Parametrization data

After compilation and before running, one must fill parameters in namelists files and build data files.

namelist files

The namelist variables are dispatches in several files, depending on themes and code organization. There are :

• paramain.txt : general namelist for the configuration (shared with all ranks) (paramain.txt)
• paracom.txt : shared with all ranks (paracom.txt)
• paraspec.txt : different for each rank (paraspec.txt)
• parasubs.txt : need if transport substances (key_substance) (parasubs.txt : namelist for substances)
• parasedim.txt : need if sediment using (key_sedim)(namelist for sediment : parasedim.txt)
• parabiolo.txt : need if using modules for biology (key_biolo) (Paramètres dédiés aux applications ECO-MARS (parabiolo.txt))
• paraconta.txt : need if using modules for contaminant (key_contaminant)

Namelist variables listed by theme

Definition of each variable is given into each namelist file

Theme Dates

namelist	namelist file	variable	CPPkey	Observations
nmlmain	paramain.txt	date_ref = ‘01-Jan-1900 00:00:00‘		Do not change
namdate	paracom.txt	date_start = ‘06/03/2005 00:00:00’ date_end = ‘09/03/2005 00:00:00’		simulatin starting date simulation finishing date
namdat3d	paraspec.txt	date_start3d = ‘03/02/2006 12:00:00’ date_startagrif = ‘05/02/2008 12:00:00’ date_startshift = 0.0		3D run starting date (== or > date_start) AGRIF zoom starting date Rank management

Theme General

namelist	namelist file	variable	CPPkey	Observations
nmlmain	paramain.txt	comdir = ‘../’ jhemisph=1		./ without rank OR ../if ranks 1/-1 in North/South hemisphere
nmlhead	paracom.txt	file_head = ‘../../inputs/head.cool‘ confname_mother = ‘cool’ confname = ‘cool’ suffix = ‘V10.4’		example congif “cool”
namriv	paraspec.txt	icon=2		/=2 to make tests on buoyancy impact (3D)
namparanum |	paraspec.txt	l_modele2d=.true. cflcrt=0.6		If set to .true., 2D run even though kmax>1

Theme SIGMA

namelist	namelist file	variable	CPPkey	Observations
namgridsig	paraspec.txt	l_equisig=.true. sig(1)=0.05 hc = 5. (meters) b_sig theta_sig grid_angle l_corio_cst=.false.	key_grid_rotated	(3D) (3D) if generalized sigma 0< Bottom control <1 (Genralized sigma) 0< Surface control <20 (Genralized sigma)

Theme TIME STEPS

namelist	namelist file	variable	CPPkey	Observations
namparanum	paraspec.txt	dtini=400.d0 dtmin=200.d0 dtmax=800.d0		dtmin < dt < dtmax if generalized sigma

Theme TIME INTERPOLATION

namelist	namelist file	variable	CPPkey	Observations
nmlinterp	paramain.txt	perchrono=0.1 tobs=12.0 (hours) l_champroche=.false.		Used if reading of one data.dat file DO NOT USE

Theme BATHYMETRY

namelist	namelist file	variable	CPPkey	Observations
nambathy	paraspec.txt	file_bathy=’../../inputs/hxhy.cool0’ name_bathy_hx=’HX‘ name_bathy_hy=’HY‘ name_bathy_h0=’H0‘ l_bathy_meanlev=.false. name_bathy_meanlev=’nmoy’ mslshift=0.0 bathy_nbsmooth=0 l_bathy_comb=.false. l_bathy_pit=.false. hminim=-9.9 hrdef=20.0 h0fond=0.01 dhj=0.05 hminkxky=0.5 l_tssubadv_over_smalldepth=.true. hm=1.0 l_bathy_save=.false. fwetmin =1.0 file_bathy_child	key_netcdf key_netcdf key_netcdf	should not be changed

Theme RESTART

namelist	namelist file	variable	CPPkey	Observations
nmlrestart	paramain.txt	name_in_dt = ‘DT’ name_in_xe = ‘XE‘ ....
namreprise	paraspec.txt	l_initfromfile file_init = ‘save.nc‘ l_init_restart=.false. l_init_rtime=.false. l_init_rdt=.false. l_init_rssh=.false. l_init_rbtvel=.false. l_init_r3dvel=.false. l_init_rwz=.false l_init_rturb=.false. l_init_rsal=.false. l_init_rtemp=.false.		Set all the boolean to .true. to get exact results when restarting from a restart file after a break in the simulation. To read an input file prepared from extract program specify which variables you want to read and define l_init_restart=.false.

Theme OUTPUT

namelist	namelist file	variable	CPPkey	Observations
nmloutput	paramain.txt	l_maxu=.true. name_out_h0=’h0‘ ‘.... ‘		Maximum velocities are printed on the screen (iscreen=6) or in the listing file (iscreen=12)
namoutput	paraspec.txt	file_output= ‘./output.dat’ iscreen=12 iscreenlog=18 iwarnlog=16 ierrorlog=17 out_dir l_out_nc4par l_out_pack	-Dkey_MPI_2D	Get it empty The simulation is stopped if an error occurs. The error si described in file error_suffix.log True : each cpu writes its local domain in a unique global file True : the data values are packed, i.e. saved in short precision Packed_value = NINT((value- offset)/scale_factor

Theme SAVING

namelist	namelist file	variable	CPPkey	Observations
nasaverestart	paraspec.txt	l_saverestart_1file = .false. l_saverestart_bydate = .false. file_saverestart= ‘save.nc’ saverestart_step = 1.0d0

Theme OPEN BOUNDARY CONDITIONS

namelist	namelist file	variable	CPPkey	Observations
namobc	paraspec.txt	l_obc_ogcm_rssh=.false. l_obc_ogcm_rt=.false. l_obc_ogcm_rs=.false. l_obc_ogcm_rc=.false. l_obc_ogcm_ruv=.false. l_obc_ogcm_ruvz=.false. l_obc_relax=.false. obc_coefrel=0.7e-05 l_obc_cyc=.true. l_obc_cycl_x/y=.false. l_obc_mars=.true. l_obc_char=.true. l_obc_diri=.true. l_obc_tide=.true. l_obc_ogcm=.true. l_tide_harmcompo=.true. l_obc2drank_save=.true. l_obc_south=.false. file_obc_ogcm_s=’./‘ l_obc_north=.false. file_obc_ogcm_n=’./‘ l_obc_east=.false. file_obc_ogcm_e=’./‘ l_obc_west=.false. file_obc_ogcm_w=’./‘	key_tide_fes2004 or…	Reading of data issued from another MARS configuration or another model. Data are spatially interpolated off-line with the use of the program named extract. Data are interpolated on time during the run l_obc_rssh=.true., the ssh relative to the mean circulation comes from a coarser model l_obc_cyc=.true., If periodic zonal/meridional periodicity No gradient of velocity at open boundary Characteristics method Dirichlet OBCs come from a previous rank OBCs come from an OGCM Saving of open boundary condition (rank)

Theme RIVERS, TRAJECTORIES, TRACKPOINTS, DIAGNOSTIC

namelist	namelist file	variable	CPPkey	Observations
namriv	paraspec.txt	file_river=’../../inputs/.dat’ icon=2
namtraj	paraspec.txt	file_trajec=’tache.dat’ itypetraj = 3 ndtz = 50
namdiag	paraspec.txt	l_diag=.false. date_startdiag = ‘01/01/1996 00:00:00’ date_enddiag = ‘02/01/2001 18:00:01’ file_diag=’diag.gdg51’ l_points=.false. file_point=’points.dat’

Theme TIDE

namelist	namelist file	variable	CPPkey	Observations
namtide	paracom.txt	l_tide_M2harm=.false. l_tide_M2statcoef=.T. tide_M2coef=0.0 file_tide_M2coef=’bidon.dat‘ file_tide_harmcp=’../../inputs/fes2004.nc‘ or file_tide_harmcp=’../../inputs/schwiderski.nc’ l_tide_admittance=.false. l_genpot=.false.	key_tide_fes2004 key_tide_schwid key_tide_fes2004 key_tide_schwid	effective if l_tide_M2harm=.true. effective if l_tide_M2harm=.T. + l_tide_M2statcoef=.F.

Theme ATMOSPHERICAL FIELDS

namelist	namelist file	variable	CPPkey	Observations
nammeteo	paraspec.txt	imeteo_dragtype=0 imeteo_exchtype=0 paref=101500.0 cds=0.0012 l_sflx_rpa=.false. ... name_sflx_sat=‘sat‘ ...		type of surface drag coefficient 0 -> constant value (= cds) if imeteo_exchtype=0 1 -> large and pond (1981) 2 -> smith and banke (1975) 3 -> geernaert et al. (1986) 4 -> charnock’s relation (1955) dependency on air-sea temperature difference for surf drag coefficient and thermal exchange coefficient = 0 -> no dependence on tdif = 1 -> as function of tdif imeteo_dragtype and imeteo_exchtype not used if l_meteo_hom=T or l_meteo_stat=T

Theme WIND FIELD

namelist	namelist file	variable	CPPkey	Observations
nammeteoc	paracom.txt	l_meteo_stat = .true. l_meteo_hom = .true. wind_veloc = 0.0 wind_dir = 275.0 file_meteo = ‘bidon.dat’		To use constant wind field or to read a file .dat

Theme RADIATIVE HEAT FLUX

namelist	namelist file	variable	CPPkey	Observations
namthermo	paraspec.txt	l_sflx_radlossbot=.false. l_sflx_solarcst=.true. sflx_solarcst=0.0

Theme STATE EQUATION

namelist	namelist file	variable	CPPkey	Observations
nmlthermo	paramain.txt	rhoref=1027.34 saliref=35.5 tetaref=10.0 l_stateeq_lin=.true. saliref_lin=35.5 tetaref_lin=10.0		3D 3D 3D

Theme THERMODYNAMICS

namelist	namelist file	variable	CPPkey	Observations
nmlthermo	paramain.txt	rhoair=1.25 chp=3986.0 coext=0.1

Theme EQUATION OF MOVEMENT

namelist	namelist file	variable	CPPkey	Observations
namfrot	paraspec.txt	l_incbotstress=.true. botstressmax=3.0		2D

Theme ADVECTION OF TRACERS

namelist	namelist file	variable	CPPkey	Observations
nmladvtra	paramain.txt	qmax = 8.0 qmaxz = 10.0		3D

Theme VISCOSITY

namelist	namelist file	variable	CPPkey	Observations
namvisc	paraspec.txt	l_smagor=.false. vismin=0.1 vismax=700.0 cosmag=0.27 fvisc=5.0 sponge_nbcell=5 vismul=5.0 l_spongs=.false. l_spongn=.false. l_sponge=.false. l_spongw=.false.		3D vismin, vismax, cosmag used for l_smagor=T

Theme DIFFUSION

namelist	namelist file	variable	CPPkey	Observations
namdiff	paraspec.txt	kx = 1.0 ky = 1.0

Theme TURBULENCE

namelist	namelist file	variable	CPPkey	Observations
namturb	paraspec.txt	z0bot=0.0035 z0surf hminfrot hmaxfrot turb_nbeq =0 turb_0eq_option =2 turb_2eq_option=2 bgdiff=1.0e-6 nzinit=1.0e-4 kzinit=1.0e-4 l_stability=.false.		3D 3D 2D 2D 2D 3D 3D if turb_nbeq=2 3D 3D 3D

Theme NETCDF REFERENCE (OCO 1.2)

namelist	namelist file	variable	CPPkey	Observations
nmlconvention	paramain.txt	riog_valid_min ...=-50.0 riog_valid_max ...=5000.0 cg_conv_title=CONF cg_conv ....

• paramain.txt
• paracom.txt
• paraspec.txt
• parasubs.txt : namelist for substances