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File '''ocean.in''' is the standard input file to any model run. This file sets many of the parameters that are not specified at compile time, including the names of additional input file names (e.g. netcdf forcing files and input files for application modules such as [[stations.in]], [[floats.in]] and [[biology.in]]), output netcdf files names, and parameters and logical flags to control the frequency of output. Some model options, such as the [[GLS_MIXING]] vertical turbulence closure also have parameters set within '''ocean.in'''. | File '''ocean.in''' is the standard input file to any model run. This file sets many of the parameters that are not specified at compile time, including the names of additional input file names (e.g. netcdf forcing files and input files for application modules such as [[stations.in]], [[floats.in]] and [[biology.in]]), output netcdf files names, and parameters and logical flags to control the frequency of output. Some model options, such as the [[GLS_MIXING]] vertical turbulence closure also have parameters set within '''ocean.in'''. | ||
Revision as of 19:03, 8 December 2006
File ocean.in is the standard input file to any model run. This file sets many of the parameters that are not specified at compile time, including the names of additional input file names (e.g. netcdf forcing files and input files for application modules such as stations.in, floats.in and biology.in), output netcdf files names, and parameters and logical flags to control the frequency of output. Some model options, such as the GLS_MIXING vertical turbulence closure also have parameters set within ocean.in.
Important notes on the ocean.in file syntax:
Comment lines are allowed and begin with an exclamation mark (!) in column one. Comments may appear to the right of a parameter specification to improve the documentation of your choices. All comments will ignored during reading. Blank lines are also allowed and ignored. Continuation lines in a parameter specification are allowed using a backslash (\).
Input parameters can be entered in ANY order, provided that the parameter KEYWORD (usually, upper case) is typed correctly followed by "=" or "==" symbols. Parameters that are not used can be omitted from the list, so the ocean.in file for a specific application can be very concise.
In multiple levels of nesting and/or multiple connected domains (not yet implemented), "Ngrids" entries are expected for some of these parameters. The double equals symbols "==" syntax is for those parameters which will need to be assigned distinct values for each grid in multiple grid applications. The order of the entries for multigrid parameters is extremely important. It must follow the same order (1:Ngrids) as in the state variable declaration.
Frequently, more than one value is required for a parameter. If fewer values are provided, the last value is assigned for the entire parameter array. For convenience, the multiplication symbol (*) without blank spaces in between is allowed for a repeated value in a long list specification.
For example, in a three grids nested application AKT_BAK must be specified for temperature and salinity for all three grids, i.e. six values in total.
The line:
AKT_BAK == 2*1.0d-6 2*5.0d-6 2*3.0d-6 ! m2/s
indicates that the first two entries of array AKT_BAK will have the same value of "1.0d-6" for grid 1, the next two entries will have the same value of "5.0d-6" for grid 2, and grid 3 will use "3.0d-6". Thus the line is short-hand for:
AKT_BAK == 1.0d-6 1.0d-6 5.0d-6 5.0d-6 3.0d-6 3.0d-6 ! m2/s
The comment at the end is provided as a reminder of the correct units for this parameter.
The text below shows the entries in the default ocean.in file, with links to more detailed explanation where required.
Application title. This string will be saved in the output netcdf files. A backslash continuation character is allowed
TITLE = ROMS/TOMS 3.0 - Wind-Driven Upwelling/Downwelling \
over a Periodic Channel
Input variable information file name. This file needs to be processed first so all information arrays can be initialized properly.
VARNAME = ROMS/External/varinfo.dat
Domain decomposition parameters for serial, distributed-memory or shared-memory configurations used to determine tile horizontal range indices (Istr,Iend) and (Jstr,Jend), [1:Ngrids].
NtileI == 1 ! I-direction partition NtileJ == 4 ! J-direction partition
Time-Stepping parameters.
NTIMES = 1440 DT == 300.0d0 NDTFAST == 30
Model iteration loops parameters.
ERstr = 1
ERend = 1
Nouter = 1
Ninner = 1
Nintervals = 1
Number of eigenvalues (NEV) and eigenvectors (NCV) to compute for the Lanczos/Arnoldi problem in the Generalized Stability Theory (GST) analysis. NCV must be greater than NEV (see documentation below).
NEV = 2 ! Number of eigenvalues
NCV = 10 ! Number of eigenvectors
Input/Output parameters.
NRREC = 0 LcycleRST == T NRST == 288 NSTA == 1 NFLT == 1 NINFO == 1
Output history, average, diagnostic files parameters.
LDEFOUT == T NHIS == 72 NDEFHIS == 0 NTSAVG == 1 NAVG == 72 NDEFAVG == 0 NTSDIA == 1 NDIA == 72 NDEFDIA == 0
Output tangent linear and adjoint models parameters.
LcycleTLM == F
NTLM == 72
NDEFTLM == 0
LcycleADJ == F
NADJ == 72
NDEFADJ == 0
Output check pointing GST restart parameters.
LrstGST = F ! GST restart switch
MaxIterGST = 500 ! maximun number of iterations
NGST = 10 ! check pointing interval
Relative accuracy of the Ritz values computed in the GST analysis.
Ritz_tol = 1.0d-15
Harmonic/biharmonic horizontal diffusion of all active and passive (dye) tracers: [1:NAT+NPT,Ngrids]. Diffusion coefficients for biology variables are set in biology.in
TNU2 == 0.0d0 0.0d0 ! m2/s TNU4 == 2*0.0d0 ! m4/s
Harmononic/biharmonic, horizontal viscosity coefficient: [Ngrids]. Only used if the appropriate CPP options are defined.
VISC2 == 0.0d0 ! m2/s VISC4 == 0.0d0 ! m4/s
Background vertical mixing coefficients for active and passice (dye) tracers: [1:NAT+NPT,Ngrids]
AKT_BAK == 1.0d-6 1.0d-6 ! m2/s
Background vertical mixing coefficient for momentum: [Ngrids]. For more information on the vertical mixing closure options see
AKV_BAK == 1.0d-5 ! m2/s
Turbulent closure parameters.
AKK_BAK == 5.0d-6 ! m2/s AKP_BAK == 5.0d-6 ! m2/s TKENU2 == 0.0d0 ! m2/s TKENU4 == 0.0d0 ! m4/s
Generic length-scale turbulence closure parameters. See GLS_MIXING
GLS_P == 3.0d0 ! K-epsilon
GLS_M == 1.5d0
GLS_N == -1.0d0
GLS_Kmin == 7.6d-6
GLS_Pmin == 1.0d-12
GLS_CMU0 == 0.5477d0
GLS_C1 == 1.44d0
GLS_C2 == 1.92d0
GLS_C3M == -0.4d0
GLS_C3P == 1.0d0
GLS_SIGK == 1.0d0
GLS_SIGP == 1.30d0
Constants used in momentum stress computation.
RDRG == 3.0d-04 ! m/s (requires CPP option
RDRG2 == 3.0d-03 ! nondimensional
Zob == 0.02d0 ! m
Zos == 0.02d0 ! m
Various parameters.
WTYPE == 1 ! Jerlov water type sets vertical depth scale for shortwave radiation absorption LEVSFRC == 15 LEVBFRC == 1
Vertical S-coordinates parameters, [1:Ngrids].
THETA_S == 3.0d0 ! 0 < THETA_S < 20 THETA_B == 0.0d0 ! 0 < THETA_B < 1 TCLINE == 50.0d0 ! m
Mean Density and Brunt-Vaisala frequency.
RHO0 = 1025.0d0 ! kg/m3
BVF_BAK = 1.0d-4 ! 1/s2
Time-stamp assigned for model initialization, reference time origin for tidal forcing, and model reference time for output NetCDF units attribute.
DSTART = 0.0d0 ! days TIDE_START = 0.0d0 ! days TIME_REF = 0.0d0 ! yyyymmdd.dd
Nudging/relaxation time scales, inverse scales will be computed internally, [1:Ngrids].
TNUDG == 2*0.0d0 ! days
ZNUDG == 0.0d0 ! days
M2NUDG == 0.0d0 ! days
M3NUDG == 0.0d0 ! days
Factor between passive (outflow) and active (inflow) open boundary conditions, [1:Ngrids]. If OBCFAC > 1, nudging on inflow is stronger than on outflow (recommended).
OBCFAC == 0.0d0 ! nondimensional
Linear equation of State parameters:
R0 == 1027.0d0 ! kg/m3
T0 == 10.0d0 ! Celsius
S0 == 35.0d0 ! PSU
TCOEF == 1.7d-4 ! 1/Celsius
SCOEF == 7.6d-4 ! 1/PSU
Slipperiness parameter: 1.0 (free slip) or -1.0 (no slip)
GAMMA2 = 1.0d0
Starting (DstrS) and ending (DendS) day for adjoint sensitivity forcing. DstrS must be less or equal to DendS. If both values are zero, their values are reset internally to the full range of the adjoint integration.
DstrS == 0.0d0 ! starting day
DendS == 0.0d0 ! ending day
Starting and ending vertical levels of the 3D adjoint state variables whose sensitivity is required.
KstrS == 1 ! starting level
KendS == 1 ! ending level
Logical switches (TRUE/FALSE) to specify the adjoint state variables whose sensitivity is required.
Lstate(isFsur) == F ! free-surface
Lstate(isUbar) == F ! 2D U-momentum
Lstate(isVbar) == F ! 2D V-momentum
Lstate(isUvel) == F ! 3D U-momentum
Lstate(isVvel) == F ! 3D V-momentum
Logical switches (TRUE/FALSE) to specify the adjoint state tracer variables whose sensitivity is required (NT values are expected).
Lstate(isTvar) == F F ! tracers
Stochastic optimals time decorrelation scale (days) assumed for red noise processes.
SO_decay == 2.0d0 ! days
Logical switches (TRUE/FALSE) to specify the state surface forcing variable whose stochastic optimals is required.
SOstate(isUstr) == T ! surface u-stress
SOstate(isVstr) == T ! surface v-stress
Logical switches (TRUE/FALSE) to specify the surface tracer forcing variable whose stochastic optimals is required (NT values are expected).
SOstate(isTsur) == F F ! surface tracer flux
Stochastic optimals surface forcing standard deviation for dimensionalization.
SO_sdev(isUstr) == 1.0d0 ! surface u-stress
SO_sdev(isVstr) == 1.0d0 ! surface v-stress
SO_sdev(isTsur) == 1.0d0 1.0d0 ! NT surface tracer flux
Logical switches (TRUE/FALSE) to activate writing of fields into HISTORY output file. If CPP option AVERAGES is defined, these switches will cause the same data to be averaged and written to the averages file.
Hout(idUvel) == T ! 3D U-velocity
Hout(idVvel) == T ! 3D V-velocity
Hout(idWvel) == T ! 3D W-velocity
Hout(idOvel) == T ! omega vertical velocity
Hout(idUbar) == T ! 2D U-velocity
Hout(idVbar) == T ! 2D V-velocity
Hout(idFsur) == T ! free-surface
Hout(idTvar) == T T ! temperature and salinity
Hout(idUsms) == F ! surface U-stress
Hout(idVsms) == F ! surface V-stress
Hout(idUbms) == F ! bottom U-stress
Hout(idVbms) == F ! bottom V-stress
Hout(idUbrs) == F ! bottom U-current stress
Hout(idVbrs) == F ! bottom V-current stress
Hout(idUbws) == F ! bottom U-wave stress
Hout(idVbws) == F ! bottom V-wave stress
Hout(idUbcs) == F ! bottom max wave-current U-stress
Hout(idVbcs) == F ! bottom max wave-current V-stress
Hout(idUbot) == F ! bed wave orbital U-velocity
Hout(idVbot) == F ! bed wave orbital V-velocity
Hout(idUbur) == F ! bottom U-velocity above bed
Hout(idVbvr) == F ! bottom V-velocity above bed
Hout(idTsur) == F F ! surface net heat and salt flux
Hout(idLhea) == F ! latent heat flux
Hout(idShea) == F ! sensible heat flux
Hout(idLrad) == F ! longwave radiation flux
Hout(idSrad) == F ! shortwave radiation flux
Hout(idevap) == F ! evaporation rate
Hout(idrain) == F ! precipitation rate
Hout(idDano) == F ! density anomaly
Hout(idVvis) == F ! vertical viscosity
Hout(idTdif) == F ! vertical T-diffusion
Hout(idSdif) == F ! vertical Salinity diffusion
Hout(idHsbl) == F ! depth of surface boundary layer
Hout(idHbbl) == F ! depth of bottom boundary layer
Hout(idMtke) == F ! turbulent kinetic energy
Hout(idMtls) == F ! turbulent length scale
Logical switches (TRUE/FALSE) to activate writing of extra inert passive tracers other than biological and sediment tracers. An inert passive tracer is one that it is only advected and diffused. Other processes are ignored. These tracers include, for example, dyes, pollutants, oil spills, etc. NPT values are expected. However, these switches can be activated using compact parameter specification.
Hout(inert) == T ! inert passive tracers
Logical switches (TRUE/FALSE) to activate writing of exposed sediment layer properties into HISTORY output file. Currently, MBOTP properties are expected for the bottom boundary layer and/or sediment models:
Hout(idBott(isd50)), isd50 = 1 ! mean grain diameter Hout(idBott(idens)), idens = 2 ! mean grain density Hout(idBott(iwsed)), iwsed = 3 ! mean settling velocity Hout(idBott(itauc)), itauc = 4 ! critical erosion stress Hout(idBott(irlen)), irlen = 5 ! ripple length Hout(idBott(irhgt)), irhgt = 6 ! ripple height Hout(idBott(ibwav)), ibwav = 7 ! wave excursion amplitude Hout(idBott(izdef)), izdef = 8 ! default bottom roughness Hout(idBott(izapp)), izapp = 9 ! apparent bottom roughness Hout(idBott(izNik)), izNik = 10 ! Nikuradse bottom roughness Hout(idBott(izbio)), izbio = 11 ! biological bottom roughness Hout(idBott(izbfm)), izbfm = 12 ! bed form bottom roughness Hout(idBott(izbld)), izbld = 13 ! bed load bottom roughness Hout(idBott(izwbl)), izwbl = 14 ! wave bottom roughness Hout(idBott(iactv)), iactv = 15 ! active layer thickness Hout(idBott(ishgt)), ishgt = 16 ! saltation height
1 1 1 1 1 1 1
1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6
Hout(idBott) == T T T T T T T T T F F F F F F F
Generic User parameters, [1:NUSER].
NUSER = 0
USER = 0.d0
Input NetCDF file names, [1:Ngrids].
GRDNAME == ocean_grd.nc
ININAME == ocean_ini.nc
ITLNAME == ocean_itl.nc
IRPNAME == ocean_irp.nc
IADNAME == ocean_iad.nc
CLMNAME == ocean_clm.nc
BRYNAME == ocean_bry.nc
FWDNAME == ocean_fwd.nc
ADSNAME == ocean_ads.nc
Input forcing NetCDF file name(s). The USER has the option to enter several files names per each nested grid. For example, the USER may have a different files for wind products, heat fluxes, rivers, tides, etc. The model will scan the file list and will read the needed data from the first file in the list containing the forcing field. Therefore, the order of the file names is very important. If multiple forcing files per grid, enter first all the file names for grid 1, then grid 2, and so on. Use a single line per entry with a continuation (\) symbol at the each entry, except the last one.
NFFILES == 1 ! number of forcing files
FRCNAME == ocean_frc.nc ! forcing file 1, grid 1
Output NetCDF file names, [1:Ngrids].
GSTNAME == ocean_gst.nc
RSTNAME == ocean_rst.nc
HISNAME == ocean_his.nc
TLMNAME == ocean_tlm.nc
TLFNAME == ocean_tlf.nc
ADJNAME == ocean_adj.nc
AVGNAME == ocean_avg.nc
DIANAME == ocean_dia.nc
STANAME == ocean_sta.nc
FLTNAME == ocean_flt.nc
Input ASCII parameter filenames.
APARNAM = ROMS/External/assimilation.in
SPOSNAM = ROMS/External/stations.in
FPOSNAM = ROMS/External/floats.in
BPARNAM = ROMS/External/bioFasham.in
SPARNAM = ROMS/External/sediment.in
USRNAME = ROMS/External/MyFile.dat
