Commit 20015aff authored by Gwenaelle Gremion's avatar Gwenaelle Gremion
Browse files

Code commenté

parent c946efdb
......@@ -10,20 +10,22 @@
! 4: Fasham et al. 1990 (7 variables)
! 5: IOW-ERGOM MaBenE version (9 variables)
! 6: ISMER model (9 variables)
! 7: GSJ model (11 variables)
! 8: Ariadna Nocera's model (tbd)
! 7: The GSJ model, modified from ISMER
! 8: The model of Ariadna Celina Nocera, modified from Fasham
! 9: The model with four detrital compartments
! 10: The model for the north Water polynya - NPZ4D (14 Variables)
!
! bio_eulerian -> state variables are Eulerian (.true./.false.)
!
! cnpar -> Cranck-Nicolson parameter for vertical diffusion
!
! w_adv_discr -> advection scheme for vertical motion
! 1: first order upstream
! 2: not coded yet
! 3: third-order polynomial
! 4: TVD with Superbee limiter
! 5: TVD with MUSCL limiter
! 6: TVD with ULTIMATE QUICKEST
! w_adv_discr -> advection scheme for vertical motion - case as in adv_center.F90 (method)
! 1: first order upstream - case (UPSTREAM)
! 2: not coded yet -
! 3: third-order polynomial - case (P1)
! 4: TVD with Superbee limiter - case (Superbee)
! 5: TVD with MUSCL limiter - case (MUSCL)
! 6: TVD with ULTIMATE QUICKEST - case ((P2),(P2_PDM))
!
! ode_method -> ODE scheme for source and sink dynamics
! 1: first-order explicit (not positive)
......@@ -45,16 +47,17 @@
! bio_lagrange_mean -> averaging Lagrangian conc. on output (.true./.false.)
!
! bio_npar -> total number of Lagrangian particles
!
!-------------------------------------------------------------------------------
&bio_nml
bio_calc= .true.
bio_model= 2
bio_model= 10
bio_eulerian= .true.
cnpar= 1.0
w_adv_discr= 6
ode_method= 8
w_adv_discr= 6 ! 4
ode_method= 10 !11
split_factor= 1
bioshade_feedback= .true.
bio_lagrange_mean= .false.
bio_npar= 100000
bio_lagrange_mean= .true.
bio_npar= 10000
/
#$Id$
!-------------------------------------------------------------------------------
! Fasham et al. biological model with modifications by Kuehn and Radach
!
! numc= number of compartments for geobiochemical model
!************************DESCRIPTIONS OF THE PARAMETERS*************************
!-------------------------------------------------------------------------------
! Bio_polynow model, based on Fasham et al. 1990, and modified by Gremion G. and Dumont D.
!
! numc = number of compartments for geobiochemical model [-]
! dt_bio = time step in seconds - Have to be the same as dt in gotmrun.nml [s]
! splitfac_bio = Split factor - Have to be the same as split_Factor in bio.nml [-]
!
! p_initial= initial phytoplankton concentration [mmol n/m3]
! z_initial= initial zooplakton concentration [mmol n/m3]
! b_initial= initial bacteria concentration [mmol n/m3]
! dph_initial= initial dph concentration [mmol n/m3]
! dzo_initial= initial dzo concentration [mmol n/m3]
! fp_initial= initial fp concentration [mmol n/m3]
! msn_initial= initial dzo concentration [mmol n/m3]
! n_initial= *** see obs.nml *** [mmol n/m3]
! a_initial= *** see obs.nml *** [mmol n/m3]
! l_initial= initial LDON concentration [mmol n/m3]
! p0 = minimum phytoplankton concentration [mmol n/m3]
! z0 = minimum zooplakton concentration [mmol n/m3]
! b0 = minimum bacteria concentration [mmol n/m3]
! mu5 = nitrification rate [1/day] !!GG-CHG1
! vp = maximum phytoplankton uptake rate [1/day]
! alpha = slope of the PI-curvea [m2/(W day)]
! inib = inhibition slope of the PI-curve (positive) [m2/(W day)]
! kc = attenuation constant for the self shading effect [m**2/mmol N]
! k1 = half saturation constant nitrate uptake [mmol n/m3]
! k2 = half saturation constant ammonium uptake [mmol n/m3]
! mu1 = phytoplankton mortality rate [1/day]
! k5 = half saturation constant phytoplankton mortality [mmol n/m3]
! gamma = exudation fraction [-]
! capt = Percentage of living phyto. captured in msn [%/day] - GG-D
! sp_mort = Phytoplankton non grazing mortality [1/day] - GG-D
! sp_mort2 = Quadratic mortality/aggrgation rate coefficient [1/day] - GG-D
! w_p = phytoplankton settling velocity [m/day]
! stip = Stickiness of choosen Phytoplankton species [-] - GG-D
! stidph = Stickiness of dead Phytoplankton [-] - GG-D
! gmax = maximum ingestion rate [1/day]
! k3 = half saturation constant ingestion [mmol n/m3]
! beta = grazing efficiency [-]
! betamsn = grazing efficiency on marine snow [-] - GG-D
! mu2 = maximum zooplankton loss rate [1/day]
! k6 = half saturation zooplankton loss [mmol n/m3]
! delta = fractional zooplankton loss to LDON [-]
! epsi = fractional zooplankton loss to ammonium [-]
! r1 = grazing preference phytoplankton [-]
! r2 = grazing preference bacteria [-]
! r3 = grazing preference dead phytoplankton (dph) [-] - GG-D
! r4 = grazing preference dead zooplankton (dzo) [-] - GG-D
! r5 = grazing preference fecal pellets (fp) [-] - GG-D
! r6 = grazing preference marine snow (msn) [-] - GG-D
!zingest = Proportion of grazed matter added to zoo. biomass [-] - GG-D
! eg = Percentage of eggestion [%/day] - GG-D
! stidzo = Stickiness of choosen zooplankton species [-] - GG-D
! stifp = Stickiness of fecal pellets [-] - GG-D
! pmin = intensity rariadtion in the water column
! w_zmax = Max. swimming speed for zoo (not exceed 320) [1/day]
! bertha = amplitud coefficient
! parcrit =min. phyto concentration needed for zooplankton
! vb = maximum bacterial uptake rate [1/day]
! k4 = half saturation bacterial uptake [mmol n/m3]
! mu3 = bacteria excretion rate [1/day]
! eta = uptake ratio ammonium:LDON [-]
! mbac = Percentage of bacerias captured in msn [%/day] - GG-D
! dphlossl = Dph breakdown rate [%/day] - GG-D
! dzolossl = Percentage of Dzo loss in LDON [%/day] - GG-D
! dzolossb = Percentage of Dzo loss in bacteria respiration [%/day] - GG-D
! fplossl = Percentage of fp loss in LDON [%/day] - GG-D
! fplossb = Percentage of fp loss in bacteria respiration [%/day] - GG-D
! w_d1 = [1/day]
! w_d2 = [1/day]
! w_d3 = [1/day]
! w_d4 = [1/day]
! mldon = Percentage of LDON used to constitute matrice of msn [%/day] - GG-D
!lmin = LDON limit concentration to become the matrix of msn [mmol n/m3]- GG-D
!Coag_coef = Specification by user of utilisation of model calculated Coagulation coefficient(false) or given parameter(true) [true.false] - GG-D
!betap = Coagulation coefficient of Phytoplankton [1/day]- GG-D
!betadph = Coagulation coefficient of dead Phytoplankton [1/day]- GG-D
!betadzo = Coagulation coefficient of deadzooplankton [1/day]- GG-D
!betafp = Coagulation coefficient of fecal pellets [1/day]- GG-D
!-------------------------------------------------------------------------------
! INITIAL and Minimum concentration for the variables
!-------------------------------------------------------------------------------
&bio_polynow_nml
numc= 10
p_initial= 0.012
z_initial= 0.012
b_initial= 0.001
dph_initial= 0.012
dzo_initial= 0.012
fp_initial= 0.012
msn_initial= 0.012
l_initial= 0.1
p0= 0.0001
z0= 0.0001
b0= 0.0001
mu5= 0.1
vp= 0.3
alpha= 0.04
inib= 0.06
kc= 0.03
k1= 1.0
k2= 0.8
mu1= 0.05
k5= 0.2
gamma= 0.0
capt= 0.0
sp_mort= 0.0
sp_mort2= 0.0
w_p= 0.5
stip= 0.0
stidph= 0.0
gmax= 0.6
k3= 1.0
beta= 0.625
betamsn= 0.0
mu2= 0.3
k6= 0.2
delta= 0.0
epsi= 0.70
r1= 0.1
r2= 0.2
r3= 0.3
r4= 0.1
r5= 0.2
r6= 0.1
zingest= 0.0
eg= 0.0
stidzo= 0.0
stifp= 0.0
pmin= 0.7
w_zmax= 320
bertha= 0.05
parcrit= 10
vb= 0.
k4= 0.5
mu3= 0.03
eta= 0.0
mbac= 0.0
dphlossl= 0.0
dzolossl= 0.0
dzolossb= 0.0
fplossl= 0.0
fplossb= 0.0
w_d1= 0
w_d2= 0
w_d3= 0
w_d4= 0
mldon= 0.0
lmin= 0.0
coag_coef= .false.
betap= 0.0
betadph= 0.0
betadzo= 0.0
betafp= 0.0
/
!
! p_init_value = Initial concentration of phytoplankton is a constant values(=1.0) (If it is a profile(=0.0)
! p_initial = Initial phytoplankton concentration [mmol n/m3]
! z_p_gauss_init = depth for the curve of the gaussian curve [m]
! sigma_p = value for the size of the dome on the gaussian curve [-]
!
!zoo_init_value = Initial concentration of zooplankton is a constant values(=1.0) (If it is a profile(=0.0)
! z_initial = Initial zooplakton concentration [mmol n/m3]
!z_zoo_gauss_init = depth for the curve of the gaussian curve [m]
! sigma_zoo = value for the size of the dome on the gaussian curve [-]
!
! b_initial = Initial bacteria concentration [mmol n/m3]
!
! dph_init_value = Initial concentration of dead phytoplankton is a constant values(=1.0) (If it is a profile(=0.0))
! dph_initial = Initial dead phytoplankton concentration [mmol n/m3]
! z_dph_gauss_init= depth for the curve of the gaussian curve [m]
! sigma_dph = value for the size of the dome on the gaussian curve [-]
!
! dzo_init_value = Initial concentration of dead phytoplankton is a constant values(=1.0) (If it is a profile(=0.0))
! dzo_initial = Initial dead phytoplankton concentration [mmol n/m3]
! z_dzo_gauss_init= depth for the curve of the gaussian curve [m]
! sigma_dzo = value for the size of the dome on the gaussian curve [-]
!
! fp_init_value = Initial concentration of dead phytoplankton is a constant values(=1.0) (If it is a profile(=0.0))
! fp_initial = Initial dead phytoplankton concentration [mmol n/m3]
! z_fp_gauss_init = depth for the curve of the gaussian curve [m]
! sigma_fp = value for the size of the dome on the gaussian curve [-]
!
! msn_init_value = Initial concentration of dead phytoplankton is a constant values(=1.0) (If it is a profile(=0.0))
! msn_initial = Initial dead phytoplankton concentration [mmol n/m3]
! z_msn_gauss_init= depth for the curve of the gaussian curve [m]
! sigma_msn = value for the size of the dome on the gaussian curve [-]
!
! n_initial= *** see obs.nml *** [mmol n/m3]
! a_initial= *** see obs.nml *** [mmol n/m3]
! l_initial= initial LDON concentration [mmol n/m3]
! p0 = minimum phytoplankton concentration [mmol n/m3]
! z0 = minimum zooplakton concentration [mmol n/m3]
! b0 = minimum bacteria concentration [mmol n/m3]
! mu5 = nitrification rate [1/day]
!-----------------------------------------------------------------------------------
!! PHYTOPLANKTON and Dead Phytoplankton
!-----------------------------------------------------------------------------------
! vp = maximum phytoplankton uptake rate [1/day]
! alpha = slope of the PI-curvea [m2/(W day)]
! inib = inhibition slope of the PI-curve (positive) [m2/(W day)]
! kc = attenuation constant for the self shading effect [m**2/mmol N]
! k1 = half saturation constant nitrate uptake [mmol n/m3]
! k2 = half saturation constant ammonium uptake [mmol n/m3]
! mu1 = phytoplankton mortality rate [1/day]
! k5 = half saturation constant phytoplankton mortality [mmol n/m3]
! gamma = exudation fraction [-]
! txloss_p = min aggregation loss rate of phytoplankton [1/day]
!txloss_dph = min aggregation loss rate of dead phytoplankton [1/day]
!-----------------------------------------------------------------------------------
!! ZOOPLANKTON and Dead zooplankton & Fecal pellets
!-----------------------------------------------------------------------------------
! gmax = maximum ingestion rate [1/day]
! k3 = half saturation constant ingestion [mmol n/m3]
! beta = grazing efficiency (beta =1 zooplankton eat everything) [-]
! mu2 = maximum zooplankton loss rate [1/day]
! k6 = half saturation zooplankton loss [mmol n/m3]
! delta = fractional zooplankton loss to LDON [-]
! epsi = fractional zooplankton loss to ammonium [-]
! eg = fractional zooplankton loss by eggestion [-]
! r1 = grazing preference phytoplankton [-]
! r2 = grazing preference bacteria [-]
! r3 = grazing preference dead phytoplankton (dph) [-]
! r4 = grazing preference dead zooplankton (dzo) [-]
! r5 = grazing preference fecal pellets (fp) [-]
! r6 = grazing preference marine snow (msn) [-]
!txloss_dzo = min aggregation loss rate of dead zooplankton [1/day]
!txloss_fp = min aggregation loss rate of fecal pellets [1/day]
!-----------------------------------------------------------------------------------
!! Zooplankton Vertical migration
!-----------------------------------------------------------------------------------
! Migra_zoo = Zooplankton can migrate in the water column (.true. =1.0/.false.= 0.0)
! pmin = intensity radiation in the water column
! w_zmax = Max. swimming speed for zoo (not exceed 320) [1/day]
! bertha = amplitud coefficient
! parcrit = min. phyto concentration needed for zooplankton
!-----------------------------------------------------------------------------------
!! Bacterias/LDON/Detritus
!-----------------------------------------------------------------------------------
! vb = maximum bacterial uptake rate [1/day]
!remi = remineralisation rate [1/day]
! k4 = half saturation bacterial uptake [mmol n/m3]
! mu3 = bacteria excretion rate [1/day]
! eta = uptake ratio ammonium:LDON [-]
! mbac = Loss rate of bacerias captured in msn [1/day]
! dphlossb = Dph loss rate by bacteria respiration [1/day]
! dphlossl = Dph leackage rate (Dph loss in LDON) [1/day]
! dzolossl = Dzo leackage rate (Dzo loss in LDON) [1/day]
! dzolossb = Dzo loss rate by bacteria respiration [1/day]
! fplossl = Fp leackage rate (Fp loss in LDON) [1/day]
! fplossb = Fp loss rate by bacteria respiration [1/day]
! leak = loss rate of msn to LDON [1/day]
! mldon = Loss rate of LDON captured in msn [1/day]
! lmin = LDON limit concentration to become the matrix of msn [mmol n/m3]
!-----------------------------------------------------------------------------------
!! Settling parameters
!-----------------------------------------------------------------------------------
!Phys_w = Physical environment is use to calcule settling speed of particles (no Msn)
! 0: Calculated by value from the .nml (w_msn)
! 1: Stokes's law from Ghosh et al 2013 (Msn is considered as a sphere)
! 2: Modified Stoke's law (For cylindrical particles) from McDonnell et al 2010
! 3: Power law evolution from Alldredge and Gotschalk, 1988 based on Kajihara 1971 and from Komar 1981
! 4: Stokes law for high reynolds number + Corey Shape Factor [Komar 1978]
!w_msnow = Marine snow settling velocity calculated by our equations
! 0: Calculated by value from the .nml (w_msn)
! 1: Stokes's law from Ghosh et al 2013 (Msn is considered as a sphere)
! 2: Modified Stoke's law (For cylindrical particles) from McDonnell et al 2010
! 3: Power law evolution from Alldredge and Gotschalk, 1988 based on Kajihara 1971 and from Komar 1981
! 4: Stokes law for high reynolds number + Corey Shape Factor [Komar 1978]
! 5: Non spherical particles (VanRijn 1993)
! 6: Non spherical particles depending on the diameter value of msn (VanRijn 1993)
! w_p = [negative] phytoplankton settling velocity [m/day]
! w_dph = [negative] Dead phytoplankton settling velocity [m/day]
! w_dzo = [negative] Dead zooplankton settling velocity [m/day]
! w_fp = [negative] Fecal pellets settling velocity [m/day]
! w_msn = [negative] Msn settling velocity [m/day]
! rho_p = Density of phytoplankton particle (kg/m3)
!rho_dph = Density of dead phytoplankton particle (kg/m3)
!rho_dzo = Density of zooplankton particle (kg/m3)
!rho_fp = Density of dead zooplankton particle (kg/m3)
!rho_msn = Density marine snow particle (kg/m3)
!-----------------------------------------------------------------------------------
!! COAGULATION
!-----------------------------------------------------------------------------------
!Coag_coef = Coagulation by the model (1.0) - Specified by the user (0.0)[-]
!betap_p = Coagulation coefficient of Phytoplankton with itself [m-3/d]
!betap_dph = Coag. coeff. of Phy with Dph [m-3/d]
!betap_dzo = Coag. coeff. of Phy with Dzo [m-3/d]
!betap_fp = Coag. coeff. of Phy with Fp [m-3/d]
!betadph_dph = Coag. coeff. of Dph with itself [m-3/d]
!betadph_dzo = Coag. coeff. of Dph with Dzo [m-3/d]
!betadph_fp = Coag. coeff. of Dph with Fp [m-3/d]
!betadzo_dzo = Coag. coeff. of Dzo with itself [m-3/d]
!betadzo_fp = Coag. coeff. of Dzo with Fp [m-3/d]
!betafp_fp = Coag. coeff. of Fp with itself [m-3/d]
!betaBr = 1.0 : Allow calcul of the kernel coeff. only with the brownian motion(require Coag_coef and betaSh and beta Ds =0) [-]
!betaSh = 1.0 : Allow calcul of the kernel coeff. only with the shear (require Coag_coef and betaBr and betaDs =0) [-]
!betaDs = 1.0 : Allow calcul of the kernel coeff. only with the diffential settling(require Coag_coef and betaBr and betaSh=0) [-]
!eps_const = choice of utilisation of a constant eps value (1.0)
!eps_n = value of the eps if eps_const=1.0 [m2/s3]
!cons_min = Minimal concentration of Msn to increase its size by coagulation
! sti_cst = Stickiness cst (1.0) of calculated by the model (0.0) [-]
! stip_p = Stickiness of Phytoplankton particles between themselves [-]
! stip_dph = Stickiness of Phy with dead Phytoplankton [-]
! stip_dzo = Stickiness of Phy with dead zooplankton [-]
! stip_fp = Stickiness of Phy with fecal pellets [-]
! stidph_dph = Stickiness of Phytoplankton particles between themselves [-]
! stidph_dzo = Stickiness of dead Phytoplankton with dead zoo [-]
! stidph_fp = Stickiness of dead Phytoplankton with fecal pellets [-]
! stidzo_dzo = Stickiness of dead zooplankton particles with themselves [-]
! stidzo_fp = Stickiness of dead zooplankton species with fecal pellets [-]
! stifp_fp = Stickiness of fecal pellets with themselves [-]
!-----------------------------------------------------------------------------------
!! COLLISION RATE AND SETTLING
!-----------------------------------------------------------------------------------
! CSF = the Corey shape factor of marine snow [Nasiha 2018] [-]
!size_rand = sizes of the particles are chosen randomly(1.0) or not(0.0) [-]
!size_phy_us = radius of phytoplankton particles (considering as a sphere) [m]
!size_phy_up = Max radius of phytoplankton particles (considering as a sphere) [m]
!size_dph_us = radius of DPh particles (considering as a sphere) [m]
!size_dph_up = Max radius of Dph particles (considering as a sphere) [m]
!size_dzo_us = radius of dead zoo particles (considering as a sphere) [m]
!size_dzo_up = Max radius of dead zoo particles (considering as a sphere) [m]
!size_fp_us = radius of fecal pellets particles (considering as a sphere) [m]
!size_fp_up = Max radius of fecal pellets particles (considering as a sphere) [m]
!dm_msn = allow the calculation of maximum diameter by eps level [1.0] [-]
!coef1 = cst for maximum msn size for dissagregation (Alldrege 1990) (use with dm_msn =1.0) [-]
!coef2 = exponent for maximum msn size for dissagregation (Alldrege 1990)(use with dm_msn =1.0) [-]
!diam_msn_us = maximal diameter of msn [m]
!coef3 = cst for utilisation of the flocculation settling range for ws equation (Metha 1989) [-]
!Cons_max = Maximum concentration for msn to follow settling following w_msnow from 0 to 4 [-]
!dynvis = dynamic viscosity [Pa.s]
!kinvis = kinematic viscosity [m²/s]
!kB = Boltzmann constant [J/K]
!-----------------------------------------------------------------------------------
! FRAGMENTATION
!-----------------------------------------------------------------------------------
!Frag_meth = Fragmentation occurs (1.0) or not (0.0) [-]
!swim_brk = Fragmentation rate by swimming zooplankton [1/d]
!Floc_coef = Floc strength coefficient [-]
!Daugther_part = Daughter particles formation by fragmentation (1.0 --> percentage) (0.0 --> Size/3) [-]
!-----------------------------------------------------------------------------------
!
!************************VALUES FOR THE PARAMETERS*********************************
&bio_polynow_nml
numc = 14
dt_bio = 30
splitfac_bio = 1.0
depth_bio = 100
!-----INITIAL and Minimum concentration for the variables
p_init_value = 0.0
p_initial = 0.0
z_p_gauss_init = 90.0
sigma_p = 2.0
zoo_init_value = 0.0
z_initial = 0.0
z_zoo_gauss_init = 90
sigma_zoo = 2.0
b_initial = 0.00
dph_init_value = 0.0
dph_initial = 30.0
z_dph_gauss_init = 90
sigma_dph = 2.0
dzo_init_value = 0.0
dzo_initial = 0.0
z_dzo_gauss_init = 90
sigma_dzo = 2.0
fp_init_value = 0.0
fp_initial = 30.0
z_fp_gauss_init = 90
sigma_fp = 2.0
msn_init_value = 1.0
msn_initial = 0.0
z_msn_gauss_init = 0.0
sigma_msn = 0.0
l_initial = 0.1
p0 = 0.0001
z0 = 0.0001
b0 = 0.0001
mu5 = 0.0 ! 0.1
!-----Phytoplankton and dead-phytoplankton
vp = 0.0 !0.3
alpha = 0.04
inib = 0.06
kc = 0.03
k1 = 1.0
k2 = 0.8
mu1 = 0.0 !0.05
k5 = 0.2
gamma = 0.0
txloss_p = 1.0
txloss_dph = 1.0
!-----Zooplankton
gmax = 0.0 !0.6
k3 = 1.0
beta = 0.625
mu2 = 0.0 ! 0.3
k6 = 0.2
delta = 0.15
epsi = 0.1
eg = 0.3
r1 = 0.5
r2 = 0.0
r3 = 0.29
r4 = 0.1
r5 = 0.01
r6 = 0.1
txloss_dzo = 0.05
txloss_fp = 0.05
Migra_zoo = 0.0
pmin = 0.7
w_zmax = 250
bertha = 0.05
parcrit = 10
!-----Bacterias and LDON
vb = 0.0 !0.1
remi = 0.0 !0.1
k4 = 0.5
mu3 = 0.0 !0.03
eta = 0.0
mbac = 0.0
dphlossb = 0.01
dphlossl = 0.01
dzolossl = 0.01
dzolossb = 0.01
fplossl = 0.01
fplossb = 0.01
leak = 0.1
mldon = 0.0 !0.01
lmin = 0.1
!----- Detritus/Settling
Phys_w = 4.0
w_msnow = 4.0
w_p = -0.5
w_dph = -0.1
w_dzo = -49
w_fp = -10
w_msn = -14.9
rho_p = 1330 !824.0
rho_dph = 1330 !800.0
rho_dzo = 1059 !800.0
rho_fp = 1059 !800.0
rho_msn = 1000 !900.0
!----- Coagulation
Coag_coef = 1.0
betap_p = 1.0
betap_dph = 1
betap_dzo = 1
betap_fp = 1
betadph_dph = 1
betadph_dzo = 1
betadph_fp = 1
betadzo_dzo = 1
betadzo_fp = 1
betafp_fp = 1
betaBr = 0.0
betaSh = 0.0
betaDs = 0.0
eps_const = 1.0
eps_n = 1.0e-7 !1e-4 !1.0e-8
cons_min = 0.00000001 !0.0001 !0.000001
sti_cst = 1.0
stip_p = 1.0
stip_dph = 1.0
stip_dzo = 1.0
stip_fp = 1.0
stidph_dph = 1.0
stidph_dzo = 1.0
stidph_fp = 1.0
stidzo_dzo = 1.0
stidzo_fp = 1.0
stifp_fp = 1.0
!----- Settling
CSF = 0.5
size_rand = 0.0
size_phy_us = 0.00001 !0.01 !0.00001 ! 0.001
size_phy_up = 0.0001
size_dph_us = 0.00001 !5.00e-06 !5.00e-07
size_dph_up = 5.00e-5
size_dzo_us = 0.0001 !0.0001
size_dzo_up = 0.0001
size_fp_us = 2.50e-05
size_fp_up = 2.50e-05
dm_msn = 0.0
coef1 = 4.40
coef2 = 0.14
diam_msn_us = 0.002 !0.075 (Alldrege 1988) !0.01 ![10mm]
coef3 = 1.0
cons_max = 0.2490
dynvis = 1.79E-03
kinvis = 1.519e-6
kB = 1.3806488e-23
!-----Fragmentation
Frag_meth = 0.0
swim_brk = 0.01
Floc_coef = 1.0
Daugther_part = 0.0
/
......@@ -48,8 +48,8 @@
use bio_mab, only : init_bio_mab,init_var_mab,var_info_mab
use bio_mab, only : light_mab,surface_fluxes_mab,do_bio_mab
use bio_polynow, only : init_bio_polynow,init_var_polynow,var_info_polynow !GG-A
use bio_polynow, only : light_polynow,do_bio_polynow !GG-A
use bio_polynow, only : init_bio_polynow,init_var_polynow,var_info_polynow
use bio_polynow, only : light_polynow,do_bio_polynow
use output, only : out_fmt,write_results,ts
......@@ -360,7 +360,7 @@
call var_info_npzd4()
case (10) ! The model for the north Water polynya - NPZD- Sedimentation GG-A
case (10) ! The model for the north Water polynya - NPZ4D- Sedimentation
call init_bio_polynow(namlst,'bio_polynow.nml',unit)
......@@ -514,9 +514,6 @@
if (present(w_)) w = w_
if (present(w_adv_ctr_)) w_adv_ctr = w_adv_ctr_
return
end subroutine set_env_bio
!EOC
......@@ -594,6 +591,7 @@
! !LOCAL VARIABLES:
integer, parameter :: adv_mode_0=0
integer, parameter :: adv_mode_1=1
integer, parameter :: adv_mode_3=3 ! Specific for Bio_model =10 , for Msn concentration and size
REALTYPE :: Qsour(0:nlev),Lsour(0:nlev)
REALTYPE :: RelaxTau(0:nlev)
REALTYPE :: dt_eff
......@@ -670,8 +668,29 @@
do i=1,nlev
cc(1,i) = nit(i)
end do
else
! do advection step due to settling or rising
! Specific advection scheme for Bio_model =10 , for Msn concentration (10) and size (14)
else if (j==10 .and. bio_model ==10) then
call adv_center(nlev,dt,h,h,ws(j,:),flux, &
flux,_ZERO_,_ZERO_,w_adv_discr,adv_mode_3,cc(j,:))
else if (j==14 .and. bio_model ==10) then
call adv_center(nlev,dt,h,h,ws(j,:),flux, &
flux,_ZERO_,_ZERO_,w_adv_discr,adv_mode_3,cc(j,:))
! Specific advection scheme for Bio_model =10 , for nitrate (5) and ammonium (6)
else if (j ==5 .and. bio_model==10) then
do i=1,nlev
cc(j,i) = nit(i)
end do
else if (j ==6 .and. bio_model==10) then
do i=1,nlev
cc(j,i) = amm(i)
end do
else
! do advection step due to settling or rising for all the other variables
call adv_center(nlev,dt,h,h,ws(j,:),flux, &
flux,_ZERO_,_ZERO_,w_adv_discr,adv_mode_1,cc(j,:))
......@@ -873,9 +892,6 @@
if (allocated(Flux_D2)) deallocate(Flux_D2)
if (allocated(Flux_D3)) deallocate(Flux_D3)
if (allocated(size_msnow)) deallocate(size_msnow)
if (allocated(w_msn_lev)) deallocate(w_msn_lev)
! The external provide arrays