roms.in
File ocean.in is the ROMS standard input file to any model run. This file sets the application spatial dimensions and many of the parameters that are not specified at compile time, including parallel tile decomposition, time-stepping, physical coefficients and constants, vertical coordinate set-up, logical switches and flags to control the frequency of output, the names of input and output NetCDF files, and additional input scripts names for data assimilation, stations, floats trajectories, ecosystem models, and sediment model.
This standard input ASCII file is organized in several sections as shown below, with links to more detailed explanation where required.
Notice: A detailed information about ROMS input script file syntax can be found here.
Notice: A default ocean.in input script is provided in the User/External subdirectory. Also there are several standard input scripts in the ROMS/External subdirectory which are used in the distributed test cases. They are usually named ocean_app.in where app is the lowercase of the test case cpp option.
Configuration Parameters
- Application title. This string will be saved in the output NetCDF files. TITLE = Wind-Driven Upwelling/Downwelling over a Periodic Channel
- C-preprocessing Flag to define the specific configuration. In versions up to 2.3 this flag was one of the predefined model applications that headed the cppdefs.h file. You must make the value of MyAppCPP below consistent with variable ROMS_APPLICATION in the makefile. ROMS converts the ROMS_APPLICATION variable to lowercase to determine the name of the file to include. To see the options used in the predefined applications browse the files in ROMS/Include.
Notice: It is recommended that users setting up their own configuration by creating a new file e.g. myproject.h to hold CPP options and keep this either in User/Include or a separate directory that is indicated by the MY_HEADER_DIR macro definition in makefile.
Warning: If you copy a predefined application from ROMS/Include as a template for your application you must rename it. You cannot stop ROMS from first looking in ROMS/Include, in which case any edits you make will get shadowed and your changes will not be used.
- 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
- Grid dimension parameters. These are used to dynamically allocate all model state variables upon execution.Lm == 41 ! Number of I-direction INTERIOR RHO-points
Mm == 80 ! Number of J-direction INTERIOR RHO-points
N == 16 ! Number of vertical levels
Nbed = 0 ! Number of sediment bed layers
NAT = 2 ! Number of active tracers (usually, 2)
NPT = 0 ! Number of inactive passive tracers
NCS = 0 ! Number of cohesive (mud) sediment tracers
NNS = 0 ! Number of non-cohesive (sand) sediment tracers
- 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] values are expected.
Time-Stepping and Iterations Parameters
- Time-stepping parameters.
- Model iteration loops parameters.ERstr = 1 ! Starting perturbation or iteration
ERend = 1 ! Ending perturbation or iteration
Nouter = 1 ! Maximum number of 4DVar outer loop iterations
Ninner = 1 ! Maximum number of 4DVar inner loop iterations
Nintervals = 1 ! Number of stochastic optimals interval divisions
- 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. Notice: At present, there is no a-priori analysis to guide the selection of NCV relative to NEV. The only formal requirement is that NCV > NEV. However in optimal perturbations, it is recommended to have NCV ≥ 2*NEV. In Finite Time Eigenmodes (FTE) and Adjoint Finite Time Eigenmodes (AFTE) the requirement is to have NCV ≥ 2*NEV+1. The efficiency of calculations depends critically on the combination of NEV and NCV. If NEV is large (greater than 10 say), you can use NCV=2*NEV+1 but for NEV small (less than 6) it will be inefficient to use NCV=2*NEV+1. In complicated applications, you can start with NEV=2 and NCV=10. Otherwise, it will iterate for very long time.
Output Frequency Parameters
- Flags controlling the frequency of output.NRREC = 0 ! Model restart flag
LcycleRST == T ! Switch to recycle restart time records
NRST == 288 ! Number of time-steps between restart records
NSTA == 1 ! Number of time-steps between stations records
NFLT == 1 ! Number of time-steps between floats records
NINFO == 1 ! Number of time-steps between information diagnostics
- Output history, average, diagnostic files parameters.LDEFOUT == T ! File creation/append switch
NHIS == 72 ! Number of time-steps between history records
NDEFHIS == 0 ! Number of time-steps between creation of new history file
NTSAVG == 1 ! Starting averages time-step
NAVG == 72 ! Number of time-steps between averages records
NDEFAVG == 0 ! Number of time-steps between creation of new averages file
NTSDIA == 1 ! Starting diagnostics time-step
NDIA == 72 ! Number of time-steps between diagnostics records
NDEFDIA == 0 ! Number of time-steps between creation of new diagnostics file
- Output tangent linear and adjoint models parameters.LcycleTLM == F ! Switch to recycle TLM time records
NTLM == 72 ! Number of time-steps between TLM records
NDEFTLM == 0 ! Number of time-steps between creation of new TLM file
LcycleADJ == F ! Switch to recycle ADM time records
NADJ == 72 ! Number of time-steps between ADM records
NDEFADJ == 0 ! Number of time-steps between creation of new ADM file
- Output check pointing GST restart parameters.LrstGST = F ! GST restart switch
MaxIterGST = 500 ! maximum number of iterations
NGST = 10 ! check pointing interval
Physical and Numerical Parameters
- 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 and sediment tracers are set in their respective input scripts.
- Harmonic/biharmonic, horizontal viscosity coefficient: [1:Ngrids values are expected. Only used if the appropriate CPP options are defined.
- Background vertical mixing coefficients for active and passive (dye) tracers: [1:NAT+NPT,Ngrids] values are expected.AKT_BAK == 1.0d-6 1.0d-6 ! m2/s
- Background vertical mixing coefficient for momentum: [1:Ngrids] values are expected.AKV_BAK == 1.0d-5 ! m2/s
- Turbulent closures parameters.
- Generic length-scale turbulence closure parameters. This parameters are used when GLS_MIXING is activated.
- Constants used in surface turbulent kinetic energy flux computation.CHARNOK_ALPHA == 1400.0d0 ! Charnok surface roughness
ZOS_HSIG_ALPHA == 0.5d0 ! Roughness from wave amplitude
SZ_ALPHA == 0.25d0 ! roughness from wave dissipation
CRGBAN_CW == 100.0d0 ! Craig and Banner wave breaking
- Constants used in momentum stress computation.
- Height (m) of atmospheric measurements for Bulk fluxes parameterization.
- Minimum depth for wetting and drying.DCRIT == 0.10d0 ! 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
and
