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Commit ccf76ae0 authored by Nicolas Martin's avatar Nicolas Martin :speech_balloon:
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nam_asminc 0 → 100644
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!-----------------------------------------------------------------------
&nam_asminc ! assimilation increments ('key_asminc')
!-----------------------------------------------------------------------
ln_bkgwri = .false. ! Logical switch for writing out background state
ln_trainc = .false. ! Logical switch for applying tracer increments
ln_dyninc = .false. ! Logical switch for applying velocity increments
ln_sshinc = .false. ! Logical switch for applying SSH increments
ln_asmdin = .false. ! Logical switch for Direct Initialization (DI)
ln_asmiau = .false. ! Logical switch for Incremental Analysis Updating (IAU)
nitbkg = 0 ! Timestep of background in [0,nitend-nit000-1]
nitdin = 0 ! Timestep of background for DI in [0,nitend-nit000-1]
nitiaustr = 1 ! Timestep of start of IAU interval in [0,nitend-nit000-1]
nitiaufin = 15 ! Timestep of end of IAU interval in [0,nitend-nit000-1]
niaufn = 0 ! Type of IAU weighting function
ln_salfix = .false. ! Logical switch for ensuring that the sa > salfixmin
salfixmin = -9999 ! Minimum salinity after applying the increments
nn_divdmp = 0 ! Number of iterations of divergence damping operator
/
nam_btb 0 → 100644
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!-----------------------------------------------------------------------
&nam_btb ! parameters for bioturbation and bioirrigation
!-----------------------------------------------------------------------
dbiot = 8. ! Bioturbation coefficient (in cm2/yr)
ln_btbz = .true. ! Depth varying bioturbation
dbtbzsc = 5.0 ! 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 = 2.0 ! Vertical scale of the attentuation of bioirrigation [cm]
/
nam_dia25h 0 → 100644
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!-----------------------------------------------------------------------
&nam_dia25h ! 25h Mean Output (default: OFF)
!-----------------------------------------------------------------------
ln_dia25h = .false. ! Choose 25h mean output or not
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nam_diadct 0 → 100644
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!-----------------------------------------------------------------------
&nam_diadct ! transports through some sections (default: OFF)
!-----------------------------------------------------------------------
ln_diadct = .false. ! Calculate transport thru sections or not
nn_dct = 15 ! time step frequency for transports computing
nn_dctwri = 15 ! time step frequency for transports writing
nn_secdebug = 112 ! 0 : no section to debug
! ! -1 : debug all section
! ! 0 < n : debug section number n
/
nam_diased 0 → 100644
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!-----------------------------------------------------------------------
&nam_diased ! Diagnostic arrays
!-----------------------------------------------------------------------
!
seddiag3d(1) = 'SedpH ' , 'pH ', '- '
seddiag3d(2) = 'SedCO3por ' , 'Dissolved CO3 concentration ', 'mol/L'
seddiag3d(3) = 'SaturCO3 ' , 'CO3 saturation ', '-'
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) = 'FlxPOC ' , 'POC burial flux ', 'mol/cm2/s'
seddiag2d(15) = 'FlxPOS ' , 'POS burial flux ', 'mol/cm2/s'
seddiag2d(16) = 'FlxPOR ' , 'POR burial flux ', 'mol/cm2/s'
seddiag2d(17) = 'FlxCaCO3 ' , 'Calcite burial flux ', 'mol/cm2/s'
seddiag2d(18) = 'FlxBSi ' , 'BSi burial flux ', 'mol/cm2/s'
seddiag2d(19) = 'FlxClay ' , 'Clay burial flux ', 'mol/cm2/s'
seddiag2d(20) = 'Flxtot ' , 'Total burial flux ', 'mol/cm2/s'
seddiag2d(21) = 'dzdep ' , 'Sedimentation rate ', 'cm/s'
seddiag2d(22) = 'Rstepros ' , 'Number of iterations ', '-'
/
nam_geom 0 → 100644
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!-----------------------------------------------------------------------
&nam_geom ! Characteristics of the sediment columns
!-----------------------------------------------------------------------
jpksed = 18 ! Number of vertical layers
sedzmin = 0.1 ! Minimum vertical spacing
sedhmax = 15.0 ! Maximum depth of the sediment
sedkth = 9.0 ! Default parameters
sedacr = 2.0 ! 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)
/
nam_inorg 0 → 100644
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!-----------------------------------------------------------------------
&nam_inorg ! Inorganic chemistry in sediments (CacO3, Si)
!-----------------------------------------------------------------------
rcopal = 1.25 ! Reactivity for clay [l.mol-1.an-1]
rccal = 0.1 ! 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
/
nam_poc 0 → 100644
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!-----------------------------------------------------------------------
&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 = 0.05 ! Ration of Fe bound P
rcorgl = 10. ! Reactivity for labile POC [an-1]
rcorgs = 0.1 ! Reactivity for semi-refractory POC [an-1]
rcorgr = 1.E-4 ! Reactivity for refractory POC [an-1]
rcnh4 = 1E7 ! Reactivity for O2/NH4 [l.mol-1.an-1]
rch2s = 1E8 ! 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-4 ! Precipitation of FeS [mol.l-1.an-1]
rcfesd = 1.E-3 ! Dissolution of FeS [an-1]
xksedo2 = 1.E-6 ! Half-saturation constant for oxic remin [mol/l]
xksedno3 = 5.E-6 ! Half-saturation constant for denitrification [mol/l]
xksedfeo = 0.006 ! Half-saturation constant for iron remin [%]
xksedso4 = 5E-4 ! Half-saturation constant for SO4 remin [mol/l]
/
nam_rst 0 → 100644
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!-----------------------------------------------------------------------
&nam_rst ! parameters for restarting the sediment module
!-----------------------------------------------------------------------
ln_rst_sed = .false. ! restart flag
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
/
nam_run 0 → 100644
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!-----------------------------------------------------------------------
&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-4 ! Tolerance for the absolute error
rosrtol = 1.E-4 ! Tolerance for the relative error
/
nam_tide 0 → 100644
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!-----------------------------------------------------------------------
&nam_tide ! tide parameters (default: OFF)
!-----------------------------------------------------------------------
ln_tide = .false. ! Activate tides
nn_tide_var = 1 ! Variant of tidal parameter set and tide-potential computation
! ! (1: default; 0: compatibility with previous versions)
ln_tide_dia = .false. ! Enable tidal diagnostic output
ln_tide_pot = .false. ! use tidal potential forcing
rn_tide_gamma = 0.7 ! Tidal tilt factor
ln_scal_load = .false. ! Use scalar approximation for
rn_scal_load = 0.094 ! load potential
ln_read_load = .false. ! Or read load potential from file
cn_tide_load = 'tide_LOAD_grid_T.nc' ! filename for load potential
!
ln_tide_ramp = .false. ! Use linear ramp for tides at startup
rn_tide_ramp_dt = 0. ! ramp duration in days
sn_tide_cnames(1) = 'DUMMY' ! name of constituent - all tidal components must be set in namelist_cfg
/
nam_trased 0 → 100644
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!-----------------------------------------------------------------------
&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) = 'SedPOC ' , 'POC Concentration ', '%'
sedsol(4) = 'SedPOS ' , 'Semi-ref POC Concentration ', '%'
sedsol(5) = 'SedPOR ' , 'Refractory POC Concentration ', '%'
sedsol(6) = 'SedCaCO3' , 'Calcite Concentration ', '%'
sedsol(7) = 'SedBSi ' , 'Biogenic Silicate Concentration ', '%'
sedsol(8) = 'SedClay ' , 'Clay 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'
/
nam_trc_age 0 → 100644
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! Variable setting
ctrcnm (jp_age) = 'Age'
ctrcln (jp_age) = 'Sea water age since surface contact'
ctrcun (jp_age) = 'year'
ln_trc_ini(jp_age) = .false.
ln_trc_sbc(jp_age) = .false.
ln_trc_cbc(jp_age) = .false.
ln_trc_obc(jp_age) = .false.
nam_vvl 0 → 100644
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!-----------------------------------------------------------------------
&nam_vvl ! vertical coordinate options (default: z-star)
!-----------------------------------------------------------------------
ln_vvl_zstar = .true. ! z-star vertical coordinate
ln_vvl_ztilde = .false. ! z-tilde vertical coordinate: only high frequency variations
ln_vvl_layer = .false. ! full layer vertical coordinate
ln_vvl_ztilde_as_zstar = .false. ! ztilde vertical coordinate emulating zstar
ln_vvl_zstar_at_eqtor = .false. ! ztilde near the equator
rn_ahe3 = 0.0 ! thickness diffusion coefficient
rn_rst_e3t = 30.0 ! ztilde to zstar restoration timescale [days]
rn_lf_cutoff = 5.0 ! cutoff frequency for low-pass filter [days]
rn_zdef_max = 0.9 ! maximum fractional e3t deformation
ln_vvl_dbg = .false. ! debug prints (T/F)
/
namage 0 → 100644
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!-----------------------------------------------------------------------
&namage ! AGE
!-----------------------------------------------------------------------
rn_age_depth = 10 ! depth over which age tracer reset to zero
rn_age_kill_rate = -0.000138888 ! = -1/7200 recip of relaxation timescale (s) for age tracer shallower than age_depth
/
namagrif 0 → 100644
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!-----------------------------------------------------------------------
&namagrif ! AGRIF zoom ("key_agrif")
!-----------------------------------------------------------------------
ln_agrif_2way = .true. ! activate two way nesting
ln_init_chfrpar = .false. ! initialize child grids from parent
ln_vert_remap = .false. ! use vertical remapping
ln_spc_dyn = .true. ! use 0 as special value for dynamics
ln_chk_bathy = .true. ! =T check the parent bathymetry
rn_sponge_tra = 0.002 ! coefficient for tracer sponge layer []
rn_sponge_dyn = 0.002 ! coefficient for dynamics sponge layer []
rn_trelax_tra = 0.01 ! inverse of relaxation time (in steps) for tracers []
rn_trelax_dyn = 0.01 ! inverse of relaxation time (in steps) for dynamics []
/
namalb 0 → 100644
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!------------------------------------------------------------------------------
&namalb ! albedo parameters
!------------------------------------------------------------------------------
! ! ! obs range (cloud-sky)
rn_alb_sdry = 0.85 ! dry snow albedo : 0.85 -- 0.87
rn_alb_smlt = 0.75 ! melting snow albedo : 0.72 -- 0.82
rn_alb_idry = 0.60 ! dry ice albedo : 0.54 -- 0.65
rn_alb_imlt = 0.50 ! bare puddled ice albedo : 0.49 -- 0.58
rn_alb_dpnd = 0.27 ! ponded ice albedo : 0.10 -- 0.30
rn_alb_hpiv = 1.00 ! pivotal ice thickness in m (above which albedo is constant)
/
nambbc 0 → 100644
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!-----------------------------------------------------------------------
&nambbc ! bottom temperature boundary condition (default: OFF)
!-----------------------------------------------------------------------
ln_trabbc = .false. ! Apply a geothermal heating at the ocean bottom
nn_geoflx = 2 ! geothermal heat flux: = 1 constant flux
! ! = 2 read variable flux [mW/m2]
rn_geoflx_cst = 86.4e-3 ! Constant value of geothermal heat flux [mW/m2]
cn_dir = './' ! root directory for the geothermal data location
!___________!_________________________!___________________!___________!_____________!________!___________!__________________!__________!_______________!
! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ ! weights filename ! rotation ! land/sea mask !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! ! pairing ! filename !
sn_qgh ='geothermal_heating.nc' , -12. , 'heatflow', .false. , .true. , 'yearly' , '' , '' , ''
/
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!-----------------------------------------------------------------------
&nambbl ! bottom boundary layer scheme (default: OFF)
!-----------------------------------------------------------------------
ln_trabbl = .false. ! Bottom Boundary Layer parameterisation flag
nn_bbl_ldf = 1 ! diffusive bbl (=1) or not (=0)
nn_bbl_adv = 0 ! advective bbl (=1/2) or not (=0)
rn_ahtbbl = 1000. ! lateral mixing coefficient in the bbl [m2/s]
rn_gambbl = 10. ! advective bbl coefficient [s]
/
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!-----------------------------------------------------------------------
&nambdy ! unstructured open boundaries (default: OFF)
!-----------------------------------------------------------------------
ln_bdy = .false. ! Use unstructured open boundaries
nb_bdy = 0 ! number of open boundary sets
ln_coords_file = .true. ! =T : read bdy coordinates from file
cn_coords_file = 'coordinates.bdy.nc' ! bdy coordinates files
ln_mask_file = .false. ! =T : read mask from file
cn_mask_file = '' ! name of mask file (if ln_mask_file=.TRUE.)
cn_dyn2d = 'none' !
nn_dyn2d_dta = 0 ! = 0, bdy data are equal to the initial state
! ! = 1, bdy data are read in 'bdydata .nc' files
! ! = 2, use tidal harmonic forcing data from files
! ! = 3, use external data AND tidal harmonic forcing
cn_dyn3d = 'none' !
nn_dyn3d_dta = 0 ! = 0, bdy data are equal to the initial state
! ! = 1, bdy data are read in 'bdydata .nc' files
cn_tra = 'none' !
nn_tra_dta = 0 ! = 0, bdy data are equal to the initial state
! ! = 1, bdy data are read in 'bdydata .nc' files
cn_ice = 'none' !
nn_ice_dta = 0 ! = 0, bdy data are equal to the initial state
! ! = 1, bdy data are read in 'bdydata .nc' files
!
ln_tra_dmp =.false. ! open boudaries conditions for tracers
ln_dyn3d_dmp =.false. ! open boundary condition for baroclinic velocities
rn_time_dmp = 1. ! Damping time scale in days
rn_time_dmp_out = 1. ! Outflow damping time scale
nn_rimwidth = 10 ! width of the relaxation zone
ln_vol = .false. ! total volume correction (see nn_volctl parameter)
nn_volctl = 1 ! = 0, the total water flux across open boundaries is zero
/
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