Data Files specific for MET&OR module¶
- Some parameters are definied in a Namelist File : paraconta.txt
- Each contaminant, or each species of one contaminant, can be defined in variable.dat : Defined simulated substances.
- Or, one contaminant is declared in variable.dat : Defined simulated substances as “CONTA” and its specifications, different specis and reactions for each one, are given in an other file, specific of this contaminant. (MET&OR Data File : library of contaminant)
- Definitions of all reactions are given in MET&OR Data File : reaction.dat.
Namelist File : paraconta.txt¶
+--------------+-------------------+--------------------------------------------------------------------------------------+
| namelist | variable | |
+--------------+-------------------+--------------------------------------------------------------------------------------+
| namconta | filereaction | filename for data concerning biochemical reactions |
| | minpt_mes_re5 | min of SM (g/L) below which dissolved/particulate (D/P) partition is not calculated |
| | minpt_conta | min of exchangeable contaminant concentration below which no D/P partition |
| | fileconta1 | filename describing characteristics of the first simulated contaminant |
| | fileconta2 | |
| | fileconta3 | others filename if several contaminants are simulated (max=5) |
| | fileconta4 | needed if substance type "CONTA" is choose in variable.dat |
| | fileconta5 | |
| | l_sorfluxreac | not used currently |
| | thick_volat | layer thickness over which volatilization is possible |
| | massmol_h2o | molecular weight of H20 |
| | massmol_co2 | molecular weight of CO2 |
| | massmol_o2 | molecular weight of O2 |
| | cf_difwat_co2 | Diffusivity in water for CO2 |
| | cf_difwat_o2 | Diffusivity in water for O2 |
| | cf_difair_h2o | Diffusivity of H2O à 25°C |
| | cst_gas_univ | universal constant of gaz R(Pa m3/mole °K) |
| namspecies | ... | not used currently |
+--------------+-------------------+--------------------------------------------------------------------------------------+
MET&OR Data File : reaction.dat¶
See informations of Type of reactions simulated in module MET&OR
- After the description of the file (until the line of stars), giving the parameters of each reaction.
- Each reaction is separated from the previous one by a line of “=”.
- Examples of parameters for each type of reaction are given below .
BEGINNING OF THE FILE DESCRIPTION
data file to define biochemical reactions (D_Key_contaminant)
first define all reactions of type REAC1 (1), then GENERIC (2), then REVERSE (3)
then VOLATIL (4), then PAR_EQ (5),
REAC_1 : simple constant cinetic of order 1 (exemple :degradation : dC/dt=aµC)
only one reactive variable
11 lines per reaction of type 1
(see modele in modele_reaction_REAC1.dat)
GENERIC : cinetic with limiting functions and possibility of exponent for concentratins
one or several reactive variable
13 lines per reaction of type 2 + 1 line of comments
+ 3 lines per reactive variable + 1 line of comments
+ 3 lines per limiting functions of type 1 and 2
+ 2 lines per limiting functions of type 3
(see modele in modele_reaction_GEN.dat)
REVERSIBLE : simple (order 1) reversible reaction between 2 variables
13 lines per reaction of type 3
(see modele in modele_reaction_REVERS.dat)
VOLATIL : reaction of volatilization from water (dissolved variable) to air
9 lines per reaction of type 4
(see modele in modele_reaction_VOL.dat)
PARTAGE_EQ : distribution at equilibrium (exemple : dissolved/particulate)
17 lines per reaction of type 5 + 1 line of comments
+ 8 lines per reactive variable (in addition of the free dissolved)
(see modele in modele_reaction_PART.dat)
END OF FILE DESCRIPTION
*****************************************************************************
degradation_cdp !| name of the reaction
REAC_1 !| reaction type
.true. !| integration of dc in advection equation (false : time splitting)
cdp !| active variable name
0.005 !| maxi cinetic at reference temperature (in second-1)
-1. !| stochio coeff. with sign of the reaction (+ if source, - if consumer)
.true. !| temperature dependence
1 !| type of arrhenius law (0 : teta : 1 : exponential)
1 !| teta (=1 if law type 1)
20. !| reference temperature
15 !| xeta if law type 0 (xeta=1 or 10) or sigma (if law type 1)
=======================================================================
test gen !| reaction name
GENERIC !| reaction type
.true. !| integration of dc in advection equation (false : time splitting)
2 !| number of variable affected by this reaction (reactive variable)
6.e-7 !| maxi cinetic at reference temperature (in second-1)
.true. !| constant cinetic (if false, one must program the variation)
.true. !| constant stochio coefs (if false, one must program the variation)
1 !| number de limiting functions
.true. !| temperature dependence
1 !| type of arrhenius law (0 : teta : 1 : exponential)
1 !| teta (=1 if law type 1)
20. !| reference temperature
15 !| xeta if law type 0 (xeta=1 or 10) or sigma (if law type 1)
== reactives variables below (3 lines per each)
cdl !| first reactive variable name
-1. !| stochio coeff. with sign of the reaction (+ if source, - if consumer)
1 !| concentration exponent in the reaction
cdp1 !| second reactive variable name
+1. !| stochio coeff. with sign of the reaction (+ if source, - if consumer)
0 !| concentration exponent in the reaction
== limiting functions below (3 lines for types 1 and 2, 2 lines for type 3)
1 !| type of first limiting function
0.5 !| half saturation constant or half inhibition constant
MES1 !| limiting variable name
=======================================================================
desorption !| reaction name
REVERSIBLE !| reaction type
.false. !| integration of dc in advection equation (false : time splitting)
0.5 !| rate constant at reference temperature (in day-1)
20. !| concentration at equilibrium for the firt active variable (masse/masse)
.false. !| temperature dependence
1 !| type of arrhenius law (0 : teta : 1 : exponential)
1 !| teta (=1 if law type 1)
20. !| reference temperature
1 !| xeta if law type 0 (xeta=1 or 10) or sigma (if law type 1)
== name of reactives variables below (1 lines per each)
cdp2 !| first reactive variable name
cdp1 !| second reactive variable name
=======================================================================
test_part !| reaction name
PARTAG_EQ !| reaction type
.false. !| always false because always time splitting processing
3 !| number of variable affected by this reaction
.false. !| temperature dependence
1 !| type of arrhenius law (0 : teta : 1 : exponential)
1 !| teta (=1 if law type 1)
20. !| reference temperature
15 !| xeta if law type 0 (xeta=1 or 10) or sigma (if law type 1)
false !| PCE effect
0.,0. !| coefficents a1 and a2 for PCE effect
false !| SALTING OUT effect
0.,0. !| limit salinity and coefficient b for SALTING OUT effect
false !| Ln(Kd)=f(ln(salinity+1)) issued from MOCO or from Turner
5,2. !| parameters for the law f(ln(salinity+1)) : ndeg, KD0, (see above)
-0.07345,0.7601,-2.99,5.5264,-6.160,5.475 !| parameters for the law f(ln(salinity+1)) : x(i)i=1,ndeg (see above)
cdl !| name of the free dissolved variable
== reactives variables below (4 lines per each)
cdp1 !| name of reactive variable in equilibrium with free dissolved variable
MES1 !| corresponding substrate associated with this reactive variable (SMtot if total SM)
true !| partition coef in L/G , false in log10(mL/G)
50 !| partition Coef related with the substrate
cdd !| name of reactive variable in equilibrium with free dissolved variable
MOD !| corresponding substrate associated with this reactive variable (SMtot if total SM)
true !| partition coef in L/G , false in log10(mL/G)
100. !| partition Coef related with the substrate
=======================================================================
volatilisation !| name of the reaction
VOLATIL !| reaction type
.true . !| integration of dc in advection equation (false : time splitting)
cdl !| active variable name
112.41 !| molecular mass (g) ',
0. !| Schmidt number in water
0. !| Diffusivity in air
0. !| Henry constant (Pa.m3/mol) (used if different of 0)
0.3 !| or adimensional Henry constant (used if dimensional Henry constant =0)
0. !| facteur B dans la relation Staudinger f(T) (correction de henry)
0.3 !| Constante de salting out (L/mol) Setschenow (correction de henry)
true !|KLdif(O2) : true pour formule de Churchill ou false pour formule de O Connor
true !|KLsal(O2) : true pour prise en compte de l effet salinite -formule de Wen
1 !|KLvent(CO2) : 1 si formule de Schwartzenbach; 2 si Wanninkhof: 3 si Nightingale
true !|KLcor : true pour correction transfert liquide par masse molaire ou false par nbre de Schmidt
-0.5 !|xnl : exposant terme correctif transfert liquide (-0.5 a -1)
false !|Kgcor : true pour correction transfert gazeux par diffusivité ou false par masse molaire
-0.5 !|xng : exposant terme correctif transfert gazeux (0.5 à 1 si diffusivite; -0.5 si massmolaire)
=======================================================================
MET&OR Data File : library of contaminant¶
DEBUT DESCRIPTIF DU FICHIER
Bibliotheque des donnees pour chaque contaminant
Ici Cadmium exemple mais avec données fictives
FIN DESCRIPTIF DU FICHIER
***************************************************
Cd !|name of the contaminant
microg/m3 !| unit used for this contaminant (/m3)','
112.41 !|molecular mass (g) ',
0. !|Schmidt number in water
0. !|molecular diffusion in water
0. !|Diffusivity in air
0.3 !|Henry constant (Pa.m3/mol)
0. !|or adimensional Henry constant 9.e-3
0. !|facteur B dans la relation Staudinger f(T) (correction de henry)
0.3 !|Constante de salting out (L/mol) Setschenow (correction de henry)
2 !|nombre d especes dissoutes (avec espece libre)
1 !|nombre d especes particulaires - sorption a l equilibre
1 !|nombre d especes particulaires - sorption non equilibre
1 !|nombre d especes particulaires SANS sorption/desorption
variation du processus de partage dissous/particulaire avec la température, la salinite et/ou les MES
.false. !| influence temperature (loi d arrhenius) (.false. : pas d'influence)
1 !| type de la loi d arrhenius (1 : loi teta : 2 : loi exponentionnelle)
1 !| teta (=1 si loi 2)
20. !| temperature de reference pour loi d arrhenius
1 !| xeta (loi 1 xeta=1 ou 10) ou sigma (loi 2)
false !| effect PCE
0.,0. !| coefficents x1 and x2 for effect PCE
false !| effect SALTING OUT
0.,0. !| limit salinity and coefficient x2 for effect SALTING OUT
false !| SALTING OUT effect
0.,0. !| limit salinity and coefficient b for SALTING OUT effect
infos sur la premiere espece DISSOUTE (la diss libre)
Cdd_l !|nom de l espece dissoute libre
0. !|HYDOLYSE cinetique (/day)
0. !|PHOTOLYSE cinetique (/day)
0.0 !|BIODEGRADATION cinetique (/day)
infos sur les autres DISSOUTEs si il y en a (7 lignes par espece)
Cdd !|nom de l espece dissoute du contaminant
MOD !|nom du substrat dissous lié au contaminant
true !|partition coef in L/G , false in log10(mL/G)
100. !|Log10 du Coef de partage vis à vis de ce substrat '
0. !|HYDOLYSE cinetique (/day)
0. !|PHOTOLYSE cinetique (/day)
0. !|BIODEGRADATION cinetique (/day)
infos sur chaque espece PARTICULAIRE a l EQUILIBRE (12 lignes/espece + 4/domaine non linéaire )
Cdp !|nom de l espece du contaminant
MES1 !|nom du substrat lié au contaminant
.,.,.,. !|fraction aux limites Nord, Est, Sud et Ouest
0. !|fraction dans le flux atmosphérique
0. !|fraction /conc totale du contaminant dans l'eau de pluie
true !|partition coef in L/G , false in log10(mL/G)
50. !|Log10 du Coef de partage vis à vis de ce substrat '
1 !|nombre de domaine NON LINEAIRE
4 lignes PAR DOMAINE NON lineaire POUR LES DEFINIR SI BESOIN
0.1 !|fraction de domaine non lineaire
false !|true si Kf ou Kl exprime en LOG , false sinon (l/g)
0.2309 !| paramètre Kl ou Kf ,0.0175
0.737 !|Qmax si Langmuir ou n si Freunlich ',38.95
0. !|HYDOLYSE cinetique (/day)
0. !|PHOTOLYSE cinetique (/day)
0. !|BIODEGRADATION cinetique (/day)
infos sur chaque espece PARTICULAIRE LINEAIRE traitee en CINETIQUE (9 lignes/espece )
Cdpcin !|nom de l espece particulaire du contaminant
Cdp !|nom de l espece associée a l equilibre
0.5 !|fraction initiale /conc totale du contaminant
.,.,.,. !|fraction aux limites Nord, Est, Sud et Ouest
0. !|fraction dans le flux atmosphérique
0. !|fraction /conc totale du contaminant dans l'eau de pluie
0.5 !|Constante de vitesse (/jour)
20. !|concentration a l'equilibre de l'espece (en masse/kg de particules liées)
.true. !| integration in advection equation (false : time splitting)
infos sur chaque espece PARTICULAIRE NON ECHANGEABLE (10 lignes/espece )
CdpNE !|nom de l espece particulaire du contaminant
MES1 !|nom de la variable particulaire constitutive associee
0.5 !|fraction initiale /conc totale du contaminant dans l'eau
.,.,.,. !|fraction aux limites Nord, Est, Sud et Ouest
0. !|fraction dans le flux atmosphérique
0. !|fraction /conc totale du contaminant dans l'eau de pluie
true !|partition coef in L/G , false in log10(mL/G)
0. !|HYDOLYSE cinetique (/day)
0. !|PHOTOLYSE cinetique (/day)
0. !|BIODEGRADATION cinetique (/day)
data for VOLATILIZATION process (8 lines)
true !| prise en compte de la volatilisation (false si non :les donnees des lignes suivantes ne seront pas utilisees)
true !|KLdif(O2) : true pour formule de Churchill ou false pour formule de O Connor
true !|KLsal(O2) : true pour prise en compte de l effet salinite -formule de Wen
1 !|KLvent(CO2) : 1 si formule de Schwartzenbach; 2 si Wanninkhof: 3 si Nightingale
true !|KLcor : true pour correction transfert liquide par masse molaire ou false par nbre de Schmidt
-0.5 !|nL : exposant terme correctif transfert liquide (-0.5 a -1)
false !|Kgcor : true pour correction transfert gazeux par diffusivité ou false par masse molaire
-0.5 !|nL : exposant terme correctif transfert gazeux (0.5 à 1 si diffusivite; -0.5 si massmolaire)
data for additional reactions type GENERIC between contaminant's species
0 !|number of additional reactions
migration !|nom de la reaction
.true. !|traitement dans l equation de transport, sinon false : traitement après
2 !|nombre de variables affectees par cette reaction ( variables reactives)
0.1 !| cinetique maximum a la temperature de reference (en jour-1)
.true. !| cinetique constante (.true) sinon il faudra programmer la variation
.true. !| coefs stochios constant (.true) sinon il faudra programmer la variation
1 !| nombre de fonctions limitantes pour cette reaction
.false. !| influence temperature (loi d arrhenius) (.false. : pas d'influence)
1 !| type de la loi d arrhenius (1 : loi teta : 2 : loi exponentionnelle)
1 !| teta (=1 si loi 2)
20. !| temperature de reference pour loi d arrhenius
1 !| xeta (loi 1 xeta=1 ou 10) ou sigma (loi 2)
== variables reactives (3 lignes pour chacune - les unes apres les autres)
CdpNE !| nom de la premiere espece reactive
-1. !| coeff. stochiometrique et signe (+ si source, - si puits=consommation)
1 !| exposant de la concentration dans la reaction
Cdd !| nom de la deuxieme espece reactive
+1. !| coeff. stochiometrique et signe (+ si source, - si puits=consommation)
0 !| exposant de la concentration dans la reaction
== fonctions limitantes (3 lignes pour type1 et 2, 2 lignes pour type 3 - les unes apres les autres)
1 !| type of first limiting function
0.5 !| half saturation constant or half inhibition constant
MES1 !| limiting variable name