PISCES Model
All PISCES model parameters and options are accessible in the namelist_pisces_ref file. These parameters are organized by biogeochemical process, and by model version for some, as shown below.
All namelist blocks whose names start with nampis are used by the three versions of PISCES (unless specified in the comments section of the namelist block).
The other namelist blocks are specific to each version:
namp2zfor PISCES-Simplenamp4zfor PISCES-Operationalnamp5zfor PISCES-Research
First, we present the namelist_pisces_ref file distributed with the NEMO model, followed by the sections of the namelist distributed with CROCO that differ from the one distributed with NEMO.
Methodology for namelist parameter changes
To modify the PISCES namelist parameters, we strongly advise you to copy them to the namelist_pisces_cfg file, in the same namelist block, as this file references the namelist settings specific to your configuration. You can then modify them according to your configuration and the biogeochemical adjustments you want to make.
NEMO
Here we describe the namelist parameters by block section of the namelist_pisces_ref distributed with NEMO version 5.0 (branch 5.0 of the NEMO git repository).
Version Selection
nampismod
In nampismod, you select the version of PISCES you want: PISCES-Simple, PISCES-Operational or PISCES-Research. PISCES-Operational is enabled by default. Only one version of PISCES can be enabled at a time.
You can also choose to activate prognostic ligands (only for PISCES-Operational and PISCES-Research) and the sedimentary module (only for PISCES-Operational).
!-----------------------------------------------------------------------
&nampismod ! Model used
!-----------------------------------------------------------------------
ln_p2z = .false. ! LOBSTER model used
ln_p4z = .true. ! PISCES model used
ln_p5z = .false. ! PISCES QUOTA model used
ln_ligand = .false. ! Enable organic ligands
ln_sediment = .false. ! Enable sediment module
Air-Sea Exchange
nampisext
In nampisext, you can prescribe either a constant value for the atmospheric partial pressure of CO\(_2\) (ppm) or a value that changes over time based on a file (e.g., industrial period). By default, a constant pre-industrial value of 280 ppm for pCO\(_2^{atm}\) is applied. In both cases, the values are uniform over the configuration grid.
!-----------------------------------------------------------------------
&nampisext ! air-sea exchange
!-----------------------------------------------------------------------
ln_co2int = .false. ! read atm pco2 from a file (T) or constant (F)
atcco2 = 280. ! Constant value atmospheric pCO2 - ln_co2int = F
clname = 'atcco2.txt' ! Name of atm pCO2 file - ln_co2int = T
nn_offset = 0 ! Offset model-data start year - ln_co2int = T
! ! If your model year is iyy, nn_offset=(years(1)-iyy)
! ! then the first atmospheric CO2 record read is at years(1)
Atmospheric Settings
nampisatm
In nampisatm, you can enable either constant or spatially variable atmospheric pressure (2D) over the configuration grid (ln_presatm). You can also enable a spatially variable (2D) atmospheric CO\(_2\) partial pressure file (ln_presatmco2) instead of a uniform value (see nampisext). You can define both 2D file names (sn_patm, sn_atmco2) and their frequencies (monthly, hourly) as well as the directory where the file(s) is/are located (cn_dir).
!-----------------------------------------------------------------------
&nampisatm ! Atmospheric pressure
!-----------------------------------------------------------------------
! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename !
sn_patm = 'presatm.orca2' , 24. , 'presatm' , .true. , .true. , 'yearly' , '' , '' , ''
sn_atmco2 = 'presatmco2' , -1. , 'xco2' , .true. , .true. , 'yearly' , '' , '' , ''
cn_dir = './' ! root directory for the location of the dynamical files
!
ln_presatm = .false. ! constant atmopsheric pressure (F) or from a file (T)
ln_presatmco2 = .false. ! Read spatialized atm co2 files [ppm] if TRUE
Biological Settings
nampisbio
In nampisbio are defined the time-splitting parameter for biological processes (nrdttrc, see Time Stepping paragraph), set by default to the same frequency as the time step of the ocean model, the sinking velocities of small and big particles (wsbioand wsbio2 in m/day), the Fe:C ratios for both zooplankton size-classes, and their N:C and P:C ratios for PISCES-Research (p5z). Options specific to explicit ligand production (ln_ligand) are also defined in this block.
!-----------------------------------------------------------------------
&nampisbio ! biological parameters
!-----------------------------------------------------------------------
nrdttrc = 1 ! time step frequency for biology
wsbio = 2. ! POC sinking speed
xkmort = 1.E-7 ! half saturation constant for mortality
feratz = 10.E-6 ! Fe/C in zooplankton
feratm = 15.E-6 ! Fe/C in mesozooplankton
wsbio2 = 50. ! Big particles sinking speed
wsbio2max = 50. ! Big particles maximum sinking speed
wsbio2scale = 5000. ! Big particles length scale of sinking
! ! ln_ligand enabled
ldocp = 1.E-4 ! Phyto ligand production per unit doc
ldocz = 1.E-4 ! Zoo ligand production per unit doc
lthet = 1.0 ! Proportional loss of ligands due to Fe uptake
! ! ln_p5z enabled
no3rat3 = 0.1367 ! N/C ratio in zooplankton
po4rat3 = 0.00855 ! P/C ratio in zooplankton
Nutrient Limitation
namp2zlim, namp4zlim, namp5zlim
In namp*zlim are defined the nutrient limitation parameters for each PISCES version. This parameters encompass the nutrient half-saturation constants for each phytoplankton modelled group, their size criterias and size ratios, the calcite mean rain ratio, the half-saturation constant for anoxia, and the C associated with.
namp2zlim (PISCES-Simple)
-----------------------------------------------------------------------
&namp2zlim ! parameters for nutrient limitations for PISCES reduced - ln_p2z
!-----------------------------------------------------------------------
concnno3 = 1.E-6 ! Nitrate half saturation of nanophytoplankton
concnfer = 1.E-10 ! Iron half saturation for phyto
concbno3 = 3.E-7 ! Nitrate half saturation for DOC remin.
concbfe = 5.E-11 ! Iron half-saturation for DOC remin.
xsizephy = 2.E-6 ! Minimum size criteria for phyto
xsizern = 10.0 ! Size ratio for nanophytoplankton
xkdoc = 417.E-6 ! half-saturation constant of DOC remineralization
caco3r = 0.07 ! mean rain ratio
oxymin = 1.E-6 ! Half-saturation constant for anoxia
namp4zlim (PISCES-Operational)
!-----------------------------------------------------------------------
&namp4zlim ! parameters for nutrient limitations for PISCES std - ln_p4z
!-----------------------------------------------------------------------
concnno3 = 1.E-6 ! Nitrate half saturation of nanophytoplankton
concdno3 = 3.E-6 ! Nitrate half saturation for diatoms
concnnh4 = 1.E-6 ! NH4 half saturation for phyto
concdnh4 = 3.E-6 ! NH4 half saturation for diatoms
concnfer = 1.5E-9 ! Iron half saturation for phyto
concdfer = 4.5E-9 ! Iron half saturation for diatoms
concbfe = 4.E-11 ! Iron half-saturation for DOC remin.
concbnh4 = 3.E-7 ! NH4 half saturation for DOC remin.
concbno3 = 3.E-7 ! Nitrate half saturation for DOC remin.
xsizedia = 1.E-6 ! Minimum size criteria for diatoms
xsizephy = 1.E-6 ! Minimum size criteria for phyto
xsizern = 3.0 ! Size ratio for nanophytoplankton
xsizerd = 4.0 ! Size ratio for diatoms
xksi1 = 8.E-6 ! half saturation constant for Si uptake
xksi2 = 20.E-6 ! half saturation constant for Si/C
xkdoc = 417.E-6 ! half-saturation constant of DOC remineralization
qnfelim = 10.E-6 ! Optimal quota of phyto
qdfelim = 10.E-6 ! Optimal quota of diatoms
caco3r = 0.12 ! mean rain ratio
oxymin = 1.E-6 ! Half-saturation constant for anoxia
ratchl = 10.0 ! C associated with Chlorophyll
namp5zlim (PISCES-Research)
!-----------------------------------------------------------------------
&namp5zlim ! parameters for nutrient limitations PISCES QUOTA - ln_p5z
!-----------------------------------------------------------------------
concnno3 = 2.E-6 ! Nitrate half saturation of nanophytoplankton
concpno3 = 7.E-7 ! Nitrate half saturation of picophytoplankton
concdno3 = 3.E-6 ! Phosphate half saturation for diatoms
concnnh4 = 2.E-6 ! NH4 half saturation for phyto
concpnh4 = 7.E-7 ! NH4 half saturation for picophytoplankton
concdnh4 = 3.E-6 ! NH4 half saturation for diatoms
concnpo4 = 12.E-6 ! PO4 half saturation for phyto
concppo4 = 4.E-6 ! PO4 half saturation for picophytoplankton
concdpo4 = 18.E-6 ! PO4 half saturation for diatoms
concnfer = 3.E-9 ! Iron half saturation for phyto
concpfer = 1.E-9 ! Iron half saturation for picophytoplankton
concdfer = 4.5E-9 ! Iron half saturation for diatoms
concbfe = 4.E-11 ! Half-saturation for Fe limitation of Bacteria
concbnh4 = 3.E-7 ! NH4 half saturation for phyto
concbno3 = 3.E-7 ! Phosphate half saturation for diatoms
concbpo4 = 3.E-7 ! Phosphate half saturation for bacteria
xsizedia = 1.E-6 ! Minimum size criteria for diatoms
xsizephy = 1.E-6 ! Minimum size criteria for phyto
xsizepic = 5.E-7 ! Minimum size criteria for picophyto
xsizern = 2.0 ! Size ratio for nanophytoplankton
xsizerp = 1.5 ! Size ratio for picophytoplankton
xsizerd = 4.0 ! Size ratio for diatoms
xksi1 = 8.E-6 ! half saturation constant for Si uptake
xksi2 = 20.E-6 ! half saturation constant for Si/C
xkdoc = 417.E-6 ! half-saturation constant of DOC remineralization
caco3r = 0.2 ! mean rain ratio
oxymin = 1.E-6 ! Half-saturation constant for anoxia
ratchl = 10.0 ! C associated with Chlorophyll
PISCES-Research Quotas
namp5zquota
PISCES-Research (full quota version) has an additional namelist section (compared to p2z and p4z) allowing to manage its variable Redfield ratios. Thus, namp5zquota contains the minimum, maximum and optimal quota values of Iron (Fe), nitrogen (N), and phosphorus (P) for the three groups of phytoplankton (picophytoplankton, nanophtoplankton and diatoms) modelled in PISCES-Research.
!-----------------------------------------------------------------------
&namp5zquota ! parameters for nutrient limitations PISCES quota - ln_p5z
!-----------------------------------------------------------------------
qfnopt = 10.E-6 ! Optimal Fe quota of nanophyto
qfpopt = 10.E-6 ! Optimal Fe quota of picophyto
qfdopt = 10.E-6 ! Optimal quota of diatoms
qnnmin = 0.69 ! Minimal N quota for nano
qnnmax = 1.35 ! Maximal N quota for nano
qpnmin = 0.24 ! Minimal P quota for nano
qpnmax = 1.35 ! Maximal P quota for nano
qnpmin = 0.9 ! Minimal N quota for pico
qnpmax = 1.35 ! Maximal N quota for pico
qppmin = 0.2 ! Minimal P quota for pico
qppmax = 1.1 ! Maximal P quota for pico
qndmin = 0.63 ! Minimal N quota for diatoms
qndmax = 1.35 ! Maximal N quota for diatoms
qpdmin = 0.24 ! Minimal P quota for diatoms
qpdmax = 1.67 ! Maximal P quota for diatoms
qfnmax = 60.E-6 ! Maximal Fe quota for nano
qfpmax = 60.E-6 ! Maximal Fe quota for pico
qfdmax = 60.E-6 ! Maximal Fe quota for diatoms
Light Availability
nampisopt
In nampisopt, you can choose to use a spatially variable (2D) photosynthetically available radiation file (ln_varpar) and its frequency. You can set the fraction of shortwave radiation as photosynthetically available radiation (parlux). You can also enable the impact of the diurnal cycle (and its associated effect on the mixed-layer depth) on primary productivity (ln_p4z_dcyc).
!-----------------------------------------------------------------------
&nampisopt ! parameters for optics
!-----------------------------------------------------------------------
! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename !
sn_par = 'par.orca' , 24. , 'fr_par' , .true. , .true. , 'yearly' , '' , '' , ''
cn_dir = './' ! root directory for the location of the dynamical files
ln_varpar = .true. ! boolean for PAR variable
parlux = 0.43 ! Fraction of shortwave as PAR
ln_p4z_dcyc = .false. ! Diurnal cycle in PISCES
Phytoplankton Growth
namp2zprod, namp4zprod, namp5zprod
In namp*zprod are defined the phytoplankton growth rate parameters for each phytoplankton group modelled by each version of PISCES. This includes the slope value of the photosynthesis-to-irradiance ratio, excretion rates and min/max Chl:C ratios for each phytoplankton group, the basal respiration rate of phytoplankton (common to all phytoplankton groups) and the mean Si:C ratio for diatoms.
namp2zprod (PISCES-Simple)
!-----------------------------------------------------------------------
&namp2zprod ! parameters for phytoplankton growth for PISCES reduced - ln_p2z
!-----------------------------------------------------------------------
pislopen = 4. ! P-I slope
excretn = 0.05 ! excretion ratio of phytoplankton
bresp = 0.03 ! Basal respiration rate
chlcnm = 0.033 ! Maximum Chl/C in nanophytoplankton
chlcmin = 0.0025 ! Minimum Chl/c in phytoplankton
namp4zprod (PISCES-Operational)
!-----------------------------------------------------------------------
&namp4zprod ! parameters for phytoplankton growth for PISCES std - ln_p4z
!-----------------------------------------------------------------------
pislopen = 3.5 ! P-I slope
pisloped = 3.5 ! P-I slope for diatoms
excretn = 0.05 ! excretion ratio of phytoplankton
excretd = 0.05 ! excretion ratio of diatoms
bresp = 0.03 ! Basal respiration rate
chlcmin = 0.0025 ! Minimum Chl/c in phytoplankton
fecnm = 60.E-6 ! Maximum Fe/C in nanophytoplankton
fecdm = 60.E-6 ! Maximum Fe/C in diatoms
grosip = 0.11 ! mean Si/C ratio
namp5zprod (PISCES-Research)
!-----------------------------------------------------------------------
&namp5zprod ! parameters for phytoplankton growth for PISCES quota- ln_p5z
!-----------------------------------------------------------------------
pislopen = 5 ! P-I slope of nanophytoplankton
pislopep = 5 ! P-I slope for picophytoplankton
pisloped = 5 ! P-I slope for diatoms
excretn = 0.05 ! excretion ratio of phytoplankton
excretp = 0.05 ! excretion ratio of picophytoplankton
excretd = 0.05 ! excretion ratio of diatoms
bresp = 0.03 ! Basal respiration rate
chlcmin = 0.0025 ! Minimum Chl/c in phytoplankton
grosip = 0.13 ! mean Si/C ratio
Phytoplankton Mortality
namp2zmort, namp4zmort, namp5zmort
In namp*zmort are defined the parameters for the linear and quadratic mortality terms of phytoplankton groups modelled by each version of PISCES.
namp2zmort (PISCES-Simple)
!-----------------------------------------------------------------------
&namp2zmort ! parameters for phytoplankton sinks for PISCES std - ln_p2z
!-----------------------------------------------------------------------
wchln = 0.02 ! quadratic mortality of phytoplankton
mpratn = 0.01 ! phytoplankton mortality rate
namp4zmort (PISCES-Operational)
!-----------------------------------------------------------------------
&namp4zmort ! parameters for phytoplankton sinks for PISCES std - ln_p4z
!-----------------------------------------------------------------------
wchln = 0.01 ! quadratic mortality of phytoplankton
wchld = 0.03 ! maximum quadratic mortality of diatoms
mpratn = 0.01 ! phytoplankton mortality rate
mpratd = 0.01 ! Diatoms mortality rate
namp5zmort (PISCES-Research)
!-----------------------------------------------------------------------
&namp5zmort ! parameters for phytoplankton sinks for PISCES quota - ln_p5z
!-----------------------------------------------------------------------
wchln = 0.01 ! quadratic mortality of nanophytoplankton
wchlp = 0.01 ! quadratic mortality of picophytoplankton
wchld = 0.03 ! maximum quadratic mortality of diatoms
mpratn = 0.01 ! nanophytoplankton mortality rate
mpratp = 0.01 ! picophytoplankton mortality rate
mpratd = 0.01 ! Diatoms mortality rate
Mesozooplankton
namp4zmes, namp5zmes
In namp*zmes are defined all the parameters of the mesozooplankton for PISCES-Operational and PISCES-Research. This includes grazing, exsudation, mortality and flux-feeding rates, food preferencies (phytoplankton, zooplankton, organic particles), the associated different feeding threshold, growth efficiency, predation window size,...
The parameterization of the diurnal vertical migration (DVM) of mesoozoplankton can also be enabled (ln_dvm_meso), as well as the fraction of mesozooplankton that performs this migration.
namp4zmes (PISCES-Operational)
!-----------------------------------------------------------------------
&namp4zmes ! parameters for mesozooplankton for PISCES std - ln_p4z
!-----------------------------------------------------------------------
part2 = 0.75 ! part of calcite not dissolved in mesozoo guts
grazrat2 = 0.5 ! maximal mesozoo grazing rate
resrat2 = 0.005 ! exsudation rate of mesozooplankton
mzrat2 = 0.01 ! mesozooplankton mortality rate
xpref2d = 1. ! mesozoo preference for diatoms
xpref2n = 0.45 ! mesozoo preference for nanophyto.
xpref2z = 1. ! mesozoo preference for microzoo.
xpref2c = 0.3 ! mesozoo preference for poc
xpref2m = 0.0 ! mesozoo preference for meso
xthresh2zoo = 1.E-8 ! zoo feeding threshold for mesozooplankton
xthresh2dia = 1.E-8 ! diatoms feeding threshold for mesozooplankton
xthresh2phy = 1.E-8 ! nanophyto feeding threshold for mesozooplankton
xthresh2poc = 1.E-8 ! poc feeding threshold for mesozooplankton
xthresh2mes = 1.E-8 ! meso feeding threshold for mesozooplankton
xthresh2 = 3.E-7 ! Food threshold for grazing
xkgraz2 = 20.E-6 ! half saturation constant for meso grazing
epsher2 = 0.4 ! Efficicency of Mesozoo growth
epsher2min = 0.4 ! Minimum efficiency of mesozoo growth
sigma2 = 0.67 ! Fraction of mesozoo excretion as DOM
unass2 = 0.3 ! non assimilated fraction of P by mesozoo
grazflux = 3.e3 ! flux-feeding rate
xsigma2 = 0.5 ! Predation window size
xsigma2del = 0.5 ! Predation window size scaling
ln_dvm_meso = .false. ! Activates DVM for mesozooplankton
xfracmig = 0.3 ! Fraction of mesozooplankton performing DVM
namp5zmes (PISCES-Research)
!-----------------------------------------------------------------------
&namp5zmes ! parameters for mesozooplankton
!-----------------------------------------------------------------------
part2 = 0.75 ! part of calcite not dissolved in mesozoo guts
grazrat2 = 0.5 ! maximal mesozoo grazing rate
bmetexc2 = .true. ! Metabolic use of excess carbon
resrat2 = 0.003 ! exsudation rate of mesozooplankton
lmzrat2 = 0.003 ! Linear mortality rate of mesozooplankton
mzrat2 = 0.01 ! mesozooplankton mortality rate
xpref2d = 1. ! meso preference for diatoms
xpref2n = 0.75 ! meso preference for nano
xpref2z = 1. ! meso preference for zoo
xpref2m = 0. ! meso preference for zoo
xpref2c = 0.3 ! meso preference for poc
xthresh2zoo = 1.E-8 ! zoo feeding threshold for mesozooplankton
xthresh2dia = 1.E-8 ! diatoms feeding threshold for mesozooplankton
xthresh2phy = 1.E-8 ! nanophyto feeding threshold for mesozooplankton
xthresh2mes = 1.E-8 ! meso feeding threshold for mesozooplankton
xthresh2poc = 1.E-8 ! poc feeding threshold for mesozooplankton
xthresh2 = 3.E-7 ! Food threshold for grazing
xkgraz2 = 20.E-6 ! half sturation constant for meso grazing
epsher2 = 0.5 ! Efficicency of Mesozoo growth
epsher2min = 0.5 ! Minimum efficiency of mesozoo growth
ssigma2 = 0.67 ! Fraction excreted as semi-labile DOM
srespir2 = 0.15 ! Active respiration
unass2c = 0.3 ! non assimilated fraction of C by mesozoo
unass2n = 0.3 ! non assimilated fraction of N by mesozoo
unass2p = 0.3 ! non assimilated fraction of P by mesozoo
xsigma2 = 0.5 ! Predation window size
xsigma2del = 0.5 ! Predation window size scaling
grazflux = 3.E3 ! flux-feeding rate
ln_dvm_meso = .false. ! Activates DVM for mesozooplankton
xfracmig = 0.25 ! Fraction of mesozooplankton performing DVM
Microzooplankton
namp2zzoo, namp4zzoo, namp5zzoo
In namp*zzoo are defined all the parameters of the microzooplankton for each PISCES version. This includes grazing and mortality rates, food preferencies (nanophytoplankton, organic particles), the associated different feeding threshold, growth efficiency, grazing half-saturation constant, predation window size, non assimilated fraction of phytoplankton,...
namp2zzoo (PISCES-Simple)
!-----------------------------------------------------------------------
&namp2zzoo ! parameters for microzooplankton for PISCES reduced - ln_p2z
!-----------------------------------------------------------------------
part = 0.75 ! part of calcite not dissolved in microzoo guts
grazrat = 2.0 ! maximal zoo grazing rate
resrat = 0.02 ! Linear mortality rate of zooplankton
mzrat = 0.02 ! zooplankton mortality rate
xprefc = 0.15 ! Microzoo preference for POM
xprefn = 1. ! Microzoo preference for Nanophyto
xprefz = 0.0 ! Microzoo preference for Microzoo
xthreshphy = 1.E-8 ! Nanophyto feeding threshold for microzooplankton
xthreshpoc = 1.E-8 ! POC feeding threshold for microzooplankton
xthreshzoo = 1.E-8 ! Microzoo feeding threshold for microzooplankton
xthresh = 3.E-7 ! Food threshold for feeding
xkgraz = 20.E-6 ! half sturation constant for grazing
epsher = 0.4 ! Efficiency of microzoo growth
epshermin = 0.4 ! Minimum efficiency of microzoo growth
sigma1 = 0.6 ! Fraction of microzoo excretion as DOM
unass = 0.3 ! non assimilated fraction of phyto by zoo
namp4zzoo (PISCES-Operational)
!-----------------------------------------------------------------------
&namp4zzoo ! parameters for microzooplankton for PISCES std - ln_p4z
!-----------------------------------------------------------------------
part = 0.75 ! part of calcite not dissolved in microzoo guts
grazrat = 2.0 ! maximal zoo grazing rate
resrat = 0.02 ! Linear mortality rate of zooplankton
mzrat = 0.01 ! zooplankton mortality rate
xprefc = 0.15 ! Microzoo preference for POM
xprefn = 1.0 ! Microzoo preference for Nanophyto
xprefd = 0.9 ! Microzoo preference for Diatoms
xprefz = 0.0 ! Microzoo preference for Microzoo
xthreshdia = 1.E-8 ! Diatoms feeding threshold for microzooplankton
xthreshphy = 1.E-8 ! Nanophyto feeding threshold for microzooplankton
xthreshpoc = 1.E-8 ! POC feeding threshold for microzooplankton
xthreshzoo = 1.E-8 ! Microzoo feeding threshold for microzooplankton
xthresh = 3.E-7 ! Food threshold for feeding
xkgraz = 20.E-6 ! half sturation constant for grazing
epsher = 0.4 ! Efficiency of microzoo growth
epshermin = 0.4 ! Minimum efficiency of microzoo growth
sigma1 = 0.67 ! Fraction of microzoo excretion as DOM
unass = 0.3 ! non assimilated fraction of phyto by zoo
xsigma = 0.5 ! Predation window size
xsigmadel = 0.5 ! Predation window size scaling
namp5zzoo (PISCES-Research)
!-----------------------------------------------------------------------
&namp5zzoo ! parameters for microzooplankton
!-----------------------------------------------------------------------
part = 0.75 ! part of calcite not dissolved in microzoo gutsa
grazrat = 2.0 ! maximal zoo grazing rate
bmetexc = .true. ! Metabolic use of excess carbon
resrat = 0.01 ! exsudation rate of zooplankton
lmzrat = 0.01 ! Linear mortality rate of zooplankton
mzrat = 0.01 ! zooplankton mortality rate
xprefc = 0.15 ! Microzoo preference for POM
xprefn = 0.95 ! Microzoo preference for Nanophyto
xprefp = 1.0 ! Microzoo preference for picophyto
xprefd = 0.85 ! Microzoo preference for Diatoms
xprefz = 0. ! Microzoo preference for microzooplankton
xthreshdia = 1.E-8 ! Diatoms feeding threshold for microzooplankton
xthreshphy = 1.E-8 ! Nanophyto feeding threshold for microzooplankton
xthreshpic = 1.E-8 ! Picophyto feeding threshold for microzooplankton
xthreshzoo = 1.E-8 ! Microzoo feeding threshold for microzooplankton
xthreshpoc = 1.E-8 ! POC feeding threshold for microzooplankton
xthresh = 3.E-7 ! Food threshold for feeding
xkgraz = 20.E-6 ! half saturation constant for grazing
epsher = 0.5 ! Efficiency of microzoo growth
epshermin = 0.5 ! Minimum efficiency of microzoo growth
ssigma = 0.67 ! Fraction excreted as semi-labile DOM
srespir = 0.15 ! Active respiration
unassc = 0.3 ! non assimilated fraction of C by zoo
unassn = 0.3 ! non assimilated fraction of N by zoo
unassp = 0.3 ! non assimilated fraction of P by zoo
xsigma = 0.5 ! Predation window size
xsigmadel = 0.5 ! Predation window size scaling
Iron Chemistry
nampisfer
In nampisfer, the concentration of diagnostic Fe ligands in seawater can be set either by a constant value (ligand concentration, in nmol L\(^{-1}\)) or by a variable ligand field diagnosed from Dissolved Organic Carbon (ln_ligvar = .true.). This also includes the scavenging (adsorption) rates of Fe on biogenic particles and dust, the constant rate of nanoparticle formation from precipitation of Fe\(^{3+}\), and the fraction of scavenged Fe added to the particulate Fe pool.
!-----------------------------------------------------------------------
&nampisfer ! parameters for iron chemistry
!-----------------------------------------------------------------------
ln_ligvar = .false. ! variable ligand concentration
xlam1 = 0.04 ! scavenging rate of Iron by biogenic particles
xlamdust = 700.0 ! Scavenging rate of Iron by dust
ligand = 1.E-9 ! Ligands concentration
kfep = 0.01 ! Nanoparticle formation rate constant
scaveff = 1.0 ! Fraction of scavenged Fe that goes to PFe
Remineralization
nampisrem
In nampisrem are defined the nitrification rate, the remineralization parameters of Si, the labile biogenic silica fraction, the Fe/C quota and half-saturation constant of bacteria, and the remineralization rates of dissolved carbon, nitrogen and phosphorus for the PISCES-Research case.
!-----------------------------------------------------------------------
&nampisrem ! parameters for remineralization
!-----------------------------------------------------------------------
nitrif = 0.05 ! NH4 nitrification rate
xsirem = 0.003 ! remineralization rate of Si
xsiremlab = 0.03 ! fast remineralization rate of Si
xsilab = 0.5 ! Fraction of labile biogenic silica
feratb = 60.E-6 ! Fe/C quota in bacteria
xkferb = 3E-10 ! Half-saturation constant for bacteria Fe/C
! ! ln_p5z
xremikc = 0.4 ! remineralization rate of DOC
xremikn = 0.4 ! remineralization rate of DON
xremikp = 0.4 ! remineralization rate of DOP
Organic Particle Degradation
nampispoc
In nampispoc are defined the parameters for the variable reactivity of particulate organic matter (Aumont et al., 20171). These parameters are applied to PISCES-Operational and PISCES-Research. By default, 15 classes of lability are set for particulate organic matter. It also includes the remineralisation rates of particulate organic carbon (POC), nitrogen (PON), and phosphorus (POP) for the PISCES-Research case.
!-----------------------------------------------------------------------
&nampispoc ! parameters for organic particles
!-----------------------------------------------------------------------
jcpoc = 15 ! Number of lability classes
rshape = 1.0 ! Shape of the gamma function
! ! ln_p5z
xremipc = 0.035 ! remineralisation rate of POC
xremipn = 0.03 ! remineralisation rate of PON
xremipp = 0.035 ! remineralisation rate of POP
Implicit Diazotrophy
nampisdiaz
In nampisdiaz the parameters for the implicit representation of diazotrophy (i.e. not explicitly resolved in the model) are defined. It includes the nitrogen fixation rate, light sensitivity and the half-saturation constant of Fe in diazotrophs.
!-----------------------------------------------------------------------
&nampisdiaz ! Namelist parameters for diazotrophy
!-----------------------------------------------------------------------
nitrfix = 2.E-7 ! Nitrogen fixation rate
diazolight = 30. ! Diazotrophs sensitivity to light (W/m2)
concfediaz = 1.5E-10 ! Diazotrophs half-saturation Cste for Iron
Warning
Implicit diazotrophy is not included in PISCES-Simple. It is only active in PISCES-Operational and PISCES-Research.
Calcite Chemistry
nampiscal
In nampiscal, the parameters relative to the dissolution of CaCO\(_3\) are defined and include the dissolution rate constant and the order of the dissolution reaction.
!-----------------------------------------------------------------------
&nampiscal ! parameters for Calcite chemistry
!-----------------------------------------------------------------------
kdca = 1000. ! calcite dissolution rate constant (1/time)
nca = 4.7 ! order of dissolution reaction (dimensionless)
External Supplies
nampisbc
In nampisbc, you can define input files for atmospheric dust deposition (sn_dust) used to estimate the spatial distribution of PO\(_4\), Si, and Fe inputs due to dust sinking along the water column, as well as Fe sources from sediments (sn_ironsed) and hydrothermal vents (sn_hydrofe). You can define their frequency (monthly, annual) and their location (cn_dir). By default, these files must be placed in the run directory.
You can enable/disable the input of Fe from sediments (ln_ironsed), sea ice (ln_ironice) and hydrothermal vents (ln_hydrofe).
The two parameters sedfeinput and distcoast are used to enhance the coastal and island input of Fe when ln_ironsed is enabled.
The two parameters mfracand wdust are respectively the Fe mineral fraction in atmospheric dust and the sinking speed of dust in the water column (m/day).
icefeinput is the fixed constant concentration of Fe in sea ice (nmol L\(^{-1}\)) used to calculate the iron flux between sea ice and sea water (ln_ironice = .true.), based on a simple parameterization from Lancelot et al. (20092).
The hratio parameter sets the Fe to \(^3\)He ratio in the case of the Fe supply of hydrothermal vents (ln_hydrofe = .true.).
lgw_rath sets the weak ligand ratio from hydrothermal sources in the case of prognostic ligands (ln_ligand = .true., see nampismod).
!-----------------------------------------------------------------------
&nampisbc ! parameters for inputs deposition
!-----------------------------------------------------------------------
! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename !
sn_dust = 'dust.orca' , -1 , 'dust' , .true. , .true. , 'yearly' , '' , '' , ''
sn_ironsed = 'bathy.orca' , -12 , 'bathy' , .false. , .true. , 'yearly' , '' , '' , ''
sn_hydrofe = 'hydrofe.orca' , -12 , 'epsdb' , .false. , .true. , 'yearly' , '' , '' , ''
!
cn_dir = './' ! root directory for the location of the dynamical files
ln_ironsed = .false. ! boolean for Fe input from sediments
ln_ironice = .false. ! boolean for Fe input from sea ice
ln_hydrofe = .false. ! boolean for from hydrothermal vents
sedfeinput = 1.E-9 ! Coastal release of Iron
distcoast = 5.E3 ! Distance off the coast for Iron from sediments
mfrac = 0.035 ! Fe mineral fraction of dust
wdust = 2.0 ! Dust sinking speed
icefeinput = 15.E-9 ! Iron concentration in sea ice
hratio = 1.E+7 ! Fe to 3He ratio assumed for vent iron supply
! ! ln_ligand
lgw_rath = 0.2 ! Weak ligand ratio from sed hydro sources
Prognostic Ligands
nampislig
In nampislig are defined all the parameters for prognostic ligands (ln_ligand enabled in nampismod). This includes the lifetime of weak and strong ligands (years), the photolysis (decomposition by light) of weak ligand, and the production of remineralized ligand.
!-----------------------------------------------------------------------
&nampislig ! Namelist parameters for ligands, nampislig
!-----------------------------------------------------------------------
rlgw = 300. ! Lifetime (years) of weak ligands
rlig = 1.E-4 ! Remin ligand production per unit C
prlgw = 3.E-4 ! Photolysis of weak ligand
rlgs = 1. ! Lifetime (years) of strong ligands
xklig = 1.E-9 ! 1/2 saturation constant of photolysis
Sediment Burial
nampissed
nampissed contains the parameters of calcite and silica burial in sediments for the sediment metamodel. This includes the minimum and variable coefficient of burial efficiency, the percentages of silica and calcite loss in the sediments, as well as the minimum and variable values of calcite dissolution at the sea floor.
!-----------------------------------------------------------------------
&nampissed ! Namelist parameters for burial in sediments ( Dune et Al. 2007 )
!-----------------------------------------------------------------------
bureffmin = 0.020 ! Minimum burial efficiency
bureffvar = 0.053 ! Variable coef. for burial efficiency
sedsilfrac = 0.03 ! percentage of silica loss in the sediments
sedcalfrac = 0.78 ! percentage of calcite loss in the sediments ( 0.78 is for river x1.5 )
sedfactcalmin = 0.3 ! Minimum value for dissolving calcite at the bottom
sedfactcalvar = 0.7 ! Variable value for dissolving calcite at the bottom
Sea-ice Tracers
nampisice
In nampisice, you have the possibility to prescribe biogeochemical tracers in sea ice. The way in which tracers are prescribed is done in the namtrc_ice block of the namelist_top_cfg file. Regarding Fe in sea ice, when its value is prescribed via this method, ln_ironce is automatically set to.false..
!-----------------------------------------------------------------------
&nampisice ! Prescribed sea ice tracers
!-----------------------------------------------------------------------
!========================================================================
! constant ocean tracer concentrations are defined in trcice_pisces.F90
! (Global, Arctic, Antarctic and Baltic)
! trc_ice_ratio : >=0 & <=1 => prescribed ice/ocean tracer concentration ratio
! : = -1 => the ice-ocean tracer concentration ratio
! follows the ice-ocean salinity ratio
! : = -2 => tracer concentration in sea ice is prescribed
! and trc_ice_prescr is used
! trc_ice_prescr : prescribed tracer concentration. used only if
! trc_ice_ratio = -2. equals -99 if not used.
! cn_trc_o : = 'GL' => use global ocean values making the Baltic
! distinction only
! : = 'AA' => use specific Arctic/Antarctic/Baltic values
!========================================================================
! sn_tri_ ! trc_ice_ratio ! trc_ice_prescr ! cn_trc_o
sn_tri_dic = -1., -99., 'AA'
sn_tri_doc = 0., -99., 'AA'
sn_tri_tal = -1., -99., 'AA'
sn_tri_oxy = -1., -99., 'AA'
sn_tri_cal = 0., -99., 'AA'
sn_tri_po4 = -1., -99., 'AA'
sn_tri_poc = 0., -99., 'AA'
sn_tri_goc = 0., -99., 'AA'
sn_tri_bfe = 0., -99., 'AA'
sn_tri_num = 0., -99., 'AA'
sn_tri_sil = -1., -99., 'AA'
sn_tri_dsi = 0., -99., 'AA'
sn_tri_gsi = 0., -99., 'AA'
sn_tri_phy = 0., -99., 'AA'
sn_tri_dia = 0., -99., 'AA'
sn_tri_zoo = 0., -99., 'AA'
sn_tri_mes = 0., -99., 'AA'
sn_tri_fer = -2., 15E-9, 'AA'
sn_tri_sfe = 0., -99., 'AA'
sn_tri_dfe = 0., -99., 'AA'
sn_tri_nfe = 0., -99., 'AA'
sn_tri_nch = 0., -99., 'AA'
sn_tri_dch = 0., -99., 'AA'
sn_tri_no3 = -1., -99., 'AA'
sn_tri_nh4 = 1., -99., 'AA'
Warning
This namelist block is not available in CROCO
Tracer Damping
nampisdmp
In nampisdmp, the restoration of nutrients (NO\(_3\), PO\(_4\), Si) and/or alkalinity to a global mean value from data can be enabled (ln_pisdmp, ln_pisdmp_alk). This restoration is done at the end of each year.
!-----------------------------------------------------------------------
&nampisdmp ! Damping
!-----------------------------------------------------------------------
ln_pisdmp = .true. ! Relaxation for some tracers to a mean value
ln_pisdmp_alk = .true. ! Relaxation of total alkalinity to a mean value
Correction of negative tracer concentration in NEMO (TOP)
In NEMO (TOP module), an artificial correction for negative concentrations of tracers can be enbaled (ln_trcrad = .true.) in the namtrc_rad block of the namelist_top_cfg
Debugging Options
nampisdbg
In nampisdbg are defined all Booleans that allow biogeochemical processes to be disabled one by one in order to facilitate the model debugging process. By default, all these processes are obviously enabled.
!-----------------------------------------------------------------------
&nampisdbg ! Namelist parameters for debugging
!-----------------------------------------------------------------------
ln_bio = .true. ! Enable biological processes
ln_flx = .true. ! Enable air-sea gas exchange
ln_sed = .true. ! Enable sediment mobilisation processes
ln_lys = .true. ! Enable carbonate chemistry
ln_fechem = .true. ! Enable Iron chemistry
ln_prod = .true. ! Enable Phyptoplankton growth rate
ln_mort = .true. ! Enable Phyptoplankton mortality
ln_micro = .true. ! Enable microzooplankton
ln_meso = .true. ! Enable mesozooplankton
ln_poc = .true. ! Enable organic particles processes
ln_agg = .true. ! Enable particles Aggregation
ln_rem = .true. ! Enable Remineralisation
ln_diaz = .true. ! Enable diazotrophy
CROCO
Here we describe only the differences between the PISCES namelist distributed with the CROCO model and the one distributed with the NEMO model. For a complete overview of the namelist, see the NEMO section above.
Unlike NEMO, the PISCES namelist no longer has the nampismod section. Indeed, in CROCO, the choice of PISCES versions is defined by cpp keys and not by Boolean flags as in NEMO.
Tracer Definition
nampistrc
The PISCES namelist (ref/cfg) includes a new namelist block called nampistrc in which the list of PISCES tracers is defined according to the selected version. Here we present the list of prognostic tracers for each PISCES version
nampistrc PISCES-Simple
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampistrc ! tracers definition
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
!
! ! name ! title of the field ! units
! ! ! !
!
tracer(1) = 'DIC ' , 'Dissolved inorganic Concentration ', 'mmol/m3'
tracer(2) = 'Alkalini' , 'Total Alkalinity Concentration ', 'meq/m3 '
tracer(3) = 'O2 ' , 'Dissolved Oxygen Concentration ', 'mmol/m3'
tracer(4) = 'POC ' , 'Small organic carbon Concentration ', 'mmol/m3'
tracer(5) = 'PHY ' , 'Nanophytoplankton Concentration ', 'mmol/m3'
tracer(6) = 'ZOO ' , 'Microzooplankton Concentration ', 'mmol/m3'
tracer(7) = 'DOC ' , 'Dissolved organic Concentration ', 'mmol/m3'
tracer(8) = 'NO3 ' , 'Nitrates Concentration ', 'mmol/m3'
tracer(9) = 'Fer ' , 'Dissolved Iron Concentration ', 'mmol/m3'
nampistrc PISCES-Operational + prognostic Ligands
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampistrc ! tracers definition
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
!
! ! name ! title of the field ! units
! ! ! !
! ! ! !
tracer(1) = 'DIC ' , 'Dissolved inorganic Concentration ', 'mmol/m3'
tracer(2) = 'Alkalini' , 'Total Alkalinity Concentration ', 'meq/m3 '
tracer(3) = 'O2 ' , 'Dissolved Oxygen Concentration ', 'mmol/m3'
tracer(4) = 'CaCO3 ' , 'Calcite Concentration ', 'mmol/m3'
tracer(5) = 'PO4 ' , 'Phosphate Concentration ', 'mmol/m3'
tracer(6) = 'POC ' , 'Small organic carbon Concentration ', 'mmol/m3'
tracer(7) = 'Si ' , 'Silicate Concentration ', 'mmol/m3'
tracer(8) = 'PHY ' , 'Nanophytoplankton Concentration ', 'mmol/m3'
tracer(9) = 'ZOO ' , 'Microzooplankton Concentration ', 'mmol/m3'
tracer(10) = 'DOC ' , 'Dissolved organic Concentration ', 'mmol/m3'
tracer(11) = 'PHY2 ' , 'Diatoms Concentration ', 'mmol/m3'
tracer(12) = 'ZOO2 ' , 'Mesozooplankton Concentration ', 'mmol/m3'
tracer(13) = 'DSi ' , 'Diatoms Silicate Concentration ', 'mmol/m3'
tracer(14) = 'Fer ' , 'Dissolved Iron Concentration ', 'mmol/m3'
tracer(15) = 'BFe ' , 'Big iron particles Concentration ', 'mmol/m3'
tracer(16) = 'GOC ' , 'Big organic carbon Concentration ', 'mmol/m3'
tracer(17) = 'SFe ' , 'Small iron particles Concentration ', 'mmol/m3'
tracer(18) = 'DFe ' , 'Diatoms iron Concentration ', 'mmol/m3'
tracer(19) = 'GSi ' , 'Sinking biogenic Silicate Concentration', 'mmol/m3'
tracer(20) = 'NFe ' , 'Nano iron Concentration ', 'mmol/m3'
tracer(21) = 'NCHL ' , 'Nano chlorophyl Concentration ', 'mg/m3'
tracer(22) = 'DCHL ' , 'Diatoms chlorophyl Concentration ', 'mg/m3'
tracer(23) = 'NO3 ' , 'Nitrates Concentration ', 'mmol/m3'
tracer(24) = 'NH4 ' , 'Ammonium Concentration ', 'mmol/m3'
tracer(25) = 'LGW ' , 'Ligands Concentration ', 'mmol/m3'
nampistrc PISCES-Research + prognostic Ligands
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampistrc ! tracers definition
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
!
! ! name ! title of the field ! units
! ! ! !
! ! ! !
tracer(1) = 'DIC ' , 'Dissolved inorganic Concentration ', 'mmol/m3'
tracer(2) = 'Alkalini' , 'Total Alkalinity Concentration ', 'meq/m3 '
tracer(3) = 'O2 ' , 'Dissolved Oxygen Concentration ', 'mmol/m3'
tracer(4) = 'CaCO3 ' , 'Calcite Concentration ', 'mmol/m3'
tracer(5) = 'PO4 ' , 'Phosphate Concentration ', 'mmol/m3'
tracer(6) = 'POC ' , 'Small organic carbon Concentration ', 'mmol/m3'
tracer(7) = 'Si ' , 'Silicate Concentration ', 'mmol/m3'
tracer(8) = 'PHY ' , 'Nanophytoplankton Concentration ', 'mmol/m3'
tracer(9) = 'ZOO ' , 'Microzooplankton Concentration ', 'mmol/m3'
tracer(10) = 'DOC ' , 'Dissolved organic Concentration ', 'mmol/m3'
tracer(11) = 'PHY2 ' , 'Diatoms Concentration ', 'mmol/m3'
tracer(12) = 'ZOO2 ' , 'Mesozooplankton Concentration ', 'mmol/m3'
tracer(13) = 'DSi ' , 'Diatoms Silicate Concentration ', 'mmol/m3'
tracer(14) = 'Fer ' , 'Dissolved Iron Concentration ', 'mmol/m3'
tracer(15) = 'BFe ' , 'Big iron particles Concentration ', 'mmol/m3'
tracer(16) = 'GOC ' , 'Big organic carbon Concentration ', 'mmol/m3'
tracer(17) = 'SFe ' , 'Small iron particles Concentration ', 'mmol/m3'
tracer(18) = 'DFe ' , 'Diatoms iron Concentration ', 'mmol/m3'
tracer(19) = 'GSi ' , 'Sinking biogenic Silicate Concentration', 'mmol/m3'
tracer(20) = 'NFe ' , 'Nano iron Concentration ', 'mmol/m3'
tracer(21) = 'NCHL ' , 'Nano chlorophyl Concentration ', 'mg/m3'
tracer(22) = 'DCHL ' , 'Diatoms chlorophyl Concentration ', 'mg/m3'
tracer(23) = 'NO3 ' , 'Nitrates Concentration ', 'mmol/m3'
tracer(24) = 'NH4 ' , 'Ammonium Concentration ', 'mmol/m3'
tracer(25) = 'LGW ' , 'Ligands Concentration ', 'mmol/m3'
tracer(26) = 'DON ' , 'Dissolved organic N Concentration ', 'mmol/m3'
tracer(27) = 'DOP ' , 'Dissolved organic P Concentration ', 'mmol/m3'
tracer(28) = 'PON ' , 'Small PON Concentration ', 'mmol/m3'
tracer(29) = 'POP ' , 'Small POP Concentration ', 'mmol/m3'
tracer(30) = 'PHYN ' , 'Nanophytoplankton N biomass ', 'mmol/m3'
tracer(31) = 'PHYP ' , 'Nanophytoplankton P biomass ', 'mmol/m3'
tracer(32) = 'DIAN ' , 'Diatoms N biomass ', 'mmol/m3'
tracer(33) = 'DIAP ' , 'Diatoms P biomass ', 'mmol/m3'
tracer(34) = 'PIC ' , 'Picophytoplankton C biomass ', 'mmol/m3'
tracer(35) = 'PICN ' , 'Picophytoplankton N biomass ', 'mmol/m3'
tracer(36) = 'PICP ' , 'Picophytoplankton P biomass ', 'mmol/m3'
tracer(37) = 'PFe ' , 'Picophytoplankton Fe biomass ', 'mmol/m3'
tracer(38) = 'PCHL ' , 'Picophytoplankton Chl biomass ', 'mg/m3'
tracer(39) = 'GON ' , 'Big PON Concentration ', 'mmol/m3'
tracer(40) = 'GOP ' , 'Big POP Concentration ', 'mmol/m3'
Particle Sedimentation
nampis_snk
The nampis_snk namelist block offers the possibility to choose between two particle sedimentation schemes: A MUSCL sedimentation scheme (ln_sink_mus) with the possibility to define the number of iterations and a semi-Lagrangian sedimentation scheme (ln_sink_slg) with three different choices of boundary conditions. Of course, the two schemes cannot be enabled at the same time.
!-----------------------------------------------------------------------
&nampis_snk ! Sedimentation of particles
!-----------------------------------------------------------------------
ln_sink_mus = .true. ! MUSCL sinking scheme
nitermax = 2 ! number of iterations for sedimentation
ln_sink_slg = .false. ! Semi-Lagrangian sinking scheme
nn_sink_lbc = 0 ! Type of boundary conditions
! ! 0 - Strictly monotonic conditions ( default )
! ! 1 - Dirichlet condition : linear continuation
! ! 2 - Neumann condition
External Supplies
nampisbc
In nampisbc, you can enable/disable the atmospheric dust deposition (ln_dust) used to estimate the spatial distribution of PO\(_4\), Si, and Fe inputs from dust, the atmospheric deposition of nitrogen (ln_ndepo) and the Fe source from sediments (ln_ironsed).
The sedfeinput parameter defines the concentration of coastal Fe (nmol l\(^{-1}\)) when ln_ironsed is enabled.
The mfracand wdust parameters are respectively the Fe mineral fraction in atmospheric dust and the sinking speed of dust in the water column (m/day).
!-----------------------------------------------------------------------
&nampisbc ! parameters for inputs deposition
!-----------------------------------------------------------------------
ln_dust = .true. ! boolean for dust input from the atmosphere
ln_ndepo = .true. ! boolean for atmospheric deposition of N
ln_ironsed = .true. ! boolean for Fe input from sediments
sedfeinput = 2.E-9 ! Coastal release of Iron
mfrac = 0.035 ! Fe mineral fraction of dust
wdust = 2.0 ! Dust sinking speed
Dust input and nitrogen deposition file
The definition of the input file for dust and nitrogen deposition croco_frcbio.nc is defined in the CROCO namelist croco.in. The file croco_frcbio.nc generated with the croco-tools, depending on your configuration, should be located in the CROCO_FILES directory of your run directory.
Restart Settings
nampisrst
In nampisrst the names and location of the PISCES restart files written and read are defined. By default, the files are located in the CROCO_FILES directory of your configuration directory.
!-----------------------------------------------------------------------
&nampisrst ! parameters for restarting
!-----------------------------------------------------------------------
cn_pisrst_in = "croco_rst_pisces_ini.nc" ! name of the input restart file name of pisces
cn_pisrst_indir = "CROCO_FILES" ! directory from which to read input pisces restarts
cn_pisrst_out = "croco_rst_pisces.nc" ! suffix of pass. restart name (output)
cn_pisrst_outdir = "CROCO_FILES" ! directory to which to write output pisces restarts
-
Olivier Aumont, Marco van Hulten, Matthieu Roy-Barman, Jean-Claude Dutay, Christian Éthé, and Marion Gehlen. Variable reactivity of particulate organic matter in a global ocean biogeochemical model. Biogeosciences, 14(9):2321–2341, 2017. doi:10.5194/bg-14-2321-2017. ↩
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C. Lancelot, A. de Montety, H. Goosse, S. Becquevort, V. Schoemann, B. Pasquer, and M. Vancoppenolle. Spatial distribution of the iron supply to phytoplankton in the southern ocean: a model study. Biogeosciences, 6(12):2861–2878, 2009. URL: https://bg.copernicus.org/articles/6/2861/2009/, doi:10.5194/bg-6-2861-2009. ↩