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Commit b5683d3d authored by Nicolas Martin's avatar Nicolas Martin :speech_balloon:
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Update of namelist blocks in preparation to 4.2 release

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doc/latex/SI3/namelists/namsbc
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......@@ -15,7 +15,7 @@
! = 2 Redistribute a single flux over categories
ln_cndflx = .false. ! Use conduction flux as surface boundary conditions (i.e. for Jules coupling)
ln_cndemulate = .false. ! emulate conduction flux (if not provided in the inputs)
nn_qtrice = 1 ! Solar flux transmitted thru the surface scattering layer:
nn_qtrice = 0 ! Solar flux transmitted thru the surface scattering layer:
! = 0 Grenfell and Maykut 1977 (depends on cloudiness and is 0 when there is snow)
! = 1 Lebrun 2019 (equals 0.3 anytime with different melting/dry snw conductivities)
/
doc/namelists/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]
/
doc/namelists/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 ', '-'
/
doc/namelists/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)
/
doc/namelists/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
/
doc/namelists/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]
/
doc/namelists/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
/
doc/namelists/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
/
doc/namelists/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'
/
doc/namelists/nam_vvl
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......@@ -10,5 +10,5 @@
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 = .true. ! debug prints (T/F)
ln_vvl_dbg = .false. ! debug prints (T/F)
/
doc/namelists/namagrif
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!-----------------------------------------------------------------------
&namagrif ! AGRIF zoom ("key_agrif")
!-----------------------------------------------------------------------
ln_spc_dyn = .true. ! use 0 as special value for dynamics
rn_sponge_tra = 2880. ! coefficient for tracer sponge layer [m2/s]
rn_sponge_dyn = 2880. ! coefficient for dynamics sponge layer [m2/s]
ln_chk_bathy = .false. ! =T check the parent bathymetry
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 []
/
doc/namelists/namalb
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......@@ -7,4 +7,5 @@
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)
/
doc/namelists/namberg
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......@@ -3,6 +3,12 @@
!-----------------------------------------------------------------------
ln_icebergs = .false. ! activate iceberg floats (force =F with "key_agrif")
!
! ! restart
cn_icbrst_in = "restart_icb" ! suffix of iceberg restart name (input)
cn_icbrst_indir = "./" ! directory from which to read input ocean restarts
cn_icbrst_out = "restart_icb" ! suffix of ocean restart name (output)
cn_icbrst_outdir = "./" ! directory from which to read output ocean restarts
!
! ! diagnostics:
ln_bergdia = .true. ! Calculate budgets
nn_verbose_level = 0 ! Turn on more verbose output if level > 0
......@@ -30,11 +36,11 @@
! ! Put a test iceberg at each gridpoint in box (lon1,lon2,lat1,lat2)
rn_test_box = 108.0, 116.0, -66.0, -58.0
ln_use_calving = .false. ! Use calving data even when nn_test_icebergs > 0
rn_speed_limit = 0. ! CFL speed limit for a berg
rn_speed_limit = 0. ! CFL speed limit for a berg (safe value is 0.4, see #2581)
!
ln_M2016 = .false. ! use Merino et al. (2016) modification (use of 3d ocean data instead of only sea surface data)
ln_icb_grd = .false. ! ground icb when icb bottom level hit oce bottom level (need ln_M2016 to be activated)
!
cn_dir = './' ! root directory for the calving data location
!___________!_________________________!___________________!___________!_____________!________!___________!__________________!__________!_______________!
! ! file name ! frequency (hours) ! variable ! time interp.! clim ! 'yearly'/ ! weights filename ! rotation ! land/sea mask !
......
doc/namelists/namc1d
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!-----------------------------------------------------------------------
&namc1d ! 1D configuration options ("key_c1d" default: PAPA station)
&namc1d ! 1D configuration options (ln_c1d =T default: PAPA station)
!-----------------------------------------------------------------------
rn_lat1d = 50 ! Column latitude
rn_lon1d = -145 ! Column longitude
ln_c1d_locpt = .true. ! Localization of 1D config in a grid (T) or independant point (F)
rn_lat1d = 50.1 ! Column latitude
rn_lon1d = -144.9 ! Column longitude
/
doc/namelists/namc1d_dyndmp
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!-----------------------------------------------------------------------
&namc1d_dyndmp ! U & V newtonian damping ("key_c1d" default: OFF)
&namc1d_dyndmp ! U & V newtonian damping (ln_c1d =T default: OFF)
!-----------------------------------------------------------------------
ln_dyndmp = .false. ! add a damping term (T) or not (F)
/
doc/namelists/namc1d_uvd
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!-----------------------------------------------------------------------
&namc1d_uvd ! data: U & V currents ("key_c1d" default: OFF)
&namc1d_uvd ! data: U & V currents (ln_c1d =T default: OFF)
!-----------------------------------------------------------------------
! ! =T read U-V fields for:
ln_uvd_init = .false. ! ocean initialisation
......
doc/namelists/namcfg
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!-----------------------------------------------------------------------
&namcfg ! parameters of the configuration (default: use namusr_def in namelist_cfg)
!-----------------------------------------------------------------------
ln_read_cfg = .false. ! (=T) read the domain configuration file
! ! (=F) user defined configuration (F => create/check namusr_def)
ln_read_cfg = .false. ! (=T) read the domain configuration file
! ! (=F) user defined configuration (F => create/check namusr_def)
cn_domcfg = "domain_cfg" ! domain configuration filename
!
ln_closea = .false. ! T => keep closed seas (defined by closea_mask field) in the
! ! domain and apply special treatment of freshwater fluxes.
! ! F => suppress closed seas (defined by closea_mask field)
! ! from the bathymetry at runtime.
! ! If closea_mask field doesn't exist in the domain_cfg file
! ! then this logical does nothing.
ln_write_cfg = .false. ! (=T) create the domain configuration file
ln_closea = .false. ! (=T => fill namclo)
! ! (=F) no control of net precip/evap over closed sea
!
ln_write_cfg = .false. ! (=T) create the domain configuration file
cn_domcfg_out = "domain_cfg_out" ! newly created domain configuration filename
!
ln_use_jattr = .false. ! use (T) the file attribute: open_ocean_jstart, if present
! ! in netcdf input files, as the start j-row for reading
ln_use_jattr = .false. ! use (T) the file attribute: open_ocean_jstart, if present
! ! in netcdf input files, as the start j-row for reading
/
doc/namelists/namctl
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!-----------------------------------------------------------------------
&namctl ! Control prints (default: OFF)
!-----------------------------------------------------------------------
sn_cfctl%l_glochk = .FALSE. ! Range sanity checks are local (F) or global (T). Set T for debugging only
sn_cfctl%l_allon = .FALSE. ! IF T activate all options. If F deactivate all unless l_config is T
sn_cfctl%l_config = .TRUE. ! IF .true. then control which reports are written with the following
sn_cfctl%l_runstat = .FALSE. ! switches and which areas produce reports with the proc integer settings.
sn_cfctl%l_trcstat = .FALSE. ! The default settings for the proc integers should ensure
sn_cfctl%l_oceout = .FALSE. ! that all areas report.
sn_cfctl%l_layout = .FALSE. !
sn_cfctl%l_prtctl = .FALSE. !
sn_cfctl%l_prttrc = .FALSE. !
sn_cfctl%l_oasout = .FALSE. !
sn_cfctl%procmin = 0 ! Minimum area number for reporting [default:0]
sn_cfctl%procmax = 1000000 ! Maximum area number for reporting [default:1000000]
sn_cfctl%procincr = 1 ! Increment for optional subsetting of areas [default:1]
sn_cfctl%ptimincr = 1 ! Timestep increment for writing time step progress info
nn_print = 0 ! level of print (0 no extra print)
nn_ictls = 0 ! start i indice of control sum (use to compare mono versus
nn_ictle = 0 ! end i indice of control sum multi processor runs
nn_jctls = 0 ! start j indice of control over a subdomain)
nn_jctle = 0 ! end j indice of control
nn_isplt = 1 ! number of processors in i-direction
nn_jsplt = 1 ! number of processors in j-direction
ln_timing = .false. ! timing by routine write out in timing.output file
ln_diacfl = .false. ! CFL diagnostics write out in cfl_diagnostics.ascii
sn_cfctl%l_runstat = .TRUE. ! switches and which areas produce reports with the proc integer settings.
sn_cfctl%l_trcstat = .FALSE. ! The default settings for the proc integers should ensure
sn_cfctl%l_oceout = .FALSE. ! that all areas report.
sn_cfctl%l_layout = .FALSE. !
sn_cfctl%l_prtctl = .FALSE. !
sn_cfctl%l_prttrc = .FALSE. !
sn_cfctl%l_oasout = .FALSE. !
sn_cfctl%procmin = 0 ! Minimum area number for reporting [default:0]
sn_cfctl%procmax = 1000000 ! Maximum area number for reporting [default:1000000]
sn_cfctl%procincr = 1 ! Increment for optional subsetting of areas [default:1]
sn_cfctl%ptimincr = 1 ! Timestep increment for writing time step progress info
nn_ictls = 0 ! start i indice of control sum (use to compare mono versus
nn_ictle = 0 ! end i indice of control sum multi processor runs
nn_jctls = 0 ! start j indice of control over a subdomain)
nn_jctle = 0 ! end j indice of control
nn_isplt = 1 ! number of processors in i-direction
nn_jsplt = 1 ! number of processors in j-direction
ln_timing = .false. ! timing by routine write out in timing.output file
ln_diacfl = .false. ! CFL diagnostics write out in cfl_diagnostics.ascii
/
doc/namelists/namdia
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......@@ -3,8 +3,8 @@
!------------------------------------------------------------------------------
ln_icediachk = .false. ! check online heat, mass & salt budgets
! ! rate of ice spuriously gained/lost at each time step => rn_icechk=1 <=> 1.e-6 m/hour
rn_icechk_cel = 100. ! check at each gridcell (1.e-4m/h)=> stops the code if violated (and writes a file)
rn_icechk_glo = 1. ! check over the entire ice cover (1.e-6m/h)=> only prints warnings
rn_icechk_cel = 1. ! check at each gridcell (1.e-06m/h)=> stops the code if violated (and writes a file)
rn_icechk_glo = 1.e-04 ! check over the entire ice cover (1.e-10m/h)=> only prints warnings
ln_icediahsb = .false. ! output the heat, mass & salt budgets (T) or not (F)
ln_icectl = .false. ! ice points output for debug (T or F)
iiceprt = 10 ! i-index for debug
......
doc/namelists/namdom
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......@@ -2,12 +2,12 @@
&namdom ! time and space domain
!-----------------------------------------------------------------------
ln_linssh = .false. ! =T linear free surface ==>> model level are fixed in time
rn_isfhmin = 1.00 ! treshold [m] to discriminate grounding ice from floating ice
!
rn_rdt = 5400. ! time step for the dynamics and tracer
rn_Dt = 5400. ! time step for the dynamics and tracer
rn_atfp = 0.1 ! asselin time filter parameter
!
ln_crs = .false. ! Logical switch for coarsening module (T => fill namcrs)
ln_c1d = .false. ! Single column domain (1x1pt) (T => fill namc1d)
!
ln_meshmask = .false. ! =T create a mesh file
ln_meshmask = .true. ! =T create a mesh file
/
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