute second aerobic parthway end ; ______________________________ Aerobic Sinthesis ______________________________________________________________________________________________________ to aerobic1 let a (sc-useful / abs (matrix:get pathway1 0 8)) ; uptaken succinate updated divided by its stoichiometric coefficient let b (am-useful / abs (matrix:get pathway1 0 4)) ; uptaken amonium updated divided by its stoichiometric coefficient let c (ox-useful / abs (matrix:get pathway1 0 0)) ; uptaken oxygen updated divided by its stoichiometric coefficient let x1 min (list a b c) ; limiting nutrient for pathway 1 in aerobic phase let nbiomass abs (matrix:get pathway1 0 6) * x1 ; Biomass generation by aerobic pathway 1 [mmol] let ndioxide abs (matrix:get pathway1 0 3) * x1 ; Carbon dioxide generation by aerobic pathway 1 [mmol] let nbicarbonate abs (matrix:get pathway1 0 5) * x1 ; Bicarbonate generation by aerobic pathway 1 [mmol] set biomass (biomass + nbiomass) ; Individual biomass update set dioxide (dioxide + ndioxide) ; Carbon dioxide local quantity update set bicarbonate (bicarbonate + nbicarbonate) ; Bicarbonate local quantity update set sc-useful (sc-useful - abs (matrix:get pathway1 0 8) * x1) ; update electron donor bacterium quantity set am-useful (am-useful - abs (matrix:get pathway1 0 4) * x1) ; update N-source bacterium quantity set ox-useful (ox-useful - abs (matrix:get pathway1 0 0) * x1) ; update electron aceptor bacterium quantity set s_aero_1 s_aero_1 + 1 ; counter to pathway 1 on aerobic phase if (sc-useful > 0) and (am-useful > 0) and (ntr-useful > 0) [aerobic2] ; if uptaken updated quantities are higher than zero the microorganism could execute second aerobic parthway end to aerobic2 let a (sc-useful / abs (matrix:get pathway2 0 8)) ; uptaken succinate updated divided by its stoichiometric coefficient let b (am-useful / abs (matrix:get pathway2 0 4)) ; uptaken amonium updated divided by its stoichiometric coefficient let c (ntr-useful / abs (matrix:get pathway2 0 0)) ; uptaken nitrate updated divided by its stoichiometric coefficient let x2 min (list a b c) ; limiting nutrient for pathway 2 in aerobic phase let nbiomass abs (matrix:get pathway2 0 6) * x2 ; Biomass generation by aerobic pathway 2 [mmol] let ndioxide abs (matrix:get pathway2 0 3) * x2 ; Carbon dioxide generation by aerobic pathway 2 [mmol] let namonium abs (matrix:get pathway2 0 9) * x2 ; Amonium generation by aerobic pathway 2 [mmol] let nbicarbonate abs (matrix:get pathway2 0 5) * x2 ; Bicarbonate generation by aerobic pathway 1 [mmol] set biomass (biomass + nbiomass) ; Individual biomass update set dioxide (dioxide + ndioxide) ; Carbon dioxide local quantity update set bicarbonate (bicarbonate + nbicarbonate) ; Bicarbonate local quantity update set amonium-medium (amonium-medium + namonium) ; Amonium uptake quantity update set sc-useful (sc-useful - abs (matrix:get pathway2 0 8) * x2) ; update electron donor bacterium quantity set am-useful (am-useful - abs (matrix:get pathway2 0 4) * x2) ; update N-source bacterium quantity set ntr-useful (ntr-useful - abs (matrix:get pathway2 0 0) * x2) ; update electron aceptor bacterium quantity set s_aero_2 s_aero_2 + 1 ; counter to pathway 2 on aerobic phase end ; ____________________________ Anaerobic phase proceeding ________________________________________________________________________________________________________ ; _____________________ Anoxics reactions are execute according to Reduction Order _______________________________________________________________________________ ; _____________________________Cellular maintenance to anoxic reaction 1 _________________________________________________________________________________________ to mant-anoxic1 let sc-mant (scm * biomass) ; Succinate celullar maintenance requirements by biomass [mmol] let ntr-mant (ntrm * biomass) ; Nitrate celullar maintenance requirements by biomass [mmol] let y min (list sc-mant sc-useful) ; takes the minimum value between maintenance requirements and uptake quantity for Succinate [mmol] let z min (list ntr-mant ntr-useful) ; takes the minimum value between maintenance requirements and uptake quantity for Nitrate [mmol] let y1 (y / abs (matrix:get rx_mant_anox1 0 8)) ; Succinate quantity by stoichometric coefficient let z1 (z / abs (matrix:get rx_mant_anox1 0 0)) ; Nitrate quantity by stoichometric coefficient let w1 min (list y1 z1) ; limiting nutrient for first anaerobic maintenance let ndioxide abs (matrix:get rx_mant_anox1 0 3) * w1 ; Carbon dioxide generation by cellular maintenance [mmol] let nbicarbonate abs (matrix:get rx_mant_anox1 0 5) * w1 ; Bicarbonate generation by cellular maintenance [mmol] let nnitrite abs (matrix:get rx_mant_anox1 0 9) * w1 ; Nitrite generation by cellular maintenance [mmol] set dioxide (dioxide + ndioxide) ; Carbon dioxide local quantity update set bicarbonate (bicarbonate + nbicarbonate) ; Bicarbonate local quantity update if ntr-mant > ntr-useful [set sc-mant2 sc-mant - abs (matrix:get rx_mant_anox1 0 8) * w1 ] ; Maintenance control set nr-useful (nr-useful + nnitrite) ; Uptaken nitrite updated set sc-useful (sc-useful - abs (matrix:get rx_mant_anox1 0 8) * w1) ; Update of Succinate uptaked [mmol] set ntr-useful (ntr-useful - abs (matrix:get rx_mant_anox1 0 0) * w1) ; Update of Nitrate uptaked [mmol] set m_anox_1 m_anox_1 + 1 ; counter to first maintenance reaction on anaerobic phase if sc-useful <= 0 [stop] ; if the succinate uptaken is lower than zero stop the microorganism metabolism until the next step time ifelse sc-mant2 > 0 [mant-anoxic2] [anoxic1] ; if maintenance is fullfiled go to biomass synthesis procedures end ; _____________________________Cellular maintenance to anoxic reaction 2 _________________________________________________________________________________________ to mant-anoxic2 let nr-mant2 (sc-mant2 * abs (matrix:get rx_mant_anox2 0 0) / abs (matrix:get rx_mant_anox2 0 8)) ; nitrite maintenance requirements from succinate maintenance requirements let y min (list sc-mant2 sc-useful) ; takes the minimum value between maintenance requirements and remaining uptaken quantity for Succinate [mmol] let z min (list nr-mant2 nr-useful) ; takes the minimum value between maintenance requirements and uptake quantity for nitrite [mmol] let y1 (y / abs (matrix:get rx_mant_anox2 0 8)) ; Succinate quantity by stoichometric coefficient let z1 (z / abs (matrix:get rx_mant_anox2 0 0)) ; Nitrite quantity by stoichometric coefficient let w2 min (list y1 z1) ; limiting nutrient for second anaerobic maintenance let ndioxide abs (matrix:get rx_mant_anox2 0 3) * w2 ; Carbon dioxide generation by cellular maintenance [mmol] let nbicarbonate abs (matrix:get rx_mant_anox2 0 5) * w2 ; Bicarbonate generation by cellular maintenance [mmol] let nmonoxide abs (matrix:get rx_mant_anox2 0 9) * w2 ; Nitric oxide generation by cellular maintenance [mmol] set dioxide (dioxide + ndioxide) ; Carbon dioxide local quantity update set bicarbonate (bicarbonate + nbicarbonate) ; Bicarbonate local quantity update set mn-useful (mn-useful + nmonoxide) ; Nitric oxide generation is added to their useful quantity if nr-mant2 > nr-useful [set sc-mant3 sc-mant2 - abs (matrix:get rx_mant_anox2 0 8) * w2 ] ; Maintenance control set sc-useful (sc-useful - w2 * abs (matrix:get rx_mant_anox2 0 8)) ; Update of Succinate uptaken [mmol] set nr-useful (nr-useful - w2 * abs (matrix:get rx_mant_anox2 0 0)) ; Update of Nitrite uptaken [mmol] set m_anox_2 m_anox_2 + 1 ; counter to second maintenance reaction on anaerobic phase if sc-useful <= 0 [stop] ; if the succinate uptaken is lower than zero stop the microorganism metabolism until the next step time ifelse sc-mant3 > 0 [mant-anoxic3] [anoxic2] ; if maintenance is fullfiled go to biomass synthesis procedures end ; _____________________________Cellular maintenance to anoxic reaction 3 _________________________________________________________________________________________ to mant-anoxic3 let mn-mant3 (sc-mant3 * abs (matrix:get rx_mant_anox3 0 0) / abs (matrix:get rx_mant_anox3 0 8)) ; nitric oxide maintenance requirements from succinate maintenance requirements let y min (list sc-mant3 sc-useful) ; takes the minimum value between maintenance requirements and remaining uptaken quantity for Succinate [mmol] let z min (list mn-mant3 mn-useful) ; takes the minimum value between maintenance requirements and uptake quantity for nitric oxide [mmol] let y1 (y / abs (matrix:get rx_mant_anox3 0 8)) ; Succinate quantity by stoichometric coefficient let z1 (z / abs (matrix:get rx_mant_anox3 0 0)) ; Nitric oxide quantity by stoichometric coefficient let w3 min (list y1 z1) ; limiting nutrient for third anaerobic maintenance let ndioxide abs (matrix:get rx_mant_anox3 0 3) * w3 ; Carbon dioxide generation by cellular maintenance [mmol] let nbicarbonate abs (matrix:get rx_mant_anox3 0 5) * w3 ; Bicarbonate generation by cellular maintenance [mmol] let ndinitrogen abs (matrix:get rx_mant_anox3 0 9) * w3 ; Nitrous oxide generation by cellular maintenance [mmol] set dioxide (dioxide + ndioxide) ; Carbon dioxide local quantity update set bicarbonate (bicarbonate + nbicarbonate) ; Bicarbonate local quantity update set dn-useful (dn-useful + ndinitrogen) ; Nitrous oxide generation is added to their useful quantity if mn-mant3 >= mn-useful [set sc-mant4 sc-mant3 - abs (matrix:get rx_mant_anox3 0 8) * w3 ] ; Maintenance control set sc-useful (sc-useful - w3 * abs (matrix:get rx_mant_anox3 0 8)) ; Update of Succinate uptaken [mmol] set mn-useful (mn-useful - w3 * abs (matrix:get rx_mant_anox3 0 0)) ; Update of Nitric oxide uptaken [mmol] set m_anox_3 m_anox_3 + 1 ; counter to third maintenance reaction on anaerobic phase if sc-useful <= 0 [stop] ; if the succinate uptaken is lower than zero stop the microorganism metabolism until the next step time ifelse sc-mant4 > 0 [mant-anoxic4] [anoxic3] ; if maintenance is fullfiled go to biomass synthesis procedures end ; _____________________________Cellular maintenance to anoxic reaction 4 _________________________________________________________________________________________ to mant-anoxic4 let dn-mant (sc-mant4 * abs (matrix:get rx_mant_anox4 0 0) / abs (matrix:get rx_mant_anox4 0 8)) ; nitrous oxide maintenance requirements from succinate maintenance requirements let y min (list sc-mant4 sc-useful) ; takes the minimum value between maintenance requirements and remaining uptaken quantity for Succinate [mmol] let z min (list dn-mant dn-useful) ; takes the minimum value between maintenance requirements and uptake quantity for nitrous oxide [mmol] let y1 (y / abs (matrix:get rx_mant_anox4 0 8)) ; Succinate quantity by stoichometric coefficient let z1 (z / abs (matrix:get rx_mant_anox4 0 0)) ; Nitrous oxide quantity by stoichometric coefficient let w4 min (list y1 z1) ; limiting nutrient for fourth anaerobic maintenance let ndioxide abs (matrix:get rx_mant_anox4 0 3) * w4 ; Carbon dioxide generation by cellular maintenance [mmol] let nbicarbonate abs (matrix:get rx_mant_anox4 0 5) * w4 ; Bicarbonate generation by cellular maintenance [mmol] let nnitrogen abs (matrix:get rx_mant_anox4 0 9) * w4 ; Nitrogen gas generation by cellular maintenance [mmol] set dioxide (dioxide + ndioxide) ; Carbon dioxide local quantity update set bicarbonate (bicarbonate + nbicarbonate) ; Bicarbonate local quantity update set nitrogen nitrogen + nnitrogen ; Nitrogen gas local quantity update set sc-useful (sc-useful - w4 * abs (matrix:get rx_mant_anox4 0 8)) ; Update of Succinate uptaken [mmol] set dn-useful (dn-useful - w4 * abs (matrix:get rx_mant_anox4 0 0)) ; Update of Nitrous oxide uptaken [mmol] set m_anox_4 m_anox_4 + 1 ; counter to fourth maintenance reaction on anaerobic phase ifelse (sc-useful > 0) and (am-useful > 0) and (dn-useful > 0) [anoxic4][stop] ; if maintenance is fullfiled go to biomass synthesis procedures end ; _____________________ Anoxics reactions are execute according to Reduction Order _______________________________________________________________________________ ; _____________________________ Biomass Synthesis to anoxic reaction 1 ___________________________________________________________________________________________ to anoxic1 let a (sc-useful / abs (matrix:get pathway3 0 8)) ; uptaken succinate updated divided by its stoichiometric coefficient let b (am-useful / abs (matrix:get pathway3 0 4)) ; uptaken amonium updated divided by its stoichiometric coefficient let c (ntr-useful / abs (matrix:get pathway3 0 0)) ; uptaken nitrate updated divided by its stoichiometric coefficient let x1 min (list a b c) ; limiting nutrient for enzimatic reaction 1 on pathway 3 in anaerobic phase let nbiomass abs (matrix:get pathway3 0 6) * x1 ; Biomass generation for enzimatic reaction 1 on pathway 3 [mmol] let ndioxide abs (matrix:get pathway3 0 3) * x1 ; Carbon dioxide generation for enzimatic reaction 1 on pathway 3 [mmol] let nnitrite abs (matrix:get pathway3 0 9) * x1 ; Nitrite generation for enzimatic reaction 1 on pathway 3 [mmol] let nbicarbonate abs (matrix:get pathway3 0 5) * x1 ; Bicarbonate generation for enzimatic reaction 1 on pathway 3 [mmol] set biomass (biomass + nbiomass) ; Individual biomass update set dioxide (dioxide + ndioxide) ; Carbon dioxide local quantity update set bicarbonate (bicarbonate + nbicarbonate) ; Bicarbonate local quantity update set nr-useful (nr-useful + nnitrite) ; Update of nitrite uptaken set sc-useful (sc-useful - abs (matrix:get pathway3 0 8) * x1) ; update electron donor bacterium quantity set am-useful (am-useful - abs (matrix:get pathway3 0 4) * x1) ; update N-source bacterium quantity set ntr-useful (ntr-useful - abs (matrix:get pathway3 0 0) * x1) ; update electron aceptor bacterium quantity set s_anox_1 s_anox_1 + 1 ; counter to first biomass synthesis reaction on anaerobic phase if (sc-useful > 0) and (am-useful > 0) and (nr-useful > 0) [anoxic2] ; if the succinate, amonium and nitrite quatities are enough go to enzimatic reaction 2 if (sc-useful > 0) and (am-useful > 0) and (mn-useful > 0) [anoxic3] ; if the succinate, amonium and nitric oxide quatities are enough go to enzimatic reaction 3 if (sc-useful > 0) and (am-useful > 0) and (dn-useful > 0) [anoxic4] ; if the succinate, amonium and nitrous oxide quatities are enough go to enzimatic reaction 4 end ; _____________________________ Biomass Synthesis to anoxic reaction 2 ___________________________________________________________________________________________ to anoxic2 let a (sc-useful / abs (matrix:get pathway4 0 8)) ; uptaken succinate updated divided by its stoichiometric coefficient let b (am-useful / abs (matrix:get pathway4 0 4)) ; uptaken amonium updated divided by its stoichiometric coefficient let c (nr-useful / abs (matrix:get pathway4 0 0)) ; uptaken nitrite updated divided by its stoichiometric coefficient let x2 min (list a b c) ; limiting nutrient for enzimatic reaction 2 on pathway 3 in anaerobic phase let nbiomass abs (matrix:get pathway4 0 6) * x2 ; Biomass generation for enzimatic reaction 2 on pathway 3 [mmol] let ndioxide abs (matrix:get pathway4 0 3) * x2 ; Carbon dioxide generation for enzimatic reaction 2 on pathway 3 [mmol] let nmonoxide abs (matrix:get pathway4 0 9) * x2 ; Nitric oxide generation for enzimatic reaction 2 on pathway 3 [mmol] let nbicarbonate abs (matrix:get pathway4 0 5) * x2 ; Bicarbonate generation for enzimatic reaction 2 on pathway 3 [mmol] set biomass (biomass + nbiomass) ; Individual biomass update set dioxide (dioxide + ndioxide) ; Carbon dioxide local quantity update set bicarbonate (bicarbonate + nbicarbonate) ; Bicarbonate local quantity update set mn-useful (mn-useful + nmonoxide) ; Update of nitric oxide uptaken set sc-useful (sc-useful - abs (matrix:get pathway4 0 8) * x2) ; update electron donor bacterium quantity set am-useful (am-useful - abs (matrix:get pathway4 0 4) * x2) ; update N-source bacterium quantity set nr-useful (nr-useful - abs (matrix:get pathway4 0 0) * x2) ; update electron aceptor bacterium quantity set s_anox_2 s_anox_2 + 1 ; counter to second biomass synthesis reaction on anaerobic phase if (sc-useful > 0) and (am-useful > 0) and (mn-useful > 0)[anoxic3] ; if the succinate, amonium and nitric oxide quatities are enough go to enzimatic reaction 3 if (sc-useful > 0) and (am-useful > 0) and (dn-useful > 0)[anoxic4] ; if the succinate, amonium and nitrous oxide quatities are enough go to enzimatic reaction 4 end ; _____________________________ Biomass Synthesis to anoxic reaction 3 ___________________________________________________________________________________________ to anoxic3 let a (sc-useful / abs (matrix:get pathway5 0 8)) ; uptaken succinate updated divided by its stoichiometric coefficient let b (am-useful / abs (matrix:get pathway5 0 4)) ; uptaken amonium updated divided by its stoichiometric coefficient let c (mn-useful / abs (matrix:get pathway5 0 0)) ; uptaken nitric oxide updated divided by its stoichiometric coefficient let x3 min (list a b c) ; limiting nutrient for enzimatic reaction 3 on pathway 3 in anaerobic phase let nbiomass abs (matrix:get pathway5 0 6) * x3 ; Biomass generation for enzimatic reaction 3 on pathway 3 [mmol] let ndioxide abs (matrix:get pathway5 0 3) * x3 ; Carbon dioxide generation for enzimatic reaction 3 on pathway 3 [mmol] let ndinitrogen abs (matrix:get pathway5 0 9) * x3 ; Nitrous oxide generation for enzimatic reaction 3 on pathway 3 [mmol] let nbicarbonate abs (matrix:get pathway5 0 5) * x3 ; Bicarbonate generation for enzimatic reaction 3 on pathway 3 [mmol] set biomass (biomass + nbiomass) ; Individual biomass update set dioxide (dioxide + ndioxide) ; Carbon dioxide local quantity update set bicarbonate (bicarbonate + nbicarbonate) ; Bicarbonate local quantity update set dn-useful (dn-useful + ndinitrogen) ; Update of nitrous oxide uptaken set sc-useful (sc-useful - abs (matrix:get pathway5 0 8) * x3) ; update electron donor bacterium quantity set am-useful (am-useful - abs (matrix:get pathway5 0 4) * x3) ; update N-source bacterium quantity set mn-useful (mn-useful - abs (matrix:get pathway5 0 0) * x3) ; update electron aceptor bacterium quantity set s_anox_3 s_anox_3 + 1 ; counter to third biomass synthesis reaction on anaerobic phase if (sc-useful > 0) and (am-useful > 0) and (dn-useful > 0)[anoxic4] ; if the succinate, amonium and nitrous oxide quatities are enough go to enzimatic reaction 4 end ; _____________________________ Biomass Synthesis to anoxic reaction 4 ___________________________________________________________________________________________ to anoxic4 let a (sc-useful / abs (matrix:get pathway6 0 8)) ; uptaken succinate updated divided by its stoichiometric coefficient let b (am-useful / abs (matrix:get pathway6 0 4)) ; uptaken amonium updated divided by its stoichiometric coefficient let c (dn-useful / abs (matrix:get pathway6 0 0)) ; uptaken nitrous oxide updated divided by its stoichiometric coefficient let x4 min (list a b c) ; limiting nutrient for enzimatic reaction 4 on pathway 3 in anaerobic phase let nbiomass abs (matrix:get pathway6 0 6) * x4 ; Biomass generation for enzimatic reaction 4 on pathway 3 [mmol] let ndioxide abs (matrix:get pathway6 0 3) * x4 ; Carbon dioxide generation for enzimatic reaction 4 on pathway 3 [mmol] let nnitrogen abs (matrix:get pathway6 0 9) * x4 ; Nitrogen gas generation for enzimatic reaction 4 on pathway 3 [mmol] let nbicarbonate abs (matrix:get pathway6 0 5) * x4 ; Bicarbonate generation for enzimatic reaction 4 on pathway 3 [mmol] set biomass (biomass + nbiomass) ; Individual biomass update set dioxide (dioxide + ndioxide) ; Carbon dioxide local quantity update set bicarbonate (bicarbonate + nbicarbonate) ; Bicarbonate local quantity update set nitrogen (nitrogen + nnitrogen) ; Nitrogen gas local quantity update set sc-useful (sc-useful - abs (matrix:get pathway6 0 8) * x4) ; update electron donor bacterium quantity set am-useful (am-useful - abs (matrix:get pathway6 0 4) * x4) ; update N-source bacterium quantity set dn-useful (dn-useful - abs (matrix:get pathway6 0 0) * x4) ; update electron aceptor bacterium quantity set s_anox_4 s_anox_4 + 1 ; counter to fourth biomass synthesis reaction on anaerobic phase end ; ____________________________ Procedure before bipartition _______________________________________________________________________________________________ to auto_consum if oxygen-medium <= abs random-normal NOX (DSTr * NOX) [ set bm (abs random-normal self_consumption_energy (DSTr * self_consumption_energy)) * steptime * biomass if mn-useful > 0 [ let mnc bm / abs (matrix:get auto_consum_NO 0 6) ; [mol electron acceptor NO] let mnc1 min (list mnc mn-useful) let ndinitrogen abs (matrix:get auto_consum_NO 0 9) * mnc1 let namonium abs (matrix:get auto_consum_NO 0 4) * mnc1 let ndioxide abs (matrix:get auto_consum_NO 0 3) * mnc1 let nbicarbonate abs (matrix:get auto_consum_NO 0 5) * mnc1 let nbiomass abs (matrix:get auto_consum_NO 0 6) * mnc1 set amonium-medium (amonium-medium + namonium) set dioxide (dioxide + ndioxide) set bicarbonate (bicarbonate + nbicarbonate) set dn-useful (dn-useful + ndinitrogen) set biomass (biomass - nbiomass) set bm bm - nbiomass set ac_mn ac_mn + 1 set mn-useful (mn-useful - mnc1) ] if (dn-useful > 0 and bm > 0) [ let dnc bm * abs (matrix:get auto_consum_N2O 0 0) / abs (matrix:get auto_consum_N2O 0 6) ; [mol electron acceptor N2O] let dnc1 min (list dnc dn-useful) let nnitrogen abs (matrix:get auto_consum_N2O 0 9) * dnc1 / abs (matrix:get auto_consum_N2O 0 0) let namonium abs (matrix:get auto_consum_N2O 0 4) * dnc1 / abs (matrix:get auto_consum_N2O 0 0) let ndioxide abs (matrix:get auto_consum_N2O 0 3) * dnc1 / abs (matrix:get auto_consum_N2O 0 0) let nbicarbonate abs (matrix:get auto_consum_N2O 0 5) * dnc1 / abs (matrix:get auto_consum_N2O 0 0) let nbiomass abs (matrix:get auto_consum_N2O 0 6) * dnc1 / abs (matrix:get auto_consum_N2O 0 0) set amonium-medium (amonium-medium + namonium) set dioxide (dioxide + ndioxide) set bicarbonate (bicarbonate + nbicarbonate) set nitrogen (nitrogen + nnitrogen) set biomass (biomass - nbiomass) set bm bm - nbiomass set ac_dn ac_dn + 1 set dn-useful (dn-useful - dnc1) ] ] end to metabolism_end ifelse sc-useful > 0 [set succinate-medium (succinate-medium + sc-useful) set sc-useful 0][set sc-useful 0] ; Release to culture medium the quantity not used ifelse am-useful > 0 [set amonium-medium (amonium-medium + am-useful) set am-useful 0][set am-useful 0] ; Release to culture medium the quantity not used ifelse ox-useful > 0 [set oxygen-medium (oxygen-medium + ox-useful) set ox-useful 0][set ox-useful 0] ; Release to culture medium the quantity not used ifelse ntr-useful > 0 [set nitrate-medium (nitrate-medium + ntr-useful) set ntr-useful 0][set ntr-useful 0] ; Release to culture medium the quantity not used ifelse nr-useful > 0 [set nitrite-medium (nitrite-medium + nr-useful) set nr-useful 0][set nr-useful 0] ; Release to culture medium the quantity not used ifelse mn-useful > 0 [set monoxide-medium (monoxide-medium + mn-useful) set mn-useful 0][set mn-useful 0] ifelse dn-useful > 0 [set dinitrogen-medium (dinitrogen-medium + dn-useful) set dn-useful 0][set dn-useful 0] set sc-mant2 0 set sc-mant3 0 set sc-mant4 0 ; Update to zero succinate internal maintenance requirements end ; ____________________________ Bipartition Procedure _______________________________________________________________________________________________ to bipartition if biomass >= biomass-reproduction ; cell division happens when a treshold value is reached [ let division-proportioning random-normal 0.50 (DSTr * 0.50) ; new bacteria differ randomly in their cell-biomass let cell-biomass-1 biomass * division-proportioning ; original biomass is not splitted equally into two halfs let cell-biomass-2 biomass - cell-biomass-1 set biomass cell-biomass-1 ; biomass for original microorganims set biomass-reproduction abs random-normal (rep_biomass) (DSTr * rep_biomass) ; setup new reproduction treshold for the original microorganism hatch 1 ; born new microorganism [ set biomass cell-biomass-2 ; biomass for newest microorganims ifelse time_now > Time_Shutdown_O2 [set color blue][set color green] set R 0 set m_aero 0 set s_aero_1 0 set s_aero_2 0 ; Reset all counters for new microorganism set m_anox_1 0 set m_anox_2 0 set m_anox_3 0 set m_anox_4 0 ; Reset all counters for new microorganism set s_anox_1 0 set s_anox_2 0 set s_anox_3 0 set s_anox_4 0 ; Reset all counters for new microorganism set ac_mn 0 set ac_dn 0 set bm 0 set biomass-reproduction abs random-normal (rep_biomass) (DSTr * rep_biomass) ; setup the reproduction treshold for the newest microorganism ] set R R + 1 ; Counter for bipartitions ] end ; ____________________________ Proceeding to simulate bioreactor agitation over the microorganism ____________________________________________________ to move if q = 0 [ setxy random-xcor random-ycor ] ; Randomly change position because bioreactor agitation end ; ____________________________ Proceeding to setup and write bioreactor graphical outputs ____________________________________________________ to do-plotting setup-monitors set-current-plot "Biomass" set-current-plot-pen "Biomass" plotxy time_now gbacteria set-current-plot "Products-CO2" set-current-plot-pen "CO2" plotxy time_now gdioxide set-current-plot "Products-N2O" set-current-plot-pen "N2O" plotxy time_now gn2o set-current-plot "Products - NO2-" set-current-plot-pen "NO2-" plotxy time_now gno2- set-current-plot "Products - NO" set-current-plot-pen "NO" plotxy time_now gno set-current-plot "Products - N2" set-current-plot-pen "N2" plotxy time_now gn2 set-current-plot "Culture Medium Nutrients" set-current-plot-pen "Succinate" plotxy time_now gsuccinate set-current-plot-pen "Amonium" plotxy time_now gamonium set-current-plot "Nitrate" set-current-plot-pen "nitrate" plotxy time_now gnitrate set-current-plot "Oxygen" set-current-plot-pen "oxygen" plotxy time_now goxygen * 32 set-current-plot "Bicarbonate" set-current-plot-pen "bicarbonate" plotxy time_now gbicarbonate set-current-plot "Bacterial-biomass-distribution" set-current-plot-pen "biomass-histogram" histogram [biomass] of bacteria set-plot-x-range fmol_small fmol_big if Denitrifying_bacterium = "P._denitrificans" [set-plot-pen-interval 0.1] if Denitrifying_bacterium = "A._xylosoxidans" [set-plot-pen-interval 0.3] set-current-plot "Metabolic_reactions" set-current-plot-pen "m_aero" plotxy time_now mean [m_aero] of bacteria set-current-plot-pen "s_aero_1" plotxy time_now mean [s_aero_1] of bacteria set-current-plot-pen "s_aero_2" plotxy time_now mean [s_aero_2] of bacteria set-current-plot-pen "m_anox_1" plotxy time_now mean [m_anox_1] of bacteria set-current-plot-pen "m_anox_2" plotxy time_now mean [m_anox_2] of bacteria set-current-plot-pen "m_anox_3" plotxy time_now mean [m_anox_3] of bacteria set-current-plot-pen "m_anox_4" plotxy time_now mean [m_anox_4] of bacteria set-current-plot-pen "s_anox_1" plotxy time_now mean [s_anox_1] of bacteria set-current-plot-pen "s_anox_2" plotxy time_now mean [s_anox_2] of bacteria set-current-plot-pen "s_anox_3" plotxy time_now mean [s_anox_3] of bacteria set-current-plot-pen "s_anox_4" plotxy time_now mean [s_anox_4] of bacteria set-current-plot-pen "R" plotxy time_now mean [R] of bacteria set-current-plot-pen "ac_mn" plotxy time_now mean [ac_mn] of bacteria set-current-plot-pen "ac_dn" plotxy time_now mean [ac_dn] of bacteria end to setup-thermodynamics if Denitrifying_bacterium = "P._denitrificans" [set carbon 3 set hydrogen 5.4 set oxygen 1.45 set b-nitrogen 0.75] if Denitrifying_bacterium = "A._xylosoxidans" [set carbon 5 set hydrogen 9 set oxygen 2.5 set b-nitrogen 1] set molecular-weight 12.011 * carbon + 1.008 * hydrogen + 16 * oxygen + 14 * b-nitrogen set e-eeq/mol (4 * carbon + hydrogen - 2 * oxygen - 3 * b-nitrogen) let b-co2 ((carbon - b-nitrogen) / e-eeq/mol) let b-hco3 (b-nitrogen / e-eeq/mol) let b-nh4 (b-nitrogen / e-eeq/mol) let b-bio (1 / e-eeq/mol) let b-h2o ((2 * carbon - oxygen + b-nitrogen) / e-eeq/mol) set dGpc (3.324 * molecular-weight / e-eeq/mol) set gamma_cells e-eeq/mol / carbon set A1 -1 * ((-29.09 / e1) + (30.9 / e1) + (dGpc / e1)) / (e1 * (-78.72 - 29.09)) set fs1 (1 / (1 + A1)) set fe1 (A1 / (1 + A1)) set yc/c1 (3.5 / gamma_cells) * fs1 set A2 -1 * ((-29.09 / e2) + (30.9 / e2) + (dGpc / e2)) / (e2 * (-35.11 - 29.09)) set fs2 (1 / (1 + A2)) set fe2 (A2 / (1 + A2)) set yc/c2 (3.5 / gamma_cells) * fs2 set A3 -1 * ((-29.09 / e3) + (30.9 / e3) + (dGpc / e3)) / (e3 * (-41.65 - 29.09)) set fs3 (1 / (1 + A3)) set fe3 (A3 / (1 + A3)) set yc/c3 (3.5 / gamma_cells) * fs3 set A4 -1 * ((-29.09 / e4) + (30.9 / e4) + (dGpc / e4)) / (e4 * (-33.718 - 29.09)) set fs4 (1 / (1 + A4)) set fe4 (A4 / (1 + A4)) set yc/c4 (3.5 / gamma_cells) * fs4 set A5 -1 * ((-29.09 / e5) + (30.9 / e5) + (dGpc / e5)) / (e5 * (-115.829 - 29.09)) set fs5 (1 / (1 + A5)) set fe5 (A5 / (1 + A5)) set yc/c5 (3.5 / gamma_cells) * fs5 set A6 -1 * ((-29.09 / e6) + (30.9 / e6) + (dGpc / e6)) / (e6 * (-133.469 - 29.09)) set fs6 (1 / (1 + A6)) set fe6 (A6 / (1 + A6)) set yc/c6 (3.5 / gamma_cells) * fs6 set donor matrix:from-row-list [[0 "d-H+" "d-e-" "d-co2" 0 "d-hco3" 0 "d-h2o" "d-succ" 0]] matrix:set donor 0 1 (1) matrix:set donor 0 2 (1) matrix:set donor 0 3 (1 / 7) matrix:set donor 0 5 (1 / 7) matrix:set donor 0 7 (-3 / 7) matrix:set donor 0 8 (-1 / 14) set b-biomass matrix:from-row-list [[0 "b-H+" "b-e-" "b-co2" "b-nh4" "b-hco3" "b-bio" "b-h2o" 0 0]] matrix:set b-biomass 0 1 (1) matrix:set b-biomass 0 2 (1) matrix:set b-biomass 0 3 (b-co2) matrix:set b-biomass 0 4 (b-nh4) matrix:set b-biomass 0 5 (b-hco3) matrix:set b-biomass 0 6 (-1 * b-bio) matrix:set b-biomass 0 7 (-1 * b-h2o) set acceptor1 matrix:from-row-list [["a1-o2" "a1-H+" "a1-e-" 0 0 0 0 "a1-h2o" 0 0]] matrix:set acceptor1 0 0 (1 / 4) matrix:set acceptor1 0 1 (1) matrix:set acceptor1 0 2 (1) matrix:set acceptor1 0 7 (-1 / 2) set acceptor2 matrix:from-row-list [["a2-no3-" "a2-H+" "a2-e-" 0 0 0 0 "a2-h2o" 0 "a2-nh4"]] matrix:set acceptor2 0 0 (1 / 8) matrix:set acceptor2 0 1 (5 / 4) matrix:set acceptor2 0 2 (1) matrix:set acceptor2 0 7 (-3 / 8) matrix:set acceptor2 0 9 (-1 / 8) set acceptor3 matrix:from-row-list [["a3-no3-" "a3-H+" "a3-e-" 0 0 0 0 "a3-h2o" 0 "a3-no2-"]] matrix:set acceptor3 0 0 (1 / 2) matrix:set acceptor3 0 1 (1) matrix:set acceptor3 0 2 (1) matrix:set acceptor3 0 7 (-1 / 2) matrix:set acceptor3 0 9 (-1 / 2) set acceptor4 matrix:from-row-list [["a4-no2-" "a4-H+" "a4-e-" 0 0 0 0 "a4-h2o" 0 "a4-no"]] matrix:set acceptor4 0 0 (1) matrix:set acceptor4 0 1 (2) matrix:set acceptor4 0 2 (1) matrix:set acceptor4 0 7 (-1) matrix:set acceptor4 0 9 (-1) set acceptor5 matrix:from-row-list [["a5-no" "a5-H+" "a5-e-" 0 0 0 0 "a5-h2o" 0 "a5-n2o"]] matrix:set acceptor5 0 0 (1) matrix:set acceptor5 0 1 (1) matrix:set acceptor5 0 2 (1) matrix:set acceptor5 0 7 (-1 / 2) matrix:set acceptor5 0 9 (-1 / 2) set acceptor6 matrix:from-row-list [["a6-n2o" "a6-H+" "a6-e-" 0 0 0 0 "a6-h2o" 0 "a6-n2"]] matrix:set acceptor6 0 0 (1 / 2) matrix:set acceptor6 0 1 (1) matrix:set acceptor6 0 2 (1) matrix:set acceptor6 0 7 (-1 / 2) matrix:set acceptor6 0 9 (-1 / 2) set pathway1 ((fe1 matrix:* acceptor1) matrix:+ (fs1 matrix:* b-biomass ) matrix:- (donor)) set pathway2 ((fe2 matrix:* acceptor2) matrix:+ (fs2 matrix:* b-biomass ) matrix:- (donor)) set pathway3 ((fe3 matrix:* acceptor3) matrix:+ (fs3 matrix:* b-biomass ) matrix:- (donor)) set pathway4 ((fe4 matrix:* acceptor4) matrix:+ (fs4 matrix:* b-biomass ) matrix:- (donor)) set pathway5 ((fe5 matrix:* acceptor5) matrix:+ (fs5 matrix:* b-biomass ) matrix:- (donor)) set pathway6 ((fe6 matrix:* acceptor6) matrix:+ (fs6 matrix:* b-biomass ) matrix:- (donor)) set auto_consum_NO acceptor5 matrix:- b-biomass set auto_consum_N2O acceptor6 matrix:- b-biomass set auto_consum_NO2- acceptor4 matrix:- b-biomass set rx_mant-aero acceptor1 matrix:- donor set rx_mant_anox1 acceptor3 matrix:- donor set rx_mant_anox2 acceptor4 matrix:- donor set rx_mant_anox3 acceptor5 matrix:- donor set rx_mant_anox4 acceptor6 matrix:- donor maximun_uptake ifelse (matrix:get pathway1 0 3) > 0 [output-print "Beware - CO2 is reagent on pathway1, please review e1 value" stop] [ifelse (matrix:get pathway2 0 3) > 0 [output-print "Beware - CO2 is reagent on pathway2, please review e2 value" stop] [ifelse (matrix:get pathway3 0 3) > 0 [output-print "Beware - CO2 is reagent on pathway3, please review e3 value" stop] [ifelse (matrix:get pathway4 0 3) > 0 [output-print "Beware - CO2 is reagent on pathway4, please review e4 value" stop] [ifelse (matrix:get pathway5 0 3) > 0 [output-print "Beware - CO2 is reagent on pathway5, please review e5 value" stop] [ifelse (matrix:get pathway6 0 3) > 0 [output-print "Beware - CO2 is reagent on pathway6, please review e6 value" stop] [output] ]]]]] end to maximun_uptake set u_succ u_max * abs mean (list (matrix:get pathway1 0 8 / matrix:get pathway1 0 6) (matrix:get pathway2 0 8 / matrix:get pathway2 0 6) (matrix:get pathway3 0 8 / matrix:get pathway3 0 6) (matrix:get pathway4 0 8 / matrix:get pathway4 0 6) (matrix:get pathway5 0 8 / matrix:get pathway5 0 6) (matrix:get pathway6 0 8 / matrix:get pathway6 0 6)) / carbon set u_nh4+ u_max * abs mean (list (matrix:get pathway1 0 4 / matrix:get pathway1 0 6) (matrix:get pathway2 0 4 / matrix:get pathway2 0 6) (matrix:get pathway3 0 4 / matrix:get pathway3 0 6) (matrix:get pathway4 0 4 / matrix:get pathway4 0 6) (matrix:get pathway5 0 4 / matrix:get pathway5 0 6) (matrix:get pathway6 0 4 / matrix:get pathway6 0 6)) / carbon set u_o2 u_max * abs (matrix:get pathway1 0 0 / matrix:get pathway1 0 6) / carbon set u_no3-a u_max * abs (matrix:get pathway2 0 0 / matrix:get pathway2 0 6) / carbon set u_no3-x (u_max * abs (matrix:get pathway3 0 0 / matrix:get pathway3 0 6) / carbon) / 4 set u_no2- (u_max * abs (matrix:get pathway4 0 0 / matrix:get pathway4 0 6) / carbon) / 4 set u_no (u_max * abs (matrix:get pathway5 0 0 / matrix:get pathway5 0 6) / carbon) / 4 set u_n2o (u_max * abs (matrix:get pathway6 0 0 / matrix:get pathway6 0 6) / carbon) / 4 end to output output-print "Adjusted Metabolic Pathways by TEEM2 (McCarty, 2007) : " output-type "Aerobic 1 : " output-type precision (matrix:get pathway1 0 8 / matrix:get pathway1 0 8) 3 output-type " (C4H4O4)2- + " output-type precision (matrix:get pathway1 0 4 / matrix:get pathway1 0 8) 3 output-type " NH4+ + " output-type precision (matrix:get pathway1 0 0 / matrix:get pathway1 0 8) 3 output-type " O2 --> " output-type precision (matrix:get pathway1 0 6 / matrix:get pathway1 0 8) 3 output-type " C'" output-type carbon output-type "'H'" output-type hydrogen output-type "'O'" output-type oxygen output-type "'N'" output-type b-nitrogen output-type " + " output-type precision (matrix:get pathway1 0 3 / matrix:get pathway1 0 8) 3 output-type " CO2 + " output-type precision (matrix:get pathway1 0 5 / matrix:get pathway1 0 8) 3 output-type " HCO3- + " output-type precision (matrix:get pathway1 0 7 / matrix:get pathway1 0 8) 3 output-print " H2O" output-type "Aerobic 2 : " output-type precision (matrix:get pathway2 0 8 / matrix:get pathway2 0 8) 3 output-type " (C4H4O4)2- + " output-type precision (matrix:get pathway2 0 4 / matrix:get pathway2 0 8) 3 output-type " NH4+ + " output-type precision (matrix:get pathway2 0 0 / matrix:get pathway2 0 8) 3 output-type " NO3- + " output-type precision (matrix:get pathway2 0 1 / matrix:get pathway2 0 8) 3 output-type " H+ + " output-type precision (matrix:get pathway2 0 7 / matrix:get pathway2 0 8) 3 output-type " H2O --> " output-type precision (matrix:get pathway2 0 6 / matrix:get pathway2 0 8) 3 output-type " C'" output-type carbon output-type "'H'" output-type hydrogen output-type "'O'" output-type oxygen output-type "'N'" output-type b-nitrogen output-type " + " output-type precision (matrix:get pathway2 0 3 / matrix:get pathway2 0 8) 3 output-type " CO2 + " output-type precision (matrix:get pathway2 0 5 / matrix:get pathway2 0 8) 3 output-type " HCO3- + " output-type precision (matrix:get pathway2 0 9 / matrix:get pathway2 0 8) 3 output-print " NH4+" output-type " Anoxic 1 : " output-type precision (matrix:get pathway3 0 8 / matrix:get pathway3 0 8) 3 output-type " (C4H4O4)2- + " output-type precision (matrix:get pathway3 0 4 / matrix:get pathway3 0 8) 3 output-type " NH4+ + " output-type precision (matrix:get pathway3 0 0 / matrix:get pathway3 0 8) 3 output-type " NO3- --> " output-type precision (matrix:get pathway3 0 6 / matrix:get pathway3 0 8) 3 output-type " C'" output-type carbon output-type "'H'" output-type hydrogen output-type "'O'" output-type oxygen output-type "'N'" output-type b-nitrogen output-type " + " output-type precision (matrix:get pathway3 0 9 / matrix:get pathway3 0 8) 3 output-type " NO2- + " output-type precision (matrix:get pathway3 0 3 / matrix:get pathway3 0 8) 3 output-type " CO2 + " output-type precision (matrix:get pathway3 0 5 / matrix:get pathway3 0 8) 3 output-type " HCO3- + " output-type precision (matrix:get pathway3 0 7 / matrix:get pathway3 0 8) 3 output-print " H2O" output-type " Anoxic 2 : " output-type precision (matrix:get pathway4 0 8 / matrix:get pathway4 0 8) 3 output-type " (C4H4O4)2- + " output-type precision (matrix:get pathway4 0 4 / matrix:get pathway4 0 8) 3 output-type " NH4+ + " output-type precision (matrix:get pathway4 0 0 / matrix:get pathway4 0 8) 3 output-type " NO2- + " output-type precision (matrix:get pathway4 0 1 / matrix:get pathway4 0 8) 3 output-type " H+ --> " output-type precision (matrix:get pathway4 0 6 / matrix:get pathway4 0 8) 3 output-type " C'" output-type carbon output-type "'H'" output-type hydrogen output-type "'O'" output-type oxygen output-type "'N'" output-type b-nitrogen output-type " + " output-type precision (matrix:get pathway4 0 9 / matrix:get pathway4 0 8) 3 output-type " NO + " output-type precision (matrix:get pathway4 0 3 / matrix:get pathway4 0 8) 3 output-type " CO2 + " output-type precision (matrix:get pathway4 0 5 / matrix:get pathway4 0 8) 3 output-type " HCO3- + " output-type precision (matrix:get pathway4 0 7 / matrix:get pathway4 0 8) 3 output-print " H2O" output-type " Anoxic 3 : " output-type precision (matrix:get pathway5 0 8 / matrix:get pathway5 0 8) 3 output-type " (C4H4O4)2- + " output-type precision (matrix:get pathway5 0 4 / matrix:get pathway5 0 8) 3 output-type " NH4+ + " output-type precision (matrix:get pathway5 0 0 / matrix:get pathway5 0 8) 3 output-type " NO --> " output-type precision (matrix:get pathway5 0 6 / matrix:get pathway5 0 8) 3 output-type " C'" output-type carbon output-type "'H'" output-type hydrogen output-type "'O'" output-type oxygen output-type "'N'" output-type b-nitrogen output-type " + " output-type precision (matrix:get pathway5 0 9 / matrix:get pathway5 0 8) 3 output-type " N2O + " output-type precision (matrix:get pathway5 0 3 / matrix:get pathway5 0 8) 3 output-type " CO2 + " output-type precision (matrix:get pathway5 0 5 / matrix:get pathway5 0 8) 3 output-type " HCO3- + " output-type precision (matrix:get pathway5 0 7 / matrix:get pathway5 0 8) 3 output-print " H2O" output-type " Anoxic 4 : " output-type precision (matrix:get pathway6 0 8 / matrix:get pathway6 0 8) 3 output-type " (C4H4O4)2- + " output-type precision (matrix:get pathway6 0 4 / matrix:get pathway6 0 8) 3 output-type " NH4+ + " output-type precision (matrix:get pathway6 0 0 / matrix:get pathway6 0 8) 3 output-type " N2O --> " output-type precision (matrix:get pathway6 0 6 / matrix:get pathway6 0 8) 3 output-type " C'" output-type carbon output-type "'H'" output-type hydrogen output-type "'O'" output-type oxygen output-type "'N'" output-type b-nitrogen output-type " + " output-type precision (matrix:get pathway6 0 9 / matrix:get pathway6 0 8) 3 output-type " N2 + " output-type precision (matrix:get pathway6 0 3 / matrix:get pathway6 0 8) 3 output-type " CO2 + " output-type precision (matrix:get pathway6 0 5 / matrix:get pathway6 0 8) 3 output-type " HCO3- + " output-type precision (matrix:get pathway6 0 7 / matrix:get pathway6 0 8) 3 output-print " H2O" output-print "Adjusted Biomass Degradation Pathways by TEEM2 (McCarty, 2007) : " output-type "Degradation of NO2-: " output-type precision (matrix:get auto_consum_NO2- 0 6 / matrix:get auto_consum_NO2- 0 6) 3 output-type " C'" output-type carbon output-type "'H'" output-type hydrogen output-type "'O'" output-type oxygen output-type "'N'" output-type b-nitrogen output-type " + " output-type precision (matrix:get auto_consum_NO2- 0 1 / matrix:get auto_consum_NO2- 0 6) 3 output-type " H+ + " output-type precision (matrix:get auto_consum_NO2- 0 0 / matrix:get auto_consum_NO2- 0 6) 3 output-type " NO2- --> " output-type precision (matrix:get auto_consum_NO2- 0 3 / matrix:get auto_consum_NO2- 0 6) 3 output-type " CO2 + " output-type precision (matrix:get auto_consum_NO2- 0 4 / matrix:get auto_consum_NO2- 0 6) 3 output-type " NH4+ + " output-type precision (matrix:get auto_consum_NO2- 0 5 / matrix:get auto_consum_NO2- 0 6) 3 output-type " HCO3- + " output-type precision (matrix:get auto_consum_NO2- 0 9 / matrix:get auto_consum_NO2- 0 6) 3 output-type " NO + " output-type precision (matrix:get auto_consum_NO2- 0 7 / matrix:get auto_consum_NO2- 0 6) 3 output-print " H2O" output-type "Degradation of NO : " output-type precision (matrix:get auto_consum_NO 0 6 / matrix:get auto_consum_NO 0 6) 3 output-type " C'" output-type carbon output-type "'H'" output-type hydrogen output-type "'O'" output-type oxygen output-type "'N'" output-type b-nitrogen output-type " + " output-type precision (matrix:get auto_consum_NO 0 0 / matrix:get auto_consum_NO 0 6) 3 output-type " NO --> " output-type precision (matrix:get auto_consum_NO 0 3 / matrix:get auto_consum_NO 0 6) 3 output-type " CO2 + " output-type precision (matrix:get auto_consum_NO 0 4 / matrix:get auto_consum_NO 0 6) 3 output-type " NH4+ + " output-type precision (matrix:get auto_consum_NO 0 5 / matrix:get auto_consum_NO 0 6) 3 output-type " HCO3- + " output-type precision (matrix:get auto_consum_NO 0 9 / matrix:get auto_consum_NO 0 6) 3 output-type " N2O + " output-type precision (matrix:get auto_consum_NO 0 7 / matrix:get auto_consum_NO 0 6) 3 output-print " H2O" output-type "Degradation of N2O : " output-type precision (matrix:get auto_consum_N2O 0 6 / matrix:get auto_consum_N2O 0 6) 3 output-type " C'" output-type carbon output-type "'H'" output-type hydrogen output-type "'O'" output-type oxygen output-type "'N'" output-type b-nitrogen output-type " + " output-type precision (matrix:get auto_consum_N2O 0 0 / matrix:get auto_consum_N2O 0 6) 3 output-type " N2O --> " output-type precision (matrix:get auto_consum_N2O 0 3 / matrix:get auto_consum_N2O 0 6) 3 output-type " CO2 + " output-type precision (matrix:get auto_consum_N2O 0 4 / matrix:get auto_consum_N2O 0 6) 3 output-type " NH4+ + " output-type precision (matrix:get auto_consum_N2O 0 5 / matrix:get auto_consum_N2O 0 6) 3 output-type " HCO3- + " output-type precision (matrix:get auto_consum_N2O 0 9 / matrix:get auto_consum_N2O 0 6) 3 output-type " N2 + " output-type precision (matrix:get auto_consum_N2O 0 7 / matrix:get auto_consum_N2O 0 6) 3 output-print " H2O" output-print "Adjusted cellular Maintenance reactions by TEEM2 (McCarty, 2007) : " output-type "Aerobic Manintenance : " output-type precision (matrix:get rx_mant-aero 0 8 / matrix:get rx_mant-aero 0 8) 3 output-type " (C4H4O4)2- + " output-type precision (matrix:get rx_mant-aero 0 0 / matrix:get rx_mant-aero 0 8) 3 output-type " O2 --> " output-type precision (matrix:get rx_mant-aero 0 3 / matrix:get rx_mant-aero 0 8) 3 output-type " CO2 + " output-type precision (matrix:get rx_mant-aero 0 5 / matrix:get rx_mant-aero 0 8) 3 output-type " HCO3- + " output-type precision (matrix:get rx_mant-aero 0 7 / matrix:get rx_mant-aero 0 8) 3 output-print " H2O" output-type "Anoxic1 Manintenance : " output-type precision (matrix:get rx_mant_anox1 0 8 / matrix:get rx_mant_anox1 0 8) 3 output-type " (C4H4O4)2- + " output-type precision (matrix:get rx_mant_anox1 0 0 / matrix:get rx_mant_anox1 0 8) 3 output-type " NO3- --> " output-type precision (matrix:get rx_mant_anox1 0 3 / matrix:get rx_mant_anox1 0 8) 3 output-type " CO2 + " output-type precision (matrix:get rx_mant_anox1 0 5 / matrix:get rx_mant_anox1 0 8) 3 output-type " HCO3- + " output-type precision (matrix:get rx_mant_anox1 0 9 / matrix:get rx_mant_anox1 0 8) 3 output-type " NO2- + " output-type precision (matrix:get rx_mant_anox1 0 7 / matrix:get rx_mant_anox1 0 8) 3 output-print " H2O" output-type "Anoxic2 Manintenance : " output-type precision (matrix:get rx_mant_anox2 0 8 / matrix:get rx_mant_anox2 0 8) 3 output-type " (C4H4O4)2- + " output-type precision (matrix:get rx_mant_anox2 0 0 / matrix:get rx_mant_anox2 0 8) 3 output-type " NO2- + " output-type precision (matrix:get rx_mant_anox2 0 1 / matrix:get rx_mant_anox2 0 8) 3 output-type " H+ --> " output-type precision (matrix:get rx_mant_anox2 0 3 / matrix:get rx_mant_anox2 0 8) 3 output-type " CO2 + " output-type precision (matrix:get rx_mant_anox2 0 5 / matrix:get rx_mant_anox2 0 8) 3 output-type " HCO3- + " output-type precision (matrix:get rx_mant_anox2 0 9 / matrix:get rx_mant_anox2 0 8) 3 output-type " NO + " output-type precision (matrix:get rx_mant_anox2 0 7 / matrix:get rx_mant_anox2 0 8) 3 output-print " H2O" output-type "Anoxic3 Manintenance : " output-type precision (matrix:get rx_mant_anox3 0 8 / matrix:get rx_mant_anox3 0 8) 3 output-type " (C4H4O4)2- + " output-type precision (matrix:get rx_mant_anox3 0 0 / matrix:get rx_mant_anox3 0 8) 3 output-type " NO --> " output-type precision (matrix:get rx_mant_anox3 0 3 / matrix:get rx_mant_anox3 0 8) 3 output-type " CO2 + " output-type precision (matrix:get rx_mant_anox3 0 5 / matrix:get rx_mant_anox3 0 8) 3 output-type " HCO3- + " output-type precision (matrix:get rx_mant_anox3 0 9 / matrix:get rx_mant_anox3 0 8) 3 output-type " N2O + " output-type precision (matrix:get rx_mant_anox3 0 7 / matrix:get rx_mant_anox3 0 8) 3 output-print " H2O" output-type "Anoxic4 Manintenance : " output-type precision (matrix:get rx_mant_anox4 0 8 / matrix:get rx_mant_anox4 0 8) 3 output-type " (C4H4O4)2- + " output-type precision (matrix:get rx_mant_anox4 0 0 / matrix:get rx_mant_anox4 0 8) 3 output-type " N2O --> " output-type precision (matrix:get rx_mant_anox4 0 3 / matrix:get rx_mant_anox4 0 8) 3 output-type " CO2 + " output-type precision (matrix:get rx_mant_anox4 0 5 / matrix:get rx_mant_anox4 0 8) 3 output-type " HCO3- + " output-type precision (matrix:get rx_mant_anox4 0 9 / matrix:get rx_mant_anox4 0 8) 3 output-type " N2 + " output-type precision (matrix:get rx_mant_anox4 0 7 / matrix:get rx_mant_anox4 0 8) 3 output-print " H2O" output-type "Biomass half reaction : " output-type precision (matrix:get b-biomass 0 3) 3 output-type " CO2 + " output-type precision (matrix:get b-biomass 0 5) 3 output-type " HCO3- + " output-type precision (matrix:get b-biomass 0 4) 3 output-type " NH4+ + " output-type precision (matrix:get b-biomass 0 1) 3 output-type " H+ + " output-type precision (matrix:get b-biomass 0 2) 3 output-type " e- --> " output-type precision (matrix:get b-biomass 0 6) 3 output-type " C'" output-type carbon output-type "'H'" output-type hydrogen output-type "'O'" output-type oxygen output-type "'N'" output-type b-nitrogen output-type " + " output-type precision (matrix:get b-biomass 0 7) 3 output-print " H2O" output-type "Donor : " output-type precision (matrix:get donor 0 3) 3 output-type " CO2 + " output-type precision (matrix:get donor 0 5) 3 output-type " HCO3- + " output-type precision (matrix:get donor 0 1) 3 output-type " H+ + " output-type precision (matrix:get donor 0 2) 3 output-type " e- --> " output-type precision (matrix:get donor 0 8) 3 output-type " (C4H4O4)2- + " output-type precision (matrix:get donor 0 7) 3 output-print " H2O" output-type "Acceptor1 : " output-type precision (matrix:get acceptor1 0 0) 3 output-type " O2 + " output-type precision (matrix:get acceptor1 0 1) 3 output-type " H+ + " output-type precision (matrix:get acceptor1 0 2) 3 output-type " e- --> " output-type precision (matrix:get acceptor1 0 7) 3 output-print " H2O" output-type "Acceptor2 : " output-type precision (matrix:get acceptor2 0 0) 4 output-type " NO3- + " output-type precision (matrix:get acceptor2 0 1) 4 output-type " H+ + " output-type precision (matrix:get acceptor2 0 2) 4 output-type " e- --> " output-type precision (matrix:get acceptor2 0 9) 4 output-type " NH4+ + " output-type precision (matrix:get acceptor2 0 7) 4 output-print " H2O" output-type "Acceptor3 : " output-type precision (matrix:get acceptor3 0 0) 4 output-type " NO3- + " output-type precision (matrix:get acceptor3 0 1) 4 output-type " H+ + " output-type precision (matrix:get acceptor3 0 2) 4 output-type " e- --> " output-type precision (matrix:get acceptor3 0 9) 4 output-type " NO2- + " output-type precision (matrix:get acceptor3 0 7) 4 output-print " H2O" output-type "Acceptor4 : " output-type precision (matrix:get acceptor4 0 0) 4 output-type " NO2- + " output-type precision (matrix:get acceptor4 0 1) 4 output-type " H+ + " output-type precision (matrix:get acceptor4 0 2) 4 output-type " e- --> " output-type precision (matrix:get acceptor4 0 9) 4 output-type " NO + " output-type precision (matrix:get acceptor4 0 7) 4 output-print " H2O" output-type "Acceptor5 : " output-type precision (matrix:get acceptor5 0 0) 4 output-type " NO + " output-type precision (matrix:get acceptor5 0 1) 4 output-type " H+ + " output-type precision (matrix:get acceptor5 0 2) 4 output-type " e- --> " output-type precision (matrix:get acceptor5 0 9) 4 output-type " N2O + " output-type precision (matrix:get acceptor5 0 7) 4 output-print " H2O" output-type "Acceptor6 : " output-type precision (matrix:get acceptor6 0 0) 4 output-type " N2O + " output-type precision (matrix:get acceptor6 0 1) 4 output-type " H+ + " output-type precision (matrix:get acceptor6 0 2) 4 output-type " e- --> " output-type precision (matrix:get acceptor6 0 9) 4 output-type " N2 + " output-type precision (matrix:get acceptor6 0 7) 4 output-print " H2O" if Output-data? = true [ if Denitrifying_bacterium = "P._denitrificans" [export-output (word (word behaviorspace-run-number"_"molecular-weight)"_I_Denitrification_V10_P.denitrificans_" ".txt")] ; Outputfile name with .txt extension and Behaviorspace numering if Denitrifying_bacterium = "A._xylosoxidans" [export-output (word (word behaviorspace-run-number"_"molecular-weight)"_I_Denitrification_V10_A.xylosoxidans_" ".txt")] ; Outputfile name with .txt extension and Behaviorspace numering ] end to to-umax set u1 gbacteria let DBM ((u1 - u0) / u0) set u DBM / steptime set u0 u1 ifelse u > u3 [set umax u set u3 umax][set umax u3 set u3 umax] end ; ---------------------------------------- Data Analysis GRI --------------------------------------------------------------------------------------------------------------------------------------- to setup-machine.learning if Denitrifying_bacterium = "P._denitrificans" [ if Experiment = "Succ_Low/Nitrate_High"[ let column_matrix_biomass 17 let row_matrix_biomass 6 set biomass_matrix matrix:make-constant row_matrix_biomass column_matrix_biomass 0 matrix:set biomass_matrix 0 0 (0) matrix:set biomass_matrix 2 0 (0.0668478) matrix:set biomass_matrix 1 0 (gbacteria) matrix:set biomass_matrix 0 1 (4) matrix:set biomass_matrix 2 1 (0.153156667) matrix:set biomass_matrix 0 2 (7) matrix:set biomass_matrix 2 2 (0.270845867) matrix:set biomass_matrix 0 3 (24) matrix:set biomass_matrix 2 3 (0.378976933) matrix:set biomass_matrix 0 4 (24.5) matrix:set biomass_matrix 2 4 (0.382777067) matrix:set biomass_matrix 0 5 (28) matrix:set biomass_matrix 2 5 (0.3668856) matrix:set biomass_matrix 0 6 (30) matrix:set biomass_matrix 2 6 (0.3259478) matrix:set biomass_matrix 0 7 (47) matrix:set biomass_matrix 2 7 (0.202443467) matrix:set biomass_matrix 0 8 (50) matrix:set biomass_matrix 2 8 (0.222480533) matrix:set biomass_matrix 0 9 (53) matrix:set biomass_matrix 2 9 (0.2103892) matrix:set biomass_matrix 0 10 (71) matrix:set biomass_matrix 2 10 (0.206589067) matrix:set biomass_matrix 0 11 (74) matrix:set biomass_matrix 2 11 (0.213671133) matrix:set biomass_matrix 0 12 (77) matrix:set biomass_matrix 2 12 (0.203998067) matrix:set biomass_matrix 0 13 (95) matrix:set biomass_matrix 2 13 (0.2109074) matrix:set biomass_matrix 0 14 (98) matrix:set biomass_matrix 2 14 (0.193115867) matrix:set biomass_matrix 0 15 (102) matrix:set biomass_matrix 2 15 (0.182060933) matrix:set biomass_matrix 0 16 (119) matrix:set biomass_matrix 2 16 (0.1694514) let column_matrix_nitrate 17 let row_matrix_nitrate 6 set nitrate_matrix matrix:make-constant row_matrix_nitrate column_matrix_nitrate 0 matrix:set nitrate_matrix 0 0 (0) matrix:set nitrate_matrix 2 0 (21.60951) matrix:set nitrate_matrix 1 0 (gnitrate) matrix:set nitrate_matrix 0 1 (4) matrix:set nitrate_matrix 2 1 (16.42224) matrix:set nitrate_matrix 0 2 (7) matrix:set nitrate_matrix 2 2 (19.884335) matrix:set nitrate_matrix 0 3 (24) matrix:set nitrate_matrix 2 3 (14.25933) matrix:set nitrate_matrix 0 4 (24.5) matrix:set nitrate_matrix 2 4 (21.196305) matrix:set nitrate_matrix 0 5 (28) matrix:set nitrate_matrix 2 5 (15.784935) matrix:set nitrate_matrix 0 6 (30) matrix:set nitrate_matrix 2 6 (19.45065) matrix:set nitrate_matrix 0 7 (47) matrix:set nitrate_matrix 2 7 (17.16744) matrix:set nitrate_matrix 0 8 (50) matrix:set nitrate_matrix 2 8 (10.15038) matrix:set nitrate_matrix 0 9 (53) matrix:set nitrate_matrix 2 9 (15.426435) matrix:set nitrate_matrix 0 10 (71) matrix:set nitrate_matrix 2 10 (7.95066) matrix:set nitrate_matrix 0 11 (74) matrix:set nitrate_matrix 2 11 (12.17988) matrix:set nitrate_matrix 0 12 (77) matrix:set nitrate_matrix 2 12 (10.57218) matrix:set nitrate_matrix 0 13 (96) matrix:set nitrate_matrix 2 13 (7.759995) matrix:set nitrate_matrix 0 14 (99) matrix:set nitrate_matrix 2 14 (13.250715) matrix:set nitrate_matrix 0 15 (102) matrix:set nitrate_matrix 2 15 (11.33085) matrix:set nitrate_matrix 0 16 (119) matrix:set nitrate_matrix 2 16 (13.93161) let column_matrix_nitrite 17 let row_matrix_nitrite 6 set nitrite_matrix matrix:make-constant row_matrix_nitrite column_matrix_nitrite 0 matrix:set nitrite_matrix 0 0 (0) matrix:set nitrite_matrix 2 0 (0.011163522) matrix:set nitrite_matrix 1 0 (gno2-) matrix:set nitrite_matrix 0 1 (3) matrix:set nitrite_matrix 2 1 (0.030220126) matrix:set nitrite_matrix 0 2 (6) matrix:set nitrite_matrix 2 2 (0.00827044) matrix:set nitrite_matrix 0 3 (24) matrix:set nitrite_matrix 2 3 (0.011981132) matrix:set nitrite_matrix 0 4 (24.5) matrix:set nitrite_matrix 2 4 (0.01827044) matrix:set nitrite_matrix 0 5 (27) matrix:set nitrite_matrix 2 5 (0.029622642) matrix:set nitrite_matrix 0 6 (30) matrix:set nitrite_matrix 2 6 (0.017295597) matrix:set nitrite_matrix 0 7 (49) matrix:set nitrite_matrix 2 7 (0.009968553) matrix:set nitrite_matrix 0 8 (52) matrix:set nitrite_matrix 2 8 (0.006320755) matrix:set nitrite_matrix 0 9 (55) matrix:set nitrite_matrix 2 9 (0.006540881) matrix:set nitrite_matrix 0 10 (72) matrix:set nitrite_matrix 2 10 (0.005408805) matrix:set nitrite_matrix 0 11 (74.5) matrix:set nitrite_matrix 2 11 (0.00663522) matrix:set nitrite_matrix 0 12 (78.5) matrix:set nitrite_matrix 2 12 (0.005220126) matrix:set nitrite_matrix 0 13 (96.5) matrix:set nitrite_matrix 2 13 (0.002924528) matrix:set nitrite_matrix 0 14 (99) matrix:set nitrite_matrix 2 14 (0.005754717) matrix:set nitrite_matrix 0 15 (102) matrix:set nitrite_matrix 2 15 (0.005377358) matrix:set nitrite_matrix 0 16 (119) matrix:set nitrite_matrix 2 16 (0.005691824) let column_matrix_nitrous_oxide 15 let row_matrix_nitrous_oxide 6 set nitrous_oxide_matrix matrix:make-constant row_matrix_nitrous_oxide column_matrix_nitrous_oxide 0 matrix:set nitrous_oxide_matrix 0 0 (0) matrix:set nitrous_oxide_matrix 2 0 (0.028413312) matrix:set nitrous_oxide_matrix 1 0 (gn2o) matrix:set nitrous_oxide_matrix 0 1 (6) matrix:set nitrous_oxide_matrix 2 1 (0.034785811) matrix:set nitrous_oxide_matrix 0 2 (24) matrix:set nitrous_oxide_matrix 2 2 (0.034617738) matrix:set nitrous_oxide_matrix 0 3 (24.5) matrix:set nitrous_oxide_matrix 2 3 (0.036901924) matrix:set nitrous_oxide_matrix 0 4 (27) matrix:set nitrous_oxide_matrix 2 4 (0.215676568) matrix:set nitrous_oxide_matrix 0 5 (49) matrix:set nitrous_oxide_matrix 2 5 (0.506300774) matrix:set nitrous_oxide_matrix 0 6 (52) matrix:set nitrous_oxide_matrix 2 6 (0.495535019) matrix:set nitrous_oxide_matrix 0 7 (55) matrix:set nitrous_oxide_matrix 2 7 (0.544601612) matrix:set nitrous_oxide_matrix 0 8 (72) matrix:set nitrous_oxide_matrix 2 8 (0.58388104) matrix:set nitrous_oxide_matrix 0 9 (74.5) matrix:set nitrous_oxide_matrix 2 9 (0.582994072) matrix:set nitrous_oxide_matrix 0 10 (78.5) matrix:set nitrous_oxide_matrix 2 10 (0.606296092) matrix:set nitrous_oxide_matrix 0 11 (96.5) matrix:set nitrous_oxide_matrix 2 11 (0.53099924) matrix:set nitrous_oxide_matrix 0 12 (99) matrix:set nitrous_oxide_matrix 2 12 (0.504279414) matrix:set nitrous_oxide_matrix 0 13 (102) matrix:set nitrous_oxide_matrix 2 13 (0.58082208) matrix:set nitrous_oxide_matrix 0 14 (119.5) matrix:set nitrous_oxide_matrix 2 14 (0.509617501) ] ; end procedure succinate low P.denitrificans if Experiment = "Succ_High/Nitrate_Low"[ let column_matrix_biomass 17 let row_matrix_biomass 6 set biomass_matrix matrix:make-constant row_matrix_biomass column_matrix_biomass 0 matrix:set biomass_matrix 0 0 (0) matrix:set biomass_matrix 2 0 (0.0033683) matrix:set biomass_matrix 1 0 (gbacteria) matrix:set biomass_matrix 0 1 (3) matrix:set biomass_matrix 2 1 (0.033683) matrix:set biomass_matrix 0 2 (6) matrix:set biomass_matrix 2 2 (0.186552) matrix:set biomass_matrix 0 3 (24) matrix:set biomass_matrix 2 3 (0.650341) matrix:set biomass_matrix 0 4 (24.5) matrix:set biomass_matrix 2 4 (0.507836) matrix:set biomass_matrix 0 5 (27) matrix:set biomass_matrix 2 5 (1.075265) matrix:set biomass_matrix 0 6 (30) matrix:set biomass_matrix 2 6 (0.8221243) matrix:set biomass_matrix 0 7 (48) matrix:set biomass_matrix 2 7 (0.4399518) matrix:set biomass_matrix 0 8 (51) matrix:set biomass_matrix 2 8 (0.598521) matrix:set biomass_matrix 0 9 (53) matrix:set biomass_matrix 2 9 (0.4161146) matrix:set biomass_matrix 0 10 (72) matrix:set biomass_matrix 2 10 (0.4000504) matrix:set biomass_matrix 0 11 (75) matrix:set biomass_matrix 2 11 (0.342012) matrix:set biomass_matrix 0 12 (79) matrix:set biomass_matrix 2 12 (0.240963) matrix:set biomass_matrix 0 13 (96) matrix:set biomass_matrix 2 13 (0.2842327) matrix:set biomass_matrix 0 14 (99) matrix:set biomass_matrix 2 14 (0.2635047) matrix:set biomass_matrix 0 15 (102) matrix:set biomass_matrix 2 15 (0.2492542) matrix:set biomass_matrix 0 16 (120) matrix:set biomass_matrix 2 16 (0.2629865) let column_matrix_nitrate 17 let row_matrix_nitrate 6 set nitrate_matrix matrix:make-constant row_matrix_nitrate column_matrix_nitrate 0 matrix:set nitrate_matrix 0 0 (0) matrix:set nitrate_matrix 2 0 (4.99825) matrix:set nitrate_matrix 1 0 (gnitrate) matrix:set nitrate_matrix 0 1 (3) matrix:set nitrate_matrix 2 1 (5.0055) matrix:set nitrate_matrix 0 2 (6) matrix:set nitrate_matrix 2 2 (5.1415) matrix:set nitrate_matrix 0 3 (24) matrix:set nitrate_matrix 2 3 (4.30925) matrix:set nitrate_matrix 0 4 (24.5) matrix:set nitrate_matrix 2 4 (4.33675) matrix:set nitrate_matrix 0 5 (27) matrix:set nitrate_matrix 2 5 (1.5245) matrix:set nitrate_matrix 0 6 (30) matrix:set nitrate_matrix 2 6 (0.1645) matrix:set nitrate_matrix 0 7 (48) matrix:set nitrate_matrix 2 7 (0.0155) matrix:set nitrate_matrix 0 8 (51) matrix:set nitrate_matrix 2 8 (0.0065) matrix:set nitrate_matrix 0 9 (53) matrix:set nitrate_matrix 2 9 (0.00325) matrix:set nitrate_matrix 0 10 (72) matrix:set nitrate_matrix 2 10 (0.004) matrix:set nitrate_matrix 0 11 (75) matrix:set nitrate_matrix 2 11 (0.008) matrix:set nitrate_matrix 0 12 (79) matrix:set nitrate_matrix 2 12 (0.003) matrix:set nitrate_matrix 0 13 (96) matrix:set nitrate_matrix 2 13 (0.0025) matrix:set nitrate_matrix 0 14 (99) matrix:set nitrate_matrix 2 14 (0.0035) matrix:set nitrate_matrix 0 15 (102) matrix:set nitrate_matrix 2 15 (0.006) matrix:set nitrate_matrix 0 16 (120) matrix:set nitrate_matrix 2 16 (0.005) let column_matrix_nitrite 17 let row_matrix_nitrite 6 set nitrite_matrix matrix:make-constant row_matrix_nitrite column_matrix_nitrite 0 matrix:set nitrite_matrix 0 0 (0) matrix:set nitrite_matrix 2 0 (0.0255) matrix:set nitrite_matrix 1 0 (gno2-) matrix:set nitrite_matrix 0 1 (3) matrix:set nitrite_matrix 2 1 (0.02075) matrix:set nitrite_matrix 0 2 (6) matrix:set nitrite_matrix 2 2 (0.03875) matrix:set nitrite_matrix 0 3 (24) matrix:set nitrite_matrix 2 3 (0.1715) matrix:set nitrite_matrix 0 4 (24.5) matrix:set nitrite_matrix 2 4 (0.091) matrix:set nitrite_matrix 0 5 (27) matrix:set nitrite_matrix 2 5 (0.19415) matrix:set nitrite_matrix 0 6 (30) matrix:set nitrite_matrix 2 6 (0.193) matrix:set nitrite_matrix 0 7 (48) matrix:set nitrite_matrix 2 7 (0.02275) matrix:set nitrite_matrix 0 8 (51) matrix:set nitrite_matrix 2 8 (0.014) matrix:set nitrite_matrix 0 9 (53) matrix:set nitrite_matrix 2 9 (0.014) matrix:set nitrite_matrix 0 10 (72) matrix:set nitrite_matrix 2 10 (0.0125) matrix:set nitrite_matrix 0 11 (75) matrix:set nitrite_matrix 2 11 (0.025) matrix:set nitrite_matrix 0 12 (79) matrix:set nitrite_matrix 2 12 (0.00975) matrix:set nitrite_matrix 0 13 (96) matrix:set nitrite_matrix 2 13 (0.01375) matrix:set nitrite_matrix 0 14 (99) matrix:set nitrite_matrix 2 14 (0.0135) matrix:set nitrite_matrix 0 15 (102) matrix:set nitrite_matrix 2 15 (0.01825) matrix:set nitrite_matrix 0 16 (120) matrix:set nitrite_matrix 2 16 (0.01725) let column_matrix_nitrous_oxide 13 let row_matrix_nitrous_oxide 6 set nitrous_oxide_matrix matrix:make-constant row_matrix_nitrous_oxide column_matrix_nitrous_oxide 0 matrix:set nitrous_oxide_matrix 0 0 (0) matrix:set nitrous_oxide_matrix 2 0 (0.003003178) matrix:set nitrous_oxide_matrix 1 0 (gn2o) matrix:set nitrous_oxide_matrix 0 1 (6) matrix:set nitrous_oxide_matrix 2 1 (0.003003178) matrix:set nitrous_oxide_matrix 0 2 (24) matrix:set nitrous_oxide_matrix 2 2 (0.000886128) matrix:set nitrous_oxide_matrix 0 3 (27) matrix:set nitrous_oxide_matrix 2 3 (0.005377157) matrix:set nitrous_oxide_matrix 0 4 (30) matrix:set nitrous_oxide_matrix 2 4 (0.002591133) matrix:set nitrous_oxide_matrix 0 5 (48) matrix:set nitrous_oxide_matrix 2 5 (0.000710695) matrix:set nitrous_oxide_matrix 0 6 (53) matrix:set nitrous_oxide_matrix 2 6 (0.000244818) matrix:set nitrous_oxide_matrix 0 7 (72) matrix:set nitrous_oxide_matrix 2 7 (0.001205919) matrix:set nitrous_oxide_matrix 0 8 (79) matrix:set nitrous_oxide_matrix 2 8 (0.000914869) matrix:set nitrous_oxide_matrix 0 9 (96) matrix:set nitrous_oxide_matrix 2 9 (0.000611436) matrix:set nitrous_oxide_matrix 0 10 (99) matrix:set nitrous_oxide_matrix 2 10 (0.001057633) matrix:set nitrous_oxide_matrix 0 11 (102) matrix:set nitrous_oxide_matrix 2 11 (0.001152196) matrix:set nitrous_oxide_matrix 0 12 (120) matrix:set nitrous_oxide_matrix 2 12 (0.00058742) ] ; End procedure succinate high P.denitrificans ] ; End bacterium procedure P.denitrificans if Denitrifying_bacterium = "A._xylosoxidans" [ if Experiment = "Succ_Low/Nitrate_High"[ let column_matrix_biomass 11 let row_matrix_biomass 6 set biomass_matrix matrix:make-constant row_matrix_biomass column_matrix_biomass 0 matrix:set biomass_matrix 0 0 (0) matrix:set biomass_matrix 2 0 (0.05182) matrix:set biomass_matrix 1 0 (gbacteria) matrix:set biomass_matrix 0 1 (6) matrix:set biomass_matrix 2 1 (0.20210) matrix:set biomass_matrix 0 2 (24) matrix:set biomass_matrix 2 2 (0.27983) matrix:set biomass_matrix 0 3 (25) matrix:set biomass_matrix 2 3 (0.25392) matrix:set biomass_matrix 0 4 (30) matrix:set biomass_matrix 2 4 (0.24692) matrix:set biomass_matrix 0 5 (48) matrix:set biomass_matrix 2 5 (0.15935) matrix:set biomass_matrix 0 6 (54) matrix:set biomass_matrix 2 6 (0.14561) matrix:set biomass_matrix 0 7 (78) matrix:set biomass_matrix 2 7 (0.11996) matrix:set biomass_matrix 0 8 (97) matrix:set biomass_matrix 2 8 (0.10830) matrix:set biomass_matrix 0 9 (102) matrix:set biomass_matrix 2 9 (0.11323) matrix:set biomass_matrix 0 10 (120) matrix:set biomass_matrix 2 10 (0.10830) let column_matrix_nitrate 12 let row_matrix_nitrate 6 set nitrate_matrix matrix:make-constant row_matrix_nitrate column_matrix_nitrate 0 matrix:set nitrate_matrix 0 0 (0) matrix:set nitrate_matrix 2 0 (21.74694) matrix:set nitrate_matrix 1 0 (gnitrate) matrix:set nitrate_matrix 0 1 (6) matrix:set nitrate_matrix 2 1 (19.54182) matrix:set nitrate_matrix 0 2 (24) matrix:set nitrate_matrix 2 2 (21.63708) matrix:set nitrate_matrix 0 3 (24.5) matrix:set nitrate_matrix 2 3 (19.77804) matrix:set nitrate_matrix 0 4 (30) matrix:set nitrate_matrix 2 4 (8.36640) matrix:set nitrate_matrix 0 5 (48) matrix:set nitrate_matrix 2 5 (6.47461) matrix:set nitrate_matrix 0 6 (54) matrix:set nitrate_matrix 2 6 (2.98806) matrix:set nitrate_matrix 0 7 (72) matrix:set nitrate_matrix 2 7 (3.13756) matrix:set nitrate_matrix 0 8 (78) matrix:set nitrate_matrix 2 8 (5.93996) matrix:set nitrate_matrix 0 9 (97) matrix:set nitrate_matrix 2 9 (4.58357) matrix:set nitrate_matrix 0 10 (102) matrix:set nitrate_matrix 2 10 (6.00180) matrix:set nitrate_matrix 0 11 (120) matrix:set nitrate_matrix 2 11 (7.00376) let column_matrix_nitrite 13 let row_matrix_nitrite 6 set nitrite_matrix matrix:make-constant row_matrix_nitrite column_matrix_nitrite 0 matrix:set nitrite_matrix 0 0 (0) matrix:set nitrite_matrix 2 0 (0.00765) matrix:set nitrite_matrix 1 0 (gno2-) matrix:set nitrite_matrix 0 1 (5) matrix:set nitrite_matrix 2 1 (0.03032) matrix:set nitrite_matrix 0 2 (24) matrix:set nitrite_matrix 2 2 (0.01729) matrix:set nitrite_matrix 0 3 (25) matrix:set nitrite_matrix 2 3 (0.02565) matrix:set nitrite_matrix 0 4 (30) matrix:set nitrite_matrix 2 4 (1.72077) matrix:set nitrite_matrix 0 5 (48) matrix:set nitrite_matrix 2 5 (4.54305) matrix:set nitrite_matrix 0 6 (54) matrix:set nitrite_matrix 2 6 (7.66966) matrix:set nitrite_matrix 0 7 (72) matrix:set nitrite_matrix 2 7 (4.84258) matrix:set nitrite_matrix 0 8 (78) matrix:set nitrite_matrix 2 8 (7.02693) matrix:set nitrite_matrix 0 9 (97) matrix:set nitrite_matrix 2 9 (6.56384) matrix:set nitrite_matrix 0 10 (99) matrix:set nitrite_matrix 2 10 (3.38517) matrix:set nitrite_matrix 0 11 (102) matrix:set nitrite_matrix 2 11 (4.96006) matrix:set nitrite_matrix 0 12 (120) matrix:set nitrite_matrix 2 12 (3.84764) let column_matrix_nitrous_oxide 12 let row_matrix_nitrous_oxide 6 set nitrous_oxide_matrix matrix:make-constant row_matrix_nitrous_oxide column_matrix_nitrous_oxide 0 matrix:set nitrous_oxide_matrix 0 0 (0) matrix:set nitrous_oxide_matrix 2 0 (0.01818) matrix:set nitrous_oxide_matrix 1 0 (gn2o) matrix:set nitrous_oxide_matrix 0 1 (6) matrix:set nitrous_oxide_matrix 2 1 (0.00771) matrix:set nitrous_oxide_matrix 0 2 (24) matrix:set nitrous_oxide_matrix 2 2 (0.00330) matrix:set nitrous_oxide_matrix 0 3 (24.5) matrix:set nitrous_oxide_matrix 2 3 (0.00559) matrix:set nitrous_oxide_matrix 0 4 (30) matrix:set nitrous_oxide_matrix 2 4 (0.28329) matrix:set nitrous_oxide_matrix 0 5 (48) matrix:set nitrous_oxide_matrix 2 5 (0.95467) matrix:set nitrous_oxide_matrix 0 6 (54) matrix:set nitrous_oxide_matrix 2 6 (1.44598) matrix:set nitrous_oxide_matrix 0 7 (72) matrix:set nitrous_oxide_matrix 2 7 (1.60833) matrix:set nitrous_oxide_matrix 0 8 (78) matrix:set nitrous_oxide_matrix 2 8 (1.02808) matrix:set nitrous_oxide_matrix 0 9 (97) matrix:set nitrous_oxide_matrix 2 9 (1.24110) matrix:set nitrous_oxide_matrix 0 10 (99) matrix:set nitrous_oxide_matrix 2 10 (16.66431) matrix:set nitrous_oxide_matrix 0 11 (102) matrix:set nitrous_oxide_matrix 2 11 (0.84064) ] ; end procedure succinate low A.xylosxidans if Experiment = "Succ_High/Nitrate_Low"[ let column_matrix_biomass 15 let row_matrix_biomass 6 set biomass_matrix matrix:make-constant row_matrix_biomass column_matrix_biomass 0 matrix:set biomass_matrix 0 0 (0) matrix:set biomass_matrix 2 0 (0.07695) matrix:set biomass_matrix 1 0 (gbacteria) matrix:set biomass_matrix 0 1 (6) matrix:set biomass_matrix 2 1 (0.20573) matrix:set biomass_matrix 0 2 (24) matrix:set biomass_matrix 2 2 (0.58194) matrix:set biomass_matrix 0 3 (24.5) matrix:set biomass_matrix 2 3 (0.50861) matrix:set biomass_matrix 0 4 (27) matrix:set biomass_matrix 2 4 (0.51043) matrix:set biomass_matrix 0 5 (31) matrix:set biomass_matrix 2 5 (0.57261) matrix:set biomass_matrix 0 6 (48) matrix:set biomass_matrix 2 6 (0.50214) matrix:set biomass_matrix 0 7 (52) matrix:set biomass_matrix 2 7 (0.42337) matrix:set biomass_matrix 0 8 (73) matrix:set biomass_matrix 2 8 (0.26083) matrix:set biomass_matrix 0 9 (75) matrix:set biomass_matrix 2 9 (0.25910) matrix:set biomass_matrix 0 10 (79) matrix:set biomass_matrix 2 10 (0.36689) matrix:set biomass_matrix 0 11 (97) matrix:set biomass_matrix 2 11 (0.31196) matrix:set biomass_matrix 0 12 (99) matrix:set biomass_matrix 2 12 (0.28838) matrix:set biomass_matrix 0 13 (102) matrix:set biomass_matrix 2 13 (0.31066) matrix:set biomass_matrix 0 14 (120) matrix:set biomass_matrix 2 14 (0.28631) let column_matrix_nitrate 14 let row_matrix_nitrate 6 set nitrate_matrix matrix:make-constant row_matrix_nitrate column_matrix_nitrate 0 matrix:set nitrate_matrix 0 0 (0) matrix:set nitrate_matrix 2 0 (5.15375) matrix:set nitrate_matrix 1 0 (gnitrate) matrix:set nitrate_matrix 0 1 (4) matrix:set nitrate_matrix 2 1 (4.68250) matrix:set nitrate_matrix 0 2 (24) matrix:set nitrate_matrix 2 2 (4.00950) matrix:set nitrate_matrix 0 3 (24.5) matrix:set nitrate_matrix 2 3 (2.40450) matrix:set nitrate_matrix 0 4 (27) matrix:set nitrate_matrix 2 4 (0.78025) matrix:set nitrate_matrix 0 5 (31) matrix:set nitrate_matrix 2 5 (0.29225) matrix:set nitrate_matrix 0 6 (49) matrix:set nitrate_matrix 2 6 (0.20075) matrix:set nitrate_matrix 0 7 (54) matrix:set nitrate_matrix 2 7 (0.13525) matrix:set nitrate_matrix 0 8 (73) matrix:set nitrate_matrix 2 8 (0.13325) matrix:set nitrate_matrix 0 9 (79) matrix:set nitrate_matrix 2 9 (0.14575) matrix:set nitrate_matrix 0 10 (97) matrix:set nitrate_matrix 2 10 (0.15725) matrix:set nitrate_matrix 0 11 (99) matrix:set nitrate_matrix 2 11 (0.10500) matrix:set nitrate_matrix 0 12 (102) matrix:set nitrate_matrix 2 12 (0.15638) matrix:set nitrate_matrix 0 13 (120) matrix:set nitrate_matrix 2 13 (0.01663) let column_matrix_nitrite 14 let row_matrix_nitrite 6 set nitrite_matrix matrix:make-constant row_matrix_nitrite column_matrix_nitrite 0 matrix:set nitrite_matrix 0 0 (0) matrix:set nitrite_matrix 2 0 (0.36863) matrix:set nitrite_matrix 1 0 (gno2-) matrix:set nitrite_matrix 0 1 (4) matrix:set nitrite_matrix 2 1 (0.65250) matrix:set nitrite_matrix 0 2 (24) matrix:set nitrite_matrix 2 2 (0.54525) matrix:set nitrite_matrix 0 3 (24.5) matrix:set nitrite_matrix 2 3 (1.01600) matrix:set nitrite_matrix 0 4 (27) matrix:set nitrite_matrix 2 4 (0.84300) matrix:set nitrite_matrix 0 5 (31) matrix:set nitrite_matrix 2 5 (0.09875) matrix:set nitrite_matrix 0 6 (49) matrix:set nitrite_matrix 2 6 (0.02325) matrix:set nitrite_matrix 0 7 (54) matrix:set nitrite_matrix 2 7 (0.01525) matrix:set nitrite_matrix 0 8 (73) matrix:set nitrite_matrix 2 8 (0.01050) matrix:set nitrite_matrix 0 9 (79) matrix:set nitrite_matrix 2 9 (0.01400) matrix:set nitrite_matrix 0 10 (97) matrix:set nitrite_matrix 2 10 (0.01450) matrix:set nitrite_matrix 0 11 (99) matrix:set nitrite_matrix 2 11 (0.18683) matrix:set nitrite_matrix 0 12 (102) matrix:set nitrite_matrix 2 12 (0.34729) matrix:set nitrite_matrix 0 13 (120) matrix:set nitrite_matrix 2 13 (0.21405) let column_matrix_nitrous_oxide 13 let row_matrix_nitrous_oxide 6 set nitrous_oxide_matrix matrix:make-constant row_matrix_nitrous_oxide column_matrix_nitrous_oxide 0 matrix:set nitrous_oxide_matrix 0 0 (0) matrix:set nitrous_oxide_matrix 2 0 (0.00006263) matrix:set nitrous_oxide_matrix 1 0 (gn2o) matrix:set nitrous_oxide_matrix 0 1 (7) matrix:set nitrous_oxide_matrix 2 1 (0.00013455) matrix:set nitrous_oxide_matrix 0 2 (24) matrix:set nitrous_oxide_matrix 2 2 (0.00019376) matrix:set nitrous_oxide_matrix 0 3 (24.5) matrix:set nitrous_oxide_matrix 2 3 (0.00024715) matrix:set nitrous_oxide_matrix 0 4 (28) matrix:set nitrous_oxide_matrix 2 4 (0.00715063) matrix:set nitrous_oxide_matrix 0 5 (47) matrix:set nitrous_oxide_matrix 2 5 (0.00192994) matrix:set nitrous_oxide_matrix 0 6 (53) matrix:set nitrous_oxide_matrix 2 6 (0.00027866) matrix:set nitrous_oxide_matrix 0 7 (74) matrix:set nitrous_oxide_matrix 2 7 (0.00045744) matrix:set nitrous_oxide_matrix 0 8 (77) matrix:set nitrous_oxide_matrix 2 8 (0.00025220) matrix:set nitrous_oxide_matrix 0 9 (95) matrix:set nitrous_oxide_matrix 2 9 (0.00027134) matrix:set nitrous_oxide_matrix 0 10 (98) matrix:set nitrous_oxide_matrix 2 10 (0.00024276) matrix:set nitrous_oxide_matrix 0 11 (102) matrix:set nitrous_oxide_matrix 2 11 (0.00053833) matrix:set nitrous_oxide_matrix 0 12 (119) matrix:set nitrous_oxide_matrix 2 12 (0.00026046) ] ; end procedure succinate high A.xylosxidans ] ; end procedure bacteria A.xylosxidans end to get_data_machine.learning if Denitrifying_bacterium = "P._denitrificans" [ if Experiment = "Succ_Low/Nitrate_High"[ if time_now = 3 [matrix:set nitrite_matrix 1 1 gno2-] if time_now = 4 [matrix:set biomass_matrix 1 1 gbacteria matrix:set nitrate_matrix 1 1 gnitrate] if time_now = 6 [matrix:set nitrite_matrix 1 2 gno2- matrix:set nitrous_oxide_matrix 1 1 gn2o] if time_now = 7 [matrix:set biomass_matrix 1 2 gbacteria matrix:set nitrate_matrix 1 2 gnitrate] if time_now = 24 [matrix:set biomass_matrix 1 3 gbacteria matrix:set nitrate_matrix 1 3 gnitrate matrix:set nitrite_matrix 1 3 gno2- matrix:set nitrous_oxide_matrix 1 2 gn2o] if time_now = 24.5 [matrix:set biomass_matrix 1 4 gbacteria matrix:set nitrate_matrix 1 4 gnitrate matrix:set nitrite_matrix 1 4 gno2- matrix:set nitrous_oxide_matrix 1 3 gn2o] if time_now = 27 [matrix:set nitrite_matrix 1 5 gno2- matrix:set nitrous_oxide_matrix 1 4 gn2o] if time_now = 28 [matrix:set biomass_matrix 1 5 gbacteria matrix:set nitrate_matrix 1 5 gnitrate] if time_now = 30 [matrix:set biomass_matrix 1 6 gbacteria matrix:set nitrate_matrix 1 6 gnitrate matrix:set nitrite_matrix 1 6 gno2-] if time_now = 47 [matrix:set biomass_matrix 1 7 gbacteria matrix:set nitrate_matrix 1 7 gnitrate] if time_now = 49 [matrix:set nitrite_matrix 1 7 gno2- matrix:set nitrous_oxide_matrix 1 5 gn2o] if time_now = 50 [matrix:set biomass_matrix 1 8 gbacteria matrix:set nitrate_matrix 1 8 gnitrate] if time_now = 52 [matrix:set nitrite_matrix 1 8 gno2- matrix:set nitrous_oxide_matrix 1 6 gn2o] if time_now = 53 [matrix:set biomass_matrix 1 9 gbacteria matrix:set nitrate_matrix 1 9 gnitrate] if time_now = 55 [matrix:set nitrite_matrix 1 9 gno2- matrix:set nitrous_oxide_matrix 1 7 gn2o] if time_now = 71 [matrix:set biomass_matrix 1 10 gbacteria matrix:set nitrate_matrix 1 10 gnitrate] if time_now = 72 [matrix:set nitrite_matrix 1 10 gno2- matrix:set nitrous_oxide_matrix 1 8 gn2o] if time_now = 74 [matrix:set biomass_matrix 1 11 gbacteria matrix:set nitrate_matrix 1 11 gnitrate] if time_now = 74.5 [matrix:set nitrite_matrix 1 11 gno2- matrix:set nitrous_oxide_matrix 1 9 gn2o] if time_now = 77 [matrix:set biomass_matrix 1 12 gbacteria matrix:set nitrate_matrix 1 12 gnitrate] if time_now = 78.5 [matrix:set nitrite_matrix 1 12 gno2- matrix:set nitrous_oxide_matrix 1 10 gn2o] if time_now = 95 [matrix:set biomass_matrix 1 13 gbacteria] if time_now = 96 [matrix:set nitrate_matrix 1 13 gnitrate] if time_now = 96.5 [matrix:set nitrite_matrix 1 13 gno2- matrix:set nitrous_oxide_matrix 1 11 gn2o] if time_now = 98 [matrix:set biomass_matrix 1 14 gbacteria] if time_now = 99 [matrix:set nitrate_matrix 1 14 gnitrate matrix:set nitrite_matrix 1 14 gno2- matrix:set nitrous_oxide_matrix 1 12 gn2o] if time_now = 102 [matrix:set biomass_matrix 1 15 gbacteria matrix:set nitrate_matrix 1 15 gnitrate matrix:set nitrite_matrix 1 15 gno2- matrix:set nitrous_oxide_matrix 1 13 gn2o] if time_now = 119 [matrix:set biomass_matrix 1 16 gbacteria matrix:set nitrate_matrix 1 16 gnitrate matrix:set nitrite_matrix 1 16 gno2-] if time_now = 119.5 [matrix:set nitrous_oxide_matrix 1 14 gn2o] ] ; end procedure succinate low P.denitrificans if Experiment = "Succ_High/Nitrate_Low"[ if time_now = 3 [matrix:set biomass_matrix 1 1 gbacteria matrix:set nitrate_matrix 1 1 gnitrate matrix:set nitrite_matrix 1 1 gno2-] if time_now = 6 [matrix:set biomass_matrix 1 2 gbacteria matrix:set nitrate_matrix 1 2 gnitrate matrix:set nitrite_matrix 1 2 gno2- matrix:set nitrous_oxide_matrix 1 1 gn2o] if time_now = 24 [matrix:set biomass_matrix 1 3 gbacteria matrix:set nitrate_matrix 1 3 gnitrate matrix:set nitrite_matrix 1 3 gno2- matrix:set nitrous_oxide_matrix 1 2 gn2o] if time_now = 24.5 [matrix:set biomass_matrix 1 4 gbacteria matrix:set nitrate_matrix 1 4 gnitrate matrix:set nitrite_matrix 1 4 gno2-] if time_now = 27 [matrix:set biomass_matrix 1 5 gbacteria matrix:set nitrate_matrix 1 5 gnitrate matrix:set nitrite_matrix 1 5 gno2- matrix:set nitrous_oxide_matrix 1 3 gn2o] if time_now = 30 [matrix:set biomass_matrix 1 6 gbacteria matrix:set nitrate_matrix 1 6 gnitrate matrix:set nitrite_matrix 1 6 gno2- matrix:set nitrous_oxide_matrix 1 4 gn2o] if time_now = 48 [matrix:set biomass_matrix 1 7 gbacteria matrix:set nitrate_matrix 1 7 gnitrate matrix:set nitrite_matrix 1 7 gno2- matrix:set nitrous_oxide_matrix 1 5 gn2o] if time_now = 51 [matrix:set biomass_matrix 1 8 gbacteria matrix:set nitrate_matrix 1 8 gnitrate matrix:set nitrite_matrix 1 8 gno2-] if time_now = 53 [matrix:set biomass_matrix 1 9 gbacteria matrix:set nitrate_matrix 1 9 gnitrate matrix:set nitrite_matrix 1 9 gno2- matrix:set nitrous_oxide_matrix 1 6 gn2o] if time_now = 72 [matrix:set biomass_matrix 1 10 gbacteria matrix:set nitrate_matrix 1 10 gnitrate matrix:set nitrite_matrix 1 10 gno2- matrix:set nitrous_oxide_matrix 1 7 gn2o] if time_now = 75 [matrix:set biomass_matrix 1 11 gbacteria matrix:set nitrate_matrix 1 11 gnitrate matrix:set nitrite_matrix 1 11 gno2-] if time_now = 79 [matrix:set biomass_matrix 1 12 gbacteria matrix:set nitrate_matrix 1 12 gnitrate matrix:set nitrite_matrix 1 12 gno2- matrix:set nitrous_oxide_matrix 1 8 gn2o] if time_now = 96 [matrix:set biomass_matrix 1 13 gbacteria matrix:set nitrate_matrix 1 13 gnitrate matrix:set nitrite_matrix 1 13 gno2- matrix:set nitrous_oxide_matrix 1 9 gn2o] if time_now = 99 [matrix:set biomass_matrix 1 14 gbacteria matrix:set nitrate_matrix 1 14 gnitrate matrix:set nitrite_matrix 1 14 gno2- matrix:set nitrous_oxide_matrix 1 10 gn2o] if time_now = 102 [matrix:set biomass_matrix 1 15 gbacteria matrix:set nitrate_matrix 1 15 gnitrate matrix:set nitrite_matrix 1 15 gno2- matrix:set nitrous_oxide_matrix 1 11 gn2o] if time_now = 120 [matrix:set biomass_matrix 1 16 gbacteria matrix:set nitrate_matrix 1 16 gnitrate matrix:set nitrite_matrix 1 16 gno2- matrix:set nitrous_oxide_matrix 1 12 gn2o] ] ; end procedure succinate high P.denitrificans ] ; End procedure bacteria P.denitrificans if Denitrifying_bacterium = "A._xylosoxidans" [ if Experiment = "Succ_Low/Nitrate_High"[ if time_now = 5 [matrix:set nitrite_matrix 1 1 gno2-] if time_now = 6 [matrix:set biomass_matrix 1 1 gbacteria matrix:set nitrate_matrix 1 1 gnitrate matrix:set nitrous_oxide_matrix 1 1 gn2o] if time_now = 24 [matrix:set biomass_matrix 1 2 gbacteria matrix:set nitrate_matrix 1 2 gnitrate matrix:set nitrite_matrix 1 2 gno2- matrix:set nitrous_oxide_matrix 1 2 gn2o] if time_now = 24.5 [matrix:set nitrate_matrix 1 3 gnitrate matrix:set nitrous_oxide_matrix 1 3 gn2o] if time_now = 25 [matrix:set biomass_matrix 1 3 gbacteria matrix:set nitrite_matrix 1 3 gno2-] if time_now = 30 [matrix:set biomass_matrix 1 4 gbacteria matrix:set nitrate_matrix 1 4 gnitrate matrix:set nitrite_matrix 1 4 gno2- matrix:set nitrous_oxide_matrix 1 4 gn2o] if time_now = 48 [matrix:set biomass_matrix 1 5 gbacteria matrix:set nitrate_matrix 1 5 gnitrate matrix:set nitrite_matrix 1 5 gno2- matrix:set nitrous_oxide_matrix 1 5 gn2o] if time_now = 54 [matrix:set biomass_matrix 1 6 gbacteria matrix:set nitrate_matrix 1 6 gnitrate matrix:set nitrite_matrix 1 6 gno2- matrix:set nitrous_oxide_matrix 1 6 gn2o] if time_now = 72 [matrix:set nitrate_matrix 1 7 gnitrate matrix:set nitrite_matrix 1 7 gno2- matrix:set nitrous_oxide_matrix 1 7 gn2o] if time_now = 78 [matrix:set biomass_matrix 1 7 gbacteria matrix:set nitrate_matrix 1 8 gnitrate matrix:set nitrite_matrix 1 8 gno2- matrix:set nitrous_oxide_matrix 1 8 gn2o] if time_now = 97 [matrix:set biomass_matrix 1 8 gbacteria matrix:set nitrate_matrix 1 9 gnitrate matrix:set nitrite_matrix 1 9 gno2- matrix:set nitrous_oxide_matrix 1 9 gn2o] if time_now = 99 [matrix:set nitrite_matrix 1 10 gno2- matrix:set nitrous_oxide_matrix 1 10 gn2o] if time_now = 102 [matrix:set biomass_matrix 1 9 gbacteria matrix:set nitrate_matrix 1 10 gnitrate matrix:set nitrite_matrix 1 11 gno2- matrix:set nitrous_oxide_matrix 1 11 gn2o] if time_now = 120 [matrix:set biomass_matrix 1 10 gbacteria matrix:set nitrate_matrix 1 11 gnitrate matrix:set nitrite_matrix 1 12 gno2-] ] ; end procedure succinate low A.Xylosoxidans if Experiment = "Succ_High/Nitrate_Low"[ if time_now = 4 [matrix:set nitrate_matrix 1 1 gnitrate matrix:set nitrite_matrix 1 1 gno2-] if time_now = 6 [matrix:set biomass_matrix 1 1 gbacteria] if time_now = 7 [matrix:set nitrous_oxide_matrix 1 1 gn2o] if time_now = 24 [matrix:set biomass_matrix 1 2 gbacteria matrix:set nitrate_matrix 1 2 gnitrate matrix:set nitrite_matrix 1 2 gno2- matrix:set nitrous_oxide_matrix 1 2 gn2o] if time_now = 24.5 [matrix:set biomass_matrix 1 3 gbacteria matrix:set nitrate_matrix 1 3 gnitrate matrix:set nitrite_matrix 1 3 gno2- matrix:set nitrous_oxide_matrix 1 3 gn2o] if time_now = 27 [matrix:set biomass_matrix 1 4 gbacteria matrix:set nitrate_matrix 1 4 gnitrate matrix:set nitrite_matrix 1 4 gno2-] if time_now = 28 [matrix:set nitrous_oxide_matrix 1 4 gn2o] if time_now = 31 [matrix:set biomass_matrix 1 5 gbacteria matrix:set nitrate_matrix 1 5 gnitrate matrix:set nitrite_matrix 1 5 gno2-] if time_now = 47 [matrix:set nitrous_oxide_matrix 1 5 gn2o] if time_now = 48 [matrix:set biomass_matrix 1 6 gbacteria] if time_now = 49 [matrix:set nitrate_matrix 1 6 gnitrate matrix:set nitrite_matrix 1 6 gno2-] if time_now = 52 [matrix:set biomass_matrix 1 7 gbacteria] if time_now = 53 [matrix:set nitrous_oxide_matrix 1 6 gn2o] if time_now = 54 [matrix:set nitrate_matrix 1 7 gnitrate matrix:set nitrite_matrix 1 7 gno2-] if time_now = 73 [matrix:set biomass_matrix 1 8 gbacteria matrix:set nitrate_matrix 1 8 gnitrate matrix:set nitrite_matrix 1 8 gno2-] if time_now = 74 [matrix:set nitrous_oxide_matrix 1 7 gn2o] if time_now = 75 [matrix:set biomass_matrix 1 9 gbacteria] if time_now = 77 [matrix:set nitrous_oxide_matrix 1 8 gn2o] if time_now = 79 [matrix:set biomass_matrix 1 10 gbacteria matrix:set nitrate_matrix 1 9 gnitrate matrix:set nitrite_matrix 1 9 gno2-] if time_now = 95 [matrix:set nitrous_oxide_matrix 1 9 gn2o] if time_now = 97 [matrix:set biomass_matrix 1 11 gbacteria matrix:set nitrate_matrix 1 10 gnitrate matrix:set nitrite_matrix 1 10 gno2-] if time_now = 98 [matrix:set nitrous_oxide_matrix 1 10 gn2o] if time_now = 99 [matrix:set biomass_matrix 1 12 gbacteria matrix:set nitrate_matrix 1 11 gnitrate matrix:set nitrite_matrix 1 11 gno2-] if time_now = 102 [matrix:set biomass_matrix 1 13 gbacteria matrix:set nitrate_matrix 1 12 gnitrate matrix:set nitrite_matrix 1 12 gno2- matrix:set nitrous_oxide_matrix 1 11 gn2o] if time_now = 119 [matrix:set nitrous_oxide_matrix 1 12 gn2o] if time_now = 120 [matrix:set biomass_matrix 1 14 gbacteria matrix:set nitrate_matrix 1 13 gnitrate matrix:set nitrite_matrix 1 13 gno2-] ] ; end procedure succinate high A.xylosoxidans ] ; end procedure bacteria A.xylosoxidans end to machine.learning if Denitrifying_bacterium = "P._denitrificans" [ if Experiment = "Succ_Low/Nitrate_High"[ matrix:set biomass_matrix 3 0 (matrix:get biomass_matrix 1 0 - matrix:get biomass_matrix 2 0) matrix:set biomass_matrix 4 0 (matrix:get biomass_matrix 1 0 + matrix:get biomass_matrix 2 0) matrix:set biomass_matrix 3 1 (matrix:get biomass_matrix 1 1 - matrix:get biomass_matrix 2 1) matrix:set biomass_matrix 4 1 (matrix:get biomass_matrix 1 1 + matrix:get biomass_matrix 2 1) matrix:set biomass_matrix 3 2 (matrix:get biomass_matrix 1 2 - matrix:get biomass_matrix 2 2) matrix:set biomass_matrix 4 2 (matrix:get biomass_matrix 1 2 + matrix:get biomass_matrix 2 2) matrix:set biomass_matrix 3 3 (matrix:get biomass_matrix 1 3 - matrix:get biomass_matrix 2 3) matrix:set biomass_matrix 4 3 (matrix:get biomass_matrix 1 3 + matrix:get biomass_matrix 2 3) matrix:set biomass_matrix 3 4 (matrix:get biomass_matrix 1 4 - matrix:get biomass_matrix 2 4) matrix:set biomass_matrix 4 4 (matrix:get biomass_matrix 1 4 + matrix:get biomass_matrix 2 4) matrix:set biomass_matrix 3 5 (matrix:get biomass_matrix 1 5 - matrix:get biomass_matrix 2 5) matrix:set biomass_matrix 4 5 (matrix:get biomass_matrix 1 5 + matrix:get biomass_matrix 2 5) matrix:set biomass_matrix 3 6 (matrix:get biomass_matrix 1 6 - matrix:get biomass_matrix 2 6) matrix:set biomass_matrix 4 6 (matrix:get biomass_matrix 1 6 + matrix:get biomass_matrix 2 6) matrix:set biomass_matrix 3 7 (matrix:get biomass_matrix 1 7 - matrix:get biomass_matrix 2 7) matrix:set biomass_matrix 4 7 (matrix:get biomass_matrix 1 7 + matrix:get biomass_matrix 2 7) matrix:set biomass_matrix 3 8 (matrix:get biomass_matrix 1 8 - matrix:get biomass_matrix 2 8) matrix:set biomass_matrix 4 8 (matrix:get biomass_matrix 1 8 + matrix:get biomass_matrix 2 8) matrix:set biomass_matrix 3 9 (matrix:get biomass_matrix 1 9 - matrix:get biomass_matrix 2 9) matrix:set biomass_matrix 4 9 (matrix:get biomass_matrix 1 9 + matrix:get biomass_matrix 2 9) matrix:set biomass_matrix 3 10 (matrix:get biomass_matrix 1 10 - matrix:get biomass_matrix 2 10) matrix:set biomass_matrix 4 10 (matrix:get biomass_matrix 1 10 + matrix:get biomass_matrix 2 10) matrix:set biomass_matrix 3 11 (matrix:get biomass_matrix 1 11 - matrix:get biomass_matrix 2 11) matrix:set biomass_matrix 4 11 (matrix:get biomass_matrix 1 11 + matrix:get biomass_matrix 2 11) matrix:set biomass_matrix 3 12 (matrix:get biomass_matrix 1 12 - matrix:get biomass_matrix 2 12) matrix:set biomass_matrix 4 12 (matrix:get biomass_matrix 1 12 + matrix:get biomass_matrix 2 12) matrix:set biomass_matrix 3 13 (matrix:get biomass_matrix 1 13 - matrix:get biomass_matrix 2 13) matrix:set biomass_matrix 4 13 (matrix:get biomass_matrix 1 13 + matrix:get biomass_matrix 2 13) matrix:set biomass_matrix 3 14 (matrix:get biomass_matrix 1 14 - matrix:get biomass_matrix 2 14) matrix:set biomass_matrix 4 14 (matrix:get biomass_matrix 1 14 + matrix:get biomass_matrix 2 14) matrix:set biomass_matrix 3 15 (matrix:get biomass_matrix 1 15 - matrix:get biomass_matrix 2 15) matrix:set biomass_matrix 4 15 (matrix:get biomass_matrix 1 15 + matrix:get biomass_matrix 2 15) matrix:set biomass_matrix 3 16 (matrix:get biomass_matrix 1 16 - matrix:get biomass_matrix 2 16) matrix:set biomass_matrix 4 16 (matrix:get biomass_matrix 1 16 + matrix:get biomass_matrix 2 16) matrix:set biomass_matrix 5 0 ((matrix:get biomass_matrix 3 0 / matrix:get biomass_matrix 4 0) ^ 2) matrix:set biomass_matrix 5 1 ((matrix:get biomass_matrix 3 1 / matrix:get biomass_matrix 4 1) ^ 2) matrix:set biomass_matrix 5 2 ((matrix:get biomass_matrix 3 2 / matrix:get biomass_matrix 4 2) ^ 2) matrix:set biomass_matrix 5 3 ((matrix:get biomass_matrix 3 3 / matrix:get biomass_matrix 4 3) ^ 2) matrix:set biomass_matrix 5 4 ((matrix:get biomass_matrix 3 4 / matrix:get biomass_matrix 4 4) ^ 2) matrix:set biomass_matrix 5 5 ((matrix:get biomass_matrix 3 5 / matrix:get biomass_matrix 4 5) ^ 2) matrix:set biomass_matrix 5 6 ((matrix:get biomass_matrix 3 6 / matrix:get biomass_matrix 4 6) ^ 2) matrix:set biomass_matrix 5 7 ((matrix:get biomass_matrix 3 7 / matrix:get biomass_matrix 4 7) ^ 2) matrix:set biomass_matrix 5 8 ((matrix:get biomass_matrix 3 8 / matrix:get biomass_matrix 4 8) ^ 2) matrix:set biomass_matrix 5 9 ((matrix:get biomass_matrix 3 9 / matrix:get biomass_matrix 4 9) ^ 2) matrix:set biomass_matrix 5 10 ((matrix:get biomass_matrix 3 10 / matrix:get biomass_matrix 4 10) ^ 2) matrix:set biomass_matrix 5 11 ((matrix:get biomass_matrix 3 11 / matrix:get biomass_matrix 4 11) ^ 2) matrix:set biomass_matrix 5 12 ((matrix:get biomass_matrix 3 12 / matrix:get biomass_matrix 4 12) ^ 2) matrix:set biomass_matrix 5 13 ((matrix:get biomass_matrix 3 13 / matrix:get biomass_matrix 4 13) ^ 2) matrix:set biomass_matrix 5 14 ((matrix:get biomass_matrix 3 14 / matrix:get biomass_matrix 4 14) ^ 2) matrix:set biomass_matrix 5 15 ((matrix:get biomass_matrix 3 15 / matrix:get biomass_matrix 4 15) ^ 2) matrix:set biomass_matrix 5 16 ((matrix:get biomass_matrix 3 16 / matrix:get biomass_matrix 4 16) ^ 2) let sum_biomass_square sum matrix:get-row biomass_matrix 5 let biomass_square sqrt ( (1 / (length matrix:get-row biomass_matrix 5)) * sum_biomass_square) set GRI_biomass (1 + biomass_square) / (1 - biomass_square) matrix:set nitrate_matrix 3 0 (matrix:get nitrate_matrix 1 0 - matrix:get nitrate_matrix 2 0) matrix:set nitrate_matrix 4 0 (matrix:get nitrate_matrix 1 0 + matrix:get nitrate_matrix 2 0) matrix:set nitrate_matrix 3 1 (matrix:get nitrate_matrix 1 1 - matrix:get nitrate_matrix 2 1) matrix:set nitrate_matrix 4 1 (matrix:get nitrate_matrix 1 1 + matrix:get nitrate_matrix 2 1) matrix:set nitrate_matrix 3 2 (matrix:get nitrate_matrix 1 2 - matrix:get nitrate_matrix 2 2) matrix:set nitrate_matrix 4 2 (matrix:get nitrate_matrix 1 2 + matrix:get nitrate_matrix 2 2) matrix:set nitrate_matrix 3 3 (matrix:get nitrate_matrix 1 3 - matrix:get nitrate_matrix 2 3) matrix:set nitrate_matrix 4 3 (matrix:get nitrate_matrix 1 3 + matrix:get nitrate_matrix 2 3) matrix:set nitrate_matrix 3 4 (matrix:get nitrate_matrix 1 4 - matrix:get nitrate_matrix 2 4) matrix:set nitrate_matrix 4 4 (matrix:get nitrate_matrix 1 4 + matrix:get nitrate_matrix 2 4) matrix:set nitrate_matrix 3 5 (matrix:get nitrate_matrix 1 5 - matrix:get nitrate_matrix 2 5) matrix:set nitrate_matrix 4 5 (matrix:get nitrate_matrix 1 5 + matrix:get nitrate_matrix 2 5) matrix:set nitrate_matrix 3 6 (matrix:get nitrate_matrix 1 6 - matrix:get nitrate_matrix 2 6) matrix:set nitrate_matrix 4 6 (matrix:get nitrate_matrix 1 6 + matrix:get nitrate_matrix 2 6) matrix:set nitrate_matrix 3 7 (matrix:get nitrate_matrix 1 7 - matrix:get nitrate_matrix 2 7) matrix:set nitrate_matrix 4 7 (matrix:get nitrate_matrix 1 7 + matrix:get nitrate_matrix 2 7) matrix:set nitrate_matrix 3 8 (matrix:get nitrate_matrix 1 8 - matrix:get nitrate_matrix 2 8) matrix:set nitrate_matrix 4 8 (matrix:get nitrate_matrix 1 8 + matrix:get nitrate_matrix 2 8) matrix:set nitrate_matrix 3 9 (matrix:get nitrate_matrix 1 9 - matrix:get nitrate_matrix 2 9) matrix:set nitrate_matrix 4 9 (matrix:get nitrate_matrix 1 9 + matrix:get nitrate_matrix 2 9) matrix:set nitrate_matrix 3 10 (matrix:get nitrate_matrix 1 10 - matrix:get nitrate_matrix 2 10) matrix:set nitrate_matrix 4 10 (matrix:get nitrate_matrix 1 10 + matrix:get nitrate_matrix 2 10) matrix:set nitrate_matrix 3 11 (matrix:get nitrate_matrix 1 11 - matrix:get nitrate_matrix 2 11) matrix:set nitrate_matrix 4 11 (matrix:get nitrate_matrix 1 11 + matrix:get nitrate_matrix 2 11) matrix:set nitrate_matrix 3 12 (matrix:get nitrate_matrix 1 12 - matrix:get nitrate_matrix 2 12) matrix:set nitrate_matrix 4 12 (matrix:get nitrate_matrix 1 12 + matrix:get nitrate_matrix 2 12) matrix:set nitrate_matrix 3 13 (matrix:get nitrate_matrix 1 13 - matrix:get nitrate_matrix 2 13) matrix:set nitrate_matrix 4 13 (matrix:get nitrate_matrix 1 13 + matrix:get nitrate_matrix 2 13) matrix:set nitrate_matrix 3 14 (matrix:get nitrate_matrix 1 14 - matrix:get nitrate_matrix 2 14) matrix:set nitrate_matrix 4 14 (matrix:get nitrate_matrix 1 14 + matrix:get nitrate_matrix 2 14) matrix:set nitrate_matrix 3 15 (matrix:get nitrate_matrix 1 15 - matrix:get nitrate_matrix 2 15) matrix:set nitrate_matrix 4 15 (matrix:get nitrate_matrix 1 15 + matrix:get nitrate_matrix 2 15) matrix:set nitrate_matrix 3 16 (matrix:get nitrate_matrix 1 16 - matrix:get nitrate_matrix 2 16) matrix:set nitrate_matrix 4 16 (matrix:get nitrate_matrix 1 16 + matrix:get nitrate_matrix 2 16) matrix:set nitrate_matrix 5 0 ((matrix:get nitrate_matrix 3 0 / matrix:get nitrate_matrix 4 0) ^ 2) matrix:set nitrate_matrix 5 1 ((matrix:get nitrate_matrix 3 1 / matrix:get nitrate_matrix 4 1) ^ 2) matrix:set nitrate_matrix 5 2 ((matrix:get nitrate_matrix 3 2 / matrix:get nitrate_matrix 4 2) ^ 2) matrix:set nitrate_matrix 5 3 ((matrix:get nitrate_matrix 3 3 / matrix:get nitrate_matrix 4 3) ^ 2) matrix:set nitrate_matrix 5 4 ((matrix:get nitrate_matrix 3 4 / matrix:get nitrate_matrix 4 4) ^ 2) matrix:set nitrate_matrix 5 5 ((matrix:get nitrate_matrix 3 5 / matrix:get nitrate_matrix 4 5) ^ 2) matrix:set nitrate_matrix 5 6 ((matrix:get nitrate_matrix 3 6 / matrix:get nitrate_matrix 4 6) ^ 2) matrix:set nitrate_matrix 5 7 ((matrix:get nitrate_matrix 3 7 / matrix:get nitrate_matrix 4 7) ^ 2) matrix:set nitrate_matrix 5 8 ((matrix:get nitrate_matrix 3 8 / matrix:get nitrate_matrix 4 8) ^ 2) matrix:set nitrate_matrix 5 9 ((matrix:get nitrate_matrix 3 9 / matrix:get nitrate_matrix 4 9) ^ 2) matrix:set nitrate_matrix 5 10 ((matrix:get nitrate_matrix 3 10 / matrix:get nitrate_matrix 4 10) ^ 2) matrix:set nitrate_matrix 5 11 ((matrix:get nitrate_matrix 3 11 / matrix:get nitrate_matrix 4 11) ^ 2) matrix:set nitrate_matrix 5 12 ((matrix:get nitrate_matrix 3 12 / matrix:get nitrate_matrix 4 12) ^ 2) matrix:set nitrate_matrix 5 13 ((matrix:get nitrate_matrix 3 13 / matrix:get nitrate_matrix 4 13) ^ 2) matrix:set nitrate_matrix 5 14 ((matrix:get nitrate_matrix 3 14 / matrix:get nitrate_matrix 4 14) ^ 2) matrix:set nitrate_matrix 5 15 ((matrix:get nitrate_matrix 3 15 / matrix:get nitrate_matrix 4 15) ^ 2) matrix:set nitrate_matrix 5 16 ((matrix:get nitrate_matrix 3 16 / matrix:get nitrate_matrix 4 16) ^ 2) let sum_nitrate_square sum matrix:get-row nitrate_matrix 5 let nitrate_square sqrt ( (1 / (length matrix:get-row nitrate_matrix 5)) * sum_nitrate_square) set GRI_nitrate (1 + nitrate_square) / (1 - nitrate_square) matrix:set nitrite_matrix 3 0 (matrix:get nitrite_matrix 1 0 - matrix:get nitrite_matrix 2 0) matrix:set nitrite_matrix 4 0 (matrix:get nitrite_matrix 1 0 + matrix:get nitrite_matrix 2 0) matrix:set nitrite_matrix 3 1 (matrix:get nitrite_matrix 1 1 - matrix:get nitrite_matrix 2 1) matrix:set nitrite_matrix 4 1 (matrix:get nitrite_matrix 1 1 + matrix:get nitrite_matrix 2 1) matrix:set nitrite_matrix 3 2 (matrix:get nitrite_matrix 1 2 - matrix:get nitrite_matrix 2 2) matrix:set nitrite_matrix 4 2 (matrix:get nitrite_matrix 1 2 + matrix:get nitrite_matrix 2 2) matrix:set nitrite_matrix 3 3 (matrix:get nitrite_matrix 1 3 - matrix:get nitrite_matrix 2 3) matrix:set nitrite_matrix 4 3 (matrix:get nitrite_matrix 1 3 + matrix:get nitrite_matrix 2 3) matrix:set nitrite_matrix 3 4 (matrix:get nitrite_matrix 1 4 - matrix:get nitrite_matrix 2 4) matrix:set nitrite_matrix 4 4 (matrix:get nitrite_matrix 1 4 + matrix:get nitrite_matrix 2 4) matrix:set nitrite_matrix 3 5 (matrix:get nitrite_matrix 1 5 - matrix:get nitrite_matrix 2 5) matrix:set nitrite_matrix 4 5 (matrix:get nitrite_matrix 1 5 + matrix:get nitrite_matrix 2 5) matrix:set nitrite_matrix 3 6 (matrix:get nitrite_matrix 1 6 - matrix:get nitrite_matrix 2 6) matrix:set nitrite_matrix 4 6 (matrix:get nitrite_matrix 1 6 + matrix:get nitrite_matrix 2 6) matrix:set nitrite_matrix 3 7 (matrix:get nitrite_matrix 1 7 - matrix:get nitrite_matrix 2 7) matrix:set nitrite_matrix 4 7 (matrix:get nitrite_matrix 1 7 + matrix:get nitrite_matrix 2 7) matrix:set nitrite_matrix 3 8 (matrix:get nitrite_matrix 1 8 - matrix:get nitrite_matrix 2 8) matrix:set nitrite_matrix 4 8 (matrix:get nitrite_matrix 1 8 + matrix:get nitrite_matrix 2 8) matrix:set nitrite_matrix 3 9 (matrix:get nitrite_matrix 1 9 - matrix:get nitrite_matrix 2 9) matrix:set nitrite_matrix 4 9 (matrix:get nitrite_matrix 1 9 + matrix:get nitrite_matrix 2 9) matrix:set nitrite_matrix 3 10 (matrix:get nitrite_matrix 1 10 - matrix:get nitrite_matrix 2 10) matrix:set nitrite_matrix 4 10 (matrix:get nitrite_matrix 1 10 + matrix:get nitrite_matrix 2 10) matrix:set nitrite_matrix 3 11 (matrix:get nitrite_matrix 1 11 - matrix:get nitrite_matrix 2 11) matrix:set nitrite_matrix 4 11 (matrix:get nitrite_matrix 1 11 + matrix:get nitrite_matrix 2 11) matrix:set nitrite_matrix 3 12 (matrix:get nitrite_matrix 1 12 - matrix:get nitrite_matrix 2 12) matrix:set nitrite_matrix 4 12 (matrix:get nitrite_matrix 1 12 + matrix:get nitrite_matrix 2 12) matrix:set nitrite_matrix 3 13 (matrix:get nitrite_matrix 1 13 - matrix:get nitrite_matrix 2 13) matrix:set nitrite_matrix 4 13 (matrix:get nitrite_matrix 1 13 + matrix:get nitrite_matrix 2 13) matrix:set nitrite_matrix 3 14 (matrix:get nitrite_matrix 1 14 - matrix:get nitrite_matrix 2 14) matrix:set nitrite_matrix 4 14 (matrix:get nitrite_matrix 1 14 + matrix:get nitrite_matrix 2 14) matrix:set nitrite_matrix 3 15 (matrix:get nitrite_matrix 1 15 - matrix:get nitrite_matrix 2 15) matrix:set nitrite_matrix 4 15 (matrix:get nitrite_matrix 1 15 + matrix:get nitrite_matrix 2 15) matrix:set nitrite_matrix 3 16 (matrix:get nitrite_matrix 1 16 - matrix:get nitrite_matrix 2 16) matrix:set nitrite_matrix 4 16 (matrix:get nitrite_matrix 1 16 + matrix:get nitrite_matrix 2 16) matrix:set nitrite_matrix 5 0 ((matrix:get nitrite_matrix 3 0 / matrix:get nitrite_matrix 4 0) ^ 2) matrix:set nitrite_matrix 5 1 ((matrix:get nitrite_matrix 3 1 / matrix:get nitrite_matrix 4 1) ^ 2) matrix:set nitrite_matrix 5 2 ((matrix:get nitrite_matrix 3 2 / matrix:get nitrite_matrix 4 2) ^ 2) matrix:set nitrite_matrix 5 3 ((matrix:get nitrite_matrix 3 3 / matrix:get nitrite_matrix 4 3) ^ 2) matrix:set nitrite_matrix 5 4 ((matrix:get nitrite_matrix 3 4 / matrix:get nitrite_matrix 4 4) ^ 2) matrix:set nitrite_matrix 5 5 ((matrix:get nitrite_matrix 3 5 / matrix:get nitrite_matrix 4 5) ^ 2) matrix:set nitrite_matrix 5 6 ((matrix:get nitrite_matrix 3 6 / matrix:get nitrite_matrix 4 6) ^ 2) matrix:set nitrite_matrix 5 7 ((matrix:get nitrite_matrix 3 7 / matrix:get nitrite_matrix 4 7) ^ 2) matrix:set nitrite_matrix 5 8 ((matrix:get nitrite_matrix 3 8 / matrix:get nitrite_matrix 4 8) ^ 2) matrix:set nitrite_matrix 5 9 ((matrix:get nitrite_matrix 3 9 / matrix:get nitrite_matrix 4 9) ^ 2) matrix:set nitrite_matrix 5 10 ((matrix:get nitrite_matrix 3 10 / matrix:get nitrite_matrix 4 10) ^ 2) matrix:set nitrite_matrix 5 11 ((matrix:get nitrite_matrix 3 11 / matrix:get nitrite_matrix 4 11) ^ 2) matrix:set nitrite_matrix 5 12 ((matrix:get nitrite_matrix 3 12 / matrix:get nitrite_matrix 4 12) ^ 2) matrix:set nitrite_matrix 5 13 ((matrix:get nitrite_matrix 3 13 / matrix:get nitrite_matrix 4 13) ^ 2) matrix:set nitrite_matrix 5 14 ((matrix:get nitrite_matrix 3 14 / matrix:get nitrite_matrix 4 14) ^ 2) matrix:set nitrite_matrix 5 15 ((matrix:get nitrite_matrix 3 15 / matrix:get nitrite_matrix 4 15) ^ 2) matrix:set nitrite_matrix 5 16 ((matrix:get nitrite_matrix 3 16 / matrix:get nitrite_matrix 4 16) ^ 2) let sum_nitrite_square sum matrix:get-row nitrite_matrix 5 let nitrite_square sqrt ( (1 / (length matrix:get-row nitrite_matrix 5)) * sum_nitrite_square) set GRI_nitrite (1 + nitrite_square) / (1 - nitrite_square) matrix:set nitrous_oxide_matrix 3 0 (matrix:get nitrous_oxide_matrix 1 0 - matrix:get nitrous_oxide_matrix 2 0) matrix:set nitrous_oxide_matrix 4 0 (matrix:get nitrous_oxide_matrix 1 0 + matrix:get nitrous_oxide_matrix 2 0) matrix:set nitrous_oxide_matrix 3 1 (matrix:get nitrous_oxide_matrix 1 1 - matrix:get nitrous_oxide_matrix 2 1) matrix:set nitrous_oxide_matrix 4 1 (matrix:get nitrous_oxide_matrix 1 1 + matrix:get nitrous_oxide_matrix 2 1) matrix:set nitrous_oxide_matrix 3 2 (matrix:get nitrous_oxide_matrix 1 2 - matrix:get nitrous_oxide_matrix 2 2) matrix:set nitrous_oxide_matrix 4 2 (matrix:get nitrous_oxide_matrix 1 2 + matrix:get nitrous_oxide_matrix 2 2) matrix:set nitrous_oxide_matrix 3 3 (matrix:get nitrous_oxide_matrix 1 3 - matrix:get nitrous_oxide_matrix 2 3) matrix:set nitrous_oxide_matrix 4 3 (matrix:get nitrous_oxide_matrix 1 3 + matrix:get nitrous_oxide_matrix 2 3) matrix:set nitrous_oxide_matrix 3 4 (matrix:get nitrous_oxide_matrix 1 4 - matrix:get nitrous_oxide_matrix 2 4) matrix:set nitrous_oxide_matrix 4 4 (matrix:get nitrous_oxide_matrix 1 4 + matrix:get nitrous_oxide_matrix 2 4) matrix:set nitrous_oxide_matrix 3 5 (matrix:get nitrous_oxide_matrix 1 5 - matrix:get nitrous_oxide_matrix 2 5) matrix:set nitrous_oxide_matrix 4 5 (matrix:get nitrous_oxide_matrix 1 5 + matrix:get nitrous_oxide_matrix 2 5) matrix:set nitrous_oxide_matrix 3 6 (matrix:get nitrous_oxide_matrix 1 6 - matrix:get nitrous_oxide_matrix 2 6) matrix:set nitrous_oxide_matrix 4 6 (matrix:get nitrous_oxide_matrix 1 6 + matrix:get nitrous_oxide_matrix 2 6) matrix:set nitrous_oxide_matrix 3 7 (matrix:get nitrous_oxide_matrix 1 7 - matrix:get nitrous_oxide_matrix 2 7) matrix:set nitrous_oxide_matrix 4 7 (matrix:get nitrous_oxide_matrix 1 7 + matrix:get nitrous_oxide_matrix 2 7) matrix:set nitrous_oxide_matrix 3 8 (matrix:get nitrous_oxide_matrix 1 8 - matrix:get nitrous_oxide_matrix 2 8) matrix:set nitrous_oxide_matrix 4 8 (matrix:get nitrous_oxide_matrix 1 8 + matrix:get nitrous_oxide_matrix 2 8) matrix:set nitrous_oxide_matrix 3 9 (matrix:get nitrous_oxide_matrix 1 9 - matrix:get nitrous_oxide_matrix 2 9) matrix:set nitrous_oxide_matrix 4 9 (matrix:get nitrous_oxide_matrix 1 9 + matrix:get nitrous_oxide_matrix 2 9) matrix:set nitrous_oxide_matrix 3 10 (matrix:get nitrous_oxide_matrix 1 10 - matrix:get nitrous_oxide_matrix 2 10) matrix:set nitrous_oxide_matrix 4 10 (matrix:get nitrous_oxide_matrix 1 10 + matrix:get nitrous_oxide_matrix 2 10) matrix:set nitrous_oxide_matrix 3 11 (matrix:get nitrous_oxide_matrix 1 11 - matrix:get nitrous_oxide_matrix 2 11) matrix:set nitrous_oxide_matrix 4 11 (matrix:get nitrous_oxide_matrix 1 11 + matrix:get nitrous_oxide_matrix 2 11) matrix:set nitrous_oxide_matrix 3 12 (matrix:get nitrous_oxide_matrix 1 12 - matrix:get nitrous_oxide_matrix 2 12) matrix:set nitrous_oxide_matrix 4 12 (matrix:get nitrous_oxide_matrix 1 12 + matrix:get nitrous_oxide_matrix 2 12) matrix:set nitrous_oxide_matrix 3 13 (matrix:get nitrous_oxide_matrix 1 13 - matrix:get nitrous_oxide_matrix 2 13) matrix:set nitrous_oxide_matrix 4 13 (matrix:get nitrous_oxide_matrix 1 13 + matrix:get nitrous_oxide_matrix 2 13) matrix:set nitrous_oxide_matrix 3 14 (matrix:get nitrous_oxide_matrix 1 14 - matrix:get nitrous_oxide_matrix 2 14) matrix:set nitrous_oxide_matrix 4 14 (matrix:get nitrous_oxide_matrix 1 14 + matrix:get nitrous_oxide_matrix 2 14) matrix:set nitrous_oxide_matrix 5 0 ((matrix:get nitrous_oxide_matrix 3 0 / matrix:get nitrous_oxide_matrix 4 0) ^ 2) matrix:set nitrous_oxide_matrix 5 1 ((matrix:get nitrous_oxide_matrix 3 1 / matrix:get nitrous_oxide_matrix 4 1) ^ 2) matrix:set nitrous_oxide_matrix 5 2 ((matrix:get nitrous_oxide_matrix 3 2 / matrix:get nitrous_oxide_matrix 4 2) ^ 2) matrix:set nitrous_oxide_matrix 5 3 ((matrix:get nitrous_oxide_matrix 3 3 / matrix:get nitrous_oxide_matrix 4 3) ^ 2) matrix:set nitrous_oxide_matrix 5 4 ((matrix:get nitrous_oxide_matrix 3 4 / matrix:get nitrous_oxide_matrix 4 4) ^ 2) matrix:set nitrous_oxide_matrix 5 5 ((matrix:get nitrous_oxide_matrix 3 5 / matrix:get nitrous_oxide_matrix 4 5) ^ 2) matrix:set nitrous_oxide_matrix 5 6 ((matrix:get nitrous_oxide_matrix 3 6 / matrix:get nitrous_oxide_matrix 4 6) ^ 2) matrix:set nitrous_oxide_matrix 5 7 ((matrix:get nitrous_oxide_matrix 3 7 / matrix:get nitrous_oxide_matrix 4 7) ^ 2) matrix:set nitrous_oxide_matrix 5 8 ((matrix:get nitrous_oxide_matrix 3 8 / matrix:get nitrous_oxide_matrix 4 8) ^ 2) matrix:set nitrous_oxide_matrix 5 9 ((matrix:get nitrous_oxide_matrix 3 9 / matrix:get nitrous_oxide_matrix 4 9) ^ 2) matrix:set nitrous_oxide_matrix 5 10 ((matrix:get nitrous_oxide_matrix 3 10 / matrix:get nitrous_oxide_matrix 4 10) ^ 2) matrix:set nitrous_oxide_matrix 5 11 ((matrix:get nitrous_oxide_matrix 3 11 / matrix:get nitrous_oxide_matrix 4 11) ^ 2) matrix:set nitrous_oxide_matrix 5 12 ((matrix:get nitrous_oxide_matrix 3 12 / matrix:get nitrous_oxide_matrix 4 12) ^ 2) matrix:set nitrous_oxide_matrix 5 13 ((matrix:get nitrous_oxide_matrix 3 13 / matrix:get nitrous_oxide_matrix 4 13) ^ 2) matrix:set nitrous_oxide_matrix 5 14 ((matrix:get nitrous_oxide_matrix 3 14 / matrix:get nitrous_oxide_matrix 4 14) ^ 2) let sum_nitrous_oxide_square sum matrix:get-row nitrous_oxide_matrix 5 let nitrous_oxide_square sqrt ( (1 / (length matrix:get-row nitrous_oxide_matrix 5)) * sum_nitrous_oxide_square) set GRI_nitrous_oxide (1 + nitrous_oxide_square) / (1 - nitrous_oxide_square) Fitness-Calculation ] ; end procedure succinate low P. denitrificans if Experiment = "Succ_High/Nitrate_Low"[ matrix:set biomass_matrix 3 0 (matrix:get biomass_matrix 1 0 - matrix:get biomass_matrix 2 0) matrix:set biomass_matrix 4 0 (matrix:get biomass_matrix 1 0 + matrix:get biomass_matrix 2 0) matrix:set biomass_matrix 3 1 (matrix:get biomass_matrix 1 1 - matrix:get biomass_matrix 2 1) matrix:set biomass_matrix 4 1 (matrix:get biomass_matrix 1 1 + matrix:get biomass_matrix 2 1) matrix:set biomass_matrix 3 2 (matrix:get biomass_matrix 1 2 - matrix:get biomass_matrix 2 2) matrix:set biomass_matrix 4 2 (matrix:get biomass_matrix 1 2 + matrix:get biomass_matrix 2 2) matrix:set biomass_matrix 3 3 (matrix:get biomass_matrix 1 3 - matrix:get biomass_matrix 2 3) matrix:set biomass_matrix 4 3 (matrix:get biomass_matrix 1 3 + matrix:get biomass_matrix 2 3) matrix:set biomass_matrix 3 4 (matrix:get biomass_matrix 1 4 - matrix:get biomass_matrix 2 4) matrix:set biomass_matrix 4 4 (matrix:get biomass_matrix 1 4 + matrix:get biomass_matrix 2 4) matrix:set biomass_matrix 3 5 (matrix:get biomass_matrix 1 5 - matrix:get biomass_matrix 2 5) matrix:set biomass_matrix 4 5 (matrix:get biomass_matrix 1 5 + matrix:get biomass_matrix 2 5) matrix:set biomass_matrix 3 6 (matrix:get biomass_matrix 1 6 - matrix:get biomass_matrix 2 6) matrix:set biomass_matrix 4 6 (matrix:get biomass_matrix 1 6 + matrix:get biomass_matrix 2 6) matrix:set biomass_matrix 3 7 (matrix:get biomass_matrix 1 7 - matrix:get biomass_matrix 2 7) matrix:set biomass_matrix 4 7 (matrix:get biomass_matrix 1 7 + matrix:get biomass_matrix 2 7) matrix:set biomass_matrix 3 8 (matrix:get biomass_matrix 1 8 - matrix:get biomass_matrix 2 8) matrix:set biomass_matrix 4 8 (matrix:get biomass_matrix 1 8 + matrix:get biomass_matrix 2 8) matrix:set biomass_matrix 3 9 (matrix:get biomass_matrix 1 9 - matrix:get biomass_matrix 2 9) matrix:set biomass_matrix 4 9 (matrix:get biomass_matrix 1 9 + matrix:get biomass_matrix 2 9) matrix:set biomass_matrix 3 10 (matrix:get biomass_matrix 1 10 - matrix:get biomass_matrix 2 10) matrix:set biomass_matrix 4 10 (matrix:get biomass_matrix 1 10 + matrix:get biomass_matrix 2 10) matrix:set biomass_matrix 3 11 (matrix:get biomass_matrix 1 11 - matrix:get biomass_matrix 2 11) matrix:set biomass_matrix 4 11 (matrix:get biomass_matrix 1 11 + matrix:get biomass_matrix 2 11) matrix:set biomass_matrix 3 12 (matrix:get biomass_matrix 1 12 - matrix:get biomass_matrix 2 12) matrix:set biomass_matrix 4 12 (matrix:get biomass_matrix 1 12 + matrix:get biomass_matrix 2 12) matrix:set biomass_matrix 3 13 (matrix:get biomass_matrix 1 13 - matrix:get biomass_matrix 2 13) matrix:set biomass_matrix 4 13 (matrix:get biomass_matrix 1 13 + matrix:get biomass_matrix 2 13) matrix:set biomass_matrix 3 14 (matrix:get biomass_matrix 1 14 - matrix:get biomass_matrix 2 14) matrix:set biomass_matrix 4 14 (matrix:get biomass_matrix 1 14 + matrix:get biomass_matrix 2 14) matrix:set biomass_matrix 3 15 (matrix:get biomass_matrix 1 15 - matrix:get biomass_matrix 2 15) matrix:set biomass_matrix 4 15 (matrix:get biomass_matrix 1 15 + matrix:get biomass_matrix 2 15) matrix:set biomass_matrix 3 16 (matrix:get biomass_matrix 1 16 - matrix:get biomass_matrix 2 16) matrix:set biomass_matrix 4 16 (matrix:get biomass_matrix 1 16 + matrix:get biomass_matrix 2 16) matrix:set biomass_matrix 5 0 ((matrix:get biomass_matrix 3 0 / matrix:get biomass_matrix 4 0) ^ 2) matrix:set biomass_matrix 5 1 ((matrix:get biomass_matrix 3 1 / matrix:get biomass_matrix 4 1) ^ 2) matrix:set biomass_matrix 5 2 ((matrix:get biomass_matrix 3 2 / matrix:get biomass_matrix 4 2) ^ 2) matrix:set biomass_matrix 5 3 ((matrix:get biomass_matrix 3 3 / matrix:get biomass_matrix 4 3) ^ 2) matrix:set biomass_matrix 5 4 ((matrix:get biomass_matrix 3 4 / matrix:get biomass_matrix 4 4) ^ 2) matrix:set biomass_matrix 5 5 ((matrix:get biomass_matrix 3 5 / matrix:get biomass_matrix 4 5) ^ 2) matrix:set biomass_matrix 5 6 ((matrix:get biomass_matrix 3 6 / matrix:get biomass_matrix 4 6) ^ 2) matrix:set biomass_matrix 5 7 ((matrix:get biomass_matrix 3 7 / matrix:get biomass_matrix 4 7) ^ 2) matrix:set biomass_matrix 5 8 ((matrix:get biomass_matrix 3 8 / matrix:get biomass_matrix 4 8) ^ 2) matrix:set biomass_matrix 5 9 ((matrix:get biomass_matrix 3 9 / matrix:get biomass_matrix 4 9) ^ 2) matrix:set biomass_matrix 5 10 ((matrix:get biomass_matrix 3 10 / matrix:get biomass_matrix 4 10) ^ 2) matrix:set biomass_matrix 5 11 ((matrix:get biomass_matrix 3 11 / matrix:get biomass_matrix 4 11) ^ 2) matrix:set biomass_matrix 5 12 ((matrix:get biomass_matrix 3 12 / matrix:get biomass_matrix 4 12) ^ 2) matrix:set biomass_matrix 5 13 ((matrix:get biomass_matrix 3 13 / matrix:get biomass_matrix 4 13) ^ 2) matrix:set biomass_matrix 5 14 ((matrix:get biomass_matrix 3 14 / matrix:get biomass_matrix 4 14) ^ 2) matrix:set biomass_matrix 5 15 ((matrix:get biomass_matrix 3 15 / matrix:get biomass_matrix 4 15) ^ 2) matrix:set biomass_matrix 5 16 ((matrix:get biomass_matrix 3 16 / matrix:get biomass_matrix 4 16) ^ 2) let sum_biomass_square sum matrix:get-row biomass_matrix 5 let biomass_square sqrt ( (1 / (length matrix:get-row biomass_matrix 5)) * sum_biomass_square) set GRI_biomass (1 + biomass_square) / (1 - biomass_square) matrix:set nitrate_matrix 3 0 (matrix:get nitrate_matrix 1 0 - matrix:get nitrate_matrix 2 0) matrix:set nitrate_matrix 4 0 (matrix:get nitrate_matrix 1 0 + matrix:get nitrate_matrix 2 0) matrix:set nitrate_matrix 3 1 (matrix:get nitrate_matrix 1 1 - matrix:get nitrate_matrix 2 1) matrix:set nitrate_matrix 4 1 (matrix:get nitrate_matrix 1 1 + matrix:get nitrate_matrix 2 1) matrix:set nitrate_matrix 3 2 (matrix:get nitrate_matrix 1 2 - matrix:get nitrate_matrix 2 2) matrix:set nitrate_matrix 4 2 (matrix:get nitrate_matrix 1 2 + matrix:get nitrate_matrix 2 2) matrix:set nitrate_matrix 3 3 (matrix:get nitrate_matrix 1 3 - matrix:get nitrate_matrix 2 3) matrix:set nitrate_matrix 4 3 (matrix:get nitrate_matrix 1 3 + matrix:get nitrate_matrix 2 3) matrix:set nitrate_matrix 3 4 (matrix:get nitrate_matrix 1 4 - matrix:get nitrate_matrix 2 4) matrix:set nitrate_matrix 4 4 (matrix:get nitrate_matrix 1 4 + matrix:get nitrate_matrix 2 4) matrix:set nitrate_matrix 3 5 (matrix:get nitrate_matrix 1 5 - matrix:get nitrate_matrix 2 5) matrix:set nitrate_matrix 4 5 (matrix:get nitrate_matrix 1 5 + matrix:get nitrate_matrix 2 5) matrix:set nitrate_matrix 3 6 (matrix:get nitrate_matrix 1 6 - matrix:get nitrate_matrix 2 6) matrix:set nitrate_matrix 4 6 (matrix:get nitrate_matrix 1 6 + matrix:get nitrate_matrix 2 6) matrix:set nitrate_matrix 3 7 (matrix:get nitrate_matrix 1 7 - matrix:get nitrate_matrix 2 7) matrix:set nitrate_matrix 4 7 (matrix:get nitrate_matrix 1 7 + matrix:get nitrate_matrix 2 7) matrix:set nitrate_matrix 3 8 (matrix:get nitrate_matrix 1 8 - matrix:get nitrate_matrix 2 8) matrix:set nitrate_matrix 4 8 (matrix:get nitrate_matrix 1 8 + matrix:get nitrate_matrix 2 8) matrix:set nitrate_matrix 3 9 (matrix:get nitrate_matrix 1 9 - matrix:get nitrate_matrix 2 9) matrix:set nitrate_matrix 4 9 (matrix:get nitrate_matrix 1 9 + matrix:get nitrate_matrix 2 9) matrix:set nitrate_matrix 3 10 (matrix:get nitrate_matrix 1 10 - matrix:get nitrate_matrix 2 10) matrix:set nitrate_matrix 4 10 (matrix:get nitrate_matrix 1 10 + matrix:get nitrate_matrix 2 10) matrix:set nitrate_matrix 3 11 (matrix:get nitrate_matrix 1 11 - matrix:get nitrate_matrix 2 11) matrix:set nitrate_matrix 4 11 (matrix:get nitrate_matrix 1 11 + matrix:get nitrate_matrix 2 11) matrix:set nitrate_matrix 3 12 (matrix:get nitrate_matrix 1 12 - matrix:get nitrate_matrix 2 12) matrix:set nitrate_matrix 4 12 (matrix:get nitrate_matrix 1 12 + matrix:get nitrate_matrix 2 12) matrix:set nitrate_matrix 3 13 (matrix:get nitrate_matrix 1 13 - matrix:get nitrate_matrix 2 13) matrix:set nitrate_matrix 4 13 (matrix:get nitrate_matrix 1 13 + matrix:get nitrate_matrix 2 13) matrix:set nitrate_matrix 3 14 (matrix:get nitrate_matrix 1 14 - matrix:get nitrate_matrix 2 14) matrix:set nitrate_matrix 4 14 (matrix:get nitrate_matrix 1 14 + matrix:get nitrate_matrix 2 14) matrix:set nitrate_matrix 3 15 (matrix:get nitrate_matrix 1 15 - matrix:get nitrate_matrix 2 15) matrix:set nitrate_matrix 4 15 (matrix:get nitrate_matrix 1 15 + matrix:get nitrate_matrix 2 15) matrix:set nitrate_matrix 3 16 (matrix:get nitrate_matrix 1 16 - matrix:get nitrate_matrix 2 16) matrix:set nitrate_matrix 4 16 (matrix:get nitrate_matrix 1 16 + matrix:get nitrate_matrix 2 16) matrix:set nitrate_matrix 5 0 ((matrix:get nitrate_matrix 3 0 / matrix:get nitrate_matrix 4 0) ^ 2) matrix:set nitrate_matrix 5 1 ((matrix:get nitrate_matrix 3 1 / matrix:get nitrate_matrix 4 1) ^ 2) matrix:set nitrate_matrix 5 2 ((matrix:get nitrate_matrix 3 2 / matrix:get nitrate_matrix 4 2) ^ 2) matrix:set nitrate_matrix 5 3 ((matrix:get nitrate_matrix 3 3 / matrix:get nitrate_matrix 4 3) ^ 2) matrix:set nitrate_matrix 5 4 ((matrix:get nitrate_matrix 3 4 / matrix:get nitrate_matrix 4 4) ^ 2) matrix:set nitrate_matrix 5 5 ((matrix:get nitrate_matrix 3 5 / matrix:get nitrate_matrix 4 5) ^ 2) matrix:set nitrate_matrix 5 6 ((matrix:get nitrate_matrix 3 6 / matrix:get nitrate_matrix 4 6) ^ 2) matrix:set nitrate_matrix 5 7 ((matrix:get nitrate_matrix 3 7 / matrix:get nitrate_matrix 4 7) ^ 2) matrix:set nitrate_matrix 5 8 ((matrix:get nitrate_matrix 3 8 / matrix:get nitrate_matrix 4 8) ^ 2) matrix:set nitrate_matrix 5 9 ((matrix:get nitrate_matrix 3 9 / matrix:get nitrate_matrix 4 9) ^ 2) matrix:set nitrate_matrix 5 10 ((matrix:get nitrate_matrix 3 10 / matrix:get nitrate_matrix 4 10) ^ 2) matrix:set nitrate_matrix 5 11 ((matrix:get nitrate_matrix 3 11 / matrix:get nitrate_matrix 4 11) ^ 2) matrix:set nitrate_matrix 5 12 ((matrix:get nitrate_matrix 3 12 / matrix:get nitrate_matrix 4 12) ^ 2) matrix:set nitrate_matrix 5 13 ((matrix:get nitrate_matrix 3 13 / matrix:get nitrate_matrix 4 13) ^ 2) matrix:set nitrate_matrix 5 14 ((matrix:get nitrate_matrix 3 14 / matrix:get nitrate_matrix 4 14) ^ 2) matrix:set nitrate_matrix 5 15 ((matrix:get nitrate_matrix 3 15 / matrix:get nitrate_matrix 4 15) ^ 2) matrix:set nitrate_matrix 5 16 ((matrix:get nitrate_matrix 3 16 / matrix:get nitrate_matrix 4 16) ^ 2) let sum_nitrate_square sum matrix:get-row nitrate_matrix 5 let nitrate_square sqrt ( (1 / (length matrix:get-row nitrate_matrix 5)) * sum_nitrate_square) set GRI_nitrate (1 + nitrate_square) / (1 - nitrate_square) matrix:set nitrite_matrix 3 0 (matrix:get nitrite_matrix 1 0 - matrix:get nitrite_matrix 2 0) matrix:set nitrite_matrix 4 0 (matrix:get nitrite_matrix 1 0 + matrix:get nitrite_matrix 2 0) matrix:set nitrite_matrix 3 1 (matrix:get nitrite_matrix 1 1 - matrix:get nitrite_matrix 2 1) matrix:set nitrite_matrix 4 1 (matrix:get nitrite_matrix 1 1 + matrix:get nitrite_matrix 2 1) matrix:set nitrite_matrix 3 2 (matrix:get nitrite_matrix 1 2 - matrix:get nitrite_matrix 2 2) matrix:set nitrite_matrix 4 2 (matrix:get nitrite_matrix 1 2 + matrix:get nitrite_matrix 2 2) matrix:set nitrite_matrix 3 3 (matrix:get nitrite_matrix 1 3 - matrix:get nitrite_matrix 2 3) matrix:set nitrite_matrix 4 3 (matrix:get nitrite_matrix 1 3 + matrix:get nitrite_matrix 2 3) matrix:set nitrite_matrix 3 4 (matrix:get nitrite_matrix 1 4 - matrix:get nitrite_matrix 2 4) matrix:set nitrite_matrix 4 4 (matrix:get nitrite_matrix 1 4 + matrix:get nitrite_matrix 2 4) matrix:set nitrite_matrix 3 5 (matrix:get nitrite_matrix 1 5 - matrix:get nitrite_matrix 2 5) matrix:set nitrite_matrix 4 5 (matrix:get nitrite_matrix 1 5 + matrix:get nitrite_matrix 2 5) matrix:set nitrite_matrix 3 6 (matrix:get nitrite_matrix 1 6 - matrix:get nitrite_matrix 2 6) matrix:set nitrite_matrix 4 6 (matrix:get nitrite_matrix 1 6 + matrix:get nitrite_matrix 2 6) matrix:set nitrite_matrix 3 7 (matrix:get nitrite_matrix 1 7 - matrix:get nitrite_matrix 2 7) matrix:set nitrite_matrix 4 7 (matrix:get nitrite_matrix 1 7 + matrix:get nitrite_matrix 2 7) matrix:set nitrite_matrix 3 8 (matrix:get nitrite_matrix 1 8 - matrix:get nitrite_matrix 2 8) matrix:set nitrite_matrix 4 8 (matrix:get nitrite_matrix 1 8 + matrix:get nitrite_matrix 2 8) matrix:set nitrite_matrix 3 9 (matrix:get nitrite_matrix 1 9 - matrix:get nitrite_matrix 2 9) matrix:set nitrite_matrix 4 9 (matrix:get nitrite_matrix 1 9 + matrix:get nitrite_matrix 2 9) matrix:set nitrite_matrix 3 10 (matrix:get nitrite_matrix 1 10 - matrix:get nitrite_matrix 2 10) matrix:set nitrite_matrix 4 10 (matrix:get nitrite_matrix 1 10 + matrix:get nitrite_matrix 2 10) matrix:set nitrite_matrix 3 11 (matrix:get nitrite_matrix 1 11 - matrix:get nitrite_matrix 2 11) matrix:set nitrite_matrix 4 11 (matrix:get nitrite_matrix 1 11 + matrix:get nitrite_matrix 2 11) matrix:set nitrite_matrix 3 12 (matrix:get nitrite_matrix 1 12 - matrix:get nitrite_matrix 2 12) matrix:set nitrite_matrix 4 12 (matrix:get nitrite_matrix 1 12 + matrix:get nitrite_matrix 2 12) matrix:set nitrite_matrix 3 13 (matrix:get nitrite_matrix 1 13 - matrix:get nitrite_matrix 2 13) matrix:set nitrite_matrix 4 13 (matrix:get nitrite_matrix 1 13 + matrix:get nitrite_matrix 2 13) matrix:set nitrite_matrix 3 14 (matrix:get nitrite_matrix 1 14 - matrix:get nitrite_matrix 2 14) matrix:set nitrite_matrix 4 14 (matrix:get nitrite_matrix 1 14 + matrix:get nitrite_matrix 2 14) matrix:set nitrite_matrix 3 15 (matrix:get nitrite_matrix 1 15 - matrix:get nitrite_matrix 2 15) matrix:set nitrite_matrix 4 15 (matrix:get nitrite_matrix 1 15 + matrix:get nitrite_matrix 2 15) matrix:set nitrite_matrix 3 16 (matrix:get nitrite_matrix 1 16 - matrix:get nitrite_matrix 2 16) matrix:set nitrite_matrix 4 16 (matrix:get nitrite_matrix 1 16 + matrix:get nitrite_matrix 2 16) matrix:set nitrite_matrix 5 0 ((matrix:get nitrite_matrix 3 0 / matrix:get nitrite_matrix 4 0) ^ 2) matrix:set nitrite_matrix 5 1 ((matrix:get nitrite_matrix 3 1 / matrix:get nitrite_matrix 4 1) ^ 2) matrix:set nitrite_matrix 5 2 ((matrix:get nitrite_matrix 3 2 / matrix:get nitrite_matrix 4 2) ^ 2) matrix:set nitrite_matrix 5 3 ((matrix:get nitrite_matrix 3 3 / matrix:get nitrite_matrix 4 3) ^ 2) matrix:set nitrite_matrix 5 4 ((matrix:get nitrite_matrix 3 4 / matrix:get nitrite_matrix 4 4) ^ 2) matrix:set nitrite_matrix 5 5 ((matrix:get nitrite_matrix 3 5 / matrix:get nitrite_matrix 4 5) ^ 2) matrix:set nitrite_matrix 5 6 ((matrix:get nitrite_matrix 3 6 / matrix:get nitrite_matrix 4 6) ^ 2) matrix:set nitrite_matrix 5 7 ((matrix:get nitrite_matrix 3 7 / matrix:get nitrite_matrix 4 7) ^ 2) matrix:set nitrite_matrix 5 8 ((matrix:get nitrite_matrix 3 8 / matrix:get nitrite_matrix 4 8) ^ 2) matrix:set nitrite_matrix 5 9 ((matrix:get nitrite_matrix 3 9 / matrix:get nitrite_matrix 4 9) ^ 2) matrix:set nitrite_matrix 5 10 ((matrix:get nitrite_matrix 3 10 / matrix:get nitrite_matrix 4 10) ^ 2) matrix:set nitrite_matrix 5 11 ((matrix:get nitrite_matrix 3 11 / matrix:get nitrite_matrix 4 11) ^ 2) matrix:set nitrite_matrix 5 12 ((matrix:get nitrite_matrix 3 12 / matrix:get nitrite_matrix 4 12) ^ 2) matrix:set nitrite_matrix 5 13 ((matrix:get nitrite_matrix 3 13 / matrix:get nitrite_matrix 4 13) ^ 2) matrix:set nitrite_matrix 5 14 ((matrix:get nitrite_matrix 3 14 / matrix:get nitrite_matrix 4 14) ^ 2) matrix:set nitrite_matrix 5 15 ((matrix:get nitrite_matrix 3 15 / matrix:get nitrite_matrix 4 15) ^ 2) matrix:set nitrite_matrix 5 16 ((matrix:get nitrite_matrix 3 16 / matrix:get nitrite_matrix 4 16) ^ 2) let sum_nitrite_square sum matrix:get-row nitrite_matrix 5 let nitrite_square sqrt ( (1 / (length matrix:get-row nitrite_matrix 5)) * sum_nitrite_square) set GRI_nitrite (1 + nitrite_square) / (1 - nitrite_square) matrix:set nitrous_oxide_matrix 3 0 (matrix:get nitrous_oxide_matrix 1 0 - matrix:get nitrous_oxide_matrix 2 0) matrix:set nitrous_oxide_matrix 4 0 (matrix:get nitrous_oxide_matrix 1 0 + matrix:get nitrous_oxide_matrix 2 0) matrix:set nitrous_oxide_matrix 3 1 (matrix:get nitrous_oxide_matrix 1 1 - matrix:get nitrous_oxide_matrix 2 1) matrix:set nitrous_oxide_matrix 4 1 (matrix:get nitrous_oxide_matrix 1 1 + matrix:get nitrous_oxide_matrix 2 1) matrix:set nitrous_oxide_matrix 3 2 (matrix:get nitrous_oxide_matrix 1 2 - matrix:get nitrous_oxide_matrix 2 2) matrix:set nitrous_oxide_matrix 4 2 (matrix:get nitrous_oxide_matrix 1 2 + matrix:get nitrous_oxide_matrix 2 2) matrix:set nitrous_oxide_matrix 3 3 (matrix:get nitrous_oxide_matrix 1 3 - matrix:get nitrous_oxide_matrix 2 3) matrix:set nitrous_oxide_matrix 4 3 (matrix:get nitrous_oxide_matrix 1 3 + matrix:get nitrous_oxide_matrix 2 3) matrix:set nitrous_oxide_matrix 3 4 (matrix:get nitrous_oxide_matrix 1 4 - matrix:get nitrous_oxide_matrix 2 4) matrix:set nitrous_oxide_matrix 4 4 (matrix:get nitrous_oxide_matrix 1 4 + matrix:get nitrous_oxide_matrix 2 4) matrix:set nitrous_oxide_matrix 3 5 (matrix:get nitrous_oxide_matrix 1 5 - matrix:get nitrous_oxide_matrix 2 5) matrix:set nitrous_oxide_matrix 4 5 (matrix:get nitrous_oxide_matrix 1 5 + matrix:get nitrous_oxide_matrix 2 5) matrix:set nitrous_oxide_matrix 3 6 (matrix:get nitrous_oxide_matrix 1 6 - matrix:get nitrous_oxide_matrix 2 6) matrix:set nitrous_oxide_matrix 4 6 (matrix:get nitrous_oxide_matrix 1 6 + matrix:get nitrous_oxide_matrix 2 6) matrix:set nitrous_oxide_matrix 3 7 (matrix:get nitrous_oxide_matrix 1 7 - matrix:get nitrous_oxide_matrix 2 7) matrix:set nitrous_oxide_matrix 4 7 (matrix:get nitrous_oxide_matrix 1 7 + matrix:get nitrous_oxide_matrix 2 7) matrix:set nitrous_oxide_matrix 3 8 (matrix:get nitrous_oxide_matrix 1 8 - matrix:get nitrous_oxide_matrix 2 8) matrix:set nitrous_oxide_matrix 4 8 (matrix:get nitrous_oxide_matrix 1 8 + matrix:get nitrous_oxide_matrix 2 8) matrix:set nitrous_oxide_matrix 3 9 (matrix:get nitrous_oxide_matrix 1 9 - matrix:get nitrous_oxide_matrix 2 9) matrix:set nitrous_oxide_matrix 4 9 (matrix:get nitrous_oxide_matrix 1 9 + matrix:get nitrous_oxide_matrix 2 9) matrix:set nitrous_oxide_matrix 3 10 (matrix:get nitrous_oxide_matrix 1 10 - matrix:get nitrous_oxide_matrix 2 10) matrix:set nitrous_oxide_matrix 4 10 (matrix:get nitrous_oxide_matrix 1 10 + matrix:get nitrous_oxide_matrix 2 10) matrix:set nitrous_oxide_matrix 3 11 (matrix:get nitrous_oxide_matrix 1 11 - matrix:get nitrous_oxide_matrix 2 11) matrix:set nitrous_oxide_matrix 4 11 (matrix:get nitrous_oxide_matrix 1 11 + matrix:get nitrous_oxide_matrix 2 11) matrix:set nitrous_oxide_matrix 3 12 (matrix:get nitrous_oxide_matrix 1 12 - matrix:get nitrous_oxide_matrix 2 12) matrix:set nitrous_oxide_matrix 4 12 (matrix:get nitrous_oxide_matrix 1 12 + matrix:get nitrous_oxide_matrix 2 12) matrix:set nitrous_oxide_matrix 5 0 ((matrix:get nitrous_oxide_matrix 3 0 / matrix:get nitrous_oxide_matrix 4 0) ^ 2) matrix:set nitrous_oxide_matrix 5 1 ((matrix:get nitrous_oxide_matrix 3 1 / matrix:get nitrous_oxide_matrix 4 1) ^ 2) matrix:set nitrous_oxide_matrix 5 2 ((matrix:get nitrous_oxide_matrix 3 2 / matrix:get nitrous_oxide_matrix 4 2) ^ 2) matrix:set nitrous_oxide_matrix 5 3 ((matrix:get nitrous_oxide_matrix 3 3 / matrix:get nitrous_oxide_matrix 4 3) ^ 2) matrix:set nitrous_oxide_matrix 5 4 ((matrix:get nitrous_oxide_matrix 3 4 / matrix:get nitrous_oxide_matrix 4 4) ^ 2) matrix:set nitrous_oxide_matrix 5 5 ((matrix:get nitrous_oxide_matrix 3 5 / matrix:get nitrous_oxide_matrix 4 5) ^ 2) matrix:set nitrous_oxide_matrix 5 6 ((matrix:get nitrous_oxide_matrix 3 6 / matrix:get nitrous_oxide_matrix 4 6) ^ 2) matrix:set nitrous_oxide_matrix 5 7 ((matrix:get nitrous_oxide_matrix 3 7 / matrix:get nitrous_oxide_matrix 4 7) ^ 2) matrix:set nitrous_oxide_matrix 5 8 ((matrix:get nitrous_oxide_matrix 3 8 / matrix:get nitrous_oxide_matrix 4 8) ^ 2) matrix:set nitrous_oxide_matrix 5 9 ((matrix:get nitrous_oxide_matrix 3 9 / matrix:get nitrous_oxide_matrix 4 9) ^ 2) matrix:set nitrous_oxide_matrix 5 10 ((matrix:get nitrous_oxide_matrix 3 10 / matrix:get nitrous_oxide_matrix 4 10) ^ 2) matrix:set nitrous_oxide_matrix 5 11 ((matrix:get nitrous_oxide_matrix 3 11 / matrix:get nitrous_oxide_matrix 4 11) ^ 2) matrix:set nitrous_oxide_matrix 5 12 ((matrix:get nitrous_oxide_matrix 3 12 / matrix:get nitrous_oxide_matrix 4 12) ^ 2) let sum_nitrous_oxide_square sum matrix:get-row nitrous_oxide_matrix 5 let nitrous_oxide_square sqrt ( (1 / (length matrix:get-row nitrous_oxide_matrix 5)) * sum_nitrous_oxide_square) set GRI_nitrous_oxide (1 + nitrous_oxide_square) / (1 - nitrous_oxide_square) Fitness-Calculation ] ; end procedure succinate high P.denitrificans ] ; End procedure bacteria P. denitrificans if Denitrifying_bacterium = "A._xylosoxidans" [ if Experiment = "Succ_Low/Nitrate_High"[ matrix:set biomass_matrix 3 0 (matrix:get biomass_matrix 1 0 - matrix:get biomass_matrix 2 0) matrix:set biomass_matrix 4 0 (matrix:get biomass_matrix 1 0 + matrix:get biomass_matrix 2 0) matrix:set biomass_matrix 3 1 (matrix:get biomass_matrix 1 1 - matrix:get biomass_matrix 2 1) matrix:set biomass_matrix 4 1 (matrix:get biomass_matrix 1 1 + matrix:get biomass_matrix 2 1) matrix:set biomass_matrix 3 2 (matrix:get biomass_matrix 1 2 - matrix:get biomass_matrix 2 2) matrix:set biomass_matrix 4 2 (matrix:get biomass_matrix 1 2 + matrix:get biomass_matrix 2 2) matrix:set biomass_matrix 3 3 (matrix:get biomass_matrix 1 3 - matrix:get biomass_matrix 2 3) matrix:set biomass_matrix 4 3 (matrix:get biomass_matrix 1 3 + matrix:get biomass_matrix 2 3) matrix:set biomass_matrix 3 4 (matrix:get biomass_matrix 1 4 - matrix:get biomass_matrix 2 4) matrix:set biomass_matrix 4 4 (matrix:get biomass_matrix 1 4 + matrix:get biomass_matrix 2 4) matrix:set biomass_matrix 3 5 (matrix:get biomass_matrix 1 5 - matrix:get biomass_matrix 2 5) matrix:set biomass_matrix 4 5 (matrix:get biomass_matrix 1 5 + matrix:get biomass_matrix 2 5) matrix:set biomass_matrix 3 6 (matrix:get biomass_matrix 1 6 - matrix:get biomass_matrix 2 6) matrix:set biomass_matrix 4 6 (matrix:get biomass_matrix 1 6 + matrix:get biomass_matrix 2 6) matrix:set biomass_matrix 3 7 (matrix:get biomass_matrix 1 7 - matrix:get biomass_matrix 2 7) matrix:set biomass_matrix 4 7 (matrix:get biomass_matrix 1 7 + matrix:get biomass_matrix 2 7) matrix:set biomass_matrix 3 8 (matrix:get biomass_matrix 1 8 - matrix:get biomass_matrix 2 8) matrix:set biomass_matrix 4 8 (matrix:get biomass_matrix 1 8 + matrix:get biomass_matrix 2 8) matrix:set biomass_matrix 3 9 (matrix:get biomass_matrix 1 9 - matrix:get biomass_matrix 2 9) matrix:set biomass_matrix 4 9 (matrix:get biomass_matrix 1 9 + matrix:get biomass_matrix 2 9) matrix:set biomass_matrix 3 10 (matrix:get biomass_matrix 1 10 - matrix:get biomass_matrix 2 10) matrix:set biomass_matrix 4 10 (matrix:get biomass_matrix 1 10 + matrix:get biomass_matrix 2 10) matrix:set biomass_matrix 5 0 ((matrix:get biomass_matrix 3 0 / matrix:get biomass_matrix 4 0) ^ 2) matrix:set biomass_matrix 5 1 ((matrix:get biomass_matrix 3 1 / matrix:get biomass_matrix 4 1) ^ 2) matrix:set biomass_matrix 5 2 ((matrix:get biomass_matrix 3 2 / matrix:get biomass_matrix 4 2) ^ 2) matrix:set biomass_matrix 5 3 ((matrix:get biomass_matrix 3 3 / matrix:get biomass_matrix 4 3) ^ 2) matrix:set biomass_matrix 5 4 ((matrix:get biomass_matrix 3 4 / matrix:get biomass_matrix 4 4) ^ 2) matrix:set biomass_matrix 5 5 ((matrix:get biomass_matrix 3 5 / matrix:get biomass_matrix 4 5) ^ 2) matrix:set biomass_matrix 5 6 ((matrix:get biomass_matrix 3 6 / matrix:get biomass_matrix 4 6) ^ 2) matrix:set biomass_matrix 5 7 ((matrix:get biomass_matrix 3 7 / matrix:get biomass_matrix 4 7) ^ 2) matrix:set biomass_matrix 5 8 ((matrix:get biomass_matrix 3 8 / matrix:get biomass_matrix 4 8) ^ 2) matrix:set biomass_matrix 5 9 ((matrix:get biomass_matrix 3 9 / matrix:get biomass_matrix 4 9) ^ 2) matrix:set biomass_matrix 5 10 ((matrix:get biomass_matrix 3 10 / matrix:get biomass_matrix 4 10) ^ 2) let sum_biomass_square sum matrix:get-row biomass_matrix 5 let biomass_square sqrt ( (1 / (length matrix:get-row biomass_matrix 5)) * sum_biomass_square) set GRI_biomass (1 + biomass_square) / (1 - biomass_square) matrix:set nitrate_matrix 3 0 (matrix:get nitrate_matrix 1 0 - matrix:get nitrate_matrix 2 0) matrix:set nitrate_matrix 4 0 (matrix:get nitrate_matrix 1 0 + matrix:get nitrate_matrix 2 0) matrix:set nitrate_matrix 3 1 (matrix:get nitrate_matrix 1 1 - matrix:get nitrate_matrix 2 1) matrix:set nitrate_matrix 4 1 (matrix:get nitrate_matrix 1 1 + matrix:get nitrate_matrix 2 1) matrix:set nitrate_matrix 3 2 (matrix:get nitrate_matrix 1 2 - matrix:get nitrate_matrix 2 2) matrix:set nitrate_matrix 4 2 (matrix:get nitrate_matrix 1 2 + matrix:get nitrate_matrix 2 2) matrix:set nitrate_matrix 3 3 (matrix:get nitrate_matrix 1 3 - matrix:get nitrate_matrix 2 3) matrix:set nitrate_matrix 4 3 (matrix:get nitrate_matrix 1 3 + matrix:get nitrate_matrix 2 3) matrix:set nitrate_matrix 3 4 (matrix:get nitrate_matrix 1 4 - matrix:get nitrate_matrix 2 4) matrix:set nitrate_matrix 4 4 (matrix:get nitrate_matrix 1 4 + matrix:get nitrate_matrix 2 4) matrix:set nitrate_matrix 3 5 (matrix:get nitrate_matrix 1 5 - matrix:get nitrate_matrix 2 5) matrix:set nitrate_matrix 4 5 (matrix:get nitrate_matrix 1 5 + matrix:get nitrate_matrix 2 5) matrix:set nitrate_matrix 3 6 (matrix:get nitrate_matrix 1 6 - matrix:get nitrate_matrix 2 6) matrix:set nitrate_matrix 4 6 (matrix:get nitrate_matrix 1 6 + matrix:get nitrate_matrix 2 6) matrix:set nitrate_matrix 3 7 (matrix:get nitrate_matrix 1 7 - matrix:get nitrate_matrix 2 7) matrix:set nitrate_matrix 4 7 (matrix:get nitrate_matrix 1 7 + matrix:get nitrate_matrix 2 7) matrix:set nitrate_matrix 3 8 (matrix:get nitrate_matrix 1 8 - matrix:get nitrate_matrix 2 8) matrix:set nitrate_matrix 4 8 (matrix:get nitrate_matrix 1 8 + matrix:get nitrate_matrix 2 8) matrix:set nitrate_matrix 3 9 (matrix:get nitrate_matrix 1 9 - matrix:get nitrate_matrix 2 9) matrix:set nitrate_matrix 4 9 (matrix:get nitrate_matrix 1 9 + matrix:get nitrate_matrix 2 9) matrix:set nitrate_matrix 3 10 (matrix:get nitrate_matrix 1 10 - matrix:get nitrate_matrix 2 10) matrix:set nitrate_matrix 4 10 (matrix:get nitrate_matrix 1 10 + matrix:get nitrate_matrix 2 10) matrix:set nitrate_matrix 3 11 (matrix:get nitrate_matrix 1 11 - matrix:get nitrate_matrix 2 11) matrix:set nitrate_matrix 4 11 (matrix:get nitrate_matrix 1 11 + matrix:get nitrate_matrix 2 11) matrix:set nitrate_matrix 5 0 ((matrix:get nitrate_matrix 3 0 / matrix:get nitrate_matrix 4 0) ^ 2) matrix:set nitrate_matrix 5 1 ((matrix:get nitrate_matrix 3 1 / matrix:get nitrate_matrix 4 1) ^ 2) matrix:set nitrate_matrix 5 2 ((matrix:get nitrate_matrix 3 2 / matrix:get nitrate_matrix 4 2) ^ 2) matrix:set nitrate_matrix 5 3 ((matrix:get nitrate_matrix 3 3 / matrix:get nitrate_matrix 4 3) ^ 2) matrix:set nitrate_matrix 5 4 ((matrix:get nitrate_matrix 3 4 / matrix:get nitrate_matrix 4 4) ^ 2) matrix:set nitrate_matrix 5 5 ((matrix:get nitrate_matrix 3 5 / matrix:get nitrate_matrix 4 5) ^ 2) matrix:set nitrate_matrix 5 6 ((matrix:get nitrate_matrix 3 6 / matrix:get nitrate_matrix 4 6) ^ 2) matrix:set nitrate_matrix 5 7 ((matrix:get nitrate_matrix 3 7 / matrix:get nitrate_matrix 4 7) ^ 2) matrix:set nitrate_matrix 5 8 ((matrix:get nitrate_matrix 3 8 / matrix:get nitrate_matrix 4 8) ^ 2) matrix:set nitrate_matrix 5 9 ((matrix:get nitrate_matrix 3 9 / matrix:get nitrate_matrix 4 9) ^ 2) matrix:set nitrate_matrix 5 10 ((matrix:get nitrate_matrix 3 10 / matrix:get nitrate_matrix 4 10) ^ 2) matrix:set nitrate_matrix 5 11 ((matrix:get nitrate_matrix 3 11 / matrix:get nitrate_matrix 4 11) ^ 2) let sum_nitrate_square sum matrix:get-row nitrate_matrix 5 let nitrate_square sqrt ( (1 / (length matrix:get-row nitrate_matrix 5)) * sum_nitrate_square) set GRI_nitrate (1 + nitrate_square) / (1 - nitrate_square) matrix:set nitrite_matrix 3 0 (matrix:get nitrite_matrix 1 0 - matrix:get nitrite_matrix 2 0) matrix:set nitrite_matrix 4 0 (matrix:get nitrite_matrix 1 0 + matrix:get nitrite_matrix 2 0) matrix:set nitrite_matrix 3 1 (matrix:get nitrite_matrix 1 1 - matrix:get nitrite_matrix 2 1) matrix:set nitrite_matrix 4 1 (matrix:get nitrite_matrix 1 1 + matrix:get nitrite_matrix 2 1) matrix:set nitrite_matrix 3 2 (matrix:get nitrite_matrix 1 2 - matrix:get nitrite_matrix 2 2) matrix:set nitrite_matrix 4 2 (matrix:get nitrite_matrix 1 2 + matrix:get nitrite_matrix 2 2) matrix:set nitrite_matrix 3 3 (matrix:get nitrite_matrix 1 3 - matrix:get nitrite_matrix 2 3) matrix:set nitrite_matrix 4 3 (matrix:get nitrite_matrix 1 3 + matrix:get nitrite_matrix 2 3) matrix:set nitrite_matrix 3 4 (matrix:get nitrite_matrix 1 4 - matrix:get nitrite_matrix 2 4) matrix:set nitrite_matrix 4 4 (matrix:get nitrite_matrix 1 4 + matrix:get nitrite_matrix 2 4) matrix:set nitrite_matrix 3 5 (matrix:get nitrite_matrix 1 5 - matrix:get nitrite_matrix 2 5) matrix:set nitrite_matrix 4 5 (matrix:get nitrite_matrix 1 5 + matrix:get nitrite_matrix 2 5) matrix:set nitrite_matrix 3 6 (matrix:get nitrite_matrix 1 6 - matrix:get nitrite_matrix 2 6) matrix:set nitrite_matrix 4 6 (matrix:get nitrite_matrix 1 6 + matrix:get nitrite_matrix 2 6) matrix:set nitrite_matrix 3 7 (matrix:get nitrite_matrix 1 7 - matrix:get nitrite_matrix 2 7) matrix:set nitrite_matrix 4 7 (matrix:get nitrite_matrix 1 7 + matrix:get nitrite_matrix 2 7) matrix:set nitrite_matrix 3 8 (matrix:get nitrite_matrix 1 8 - matrix:get nitrite_matrix 2 8) matrix:set nitrite_matrix 4 8 (matrix:get nitrite_matrix 1 8 + matrix:get nitrite_matrix 2 8) matrix:set nitrite_matrix 3 9 (matrix:get nitrite_matrix 1 9 - matrix:get nitrite_matrix 2 9) matrix:set nitrite_matrix 4 9 (matrix:get nitrite_matrix 1 9 + matrix:get nitrite_matrix 2 9) matrix:set nitrite_matrix 3 10 (matrix:get nitrite_matrix 1 10 - matrix:get nitrite_matrix 2 10) matrix:set nitrite_matrix 4 10 (matrix:get nitrite_matrix 1 10 + matrix:get nitrite_matrix 2 10) matrix:set nitrite_matrix 3 11 (matrix:get nitrite_matrix 1 11 - matrix:get nitrite_matrix 2 11) matrix:set nitrite_matrix 4 11 (matrix:get nitrite_matrix 1 11 + matrix:get nitrite_matrix 2 11) matrix:set nitrite_matrix 3 12 (matrix:get nitrite_matrix 1 12 - matrix:get nitrite_matrix 2 12) matrix:set nitrite_matrix 4 12 (matrix:get nitrite_matrix 1 12 + matrix:get nitrite_matrix 2 12) matrix:set nitrite_matrix 5 0 ((matrix:get nitrite_matrix 3 0 / matrix:get nitrite_matrix 4 0) ^ 2) matrix:set nitrite_matrix 5 1 ((matrix:get nitrite_matrix 3 1 / matrix:get nitrite_matrix 4 1) ^ 2) matrix:set nitrite_matrix 5 2 ((matrix:get nitrite_matrix 3 2 / matrix:get nitrite_matrix 4 2) ^ 2) matrix:set nitrite_matrix 5 3 ((matrix:get nitrite_matrix 3 3 / matrix:get nitrite_matrix 4 3) ^ 2) matrix:set nitrite_matrix 5 4 ((matrix:get nitrite_matrix 3 4 / matrix:get nitrite_matrix 4 4) ^ 2) matrix:set nitrite_matrix 5 5 ((matrix:get nitrite_matrix 3 5 / matrix:get nitrite_matrix 4 5) ^ 2) matrix:set nitrite_matrix 5 6 ((matrix:get nitrite_matrix 3 6 / matrix:get nitrite_matrix 4 6) ^ 2) matrix:set nitrite_matrix 5 7 ((matrix:get nitrite_matrix 3 7 / matrix:get nitrite_matrix 4 7) ^ 2) matrix:set nitrite_matrix 5 8 ((matrix:get nitrite_matrix 3 8 / matrix:get nitrite_matrix 4 8) ^ 2) matrix:set nitrite_matrix 5 9 ((matrix:get nitrite_matrix 3 9 / matrix:get nitrite_matrix 4 9) ^ 2) matrix:set nitrite_matrix 5 10 ((matrix:get nitrite_matrix 3 10 / matrix:get nitrite_matrix 4 10) ^ 2) matrix:set nitrite_matrix 5 11 ((matrix:get nitrite_matrix 3 11 / matrix:get nitrite_matrix 4 11) ^ 2) matrix:set nitrite_matrix 5 12 ((matrix:get nitrite_matrix 3 12 / matrix:get nitrite_matrix 4 12) ^ 2) let sum_nitrite_square sum matrix:get-row nitrite_matrix 5 let nitrite_square sqrt ( (1 / (length matrix:get-row nitrite_matrix 5)) * sum_nitrite_square) set GRI_nitrite (1 + nitrite_square) / (1 - nitrite_square) matrix:set nitrous_oxide_matrix 3 0 (matrix:get nitrous_oxide_matrix 1 0 - matrix:get nitrous_oxide_matrix 2 0) matrix:set nitrous_oxide_matrix 4 0 (matrix:get nitrous_oxide_matrix 1 0 + matrix:get nitrous_oxide_matrix 2 0) matrix:set nitrous_oxide_matrix 3 1 (matrix:get nitrous_oxide_matrix 1 1 - matrix:get nitrous_oxide_matrix 2 1) matrix:set nitrous_oxide_matrix 4 1 (matrix:get nitrous_oxide_matrix 1 1 + matrix:get nitrous_oxide_matrix 2 1) matrix:set nitrous_oxide_matrix 3 2 (matrix:get nitrous_oxide_matrix 1 2 - matrix:get nitrous_oxide_matrix 2 2) matrix:set nitrous_oxide_matrix 4 2 (matrix:get nitrous_oxide_matrix 1 2 + matrix:get nitrous_oxide_matrix 2 2) matrix:set nitrous_oxide_matrix 3 3 (matrix:get nitrous_oxide_matrix 1 3 - matrix:get nitrous_oxide_matrix 2 3) matrix:set nitrous_oxide_matrix 4 3 (matrix:get nitrous_oxide_matrix 1 3 + matrix:get nitrous_oxide_matrix 2 3) matrix:set nitrous_oxide_matrix 3 4 (matrix:get nitrous_oxide_matrix 1 4 - matrix:get nitrous_oxide_matrix 2 4) matrix:set nitrous_oxide_matrix 4 4 (matrix:get nitrous_oxide_matrix 1 4 + matrix:get nitrous_oxide_matrix 2 4) matrix:set nitrous_oxide_matrix 3 5 (matrix:get nitrous_oxide_matrix 1 5 - matrix:get nitrous_oxide_matrix 2 5) matrix:set nitrous_oxide_matrix 4 5 (matrix:get nitrous_oxide_matrix 1 5 + matrix:get nitrous_oxide_matrix 2 5) matrix:set nitrous_oxide_matrix 3 6 (matrix:get nitrous_oxide_matrix 1 6 - matrix:get nitrous_oxide_matrix 2 6) matrix:set nitrous_oxide_matrix 4 6 (matrix:get nitrous_oxide_matrix 1 6 + matrix:get nitrous_oxide_matrix 2 6) matrix:set nitrous_oxide_matrix 3 7 (matrix:get nitrous_oxide_matrix 1 7 - matrix:get nitrous_oxide_matrix 2 7) matrix:set nitrous_oxide_matrix 4 7 (matrix:get nitrous_oxide_matrix 1 7 + matrix:get nitrous_oxide_matrix 2 7) matrix:set nitrous_oxide_matrix 3 8 (matrix:get nitrous_oxide_matrix 1 8 - matrix:get nitrous_oxide_matrix 2 8) matrix:set nitrous_oxide_matrix 4 8 (matrix:get nitrous_oxide_matrix 1 8 + matrix:get nitrous_oxide_matrix 2 8) matrix:set nitrous_oxide_matrix 3 9 (matrix:get nitrous_oxide_matrix 1 9 - matrix:get nitrous_oxide_matrix 2 9) matrix:set nitrous_oxide_matrix 4 9 (matrix:get nitrous_oxide_matrix 1 9 + matrix:get nitrous_oxide_matrix 2 9) matrix:set nitrous_oxide_matrix 3 10 (matrix:get nitrous_oxide_matrix 1 10 - matrix:get nitrous_oxide_matrix 2 10) matrix:set nitrous_oxide_matrix 4 10 (matrix:get nitrous_oxide_matrix 1 10 + matrix:get nitrous_oxide_matrix 2 10) matrix:set nitrous_oxide_matrix 3 11 (matrix:get nitrous_oxide_matrix 1 11 - matrix:get nitrous_oxide_matrix 2 11) matrix:set nitrous_oxide_matrix 4 11 (matrix:get nitrous_oxide_matrix 1 11 + matrix:get nitrous_oxide_matrix 2 11) matrix:set nitrous_oxide_matrix 5 0 ((matrix:get nitrous_oxide_matrix 3 0 / matrix:get nitrous_oxide_matrix 4 0) ^ 2) matrix:set nitrous_oxide_matrix 5 1 ((matrix:get nitrous_oxide_matrix 3 1 / matrix:get nitrous_oxide_matrix 4 1) ^ 2) matrix:set nitrous_oxide_matrix 5 2 ((matrix:get nitrous_oxide_matrix 3 2 / matrix:get nitrous_oxide_matrix 4 2) ^ 2) matrix:set nitrous_oxide_matrix 5 3 ((matrix:get nitrous_oxide_matrix 3 3 / matrix:get nitrous_oxide_matrix 4 3) ^ 2) matrix:set nitrous_oxide_matrix 5 4 ((matrix:get nitrous_oxide_matrix 3 4 / matrix:get nitrous_oxide_matrix 4 4) ^ 2) matrix:set nitrous_oxide_matrix 5 5 ((matrix:get nitrous_oxide_matrix 3 5 / matrix:get nitrous_oxide_matrix 4 5) ^ 2) matrix:set nitrous_oxide_matrix 5 6 ((matrix:get nitrous_oxide_matrix 3 6 / matrix:get nitrous_oxide_matrix 4 6) ^ 2) matrix:set nitrous_oxide_matrix 5 7 ((matrix:get nitrous_oxide_matrix 3 7 / matrix:get nitrous_oxide_matrix 4 7) ^ 2) matrix:set nitrous_oxide_matrix 5 8 ((matrix:get nitrous_oxide_matrix 3 8 / matrix:get nitrous_oxide_matrix 4 8) ^ 2) matrix:set nitrous_oxide_matrix 5 9 ((matrix:get nitrous_oxide_matrix 3 9 / matrix:get nitrous_oxide_matrix 4 9) ^ 2) matrix:set nitrous_oxide_matrix 5 10 ((matrix:get nitrous_oxide_matrix 3 10 / matrix:get nitrous_oxide_matrix 4 10) ^ 2) matrix:set nitrous_oxide_matrix 5 11 ((matrix:get nitrous_oxide_matrix 3 11 / matrix:get nitrous_oxide_matrix 4 11) ^ 2) let sum_nitrous_oxide_square sum matrix:get-row nitrous_oxide_matrix 5 let nitrous_oxide_square sqrt ( (1 / (length matrix:get-row nitrous_oxide_matrix 5)) * sum_nitrous_oxide_square) set GRI_nitrous_oxide (1 + nitrous_oxide_square) / (1 - nitrous_oxide_square) Fitness-Calculation ] ; end procedure succinate low A. Xylosoxidans if Experiment = "Succ_High/Nitrate_Low"[ matrix:set biomass_matrix 3 0 (matrix:get biomass_matrix 1 0 - matrix:get biomass_matrix 2 0) matrix:set biomass_matrix 4 0 (matrix:get biomass_matrix 1 0 + matrix:get biomass_matrix 2 0) matrix:set biomass_matrix 3 1 (matrix:get biomass_matrix 1 1 - matrix:get biomass_matrix 2 1) matrix:set biomass_matrix 4 1 (matrix:get biomass_matrix 1 1 + matrix:get biomass_matrix 2 1) matrix:set biomass_matrix 3 2 (matrix:get biomass_matrix 1 2 - matrix:get biomass_matrix 2 2) matrix:set biomass_matrix 4 2 (matrix:get biomass_matrix 1 2 + matrix:get biomass_matrix 2 2) matrix:set biomass_matrix 3 3 (matrix:get biomass_matrix 1 3 - matrix:get biomass_matrix 2 3) matrix:set biomass_matrix 4 3 (matrix:get biomass_matrix 1 3 + matrix:get biomass_matrix 2 3) matrix:set biomass_matrix 3 4 (matrix:get biomass_matrix 1 4 - matrix:get biomass_matrix 2 4) matrix:set biomass_matrix 4 4 (matrix:get biomass_matrix 1 4 + matrix:get biomass_matrix 2 4) matrix:set biomass_matrix 3 5 (matrix:get biomass_matrix 1 5 - matrix:get biomass_matrix 2 5) matrix:set biomass_matrix 4 5 (matrix:get biomass_matrix 1 5 + matrix:get biomass_matrix 2 5) matrix:set biomass_matrix 3 6 (matrix:get biomass_matrix 1 6 - matrix:get biomass_matrix 2 6) matrix:set biomass_matrix 4 6 (matrix:get biomass_matrix 1 6 + matrix:get biomass_matrix 2 6) matrix:set biomass_matrix 3 7 (matrix:get biomass_matrix 1 7 - matrix:get biomass_matrix 2 7) matrix:set biomass_matrix 4 7 (matrix:get biomass_matrix 1 7 + matrix:get biomass_matrix 2 7) matrix:set biomass_matrix 3 8 (matrix:get biomass_matrix 1 8 - matrix:get biomass_matrix 2 8) matrix:set biomass_matrix 4 8 (matrix:get biomass_matrix 1 8 + matrix:get biomass_matrix 2 8) matrix:set biomass_matrix 3 9 (matrix:get biomass_matrix 1 9 - matrix:get biomass_matrix 2 9) matrix:set biomass_matrix 4 9 (matrix:get biomass_matrix 1 9 + matrix:get biomass_matrix 2 9) matrix:set biomass_matrix 3 10 (matrix:get biomass_matrix 1 10 - matrix:get biomass_matrix 2 10) matrix:set biomass_matrix 4 10 (matrix:get biomass_matrix 1 10 + matrix:get biomass_matrix 2 10) matrix:set biomass_matrix 3 11 (matrix:get biomass_matrix 1 11 - matrix:get biomass_matrix 2 11) matrix:set biomass_matrix 4 11 (matrix:get biomass_matrix 1 11 + matrix:get biomass_matrix 2 11) matrix:set biomass_matrix 3 12 (matrix:get biomass_matrix 1 12 - matrix:get biomass_matrix 2 12) matrix:set biomass_matrix 4 12 (matrix:get biomass_matrix 1 12 + matrix:get biomass_matrix 2 12) matrix:set biomass_matrix 3 13 (matrix:get biomass_matrix 1 13 - matrix:get biomass_matrix 2 13) matrix:set biomass_matrix 4 13 (matrix:get biomass_matrix 1 13 + matrix:get biomass_matrix 2 13) matrix:set biomass_matrix 3 14 (matrix:get biomass_matrix 1 14 - matrix:get biomass_matrix 2 14) matrix:set biomass_matrix 4 14 (matrix:get biomass_matrix 1 14 + matrix:get biomass_matrix 2 14) matrix:set biomass_matrix 5 0 ((matrix:get biomass_matrix 3 0 / matrix:get biomass_matrix 4 0) ^ 2) matrix:set biomass_matrix 5 1 ((matrix:get biomass_matrix 3 1 / matrix:get biomass_matrix 4 1) ^ 2) matrix:set biomass_matrix 5 2 ((matrix:get biomass_matrix 3 2 / matrix:get biomass_matrix 4 2) ^ 2) matrix:set biomass_matrix 5 3 ((matrix:get biomass_matrix 3 3 / matrix:get biomass_matrix 4 3) ^ 2) matrix:set biomass_matrix 5 4 ((matrix:get biomass_matrix 3 4 / matrix:get biomass_matrix 4 4) ^ 2) matrix:set biomass_matrix 5 5 ((matrix:get biomass_matrix 3 5 / matrix:get biomass_matrix 4 5) ^ 2) matrix:set biomass_matrix 5 6 ((matrix:get biomass_matrix 3 6 / matrix:get biomass_matrix 4 6) ^ 2) matrix:set biomass_matrix 5 7 ((matrix:get biomass_matrix 3 7 / matrix:get biomass_matrix 4 7) ^ 2) matrix:set biomass_matrix 5 8 ((matrix:get biomass_matrix 3 8 / matrix:get biomass_matrix 4 8) ^ 2) matrix:set biomass_matrix 5 9 ((matrix:get biomass_matrix 3 9 / matrix:get biomass_matrix 4 9) ^ 2) matrix:set biomass_matrix 5 10 ((matrix:get biomass_matrix 3 10 / matrix:get biomass_matrix 4 10) ^ 2) matrix:set biomass_matrix 5 11 ((matrix:get biomass_matrix 3 11 / matrix:get biomass_matrix 4 11) ^ 2) matrix:set biomass_matrix 5 12 ((matrix:get biomass_matrix 3 12 / matrix:get biomass_matrix 4 12) ^ 2) matrix:set biomass_matrix 5 13 ((matrix:get biomass_matrix 3 13 / matrix:get biomass_matrix 4 13) ^ 2) matrix:set biomass_matrix 5 14 ((matrix:get biomass_matrix 3 14 / matrix:get biomass_matrix 4 14) ^ 2) let sum_biomass_square sum matrix:get-row biomass_matrix 5 let biomass_square sqrt ( (1 / (length matrix:get-row biomass_matrix 5)) * sum_biomass_square) set GRI_biomass (1 + biomass_square) / (1 - biomass_square) matrix:set nitrate_matrix 3 0 (matrix:get nitrate_matrix 1 0 - matrix:get nitrate_matrix 2 0) matrix:set nitrate_matrix 4 0 (matrix:get nitrate_matrix 1 0 + matrix:get nitrate_matrix 2 0) matrix:set nitrate_matrix 3 1 (matrix:get nitrate_matrix 1 1 - matrix:get nitrate_matrix 2 1) matrix:set nitrate_matrix 4 1 (matrix:get nitrate_matrix 1 1 + matrix:get nitrate_matrix 2 1) matrix:set nitrate_matrix 3 2 (matrix:get nitrate_matrix 1 2 - matrix:get nitrate_matrix 2 2) matrix:set nitrate_matrix 4 2 (matrix:get nitrate_matrix 1 2 + matrix:get nitrate_matrix 2 2) matrix:set nitrate_matrix 3 3 (matrix:get nitrate_matrix 1 3 - matrix:get nitrate_matrix 2 3) matrix:set nitrate_matrix 4 3 (matrix:get nitrate_matrix 1 3 + matrix:get nitrate_matrix 2 3) matrix:set nitrate_matrix 3 4 (matrix:get nitrate_matrix 1 4 - matrix:get nitrate_matrix 2 4) matrix:set nitrate_matrix 4 4 (matrix:get nitrate_matrix 1 4 + matrix:get nitrate_matrix 2 4) matrix:set nitrate_matrix 3 5 (matrix:get nitrate_matrix 1 5 - matrix:get nitrate_matrix 2 5) matrix:set nitrate_matrix 4 5 (matrix:get nitrate_matrix 1 5 + matrix:get nitrate_matrix 2 5) matrix:set nitrate_matrix 3 6 (matrix:get nitrate_matrix 1 6 - matrix:get nitrate_matrix 2 6) matrix:set nitrate_matrix 4 6 (matrix:get nitrate_matrix 1 6 + matrix:get nitrate_matrix 2 6) matrix:set nitrate_matrix 3 7 (matrix:get nitrate_matrix 1 7 - matrix:get nitrate_matrix 2 7) matrix:set nitrate_matrix 4 7 (matrix:get nitrate_matrix 1 7 + matrix:get nitrate_matrix 2 7) matrix:set nitrate_matrix 3 8 (matrix:get nitrate_matrix 1 8 - matrix:get nitrate_matrix 2 8) matrix:set nitrate_matrix 4 8 (matrix:get nitrate_matrix 1 8 + matrix:get nitrate_matrix 2 8) matrix:set nitrate_matrix 3 9 (matrix:get nitrate_matrix 1 9 - matrix:get nitrate_matrix 2 9) matrix:set nitrate_matrix 4 9 (matrix:get nitrate_matrix 1 9 + matrix:get nitrate_matrix 2 9) matrix:set nitrate_matrix 3 10 (matrix:get nitrate_matrix 1 10 - matrix:get nitrate_matrix 2 10) matrix:set nitrate_matrix 4 10 (matrix:get nitrate_matrix 1 10 + matrix:get nitrate_matrix 2 10) matrix:set nitrate_matrix 3 11 (matrix:get nitrate_matrix 1 11 - matrix:get nitrate_matrix 2 11) matrix:set nitrate_matrix 4 11 (matrix:get nitrate_matrix 1 11 + matrix:get nitrate_matrix 2 11) matrix:set nitrate_matrix 3 12 (matrix:get nitrate_matrix 1 12 - matrix:get nitrate_matrix 2 12) matrix:set nitrate_matrix 4 12 (matrix:get nitrate_matrix 1 12 + matrix:get nitrate_matrix 2 12) matrix:set nitrate_matrix 3 13 (matrix:get nitrate_matrix 1 13 - matrix:get nitrate_matrix 2 13) matrix:set nitrate_matrix 4 13 (matrix:get nitrate_matrix 1 13 + matrix:get nitrate_matrix 2 13) matrix:set nitrate_matrix 5 0 ((matrix:get nitrate_matrix 3 0 / matrix:get nitrate_matrix 4 0) ^ 2) matrix:set nitrate_matrix 5 1 ((matrix:get nitrate_matrix 3 1 / matrix:get nitrate_matrix 4 1) ^ 2) matrix:set nitrate_matrix 5 2 ((matrix:get nitrate_matrix 3 2 / matrix:get nitrate_matrix 4 2) ^ 2) matrix:set nitrate_matrix 5 3 ((matrix:get nitrate_matrix 3 3 / matrix:get nitrate_matrix 4 3) ^ 2) matrix:set nitrate_matrix 5 4 ((matrix:get nitrate_matrix 3 4 / matrix:get nitrate_matrix 4 4) ^ 2) matrix:set nitrate_matrix 5 5 ((matrix:get nitrate_matrix 3 5 / matrix:get nitrate_matrix 4 5) ^ 2) matrix:set nitrate_matrix 5 6 ((matrix:get nitrate_matrix 3 6 / matrix:get nitrate_matrix 4 6) ^ 2) matrix:set nitrate_matrix 5 7 ((matrix:get nitrate_matrix 3 7 / matrix:get nitrate_matrix 4 7) ^ 2) matrix:set nitrate_matrix 5 8 ((matrix:get nitrate_matrix 3 8 / matrix:get nitrate_matrix 4 8) ^ 2) matrix:set nitrate_matrix 5 9 ((matrix:get nitrate_matrix 3 9 / matrix:get nitrate_matrix 4 9) ^ 2) matrix:set nitrate_matrix 5 10 ((matrix:get nitrate_matrix 3 10 / matrix:get nitrate_matrix 4 10) ^ 2) matrix:set nitrate_matrix 5 11 ((matrix:get nitrate_matrix 3 11 / matrix:get nitrate_matrix 4 11) ^ 2) matrix:set nitrate_matrix 5 12 ((matrix:get nitrate_matrix 3 12 / matrix:get nitrate_matrix 4 12) ^ 2) matrix:set nitrate_matrix 5 13 ((matrix:get nitrate_matrix 3 13 / matrix:get nitrate_matrix 4 13) ^ 2) let sum_nitrate_square sum matrix:get-row nitrate_matrix 5 let nitrate_square sqrt ( (1 / (length matrix:get-row nitrate_matrix 5)) * sum_nitrate_square) set GRI_nitrate (1 + nitrate_square) / (1 - nitrate_square) matrix:set nitrite_matrix 3 0 (matrix:get nitrite_matrix 1 0 - matrix:get nitrite_matrix 2 0) matrix:set nitrite_matrix 4 0 (matrix:get nitrite_matrix 1 0 + matrix:get nitrite_matrix 2 0) matrix:set nitrite_matrix 3 1 (matrix:get nitrite_matrix 1 1 - matrix:get nitrite_matrix 2 1) matrix:set nitrite_matrix 4 1 (matrix:get nitrite_matrix 1 1 + matrix:get nitrite_matrix 2 1) matrix:set nitrite_matrix 3 2 (matrix:get nitrite_matrix 1 2 - matrix:get nitrite_matrix 2 2) matrix:set nitrite_matrix 4 2 (matrix:get nitrite_matrix 1 2 + matrix:get nitrite_matrix 2 2) matrix:set nitrite_matrix 3 3 (matrix:get nitrite_matrix 1 3 - matrix:get nitrite_matrix 2 3) matrix:set nitrite_matrix 4 3 (matrix:get nitrite_matrix 1 3 + matrix:get nitrite_matrix 2 3) matrix:set nitrite_matrix 3 4 (matrix:get nitrite_matrix 1 4 - matrix:get nitrite_matrix 2 4) matrix:set nitrite_matrix 4 4 (matrix:get nitrite_matrix 1 4 + matrix:get nitrite_matrix 2 4) matrix:set nitrite_matrix 3 5 (matrix:get nitrite_matrix 1 5 - matrix:get nitrite_matrix 2 5) matrix:set nitrite_matrix 4 5 (matrix:get nitrite_matrix 1 5 + matrix:get nitrite_matrix 2 5) matrix:set nitrite_matrix 3 6 (matrix:get nitrite_matrix 1 6 - matrix:get nitrite_matrix 2 6) matrix:set nitrite_matrix 4 6 (matrix:get nitrite_matrix 1 6 + matrix:get nitrite_matrix 2 6) matrix:set nitrite_matrix 3 7 (matrix:get nitrite_matrix 1 7 - matrix:get nitrite_matrix 2 7) matrix:set nitrite_matrix 4 7 (matrix:get nitrite_matrix 1 7 + matrix:get nitrite_matrix 2 7) matrix:set nitrite_matrix 3 8 (matrix:get nitrite_matrix 1 8 - matrix:get nitrite_matrix 2 8) matrix:set nitrite_matrix 4 8 (matrix:get nitrite_matrix 1 8 + matrix:get nitrite_matrix 2 8) matrix:set nitrite_matrix 3 9 (matrix:get nitrite_matrix 1 9 - matrix:get nitrite_matrix 2 9) matrix:set nitrite_matrix 4 9 (matrix:get nitrite_matrix 1 9 + matrix:get nitrite_matrix 2 9) matrix:set nitrite_matrix 3 10 (matrix:get nitrite_matrix 1 10 - matrix:get nitrite_matrix 2 10) matrix:set nitrite_matrix 4 10 (matrix:get nitrite_matrix 1 10 + matrix:get nitrite_matrix 2 10) matrix:set nitrite_matrix 3 11 (matrix:get nitrite_matrix 1 11 - matrix:get nitrite_matrix 2 11) matrix:set nitrite_matrix 4 11 (matrix:get nitrite_matrix 1 11 + matrix:get nitrite_matrix 2 11) matrix:set nitrite_matrix 3 12 (matrix:get nitrite_matrix 1 12 - matrix:get nitrite_matrix 2 12) matrix:set nitrite_matrix 4 12 (matrix:get nitrite_matrix 1 12 + matrix:get nitrite_matrix 2 12) matrix:set nitrite_matrix 3 13 (matrix:get nitrite_matrix 1 13 - matrix:get nitrite_matrix 2 13) matrix:set nitrite_matrix 4 13 (matrix:get nitrite_matrix 1 13 + matrix:get nitrite_matrix 2 13) matrix:set nitrite_matrix 5 0 ((matrix:get nitrite_matrix 3 0 / matrix:get nitrite_matrix 4 0) ^ 2) matrix:set nitrite_matrix 5 1 ((matrix:get nitrite_matrix 3 1 / matrix:get nitrite_matrix 4 1) ^ 2) matrix:set nitrite_matrix 5 2 ((matrix:get nitrite_matrix 3 2 / matrix:get nitrite_matrix 4 2) ^ 2) matrix:set nitrite_matrix 5 3 ((matrix:get nitrite_matrix 3 3 / matrix:get nitrite_matrix 4 3) ^ 2) matrix:set nitrite_matrix 5 4 ((matrix:get nitrite_matrix 3 4 / matrix:get nitrite_matrix 4 4) ^ 2) matrix:set nitrite_matrix 5 5 ((matrix:get nitrite_matrix 3 5 / matrix:get nitrite_matrix 4 5) ^ 2) matrix:set nitrite_matrix 5 6 ((matrix:get nitrite_matrix 3 6 / matrix:get nitrite_matrix 4 6) ^ 2) matrix:set nitrite_matrix 5 7 ((matrix:get nitrite_matrix 3 7 / matrix:get nitrite_matrix 4 7) ^ 2) matrix:set nitrite_matrix 5 8 ((matrix:get nitrite_matrix 3 8 / matrix:get nitrite_matrix 4 8) ^ 2) matrix:set nitrite_matrix 5 9 ((matrix:get nitrite_matrix 3 9 / matrix:get nitrite_matrix 4 9) ^ 2) matrix:set nitrite_matrix 5 10 ((matrix:get nitrite_matrix 3 10 / matrix:get nitrite_matrix 4 10) ^ 2) matrix:set nitrite_matrix 5 11 ((matrix:get nitrite_matrix 3 11 / matrix:get nitrite_matrix 4 11) ^ 2) matrix:set nitrite_matrix 5 12 ((matrix:get nitrite_matrix 3 12 / matrix:get nitrite_matrix 4 12) ^ 2) matrix:set nitrite_matrix 5 13 ((matrix:get nitrite_matrix 3 13 / matrix:get nitrite_matrix 4 13) ^ 2) let sum_nitrite_square sum matrix:get-row nitrite_matrix 5 let nitrite_square sqrt ( (1 / (length matrix:get-row nitrite_matrix 5)) * sum_nitrite_square) set GRI_nitrite (1 + nitrite_square) / (1 - nitrite_square) matrix:set nitrous_oxide_matrix 3 0 (matrix:get nitrous_oxide_matrix 1 0 - matrix:get nitrous_oxide_matrix 2 0) matrix:set nitrous_oxide_matrix 4 0 (matrix:get nitrous_oxide_matrix 1 0 + matrix:get nitrous_oxide_matrix 2 0) matrix:set nitrous_oxide_matrix 3 1 (matrix:get nitrous_oxide_matrix 1 1 - matrix:get nitrous_oxide_matrix 2 1) matrix:set nitrous_oxide_matrix 4 1 (matrix:get nitrous_oxide_matrix 1 1 + matrix:get nitrous_oxide_matrix 2 1) matrix:set nitrous_oxide_matrix 3 2 (matrix:get nitrous_oxide_matrix 1 2 - matrix:get nitrous_oxide_matrix 2 2) matrix:set nitrous_oxide_matrix 4 2 (matrix:get nitrous_oxide_matrix 1 2 + matrix:get nitrous_oxide_matrix 2 2) matrix:set nitrous_oxide_matrix 3 3 (matrix:get nitrous_oxide_matrix 1 3 - matrix:get nitrous_oxide_matrix 2 3) matrix:set nitrous_oxide_matrix 4 3 (matrix:get nitrous_oxide_matrix 1 3 + matrix:get nitrous_oxide_matrix 2 3) matrix:set nitrous_oxide_matrix 3 4 (matrix:get nitrous_oxide_matrix 1 4 - matrix:get nitrous_oxide_matrix 2 4) matrix:set nitrous_oxide_matrix 4 4 (matrix:get nitrous_oxide_matrix 1 4 + matrix:get nitrous_oxide_matrix 2 4) matrix:set nitrous_oxide_matrix 3 5 (matrix:get nitrous_oxide_matrix 1 5 - matrix:get nitrous_oxide_matrix 2 5) matrix:set nitrous_oxide_matrix 4 5 (matrix:get nitrous_oxide_matrix 1 5 + matrix:get nitrous_oxide_matrix 2 5) matrix:set nitrous_oxide_matrix 3 6 (matrix:get nitrous_oxide_matrix 1 6 - matrix:get nitrous_oxide_matrix 2 6) matrix:set nitrous_oxide_matrix 4 6 (matrix:get nitrous_oxide_matrix 1 6 + matrix:get nitrous_oxide_matrix 2 6) matrix:set nitrous_oxide_matrix 3 7 (matrix:get nitrous_oxide_matrix 1 7 - matrix:get nitrous_oxide_matrix 2 7) matrix:set nitrous_oxide_matrix 4 7 (matrix:get nitrous_oxide_matrix 1 7 + matrix:get nitrous_oxide_matrix 2 7) matrix:set nitrous_oxide_matrix 3 8 (matrix:get nitrous_oxide_matrix 1 8 - matrix:get nitrous_oxide_matrix 2 8) matrix:set nitrous_oxide_matrix 4 8 (matrix:get nitrous_oxide_matrix 1 8 + matrix:get nitrous_oxide_matrix 2 8) matrix:set nitrous_oxide_matrix 3 9 (matrix:get nitrous_oxide_matrix 1 9 - matrix:get nitrous_oxide_matrix 2 9) matrix:set nitrous_oxide_matrix 4 9 (matrix:get nitrous_oxide_matrix 1 9 + matrix:get nitrous_oxide_matrix 2 9) matrix:set nitrous_oxide_matrix 3 10 (matrix:get nitrous_oxide_matrix 1 10 - matrix:get nitrous_oxide_matrix 2 10) matrix:set nitrous_oxide_matrix 4 10 (matrix:get nitrous_oxide_matrix 1 10 + matrix:get nitrous_oxide_matrix 2 10) matrix:set nitrous_oxide_matrix 3 11 (matrix:get nitrous_oxide_matrix 1 11 - matrix:get nitrous_oxide_matrix 2 11) matrix:set nitrous_oxide_matrix 4 11 (matrix:get nitrous_oxide_matrix 1 11 + matrix:get nitrous_oxide_matrix 2 11) matrix:set nitrous_oxide_matrix 3 12 (matrix:get nitrous_oxide_matrix 1 12 - matrix:get nitrous_oxide_matrix 2 12) matrix:set nitrous_oxide_matrix 4 12 (matrix:get nitrous_oxide_matrix 1 12 + matrix:get nitrous_oxide_matrix 2 12) matrix:set nitrous_oxide_matrix 5 0 ((matrix:get nitrous_oxide_matrix 3 0 / matrix:get nitrous_oxide_matrix 4 0) ^ 2) matrix:set nitrous_oxide_matrix 5 1 ((matrix:get nitrous_oxide_matrix 3 1 / matrix:get nitrous_oxide_matrix 4 1) ^ 2) matrix:set nitrous_oxide_matrix 5 2 ((matrix:get nitrous_oxide_matrix 3 2 / matrix:get nitrous_oxide_matrix 4 2) ^ 2) matrix:set nitrous_oxide_matrix 5 3 ((matrix:get nitrous_oxide_matrix 3 3 / matrix:get nitrous_oxide_matrix 4 3) ^ 2) matrix:set nitrous_oxide_matrix 5 4 ((matrix:get nitrous_oxide_matrix 3 4 / matrix:get nitrous_oxide_matrix 4 4) ^ 2) matrix:set nitrous_oxide_matrix 5 5 ((matrix:get nitrous_oxide_matrix 3 5 / matrix:get nitrous_oxide_matrix 4 5) ^ 2) matrix:set nitrous_oxide_matrix 5 6 ((matrix:get nitrous_oxide_matrix 3 6 / matrix:get nitrous_oxide_matrix 4 6) ^ 2) matrix:set nitrous_oxide_matrix 5 7 ((matrix:get nitrous_oxide_matrix 3 7 / matrix:get nitrous_oxide_matrix 4 7) ^ 2) matrix:set nitrous_oxide_matrix 5 8 ((matrix:get nitrous_oxide_matrix 3 8 / matrix:get nitrous_oxide_matrix 4 8) ^ 2) matrix:set nitrous_oxide_matrix 5 9 ((matrix:get nitrous_oxide_matrix 3 9 / matrix:get nitrous_oxide_matrix 4 9) ^ 2) matrix:set nitrous_oxide_matrix 5 10 ((matrix:get nitrous_oxide_matrix 3 10 / matrix:get nitrous_oxide_matrix 4 10) ^ 2) matrix:set nitrous_oxide_matrix 5 11 ((matrix:get nitrous_oxide_matrix 3 11 / matrix:get nitrous_oxide_matrix 4 11) ^ 2) matrix:set nitrous_oxide_matrix 5 12 ((matrix:get nitrous_oxide_matrix 3 12 / matrix:get nitrous_oxide_matrix 4 12) ^ 2) let sum_nitrous_oxide_square sum matrix:get-row nitrous_oxide_matrix 5 let nitrous_oxide_square sqrt ( (1 / (length matrix:get-row nitrous_oxide_matrix 5)) * sum_nitrous_oxide_square) set GRI_nitrous_oxide (1 + nitrous_oxide_square) / (1 - nitrous_oxide_square) Fitness-Calculation ] ; end procedure succinate high A. Xylosoxidans ] ; end procedure bacteria A.xylosoxidans end To Fitness-Calculation set Fitness ((GRI_nitrous_oxide - 1) ^ 2) + ((GRI_nitrite - 1) ^ 2) + ((GRI_nitrate - 1) ^ 2) + ((GRI_biomass - 1) ^ 2) End
There is only one version of this model, created about 5 years ago by Pablo Alejandro Araujo Granda.
Attached files
| File | Type | Description | Last updated | |
|---|---|---|---|---|
| INDISIM-Denitrification.png | preview | Preview for 'INDISIM-Denitrification' | about 5 years ago, by Pablo Alejandro Araujo Granda | Download |
This model does not have any ancestors.
This model does not have any descendants.