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A new Mechanistic Modular Ecological Model: Eco3M tool .

A new Mechanistic Modular Ecological Model: Eco3M tool. Presented by Christel PINAZO. Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas. LECTURE SCHEDULE. Introduction What does simulate ECO3M ? ECO3M Characteristics

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A new Mechanistic Modular Ecological Model: Eco3M tool .

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  1. A new Mechanistic Modular Ecological Model: Eco3M tool. Presented by Christel PINAZO Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  2. LECTURE SCHEDULE • Introduction • What does simulate ECO3M ? • ECO3M Characteristics • ECO3M functioning • State Variables • FLUX matrix & SELF Vector • Processes Library • Configuration files • config.ini • modele.def • Mod_process.F90 • Results

  3. LECTURE SCHEDULE • Introduction • What does simulate ECO3M ? • ECO3M Characteristics • ECO3M functioning • State Variables • FLUX matrix & SELF Vector • Processes Library • Configuration files • config.ini • modele.def • Mod_process.F90 • Results

  4. z y O x ECO3M IS USED TO CALCULATE THE BIOGEOCHEMICAL TREND TERM OF BIOGEOCHEMICAL CONCENTRATIONS : Concentration Trend term= Sources – Sinks INTRODUCTION > WHAT? FUNCTIONING CONFIGURATION RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  5. ECO3M IS USED TO CALCULATE THE BIOGEOCHEMICAL TREND TERM OF BIOGEOCHEMICAL CONCENTRATIONS : Concentration Trend term = Sources – Sinks INTRODUCTION > WHAT? FUNCTIONING CONFIGURATION RESULTS

  6. C= T° SINK = N Nutrients = SOURCE IRRADIANCE BIOGEOCHEMICAL MODEL GEOCHEMICAL MODEL Zooplanktonic N Phytoplanktonic N Grazing TREND= SOURCE - SINK Uptake Schematic Marine Ecosystem Nitrogen cycle Sediment

  7. T° State Variables N Nutrients PROCESSES IRRADIANCE BIOGEOCHEMICAL MODEL GEOCHEMICAL MODEL Zooplanktonic N Phytoplanktonic N Grazing Uptake Schematic Marine Ecosystem Nitrogen cycle Sediment

  8. Phytoplankton Zooplankton Ammonium Bacteria Detritus Nitrate DON N-P-Z-D MODELS Nutrient-Phytoplankton-Zooplankton-Detritus Fasham’s Model (1990) INTRODUCTION > WHAT? FUNCTIONING CONFIGURATION RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  9. LECTURE SCHEDULE • Introduction • What does simulate ECO3M ? • ECO3M Characteristics • ECO3M functioning • State Variables • FLUX matrix & SELF Vector • Processes Library • Configuration files • config.ini • modele.def • Mod_process.F90 • Results

  10. ECO3M CHARACTERISTICS • COUPLING WITH DIFFERENT HYDRODYNAMIC MODELS • MECHANISTIC • VARIABLE STOICHIOMETRY • MODULAR INTRODUCTION > CHARACTERISTICS FUNCTIONING CONFIGURATION RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  11. N uptake Excretion ZOO Grazing Death NH4 PHYTO Grazing Grazing Mineralisation Death Egestion Mineralisation Egestion POMsmall DON Nitrification Mineralisation POMlarge aggregation NO3 Exudation N uptake Settling Example of Eco3M configuration Nitrogen cycle

  12. Example of Eco3M configuration C, N, Chl, O cycles

  13. grazing Mineralisation nitrification P Si N N C C C C C N N N N N Mortality P P P P P Nutrient uptake Diatoms Synechococcus Si Si C N P Chl production Chl respiration Example of Eco3M configuration ZOO PHYTO POMsmall POMlarge DOM NO3 NH4 Si PO4 C, N, Chl, P, Si cycles

  14. LECTURE SCHEDULE • Introduction • What does simulate ECO3M ? • ECO3M Characteristics • ECO3M functioning • State Variables • FLUX matrix & SELF Vector • Processes Library • Configuration files • config.ini • modele.def • Mod_process.F90 • Results

  15. T° IRRADIANCE BIOGEOCHEMICAL MODEL GEOCHEMICAL MODEL STATE VARIABLE 2 STATE VARIABLE 3 STATE VARIABLE 1 Schematic Marine Ecosystem Sediment

  16. LECTURE SCHEDULE • Introduction • What does simulate ECO3M ? • ECO3M Characteristics • ECO3M functioning • State Variables • FLUX matrix & SELF Vector • Processes Library • Configuration files • config.ini • modele.def • Mod_process.F90 • Results

  17. T° IRRADIANCE BIOGEOCHEMICAL MODEL GEOCHEMICAL MODEL STATE VARIABLE 2 STATE VARIABLE 3 FLUX 2,3 FLUX 1,2 STATE VARIABLE 1 Schematic Marine Ecosystem Sediment

  18. 1 2 3 4 … 1 2 3 4 … ECO3M FUNCTIONINGMATRIX “FLUX” Matrix « FLUX » Flux1,2 Flux2,3 nvar nvar INTRODUCTION FUNCTIONING>MATRIX CONFIGURATION RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  19. T° > SELF 2 IRRADIANCE BIOGEOCHEMICAL MODEL GEOCHEMICAL MODEL STATE VARIABLE 2 STATE VARIABLE 3 FLUX 2,3 FLUX 1,2 STATE VARIABLE 1 Schematic Marine Ecosystem Sediment

  20. 1 2 3 4 … 1 2 3 4 … ECO3M FUNCTIONINGVECTOR “SELF” Matrix « FLUX » Vector « SELF » 1 Flux1,2 Flux2,3 2 Self2 nvar 3 nvar 4 … nvar INTRODUCTION FUNCTIONING>MATRIX CONFIGURATION RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  21. 1 2 3 4 … 1 2 3 4 … ECO3M FUNCTIONING Matrix « FLUX » Vector « SELF » Flux 1,3 1 Flux1,2 Flux1,3 2 Self2 nvar 3 Self3 nvar 4 … nvar INTRODUCTION FUNCTIONING>MATRIX CONFIGURATION RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  22. T° > netPP N Nutrients IRRADIANCE BIOGEOCHEMICAL MODEL GEOCHEMICAL MODEL Zooplanktonic N Phytoplanktonic N Grazing Uptake Schematic Marine Ecosystem Nitrogen cycle Sediment

  23. NO3 phyN ZooN … NO3 phyN ZooN … ECO3M FUNCTIONING Matrix « FLUX » Vector « SELF » NO3 UPT GRA phyN netPP nvar ZooN nvar … nvar INTRODUCTION FUNCTIONING>MATRIX CONFIGURATION RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  24. Derived types of the numerical code Identifier (variable #) Identifier organism State variables Name of compartment (ZOO/PHY/dissolved inorganics…) Name of sub-compartment (diatom,NO3,…) Element (C, N, P, Chl, Si …) Identifier (process #) Index (in the flux matrix) Flux value Fluxes Identifier (process #) Index (in the self vector) Self value SELF INTRODUCTION FUNCTIONING>MATRIX CONFIGURATION RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  25. LECTURE SCHEDULE • Introduction • What does simulate ECO3M ? • ECO3M Characteristics • ECO3M functioning • State Variables • FLUX matrix & SELF Vector • Processes Library • Configuration files • config.ini • modele.def • Mod_process.F90 • Results

  26. Photosynthesis(Han, 2002) Respiration(Cannell & Thornley, 2002) Specific cost (gC) of each process (NO3- uptake, NO3- reduction, growth,…) Photoacclimation(Geider, 1998) Variable Chl a / C ratio Vector « SELF » NO3 phyN netPP PChl phyChl … • LINK BETWEEN PROCESSES AND FORMULATIONS IN THE PRE-DEFINED MODEL LIBRARY • EASILY ADDING A NEW FORMULATION WITHOUT ENTERING IN THE MODEL STRUCTURE INTRODUCTION FUNCTIONING>LIBRARY CONFIGURATION RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  27. PROCESSES LIBRARY Identifier (process #) Name of process (upt,GPP,…) Name of associated fonction (f_upt,…) Number of associated parameters Name of parameters (Qmin, Qmax, KQ,…) Processes • EACH PROCESS IS DESCRIBED BY A MATHEMATICAL FORMULATION • PROGRAMED IN AN ASSOCIATED FUNCTION F_PROCESS • THE SAME PROCESS COULD BE DESCRIBED BY SEVERAL FORMULATIONS • STORED IN THE F_PROCESS LIBRARY • CONFIGURATION FILES OF THE MODEL ALLOW TO LINK EACH PROCESS • WITH ITS FORMULATION AND WITH THE ASSOCIATED F_PROCESS FUNCTION • OF THE LIBRARY INTRODUCTION FUNCTIONING>LIBRARY CONFIGURATION RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  28. LECTURE SCHEDULE • Introduction • What does simulate ECO3M ? • ECO3M Characteristics • ECO3M functioning • State Variables • FLUX matrix & SELF Vector • Processes Library • Configuration files • config.ini • modele.def • Mod_process.F90 • Results

  29. ECO3M CONFIGURATION FILES • CONFIG.INI : CONFIGURATION FILE OF THE MODEL AND OF THE SIMULATION CONDITIONS • MODELE.DEF : FILE CONTAINING LINKS BETWEEN PROCESSES AND F_PROCESS LIBRARY • MOD_PROCESS.F90 : FORTRAN FILE WHERE INCLUDE NEW F_PROCESS FUNCTION INTRODUCTION FUNCTIONING CONFIGURATION RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  30. LECTURE SCHEDULE • Introduction • What does simulate ECO3M ? • ECO3M Characteristics • ECO3M functioning • State Variables • FLUX matrix & SELF Vector • Processes Library • Configuration files • config.ini • modele.def • Mod_process.F90 • Results

  31. ECO3M CONFIG.INI SIMULATION CONDITIONS # SIMULATION NAME Simu_ICTP # SIMULATION TIME(DAY):TIME STEP(sec):TIME STEP OF BIO RESULTS SAVING(mn) 0.1:1200:1440 #600.0:1200:1440 #SPATIAL GRID DIMENSIONS (nx_min,nxmax,ny_min,ny_max,nz) #110:280:0:90:10 1:1:1:1:1 INTRODUCTION FUNCTIONING CONFIGURATION>CONFIG.INI RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  32. ECO3M CONFIG.INI MODEL DEFINITION: STATE VARIABLES # COMPARTMENT NUMBER:SUB_COMPARTMENT NUMBER: TOTAL STATE VARIABLES NUMBER 5:7:12 # COMPARTMENT NAME: SUB_COMPARTMENT NUMBER # SUB_COMPARTMENT NAME: ELEMENT phy:1 phyto:C:N:Chl bac:1 bacteries:C:N det:1 detritus:C:N mod:1 dissous:C:N # mid:3 nh4:nh4 no3:no3 O2:O2 INTRODUCTION FUNCTIONING CONFIGURATION>CONFIG.INI RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  33. ECO3M CONFIG.INI SIMULATION CONDITIONS # IRRADIANCE OR PAR FILE, FUNCTION OR CALCULATED BY PHYSICAL MODEL; JOULES TO µEINSTEIN CONVERSION:ALBEDO:SINK AT AIR/SEA INTERFACE #IRR_ISA:60:0.43:0.05:1.0 IRR_FONCTION:420:30:0.46:0.05:0.75 #IRR_CODEPHYS:0.43:0.05:1.0 # #LIGHT ATTENUATION f_lum(0.0384>0.01) #f_extinc(0.0384>0.029) # SURF=nz_max is at surface; FOND=nz_max is at the bottom SURF INTRODUCTION FUNCTIONING CONFIGURATION>CONFIG.INI RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  34. ECO3M CONFIG.INI MODEL DEFINITION: FLUX MATRIX # TOTAL NUMBER OF FLUXES IN THE MATRIX 10 # phyto C --> DOC 1;8:+;exud(0.2) # # phyto N --> DON 2;9:+;exud(0.001) # # phyto N <-- NH4 2;10:-;uptv(2.1E-5>0.2>0.05>1>1>0.2) # phyto N <-- NO3 2;11:-;uptv(8.5E-6>0.2>0.05>1>1>0.3) . . . finflux INTRODUCTION FUNCTIONING CONFIGURATION>CONFIG.INI RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  35. ECO3M CONFIG.INI MODEL DEFINITION: SELF VECTOR # TOTAL NUMBER OF SELF PROCESSES 18 # PHYTO C photosynthesis & autotrophrespiration & grazing 1:+;gppg(0.8>0.063321>0.05>0.2>8.02E-06):-;resp(1.15e-6):-;gra(4.6800E-06>5.78704E-06>1.0) # PHYTO N grazing 2:-;gra(4.6800E-06>5.78704E-06>1.0) . . # NH4 zooplankton excretion 10:+;out_modn(0.95>0.5>0.445>4.6800E-06>5.78704E-06) #O2 nitrification & photosynthesis 12:-2;nit(5.7870E-07>0.0693>30.0):+;prodO2() # # finself INTRODUCTION FUNCTIONING CONFIGURATION>CONFIG.INI RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  36. ECO3M CONFIG.INI MODEL DEFINITION: CHLOROPHYLL/CARBON RATIO # CHLOROPHYLL/CARBON RATIO # 0 = CONSTANT CHLOROPHYLL/CARBON RATIO: RATIO VALUE # 1 = VARIABLE CHLOROPHYLL/CARBON RATIO CALCULATED BY THE MODEL #0:0.225 1 INTRODUCTION FUNCTIONING CONFIGURATION>CONFIG.INI RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  37. LECTURE SCHEDULE • Introduction • What does simulate ECO3M ? • ECO3M Characteristics • ECO3M functioning • State Variables • FLUX matrix & SELF Vector • Processes Library • Configuration files • config.ini • modele.def • Mod_process.F90 • Results

  38. ECO3M MODELE.DEF # UPTAKE MODELS # Uptake (geider 98) : #upt_gei:f_upt_geid98:7:v_ref:T_ref:AE:Qmin:Qmax:n:k_demi uptv:f_upt_droop:6:upmax:Qmax:Qmin:coeff_up:up_part:ks # # GRAZING MODELS # Grazing (Holling II): #grazphiX:f_graz_hol2_mpreys_X:2:ind_pred:ind_prey # fraction phyto grazing gra:f_gra_pourc_1:3:g1:g2:choix. . . # !fin INTRODUCTION FUNCTIONING CONFIGURATION>MODELE.DEF RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  39. LECTURE SCHEDULE • Introduction • What does simulate ECO3M ? • ECO3M Characteristics • ECO3M functioning • State Variables • FLUX matrix & SELF Vector • Processes Library • Configuration files • config.ini • modele.def • Mod_process.F90 • Results

  40. ECO3M MOD_PROCESS.F90 include "../F_PROCESS/LIGHT/ATTENUATION/f_lum.inc" include "../F_PROCESS/PPB/f_ppb_geider.inc" include "../F_PROCESS/RESP/f_resp_1.inc" include "../F_PROCESS/RESP/f_resp_bac.inc" include "../F_PROCESS/PERTES/f_out1.inc" include "../F_PROCESS/PERTES/f_out_det.inc" include "../F_PROCESS/PERTES/f_out_mod.inc" include "../F_PROCESS/PERTES/f_p_zoo.inc" include "../F_PROCESS/UPT/f_upt_droop.inc" include "../F_PROCESS/UPT/f_upt_bact_droop.inc" include "../F_PROCESS/GRAZ/f_gra_pourc_1.inc" include "../F_PROCESS/GRAZ/f_gra_bact.inc" include "../F_PROCESS/GRAZ/f_gra_det.inc" INTRODUCTION FUNCTIONING CONFIGURATION>MOD_PROCESS RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas

  41. LECTURE SCHEDULE • Introduction • What does simulate ECO3M ? • ECO3M Characteristics • ECO3M functioning • State Variables • FLUX matrix & SELF Vector • Processes Library • Configuration files • config.ini • modele.def • Mod_process.F90 • Results

  42. 0.20 0.5 0.4 0.15 Chl a / C (mol m-3) E/500 (µEinstein m-2 s-1) 0.3 Chl a / C (g Chl a (mol C)-1) E/9000 (µEinstein m-2 s-1) 0.10 0.2 0.05 0.1 0 0 16 16 18 18 20 20 22 22 24 24 26 26 28 28 Time (days) Time (days) MODEL VALIDATION CHEMOSTAT EXPERIMENT Modelling of the cell Chl a / C ratio evolution of the diatom Th. weissflogii conducted in high light and low light fluctuating regime then transfered to continuous light of the same intensity data from Pawlowski (2004) model by Baklouti et al. (2006)

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