Understanding the AMM12 Namelist
The file is in sections:
!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
!! NEMO/OPA : 1 - run manager (namrun)
!! namelists 2 - Domain (namzgr, namzgr_sco, namdom, namtsd)
!! 3 - Surface boundary (namsbc, namsbc_ana, namsbc_flx, namsbc_clio, namsbc_core
!! namsbc_cpl, namtra_qsr, namsbc_rnf,
!! namsbc_apr, namsbc_ssr, namsbc_alb)
!! 4 - lateral boundary (namlbc, namcla, namobc, namagrif, nambdy, nambdy_tide)
!! 5 - bottom boundary (nambfr, nambbc, nambbl)
!! 6 - Tracer (nameos, namtra_adv, namtra_ldf, namtra_dmp)
!! 7 - dynamics (namdyn_adv, namdyn_vor, namdyn_hpg, namdyn_spg, namdyn_ldf)
!! 8 - Verical physics (namzdf, namzdf_ric, namzdf_tke, namzdf_kpp, namzdf_ddm, namzdf_tmx)
!! 9 - diagnostics (namnc4, namtrd, namspr, namflo, namptr, namhsb)
!! 10 - miscellaneous (namsol, nammpp, nammpp_dyndist, namctl)
!! 11 - Obs & Assim (namobs, nam_asminc)
!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The first part is the Run Management (note MPI directives are further down, under misc)
nn_intend : Number of time steps
nn_date0 : Date to start by
nn_write : frequency of write in the NetCDF output files
nn_stock : restart file frequency
and restart controls.
!!======================================================================
!! *** Run management namelists ***
!!======================================================================
!! namrun parameters of the run
!!======================================================================
!
!-----------------------------------------------------------------------
&namrun ! parameters of the run
!-----------------------------------------------------------------------
nn_no = 0 ! job number (no more used...)
cn_exp = "AMM12" ! experience name
nn_it000 = 1 ! first time step
nn_itend = 576 ! last time step (std 1 day = 576)
nn_date0 = 20070101 ! date at nit_0000 (format yyyymmdd) used if ln_rstart=F or (ln_rstart=T and nn_rstctl=0 or 1)
nn_leapy = 1 ! Leap year calendar (1) or not (0)
ln_rstart = .false. ! start from rest (F) or from a restart file (T)
nn_rstctl = 0 ! restart control => activated only if ln_rstart = T
! = 0 nn_date0 read in namelist ; nn_it000 : read in namelist
! = 1 nn_date0 read in namelist ; nn_it000 : check consistancy between namelist and restart
! = 2 nn_date0 read in restart ; nn_it000 : check consistancy between namelist and restart
cn_ocerst_in = "restart" ! suffix of ocean restart name (input)
cn_ocerst_out = "restart" ! suffix of ocean restart name (output)
nn_istate = 0 ! output the initial state (1) or not (0)
nn_stock = 576 ! frequency of creation of a restart file (modulo referenced to 1)
nn_write = 12 ! frequency of write in the output file (modulo referenced to nit000)
ln_dimgnnn = .false. ! DIMG file format: 1 file for all processors (F) or by processor (T)
ln_mskland = .false. ! mask land points in NetCDF outputs (costly: + ~15%)
ln_clobber = .false. ! clobber (overwrite) an existing file
nn_chunksz = 0 ! chunksize (bytes) for NetCDF file (works only with iom_nf90 routines)
/
- The next part is setting up the grid and bathymetry
vertical coordinate, switch between z and s-coordinates
rn_hmin : set minimum ocean depth
rn_e3* : to do with partial steps
rn_rdt : time step
rn_baro : barotropic time steps
rn_rd : tracer time steps
initialization of TS with input data, and damping back to that data.
!!======================================================================
!! *** Domain namelists ***
!!======================================================================
!! namzgr vertical coordinate
!! namzgr_sco s-coordinate or hybrid z-s-coordinate
!! namdom space and time domain (bathymetry, mesh, timestep)
!! namtsd data: temperature & salinity
!!======================================================================
!
!-----------------------------------------------------------------------
&namzgr ! vertical coordinate
!-----------------------------------------------------------------------
ln_zco = .false. ! z-coordinate - full steps (T/F) ("key_zco" may also be defined)
ln_zps = .false. ! z-coordinate - partial steps (T/F)
ln_sco = .true. ! s- or hybrid z-s-coordinate (T/F)
/
!-----------------------------------------------------------------------
&namzgr_sco ! s-coordinate or hybrid z-s-coordinate
!-----------------------------------------------------------------------
NOT IMPORTANT FOR Z-COORDINATES
/
!-----------------------------------------------------------------------
&namdom ! space and time domain (bathymetry, mesh, timestep)
!-----------------------------------------------------------------------
nn_bathy = 1 ! compute (=0) or read (=1) the bathymetry file
nn_closea = 0 ! remove (=0) or keep (=1) closed seas and lakes (ORCA)
nn_msh = 0 ! create (=1) a mesh file or not (=0)
rn_hmin = -3. ! min depth of the ocean (>0) or min number of ocean level (<0)
rn_e3zps_min= 20. ! partial step thickness is set larger than the minimum of
rn_e3zps_rat= 0.1 ! rn_e3zps_min and rn_e3zps_rat*e3t, with 0<rn_e3zps_rat<1
!
rn_rdt = 150. ! time step for the dynamics (and tracer if nn_acc=0)
nn_baro = 30 ! number of barotropic time step ("key_dynspg_ts")
rn_atfp = 0.1 ! asselin time filter parameter
nn_acc = 0 ! acceleration of convergence : =1 used, rdt < rdttra(k)
! =0, not used, rdt = rdttra
rn_rdtmin = 300. ! minimum time step on tracers (used if nn_acc=1)
rn_rdtmax = 300. ! maximum time step on tracers (used if nn_acc=1)
rn_rdth = 300. ! depth variation of tracer time step (used if nn_acc=1)
/
!-----------------------------------------------------------------------
&namtsd ! data : Temperature & Salinity
!-----------------------------------------------------------------------
! ! file name ! frequency (hours) ! variable ! time interp. ! clim !'yearly' or ! weights ! rotation !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing !
sn_tem = 'data_1m_potential_temperature_nomask', -1,'votemper', .true. , .true., 'yearly' , ' ' , ' '
sn_sal = 'data_1m_salinity_nomask' , -1,'vosaline', .true. , .true., 'yearly' , '' , ' '
!
cn_dir = './' ! root directory for the location of the runoff files
ln_tsd_init = .false. ! Initialisation of ocean T & S with T &S input data (T) or not (F)
ln_tsd_tradmp = .false. ! damping of ocean T & S toward T &S input data (T) or not (F)
/
Part 3 is the surface boundary conditions
ln_flx true sets fluxes from files, in namsbc_flx set file names and characteristics
ln_rnf sets runoffs, in namsbc_rnf set files and configure river inflow
left in the penetrative light formulation. Suspect it is turned off here, but docs not clear.
!!====================================================================== !! *** Surface Boundary Condition namelists *** !!====================================================================== !! namsbc surface boundary condition !! namsbc_ana analytical formulation !! namsbc_flx flux formulation !! namsbc_clio CLIO bulk formulae formulation !! namsbc_core CORE bulk formulae formulation !! namsbc_mfs MFS bulk formulae formulation !! namsbc_cpl CouPLed formulation ("key_coupled") !! namtra_qsr penetrative solar radiation !! namsbc_rnf river runoffs !! namsbc_apr Atmospheric Pressure !! namsbc_ssr sea surface restoring term (for T and/or S) !! namsbc_alb albedo parameters !!====================================================================== ! !----------------------------------------------------------------------- &namsbc ! Surface Boundary Condition (surface module) !----------------------------------------------------------------------- nn_fsbc = 1 ! frequency of surface boundary condition computation ! (also = the frequency of sea-ice model call) ln_ana = .false ! analytical formulation (T => fill namsbc_ana ) ln_flx = .true. ! flux formulation (T => fill namsbc_flx ) ln_blk_clio = .false. ! CLIO bulk formulation (T => fill namsbc_clio) ln_blk_core = .false. ! CORE bulk formulation (T => fill namsbc_core) ln_blk_mfs = .false. ! MFS bulk formulation (T => fill namsbc_mfs ) ln_cpl = .false. ! Coupled formulation (T => fill namsbc_cpl ) ln_apr_dyn = .false. ! Patm gradient added in ocean & ice Eqs. (T => fill namsbc_apr ) nn_ice = 0 ! =0 no ice boundary condition , ! =1 use observed ice-cover , ! =2 ice-model used ("key_lim3" or "key_lim2) ln_dm2dc = .false. ! daily mean to diurnal cycle on short wave ln_rnf = .true. ! runoffs (T => fill namsbc_rnf) ln_ssr = .false. ! Sea Surface Restoring on T and/or S (T => fill namsbc_ssr) nn_fwb = 0 ! FreshWater Budget: =0 unchecked ! =1 global mean of e-p-r set to zero at each time step ! =2 annual global mean of e-p-r set to zero ! =3 global emp set to zero and spread out over erp area ln_cdgw = .false. ! Neutral drag coefficient read from wave model (T => fill namsbc_wave) / !----------------------------------------------------------------------- &namsbc_ana ! analytical surface boundary condition !----------------------------------------------------------------------- NOT USED / !----------------------------------------------------------------------- &namsbc_flx ! surface boundary condition : flux formulation !----------------------------------------------------------------------- ! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! ! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! sn_utau = 'amm12_utau' , 1 , 'utau' , .false. , .false. , 'daily' , '' , '' sn_vtau = 'amm12_vtau' , 1 , 'vtau' , .false. , .false. , 'daily' , '' , '' sn_qtot = 'amm12_flx' , 3 , 'sonsfldo' , .true. , .false. , 'daily' , '' , '' sn_qsr = 'amm12_flx' , 3 , 'soshfldo' , .true. , .false. , 'daily' , '' , '' sn_emp = 'amm12_flx' , 3 , 'sowafldo' , .true. , .false. , 'daily' , '' , '' cn_dir = './fluxes/' ! root directory for the location of the flux files / !----------------------------------------------------------------------- &namsbc_clio ! namsbc_clio CLIO bulk formulae !----------------------------------------------------------------------- NOT USED !----------------------------------------------------------------------- &namsbc_core ! namsbc_core CORE bulk formulae !----------------------------------------------------------------------- NOT USED / !----------------------------------------------------------------------- &namsbc_mfs ! namsbc_mfs MFS bulk formulae !----------------------------------------------------------------------- NOT USED / !----------------------------------------------------------------------- &namsbc_cpl ! coupled ocean/atmosphere model ("key_coupled") !----------------------------------------------------------------------- NOT USED / !----------------------------------------------------------------------- &namtra_qsr ! penetrative solar radiation !----------------------------------------------------------------------- ! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! ! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! sn_chl ='chlorophyll', -1 , 'CHLA' , .true. , .true. , 'yearly' , '' , '' cn_dir = './' ! root directory for the location of the runoff files ln_traqsr = .false. ! Light penetration (T) or not (F) ln_qsr_rgb = .true. ! RGB (Red-Green-Blue) light penetration ln_qsr_2bd = .false. ! 2 bands light penetration ln_qsr_bio = .false. ! bio-model light penetration nn_chldta = 0 ! RGB : Chl data (=1) or cst value (=0) rn_abs = 0.58 ! RGB & 2 bands: fraction of light (rn_si1) rn_si0 = 0.35 ! RGB & 2 bands: shortess depth of extinction rn_si1 = 23.0 ! 2 bands: longest depth of extinction / !----------------------------------------------------------------------- &namsbc_rnf ! runoffs namelist surface boundary condition !----------------------------------------------------------------------- ! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! ! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! sn_rnf = 'amm12_rivers' , 24 , 'rorunoff', .false. , .true. , 'yearly' , '' , '' sn_cnf = 'runoff_1m_nomask' , 0 , 'socoefr0', .false. , .true. , 'yearly' , '' , '' sn_s_rnf = 'amm12_rivers' , 24 , 'rosaline', .false. , .true. , 'yearly' , '' , '' sn_t_rnf = 'amm12_rivers' , 24 , 'rotemper', .false. , .true. , 'yearly' , '' , '' sn_dep_rnf = 'amm12_rivers' , 24 , 'rodepth' , .false. , .true. , 'yearly' , '' , '' cn_dir = './' ! root directory for the location of the runoff files ln_rnf_emp = .false. ! runoffs included into precipitation field (T) or into a file (F) ln_rnf_mouth = .false. ! specific treatment at rivers mouths rn_hrnf = 15.e0 ! depth over which enhanced vertical mixing is used rn_avt_rnf = 1.e-3 ! value of the additional vertical mixing coef. [m2/s] rn_rfact = 1.e0 ! multiplicative factor for runoff ln_rnf_depth = .true. ! read in depth information for runoff ln_rnf_tem = .true. ! read in temperature information for runoff ln_rnf_sal = .true. ! read in salinity information for runoff / !----------------------------------------------------------------------- &namsbc_apr ! Atmospheric pressure used as ocean forcing or in bulk !----------------------------------------------------------------------- NOT USED / !----------------------------------------------------------------------- &namsbc_ssr ! surface boundary condition : sea surface restoring !----------------------------------------------------------------------- NOT USED / !----------------------------------------------------------------------- &namsbc_alb ! albedo parameters !----------------------------------------------------------------------- FOR ICE, NOT USED /
Section Four, Boundary Conditions
Free slip along coasts rn_shlat = 0
No cross land advection through thin pennisulas nn_cla = 0
Open Boundaries: things to change : time relaxation for the different open boundaries
Check AGRIF conditions: sponge layer in particular
Unstructured open boundaries, may be able to greatly simplify or even remove
nambdy_dta open boundary files
nambdy_tide tide files
!!====================================================================== !! *** Lateral boundary condition *** !!====================================================================== !! namlbc lateral momentum boundary condition !! namcla cross land advection !! namobc open boundaries parameters ("key_obc") !! namagrif agrif nested grid ( read by child model only ) ("key_agrif") !! nambdy Unstructured open boundaries ("key_bdy") !! namtide Tidal forcing at open boundaries ("key_bdy_tides") !!====================================================================== ! !----------------------------------------------------------------------- &namlbc ! lateral momentum boundary condition !----------------------------------------------------------------------- rn_shlat = 0 ! shlat = 0 ! 0 < shlat < 2 ! shlat = 2 ! 2 < shlat ! free slip ! partial slip ! no slip ! strong slip ln_vorlat = .false. ! consistency of vorticity boundary condition with analytical eqs. / !----------------------------------------------------------------------- &namcla ! cross land advection !----------------------------------------------------------------------- nn_cla = 0 ! advection between 2 ocean pts separates by land / !----------------------------------------------------------------------- &namobc ! open boundaries parameters ("key_obc") !----------------------------------------------------------------------- ln_obc_clim = .false. ! climatological obc data files (T) or not (F) ln_vol_cst = .true. ! impose the total volume conservation (T) or not (F) ln_obc_fla = .false. ! Flather open boundary condition nn_obcdta = 1 ! = 0 the obc data are equal to the initial state ! = 1 the obc data are read in 'obc.dta' files cn_obcdta = 'annual' ! set to annual if obc datafile hold 1 year of data ! set to monthly if obc datafile hold 1 month of data rn_dpein = 1. ! damping time scale for inflow at east open boundary rn_dpwin = 1. ! - - - west - - rn_dpnin = 1. ! - - - north - - rn_dpsin = 1. ! - - - south - - rn_dpeob = 3000. ! time relaxation (days) for the east open boundary rn_dpwob = 15. ! - - - west - - rn_dpnob = 3000. ! - - - north - - rn_dpsob = 15. ! - - - south - - rn_volemp = 1. ! = 0 the total volume change with the surface flux (E-P-R) ! = 1 the total volume remains constant / !----------------------------------------------------------------------- &namagrif ! AGRIF zoom ("key_agrif") !----------------------------------------------------------------------- nn_cln_update = 3 ! baroclinic update frequency 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] / !----------------------------------------------------------------------- &nam_tide ! tide parameters (#ifdef key_tide) !----------------------------------------------------------------------- ln_tide_pot = .true. ! use tidal potential forcing nb_harmo = 11 ! number of constituents used clname(1) = 'M2' ! name of constituent clname(2) = 'S2' clname(3) = 'N2' clname(4) = 'K1' clname(5) = 'O1' clname(6) = 'Q1' clname(7) = 'M4' clname(8) = 'K2' clname(9) = 'P1' clname(10) = 'Mf' clname(11) = 'Mm' / !----------------------------------------------------------------------- &nambdy ! unstructured open boundaries ("key_bdy") !----------------------------------------------------------------------- nb_bdy = 1 ! 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.) nn_dyn2d = 2 ! boundary conditions for barotropic fields nn_dyn2d_dta = 2 ! = 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 nn_dyn3d = 0 ! boundary conditions for baroclinic velocities nn_dyn3d_dta = 0 ! = 0, bdy data are equal to the initial state ! = 1, bdy data are read in 'bdydata .nc' files nn_tra = 1 ! boundary conditions for T and S nn_tra_dta = 0 ! = 0, bdy data are equal to the initial state ! = 1, bdy data are read in 'bdydata .nc' files 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 / !----------------------------------------------------------------------- &nambdy_dta ! open boundaries - external data ("key_bdy") !----------------------------------------------------------------------- ! ! file name ! frequency (hours) ! variable ! time interpol. ! clim ! 'yearly'/ ! weights ! rotation ! ! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! bn_ssh = 'amm12_bdyT_u2d' , 24 , 'sossheig' , .true. , .false. , 'daily' , '' , '' bn_u2d = 'amm12_bdyU_u2d' , 24 , 'vobtcrtx' , .true. , .false. , 'daily' , '' , '' bn_v2d = 'amm12_bdyV_u2d' , 24 , 'vobtcrty' , .true. , .false. , 'daily' , '' , '' bn_u3d = 'amm12_bdyU_u3d' , 24 , 'vozocrtx' , .true. , .false. , 'daily' , '' , '' bn_v3d = 'amm12_bdyV_u3d' , 24 , 'vomecrty' , .true. , .false. , 'daily' , '' , '' bn_tem = 'amm12_bdyT_tra' , 24 , 'votemper' , .true. , .false. , 'daily' , '' , '' bn_sal = 'amm12_bdyT_tra' , 24 , 'vosaline' , .true. , .false. , 'daily' , '' , '' cn_dir = 'bdydta/' ln_full_vel = .false. / !----------------------------------------------------------------------- &nambdy_tide ! tidal forcing at open boundaries !----------------------------------------------------------------------- filtide = 'bdydta/amm12_bdytide_' ! file name root of tidal forcing files tide_cpt(1) ='Q1' ! names of tidal components used tide_cpt(2) ='O1' ! names of tidal components used tide_cpt(3) ='P1' ! names of tidal components used tide_cpt(4) ='S1' ! names of tidal components used tide_cpt(5) ='K1' ! names of tidal components used tide_cpt(6) ='2N2' ! names of tidal components used tide_cpt(7) ='MU2' ! names of tidal components used tide_cpt(8) ='N2' ! names of tidal components used tide_cpt(9) ='NU2' ! names of tidal components used tide_cpt(10) ='M2' ! names of tidal components used tide_cpt(11) ='L2' ! names of tidal components used tide_cpt(12) ='T2' ! names of tidal components used tide_cpt(13) ='S2' ! names of tidal components used tide_cpt(14) ='K2' ! names of tidal components used tide_cpt(15) ='M4' ! names of tidal components used tide_speed(1) = 13.398661 ! phase speeds of tidal components (deg/hour) tide_speed(2) = 13.943036 ! phase speeds of tidal components (deg/hour) tide_speed(3) = 14.958932 ! phase speeds of tidal components (deg/hour) tide_speed(4) = 15.000001 ! phase speeds of tidal components (deg/hour) tide_speed(5) = 15.041069 ! phase speeds of tidal components (deg/hour) tide_speed(6) = 27.895355 ! phase speeds of tidal components (deg/hour) tide_speed(7) = 27.968210 ! phase speeds of tidal components (deg/hour) tide_speed(8) = 28.439730 ! phase speeds of tidal components (deg/hour) tide_speed(9) = 28.512585 ! phase speeds of tidal components (deg/hour) tide_speed(10) = 28.984106 ! phase speeds of tidal components (deg/hour) tide_speed(11) = 29.528479 ! phase speeds of tidal components (deg/hour) tide_speed(12) = 29.958935 ! phase speeds of tidal components (deg/hour) tide_speed(13) = 30.000002 ! phase speeds of tidal components (deg/hour) tide_speed(14) = 30.082138 ! phase speeds of tidal components (deg/hour) tide_speed(15) = 57.968212 ! phase speeds of tidal components (deg/hour) ln_tide_date = .true. ! adjust tidal harmonics for start date of run /
Section 5 : bottom boundaries
probably don’t have to change anything here on first cut. May need to do later to get tides correct
!!====================================================================== !! *** Bottom boundary condition *** !!====================================================================== !! nambfr bottom friction !! nambbc bottom temperature boundary condition !! nambbl bottom boundary layer scheme ("key_trabbl") !!====================================================================== ! !----------------------------------------------------------------------- &nambfr ! bottom friction !----------------------------------------------------------------------- nn_bfr = 2 ! type of bottom friction : = 0 : free slip, = 1 : linear friction ! = 2 : nonlinear friction rn_bfri1 = 4.e-4 ! bottom drag coefficient (linear case) rn_bfri2 = 2.5e-3 ! bottom drag coefficient (non linear case) rn_bfeb2 = 0.0e0 ! bottom turbulent kinetic energy background (m2/s2) ln_bfr2d = .false. ! horizontal variation of the bottom friction coef (read a 2D mask file ) rn_bfrien = 50. ! local multiplying factor of bfr (ln_bfr2d=T) ln_bfrimp = .true. ! implicit bottom friction (requires ln_zdfexp = .false. if true) / !----------------------------------------------------------------------- &nambbc ! bottom temperature boundary condition !----------------------------------------------------------------------- ln_trabbc = .false. ! Apply a geothermal heating at the ocean bottom nn_geoflx = 2 ! geothermal heat flux: = 0 no flux ! = 1 constant flux ! = 2 variable flux (read in geothermal_heating.nc in mW/m2) rn_geoflx_cst = 86.4e-3 ! Constant value of geothermal heat flux [W/m2] / !----------------------------------------------------------------------- &nambbl ! bottom boundary layer scheme !----------------------------------------------------------------------- nn_bbl_ldf = 0 ! 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] /
Section 6 : Tracers
probably nothing to change here (No TEOS!)
!!====================================================================== !! Tracer (T & S ) namelists !!====================================================================== !! nameos equation of state !! namtra_adv advection scheme !! namtra_ldf lateral diffusion scheme !! namtra_dmp T & S newtonian damping !!====================================================================== ! !----------------------------------------------------------------------- &nameos ! ocean physical parameters !----------------------------------------------------------------------- nn_eos = 0 ! type of equation of state and Brunt-Vaisala frequency ! = 0, UNESCO (formulation of Jackett and McDougall (1994) and of McDougall (1987) ) ! = 1, linear: rho(T) = rau0 * ( 1.028 - ralpha * T ) ! = 2, linear: rho(T,S) = rau0 * ( rbeta * S - ralpha * T ) rn_alpha = 2.0e-4 ! thermal expension coefficient (nn_eos= 1 or 2) rn_beta = 7.7e-4 ! saline expension coefficient (nn_eos= 2) / !----------------------------------------------------------------------- &namtra_adv ! advection scheme for tracer !----------------------------------------------------------------------- ln_traadv_cen2 = .false. ! 2nd order centered scheme ln_traadv_tvd = .true. ! TVD scheme ln_traadv_muscl = .false. ! MUSCL scheme ln_traadv_muscl2 = .false. ! MUSCL2 scheme + cen2 at boundaries ln_traadv_ubs = .false. ! UBS scheme ln_traadv_qck = .false. ! QUICKEST scheme / !---------------------------------------------------------------------------------- &namtra_ldf ! lateral diffusion scheme for tracers !---------------------------------------------------------------------------------- ! ! Operator type: ln_traldf_lap = .true. ! laplacian operator ln_traldf_bilap = .false. ! bilaplacian operator ! ! Direction of action: ln_traldf_level = .false. ! iso-level ln_traldf_hor = .true. ! horizontal (geopotential) (needs "key_ldfslp" when ln_sco=T) ln_traldf_iso = .false. ! iso-neutral (needs "key_ldfslp") ! ! Griffies parameters (all need "key_ldfslp") ln_traldf_grif = .false. ! use griffies triads ln_traldf_gdia = .false. ! output griffies eddy velocities ln_triad_iso = .false. ! pure lateral mixing in ML ln_botmix_grif = .false. ! lateral mixing on bottom ! ! Coefficients ! Eddy-induced (GM) advection always used with Griffies; otherwise needs "key_traldf_eiv" ! Value rn_aeiv_0 is ignored unless = 0 with Held-Larichev spatially varying aeiv ! (key_traldf_c2d & key_traldf_eiv & key_orca_r2, _r1 or _r05) rn_aeiv_0 = 0. ! eddy induced velocity coefficient [m2/s] rn_aht_0 = 50. ! horizontal eddy diffusivity for tracers [m2/s] rn_ahtb_0 = 0. ! background eddy diffusivity for ldf_iso [m2/s] ! (normally=0; not used with Griffies) / !----------------------------------------------------------------------- &namtra_dmp ! tracer: T & S newtonian damping !----------------------------------------------------------------------- ln_tradmp = .false. ! add a damping termn (T) or not (F) REST NOT USED /
Dynamics
note: cpp keys matter here too
AMM12 has split-explicit free surface key_dynspg_ts
key_ldfslp for s-coordinates, won’t need in z
key_zdfgls for GLS vertical mixing
Hydrostatic pressure depends on z coordinate ln_hpg
Horz Eddy viscosity set here rn_ahm_0_lap = 60.0 m2/s
Vert Eddy viscosity/diffusivity rn_avt0, rn_avm0 = 0.1e-6 m2/s
!!====================================================================== !! *** Dynamics namelists *** !!====================================================================== !! namdyn_adv formulation of the momentum advection !! namdyn_vor advection scheme !! namdyn_hpg hydrostatic pressure gradient !! namdyn_spg surface pressure gradient (CPP key only) !! namdyn_ldf lateral diffusion scheme !!====================================================================== ! !----------------------------------------------------------------------- &namdyn_adv ! formulation of the momentum advection !----------------------------------------------------------------------- ln_dynadv_vec = .true. ! vector form (T) or flux form (F) ln_dynadv_cen2= .false. ! flux form - 2nd order centered scheme ln_dynadv_ubs = .false. ! flux form - 3rd order UBS scheme / !----------------------------------------------------------------------- &namdyn_vor ! option of physics/algorithm (not control by CPP keys) !----------------------------------------------------------------------- ln_dynvor_ene = .false. ! energy conserving scheme ln_dynvor_ens = .false. ! enstrophy conserving scheme ln_dynvor_mix = .false. ! mixed scheme ln_dynvor_een = .true. ! energy & enstrophy scheme / !----------------------------------------------------------------------- &namdyn_hpg ! Hydrostatic pressure gradient option !----------------------------------------------------------------------- ln_hpg_zco = .false. ! z-coordinate - full steps ln_hpg_zps = .false. ! z-coordinate - partial steps (interpolation) ln_hpg_sco = .true. ! s-coordinate (standard jacobian formulation) ln_hpg_djc = .false. ! s-coordinate (Density Jacobian with Cubic polynomial) ln_hpg_prj = .false. ! s-coordinate (Pressure Jacobian scheme) ln_dynhpg_imp = .false. ! time stepping: semi-implicit time scheme (T) ! centered time scheme (F) / !----------------------------------------------------------------------- !namdyn_spg ! surface pressure gradient (CPP key only) !----------------------------------------------------------------------- ! ! explicit free surface ("key_dynspg_exp") ! ! filtered free surface ("key_dynspg_flt") ! ! split-explicit free surface ("key_dynspg_ts") !----------------------------------------------------------------------- &namdyn_ldf ! lateral diffusion on momentum !----------------------------------------------------------------------- ! ! Type of the operator : ln_dynldf_lap = .true. ! laplacian operator ln_dynldf_bilap = .true. ! bilaplacian operator ! Direction of action : ln_dynldf_level = .false. ! iso-level ln_dynldf_hor = .true. ! horizontal (geopotential) (require "key_ldfslp" in s-coord.) ln_dynldf_iso = .false. ! iso-neutral (require "key_ldfslp") ! Coefficient rn_ahm_0_lap = 60.0 ! horizontal laplacian eddy viscosity [m2/s] rn_ahmb_0 = 0.0 ! background eddy viscosity for ldf_iso [m2/s] rn_ahm_0_blp = -1.0e+10 ! horizontal bilaplacian eddy viscosity [m4/s] / !!====================================================================== !! Tracers & Dynamics vertical physics namelists !!====================================================================== !! namzdf vertical physics !! namzdf_ric richardson number dependent vertical mixing ("key_zdfric") !! namzdf_tke TKE dependent vertical mixing ("key_zdftke") !! namzdf_kpp KPP dependent vertical mixing ("key_zdfkpp") !! namzdf_ddm double diffusive mixing parameterization ("key_zdfddm") !! namzdf_tmx tidal mixing parameterization ("key_zdftmx") !!====================================================================== ! !----------------------------------------------------------------------- &namzdf ! vertical physics !----------------------------------------------------------------------- rn_avm0 = 0.1e-6 ! vertical eddy viscosity [m2/s] (background Kz if not "key_zdfcst") rn_avt0 = 0.1e-6 ! vertical eddy diffusivity [m2/s] (background Kz if not "key_zdfcst") nn_avb = 0 ! profile for background avt & avm (=1) or not (=0) nn_havtb = 0 ! horizontal shape for avtb (=1) or not (=0) ln_zdfevd = .false. ! enhanced vertical diffusion (evd) (T) or not (F) nn_evdm = 1 ! evd apply on tracer (=0) or on tracer and momentum (=1) rn_avevd = 100. ! evd mixing coefficient [m2/s] ln_zdfnpc = .false. ! Non-Penetrative Convective algorithm (T) or not (F) nn_npc = 1 ! frequency of application of npc nn_npcp = 365 ! npc control print frequency ln_zdfexp = .false. ! time-stepping: split-explicit (T) or implicit (F) time stepping nn_zdfexp = 3 ! number of sub-timestep for ln_zdfexp=T / !----------------------------------------------------------------------- &namzdf_ric ! richardson number dependent vertical diffusion ("key_zdfric" ) !----------------------------------------------------------------------- NOT USED / !----------------------------------------------------------------------- &namzdf_tke ! turbulent eddy kinetic dependent vertical diffusion ("key_zdftke") !----------------------------------------------------------------------- NOT USED / !------------------------------------------------------------------------ &namzdf_kpp ! K-Profile Parameterization dependent vertical mixing ("key_zdfkpp", and optionally: !------------------------------------------------------------------------ "key_kppcustom" or "key_kpplktb") NOT USED / !----------------------------------------------------------------------- &namzdf_gls ! GLS vertical diffusion ("key_zdfgls") !----------------------------------------------------------------------- rn_emin = 1.e-6 ! minimum value of e [m2/s2] rn_epsmin = 1.e-12 ! minimum value of eps [m2/s3] ln_length_lim = .true. ! limit on the dissipation rate under stable stratification (Galperin et al., 1988) rn_clim_galp = 0.53 ! galperin limit ln_crban = .true. ! Use Craig & Banner (1994) surface wave mixing parametrisation ln_sigpsi = .true. ! Activate or not Burchard 2001 mods on psi schmidt number in the wb case rn_crban = 100. ! Craig and Banner 1994 constant for wb tke flux rn_charn = 100000. ! Charnock constant for wb induced roughness length nn_tkebc_surf = 1 ! surface tke condition (0/1/2=Dir/Neum/Dir Mellor-Blumberg) nn_tkebc_bot = 1 ! bottom tke condition (0/1=Dir/Neum) nn_psibc_surf = 1 ! surface psi condition (0/1/2=Dir/Neum/Dir Mellor-Blumberg) nn_psibc_bot = 1 ! bottom psi condition (0/1=Dir/Neum) nn_stab_func = 2 ! stability function (0=Galp, 1= KC94, 2=CanutoA, 3=CanutoB) nn_clos = 1 ! predefined closure type (0=MY82, 1=k-eps, 2=k-w, 3=Gen) / !----------------------------------------------------------------------- &namzdf_ddm ! double diffusive mixing parameterization ("key_zdfddm") !----------------------------------------------------------------------- NOT USED / !----------------------------------------------------------------------- &namzdf_tmx ! tidal mixing parameterization ("key_zdftmx") !----------------------------------------------------------------------- NOT USED /
Diagnostics (see below (switched order in this namelist)
Misc.
mpi settings for blocks are here, jpni, jpnj, jpnij
!!====================================================================== !! *** Miscellaneous namelists *** !!====================================================================== !! nammpp Massively Parallel Processing ("key_mpp_mpi) !! namctl Control prints & Benchmark !! namsol elliptic solver / island / free surface !!====================================================================== ! !----------------------------------------------------------------------- &namsol ! elliptic solver / island / free surface !----------------------------------------------------------------------- nn_solv = 1 ! elliptic solver: =1 preconditioned conjugate gradient (pcg) ! =2 successive-over-relaxation (sor) nn_sol_arp = 0 ! absolute/relative (0/1) precision convergence test rn_eps = 1.e-6 ! absolute precision of the solver nn_nmin = 300 ! minimum of iterations for the SOR solver nn_nmax = 800 ! maximum of iterations for the SOR solver nn_nmod = 10 ! frequency of test for the SOR solver rn_resmax = 1.e-10 ! absolute precision for the SOR solver rn_sor = 1.92 ! optimal coefficient for SOR solver (to be adjusted with the domain) / !----------------------------------------------------------------------- &nammpp ! Massively Parallel Processing ("key_mpp_mpi) !----------------------------------------------------------------------- cn_mpi_send = 'I' ! mpi send/recieve type ='S', 'B', or 'I' for standard send, ! buffer blocking send or immediate non-blocking sends, resp. nn_buffer = 0 ! size in bytes of exported buffer ('B' case), 0 no exportation ln_nnogather= .false. ! activate code to avoid mpi_allgather use at the northfold jpni = 0 ! jpni number of processors following i (set automatically if < 1) jpnj = 0 ! jpnj number of processors following j (set automatically if < 1) jpnij = 0 ! jpnij number of local domains (set automatically if < 1) / !----------------------------------------------------------------------- &namctl ! Control prints & Benchmark !----------------------------------------------------------------------- ln_ctl = .false. ! trends control print (expensive!) 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 nn_bench = 0 ! Bench mode (1/0): CAUTION use zero except for bench ! (no physical validity of the results) nn_timing = 1 ! timing by routine activated (=1) creates timing.output file, or not (=0) /
Diagnostics
NetCDF chunking and compressions set here nn_nchunks
Float parameters would be set here too
Harmonic analysis of tidal constituents set here!
!!====================================================================== !! *** Diagnostics namelists *** !!====================================================================== !! namnc4 netcdf4 chunking and compression settings ("key_netcdf4") !! namtrd dynamics and/or tracer trends ("key_trddyn","key_trdtra","key_trdmld") !! namflo float parameters ("key_float") !! namptr Poleward Transport Diagnostics !! namhsb Heat and salt budgets !!====================================================================== ! !----------------------------------------------------------------------- &namnc4 ! netcdf4 chunking and compression settings ("key_netcdf4") !----------------------------------------------------------------------- nn_nchunks_i= 4 ! number of chunks in i-dimension nn_nchunks_j= 4 ! number of chunks in j-dimension nn_nchunks_k= 31 ! number of chunks in k-dimension ! setting nn_nchunks_k = jpk will give a chunk size of 1 in the vertical which ! is optimal for postprocessing which works exclusively with horizontal slabs ln_nc4zip = .true. ! (T) use netcdf4 chunking and compression ! (F) ignore chunking information and produce netcdf3-compatible files / !----------------------------------------------------------------------- &namtrd ! diagnostics on dynamics and/or tracer trends ("key_trddyn" and/or "key_trdtra") ! ! or mixed-layer trends or barotropic vorticity ("key_trdmld" or "key_trdvor") !----------------------------------------------------------------------- NOT USED / !----------------------------------------------------------------------- &namgap ! level mean model-data gap ('key_diagap') !----------------------------------------------------------------------- NOT USED / !----------------------------------------------------------------------- &namflo ! float parameters ("key_float") !----------------------------------------------------------------------- NOT USED / !----------------------------------------------------------------------- &namptr ! Poleward Transport Diagnostic !----------------------------------------------------------------------- ln_diaptr = .false. ! Poleward heat and salt transport (T) or not (F) ln_diaznl = .false. ! Add zonal means and meridional stream functions ln_subbas = .false. ! Atlantic/Pacific/Indian basins computation (T) or not ! (orca configuration only, need input basins mask file named "subbasins.nc" ln_ptrcomp = .false. ! Add decomposition : overturning nn_fptr = 1 ! Frequency of ptr computation [time step] nn_fwri = 15 ! Frequency of ptr outputs [time step] / !----------------------------------------------------------------------- &namhsb ! Heat and salt budgets !----------------------------------------------------------------------- ln_diahsb = .false. ! check the heat and salt budgets (T) or not (F) / !----------------------------------------------------------------------- &nam_diaharm ! Harmonic analysis of tidal constituents ('key_diaharm') !----------------------------------------------------------------------- nit000_han = 1 ! First time step used for harmonic analysis nitend_han = 75 ! Last time step used for harmonic analysis nstep_han = 15 ! Time step frequency for harmonic analysis tname(1) = 'M2' ! Name of tidal constituents tname(2) = 'K1' / !----------------------------------------------------------------------- &namdct ! transports through sections !----------------------------------------------------------------------- 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
Assimilation and Observation
no changes here
/ !!====================================================================== !! *** Observation & Assimilation namelists *** !!====================================================================== !! namobs observation and model comparison ('key_diaobs') !! nam_asminc assimilation increments ('key_asminc') !!====================================================================== ! !----------------------------------------------------------------------- &namobs ! observation usage switch ('key_diaobs') !----------------------------------------------------------------------- NOT USED / !----------------------------------------------------------------------- &nam_asminc ! assimilation increments ('key_asminc') !----------------------------------------------------------------------- NOT USED / !----------------------------------------------------------------------- &namsbc_wave ! External fields from wave model !----------------------------------------------------------------------- NOT USED / !----------------------------------------------------------------------- &namdyn_nept ! Neptune effect (simplified: lateral and vertical diffusions removed) !----------------------------------------------------------------------- ! Suggested lengthscale values are those of Eby & Holloway (1994) for a coarse model ln_neptsimp = .false. ! yes/no use simplified neptune REST NOT USED / !----------------------------------------------------------------------- &namtrj ! Handling non-linear trajectory for TAM (output for direct model, input for TAM) !----------------------------------------------------------------------- NOT USED /