Sediment Module
All parameters and options of the explicit sediment biogeochemistry modeling module of PISCES are described below for NEMO and CROCO. They are accessible in the namelist_sediment_ref file. There is no distinction in the sediment module namelist between the different versions of PISCES, as this module can only be activated with PISCES-Operational.
Methodology for namelist parameter changes
The namelist parameters of the PISCES diagenesis model can be modified, taking care to first copy them from the namelist_sediment_ref file to the namelist_sediment_cfg file, in the same namelist block.
NEMO
The reference namelist of the sediment module namelist_sediment_ref is available in the SHARED subdirectory of the cfgs directory of the NEMO source code.
Run Options
nam_run
In nam_run, two-way coupling can be enabled (ln_sed_2way) allowing fluxes at the sediment–water interface to modify PISCES ocean prognostic variables. The default setting is one-way coupling from water to sediments (ln_sed_2way = .false.). The choice between the two orders of the Rosenbrock method (3 or 4) can be made here, as can the setting of the tolerance for absolute and relative errors in the Rosenbrock method.
!-----------------------------------------------------------------------
&nam_run ! Characteristics of the simulation
!-----------------------------------------------------------------------
ln_sed_2way = .false. ! 2 way coupling with pisces
nrosorder = 3 ! Order of the rosenbrock methode (3,4)
rosatol = 1.E-3 ! Tolerance for the absolute error
rosrtol = 1.E-4 ! Tolerance for the relative error
Geometric Characteristics
nam_geom
The geometric characteristics of the sediment column are defined in nam_geom: the number of vertical layers, the minimum spacing between layers, the maximum depth of the column, the porosity of the sediments at the surface and at the bottom, and the length scale of the porosity variation.
!-----------------------------------------------------------------------
&nam_geom ! Characteristics of the sediment columns
!-----------------------------------------------------------------------
jpksed = 25 ! Number of vertical layers
sedzmin = 0.1 ! Minimum vertical spacing
sedhmax = 50.0 ! Maximum depth of the sediment
sedkth = 14.0 ! Default parameters
sedacr = 6.0 ! Default parameters
porsurf = 0.9 ! Sediment porosity at the surface
porinf = 0.75 ! Sediment porosity at infinite depth
rhox = 0.25 ! Length scale of porosity variation (cm)
Info
The horizontal grid is identical to that of the ocean model, with land points removed. The first sediment layer corresponds to the bottom layer of the water column in the ocean model. The sediment module is built on a typical vertical discretization with a variable layer thickness increasing with depth (defined in the namelist). In the default configuration, this discretization is represented by 25 vertical levels.
Prognostic Tracers
nam_trased
All prognostic tracers of the sediment module are defined in nam_trased. They are separated into solid species (sedsol in %) and dissolved species (sedwat in mol L\(^{-1}\)) :
- 11 dissolved species: O\(_2\), Si, DIC, Alkalinity, NO\(_3\), NH\(_4\), PO\(_4\), H\(_2\)S, SO\(_4\), Fe\(^{2+}\), and Ligands.
- 11 solid species: biogenic silicate (BSi), Clay, calcite, 6 different classes of Particulate Organic Carbon lability (from labile, semi-labile to refractory, ranging from 1 to 6), FeS and Fe(OH)\(^{3}\).
!-----------------------------------------------------------------------
&nam_trased ! Prognostic variables
!-----------------------------------------------------------------------
! ! ! ! !
! ! name ! title of the field ! units ! initial data from file or not !
! ! ! ! !
sedsol(1) = 'SedFeO ' , 'Fe(OH)3 Concentration ', '%'
sedsol(2) = 'SedFeS ' , 'FeS Concentration ', '%'
sedsol(3) = 'SedCaCO3' , 'Calcite Concentration ', '%'
sedsol(4) = 'SedBSi ' , 'Biogenic Silicate Concentration ', '%'
sedsol(5) = 'SedClay ' , 'Clay Concentration ', '%'
sedsol(6) = 'SedPOC1 ' , 'POC age Concentration ', '%'
sedsol(7) = 'SedPOC2 ' , 'POC age Concentration ', '%'
sedsol(8) = 'SedPOC3 ' , 'POC age Concentration ', '%'
sedsol(9) = 'SedPOC4 ' , 'POC age Concentration ', '%'
sedsol(10) = 'SedPOC5 ' , 'POC age Concentration ', '%'
sedsol(11) = 'SedPOC6 ' , 'POC age Concentration ', '%'
sedwat(1) = 'SedO2 ' , 'Dissolved Oxygen Concentration ', 'mol/L'
sedwat(2) = 'SedNO3 ' , 'Nitrates Concentration ', 'mol/L'
sedwat(3) = 'SedPO4 ' , 'Phosphate Concentration ', 'mol/L'
sedwat(4) = 'SedNH4 ' , 'Total Ammonium Concentration ', 'mol/L '
sedwat(5) = 'SedH2S ' , 'Total H2S Concentration ', 'mol/L '
sedwat(6) = 'SedSO4 ' , 'Total SO4 Concentration ', 'mol/L '
sedwat(7) = 'SedFe2 ' , 'Total Fe2+ Concentration ', 'mol/L '
sedwat(8) = 'SedAlkalini' , 'Total Alkalinity Concentration ', 'eq/L '
sedwat(9) = 'Sedligand ' , 'Total ligand Concentration ', 'mol/L '
sedwat(10) = 'SedDIC ' , 'Dissolved inorganic Concentration ', 'mol/L'
sedwat(11) = 'SedSil ' , 'Silicate Concentration ', 'mol/L'
Diagnostics
nam_diased
All diagnostics of the sediment module are defined in nam_diased. These include solid and dissolved species fluxes, the sedimentation rate, and the number of iterations from the Rosenbrock method.
!-----------------------------------------------------------------------
&nam_diased ! Diagnostic arrays
!-----------------------------------------------------------------------
!
seddiag2d(1) = 'FlxO2 ' , 'Dissolved Oxygen Flux ', 'mol/L'
seddiag2d(2) = 'FlxNO3 ' , 'Nitrates flux ', 'mol/cm2/s'
seddiag2d(3) = 'FlxPO4 ' , 'Phosphate flux ', 'mol/cm2/s'
seddiag2d(4) = 'FlxNH4 ' , 'Total Ammonium flux ', 'mol/cm2/s'
seddiag2d(5) = 'FlxH2S ' , 'Total H2S flux ', 'mol/cm2/s'
seddiag2d(6) = 'FlxSO4 ' , 'Total SO4 flux ', 'mol/cm2/s'
seddiag2d(7) = 'FlxFe2 ' , 'Total Fe2+ flux ', 'mol/cm2/s'
seddiag2d(8) = 'FlxAlkalini' , 'Total Alkalinity flux ', 'mol/cm2/s'
seddiag2d(9) = 'FlxLig ' , 'Total Ligand flux ', 'mol/cm2/s'
seddiag2d(10) = 'FlxDIC ' , 'Dissolved inorganic carbon flux ', 'mol/cm2/s'
seddiag2d(11) = 'FlxSi ' , 'Silicate flux ', 'mol/cm2/s'
seddiag2d(12) = 'FlxFeO ' , 'FeO burial flux ', 'mol/cm2/s'
seddiag2d(13) = 'FlxFeS ' , 'FeS burial flux ', 'mol/cm2/s'
seddiag2d(14) = 'FlxCaCO3 ' , 'Calcite burial flux ', 'mol/cm2/s'
seddiag2d(15) = 'FlxBSi ' , 'BSi burial flux ', 'mol/cm2/s'
seddiag2d(16) = 'FlxClay ' , 'Clay burial flux ', 'mol/cm2/s'
seddiag2d(17) = 'FlxPOC1 ' , 'POCT burial flux ', 'mol/cm2/s'
seddiag2d(18) = 'FlxPOC2 ' , 'POCT burial flux ', 'mol/cm2/s'
seddiag2d(19) = 'FlxPOC3 ' , 'POCT burial flux ', 'mol/cm2/s'
seddiag2d(20) = 'FlxPOC4 ' , 'POCT burial flux ', 'mol/cm2/s'
seddiag2d(21) = 'FlxPOC5 ' , 'POCT burial flux ', 'mol/cm2/s'
seddiag2d(22) = 'FlxPOC6 ' , 'POCT burial flux ', 'mol/cm2/s'
seddiag2d(23) = 'Flxtot ' , 'Total burial flux ', 'mol/cm2/s'
seddiag2d(24) = 'dzdep ' , 'Sedimentation rate ', 'cm/s'
seddiag2d(25) = 'Rstepros ' , 'Number of iterations ', '-'
Inorganic Compounds
nam_inorg
The chemical parameters of inorganic compounds in the sediment (clay, calcite, ligands) are defined in nam_inorg : reactivity of clay, dissolution rates of CaCO\(_3\) and ligands, and ligand/carbon ratio in the particulate organic carbon.
!-----------------------------------------------------------------------
&nam_inorg ! Inorganic chemistry in sediments (CacO3, Si)
!-----------------------------------------------------------------------
rcopal = 2.0 ! Reactivity for clay [l.mol-1.an-1]
rccal = 1.0 ! Dissolution rate of calcite [in yr-1]
rcligc = 0.1 ! Degradation rate of ligands [in yr-1]
ratligc = 1.E-4 ! L/C ratio in POC
Redox Reactions
nam_poc
In nam_poc are defined all the parameters of redox reactions in the sediment. These include the Redfield coefficients of O\(_2\), NO\(_3\), PO\(_4\) and C, the reactivity of the six classes of Particulate Organic Carbon lability relative to O\(_2\), the reactivity of NH\(_4\), H\(_2\)S, Fe\(^{2+}\) relative to O\(_2\), precipitation and dissolution of FeS, the half-saturation constants for oxic remineralization, denitrification, Fe remineralization, SO\(_4\) remineralization...
!-----------------------------------------------------------------------
&nam_poc ! parameters for the redox reactions of the sediment module
!-----------------------------------------------------------------------
redO2 = 138. ! Redfield coef for Oxygen
redNo3 = 16. ! Redfield coef for Nitrate
redPo4 = 1. ! Redfield coef for Phosphate
redC = 117. ! Redfield coef for Carbon
redfep = 0.01 ! Ration of Fe bound P
rcorg1 = 8.00 ! Reactivity for labile POC [an-1]
rcorg2 = 5.20E-1 ! Reactivity for labile POC [an-1]
rcorg3 = 3.5E-2 ! Reactivity for labile POC [an-1]
rcorg4 = 2.30E-3 ! Reactivity for labile POC [an-1]
rcorg5 = 1.5E-4 ! Reactivity for labile POC [an-1]
rcorg6 = 5.7E-6 ! Reactivity for labile POC [an-1]
rcnh4 = 5E7 ! Reactivity for O2/NH4 [l.mol-1.an-1]
rch2s = 3E8 ! Reactivity for O2/H2S [l.mol-1.an-1]
rcfe2 = 5E8 ! Reactivity for O2/Fe2+ [l.mol-1.an-1]
rcfeh2s = 1E4 ! Reactivity for FEOH/H2S [l.mol-1.an-1]
rcfeso = 2E6 ! Reactivity for FES/O2 [l.mol-1.an-1]
rcfesp = 1E-3 ! Precipitation of FeS [mol.l-1.an-1]
rcfesd = 1.E-3 ! Dissolution of FeS [an-1]
rcapat = 0.35 ! Formation rate of apatite [an-1]
xksedo2 = 1.E-6 ! Half-saturation constant for oxic remin [mol/l]
xksedno3 = 3.E-6 ! Half-saturation constant for denitrification [mol/l]
xksedfeo = 0.003 ! Half-saturation constant for iron remin [%]
xksedso4 = 1.6E-3 ! Half-saturation constant for SO4 remin [mol/l]
Bioturbation / Bioirrigation
nam_btb
In nam_btb, the parameters for bioturbation and bioirrigation are defined.
Bioturbation, i.e., the reworking of sediments by living organisms, can either vary with depth (ln_btbz = .true., default setting) or be constant along the sediment column (ln_btbz = .false.). The associated parameters are the bioturbation coefficient (dbiot) and its attenuation coefficient (dbtbzsc).
Bioirrigation, i.e., the exchange of dissolved substances between interstitial water and overlying seawater by benthic organisms, can be enabled (ln_irrig = .true., default setting) or disable. When enabled, the vertical scale of bioirrigation attenuation can also be set (xirrzsc). This block also includes the adsorption coefficents of NH\(_4\) and Fe\(^{2+}\).
!-----------------------------------------------------------------------
&nam_btb ! parameters for bioturbation and bioirrigation
!-----------------------------------------------------------------------
dbiot = 10. ! Bioturbation coefficient (in cm2/yr)
ln_btbz = .true. ! Depth varying bioturbation
dbtbzsc = 4.0 ! coefficient for btb attenuation. If no variation, depth of the mixed layer
adsnh4 = 4.16 ! Adsorption coefficient of NH4
adsfe2 = 697.0 ! Adsorption coefficient of Fe2
ln_irrig = .true. ! Bioirrigation in sediment
xirrzsc = 1.8 ! Vertical scale of the attenuation of bioirrigation [cm]
Restart Settings
nam_rst
In nam_rst, you can enable the initialization of the sediment tracers from a restart file created by a previous simulation (ln_rst_sed). You can also define the suffix and location of the written and read sediment restart files.
!-----------------------------------------------------------------------
&nam_rst ! parameters for restarting the sediment module
!-----------------------------------------------------------------------
ln_rst_sed = .false. ! restart flag
nn_rstsed = 0 ! restart control = 0 initial time step is not compared to the restart file value
! = 1 do not use the value in the restart file
! = 2 calendar parameters read in the restart file
cn_sedrst_in = "restart_sed" ! name of the input restart file name of the sediment module
cn_sedrst_indir = "." ! directory from which to read input sediment restarts
cn_sedrst_out = "restart_sed" ! suffix of pass. [sediment] restart name (output)
cn_sedrst_outdir = "." ! directory to which to write output sediment restarts
CROCO
The only difference between the sediment namelist in CROCO and NEMO is in the restart section.
Restart Settings
nam_rst
!-----------------------------------------------------------------------
&nam_rst ! parameters for restarting the sediment module
!-----------------------------------------------------------------------
ln_rst_sed = .false. ! restart flag
cn_sedrst_in = "croco_rst_sed_ini.nc" ! name of the input restart file name of the sediment module
cn_sedrst_indir = "CROCO_FILES" ! directory from which to read input sediment restarts
cn_sedrst_out = "croco_rst_sed.nc" ! suffix of pass. [sediment] restart name (output)
cn_sedrst_outdir = "CROCO_FILES" ! directory to which to write output sediment restarts