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

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

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

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

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

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

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

INTRODUCTION > WHAT?FUNCTIONINGCONFIGURATION RESULTS N-P-Z-D MODELS Fasham’s Model (1990) Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas Nutrient-Phytoplankton-Zooplankton-Detritus PhytoplanktonDONNitrate Ammonium BacteriaZooplanktonDetritus

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

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

PHYTO ZOO DON NH 4 NO 3 POM small POM large N uptake Settling Grazing Excretion Nitrification Mineralisation Grazing Death Grazing Death Egestion aggregation Mineralisation Exudation Egestion Nitrogen cycle Example of Eco3M configuration

C, N, Chl, O cycles

PHYTO ZOO DOMNH 4 NO 3 POM small POM large SiPO 4 DiatomsSynechococcus C N P C N P C N P C N P Si NN P C N P Chl C N P Si Chl Nutrient uptake grazing Mortality Mineralisation nitrification production respiration C, N, Chl, P, Si cycles Example of Eco3M configuration

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

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

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

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

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

Flux2,3 Flux1,2 …  …4 3 2  Matrix « FLUX » … 4 3 Self22  Vector « SELF » n var Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas ECO3M FUNCTIONING VECTOR “SELF” INTRODUCTION FUNCTIONING>MATRIX CONFIGURATION RESULTS

Flux 1,3 Flux1,2 …  …4 3 2  Matrix « FLUX » … 4 Self3 3 Self22  Vector « SELF » n var Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas INTRODUCTION FUNCTIONING>MATRIX CONFIGURATION RESULTS ECO3M FUNCTIONING

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

GRA UPT … Zoo N phy N NO 3 … Zoo N phy N NO 3 Matrix « FLUX » … Zoo N netPPphy N NO 3 Vector « SELF » n var Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas INTRODUCTION FUNCTIONING>MATRIX CONFIGURATION RESULTS ECO3M FUNCTIONING

Identifier (variable #) Derived types of the numerical code State variables SELF Fluxes Identifier (process #) Index (in the flux matrix) Flux value Identifier organism Name of compartment (ZOO/PHY/dissolved inorganics…) Name of sub-compartment (diatom,NO 3,…) Element (C, N, P, Chl, Si …) Identifier (process #) Index (in the self vector) Self value INTRODUCTION FUNCTIONING>MATRIX CONFIGURATION RESULTS 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 ECO3M functioning State Variables FLUX matrix & SELF Vector Processes Library Configuration files config.ini modele.def Mod_process.F90 Results

… netPPphy N NO 3 Vector « SELF » Photosynthesis Photosynthesis (Han, 2002) Respiration Respiration (Cannell & Thornley, 2002) Specific cost (gC) of each process (NO 3 - uptake, NO 3 - reduction, growth,…) phy Chl PChl Photoacclimation Photoacclimation (Geider, 1998) Variable Chl a / C ratio INTRODUCTION FUNCTIONING>LIBRARY CONFIGURATION RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas LINK BETWEEN PROCESSES AND FORMULATIONS IN THE PRE-DEFINED MODEL LIBRARY EASILY ADDING A NEW FORMULATION WITHOUT ENTERING IN THE MODEL STRUCTURE

PROCESSES LIBRARY Processes Identifier (process #) Name of process (upt,GPP,…) Name of associated fonction (f_upt,…) Number of associated parameters Name of parameters (Q min, Q max, K Q,…) 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

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

INTRODUCTION FUNCTIONING CONFIGURATION RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas -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 ECO3M CONFIGURATION FILES

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

INTRODUCTION FUNCTIONING CONFIGURATION>CONFIG.INI RESULTS Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas ECO3M CONFIG.INI # 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 SIMULATION CONDITIONS

Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas ECO3M CONFIG.INI # 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 MODEL DEFINITION: STATE VARIABLES INTRODUCTION FUNCTIONING CONFIGURATION>CONFIG.INI RESULTS

Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas ECO3M CONFIG.INI # 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 SIMULATION CONDITIONS INTRODUCTION FUNCTIONING CONFIGURATION>CONFIG.INI RESULTS

Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas ECO3M CONFIG.INI # 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 MODEL DEFINITION: FLUX MATRIX INTRODUCTION FUNCTIONING CONFIGURATION>CONFIG.INI RESULTS

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

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

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

Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas 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

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

Regional Advanced School on Physical and Mathematical Tools for the study of Marine Processes of Coastal Areas 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

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

MODEL VALIDATION CHEMOSTAT EXPERIMENT Chl a / C (g Chl a (mol C) -1 ) E/9000 (µEinstein m -2 s -1 ) Chl a / C (mol m -3 ) E/500 (µEinstein m -2 s -1 ) Time (days) Time (days) 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)