roms.in

Standard Input Script - ocean.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.
  MyAppCPP = UPWELLING
  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.
  NtileI == 1  ! I-direction partition
  NtileJ == 1  ! J-direction partition

Time-Stepping and Iterations Parameters

• Time-stepping parameters.
  NTIMES = 1440  ! Number of time steps
  DT == 300.0d0  ! Time-step size (seconds)
  NDTFAST == 30  ! Number of barotropic steps

• 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.
  NEV = 2  ! Number of eigenvalues
  NCV = 10  ! Number of eigenvectors
  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
  NSFF == 72  ! Number of time-steps between 4DVAR adjustment of surface
   ! forcing fluxes

• 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.
  TNU2 == 0.0d0 0.0d0  ! m2/s
  TNU4 == 2*0.0d0  ! m4/s

• Harmonic/biharmonic, horizontal viscosity coefficient: [1:Ngrids values are expected. 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 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.
  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. These parameters are used when GLS_MIXING is activated.
  GLS_P == 3.0d0  ! K-epsilon
  GLS_M == 1.5d0  ! Turbulent kinetic energy exponent
  GLS_N == -1.0d0  ! Turbulent length scale exponent
  GLS_Kmin == 7.6d-6  ! Minimum value of specific turbulent energy
  GLS_Pmin == 1.0d-12  ! Minimum Value of dissipation
  
  ! Closure independent constraint parameters:
  
  GLS_CMU0 == 0.5477d0  ! Stability coefficient
  GLS_C1 == 1.44d0  ! Shear production coefficient
  GLS_C2 == 1.92d0  ! Dissipation coefficient
  GLS_C3M == -0.4d0  ! Buoyancy production coefficient (minus)
  GLS_C3P == 1.0d0  ! Buoyancy production coefficient (plus)
  GLS_SIGK == 1.0d0  ! Constant Schmidt number for turbulent
   ! kinetic energy diffusivity
  GLS_SIGP == 1.30d0  ! Constant Schmidt number for turbulent
   ! generic statistical field, "psi"

• 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.
  RDRG == 3.0d-04  ! m/s
  RDRG2 == 3.0d-03  ! nondimensional
  Zob == 0.02d0  ! m
  Zos == 0.02d0  ! m

• Height (m) of atmospheric measurements for Bulk fluxes parameterization.
  BLK_ZQ == 2.0d0  ! air humidity
  BLK_ZT == 2.0d0  ! air temperature
  BLK_ZW == 10.0d0  ! winds

• Minimum depth for wetting and drying.
  DCRIT == 0.10d0  ! m

• Jerlov water type used to set vertical depth scale for shortwave radiation absorption.
  WTYPE == 1

• Deepest and shallowest levels to apply surface momentum stress as a body-force.
  LEVSFRC == 15
  LEVBFRC == 1

• 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] values are expected.
  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, [1:Ngrids] values are expected.
  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

Vertical Coordinates Parameters

• Terrain-following coordinates surface control parameter, [1:Ngrids] values are expected.
  THETA_S == 3.0d0  ! 0 < THETA_S < 20

• Terrain-following coordinates bottom control parameter, [1:Ngrids] values are expected.
  THETA_B == 0.0d0  ! 0 < THETA_B < 1

• Width of surface or bottom boundary layer in which higher vertical resolution is required during stretching.
  TCLINE == 50.0d0  ! m

Adjoint Sensitivity Parameters

• 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 tracervariables whose sensitivity is required, [1:NT,1:Ngrids] values are expected.
  Lstate(isTvar) == F F  ! tracers

Stochastic Optimals Parameters

• 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, [1:NT,1:Ngrids] 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

Output Variables Switches

• Logical switches (TRUE/FALSE) to activate writing of fields into history output file. If CPP option AVERAGES is defined, these switches will cause the samedata 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(idBath) == T  ! time-dependent bathymetry
  
  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(idW2xx) == F  ! 2D radiation stress, Sxx component
  Hout(idW2xy) == F  ! 2D radiation stress, Sxy component
  Hout(idW2yy) == F  ! 2D radiation stress, Syy component
  Hout(idU2rs) == F  ! 2D radiation U-stress
  Hout(idV2rs) == F  ! 2D radiation V-stress
  Hout(idU2Sd) == F  ! 2D U-Stokes velocity
  Hout(idV2Sd) == F  ! 2D V-Stokes velocity
  
  Hout(idW3xx) == F  ! 3D radiation stress, Sxx component
  Hout(idW3xy) == F  ! 3D radiation stress, Sxy component
  Hout(idW3yy) == F  ! 3D radiation stress, Syy component
  Hout(idW3zx) == F  ! 3D radiation stress, Szx component
  Hout(idW3zy) == F  ! 3D radiation stress, Szy component
  Hout(idU3rs) == F  ! 3D radiation U-stress
  Hout(idV3rs) == F  ! 3D radiation V-stress
  Hout(idU3Sd) == F  ! 3D U-Stokes velocity
  Hout(idV3Sd) == F  ! 3D V-Stokes velocity
  
  Hout(idWamp) == F  ! wave height
  Hout(idWlen) == F  ! wave length
  Hout(idWdir) == F  ! wave direction
  
  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. [1:NPT,1:Ngrids] 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

User Parameters

• Generic User parameters, [1:NUSER] values are expected.
  NUSER = 0
  USER = 0.d0

Input NetCDF Files

• Input NetCDF file names, [1:Ngrids] values are expected.
  GRDNAME == ocean_grd.nc  ! Grid
  ININAME == ocean_ini.nc  ! NLM initial conditions
  ITLNAME == ocean_itl.nc  ! TLM initial conditions
  IRPNAME == ocean_irp.nc  ! RPM initial conditions
  IADNAME == ocean_iad.nc  ! ADM initial conditions
  CLMNAME == ocean_clm.nc  ! Climatology
  BRYNAME == ocean_bry.nc  ! Open boundary conditions
  FWDNAME == ocean_fwd.nc  ! Forward trajectory
  ADSNAME == ocean_ads.nc  ! Adjoint sensitivity functionals

• 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 Files

• Output NetCDF file names, [1:Ngrids] files are expected.
  GSTNAME == ocean_gst.nc  ! GST analysis restart
  RSTNAME == ocean_rst.nc  ! Restart
  HISNAME == ocean_his.nc  ! History
  TLMNAME == ocean_tlm.nc  ! TLM history
  TLFNAME == ocean_tlf.nc  ! Impulse TLM forcing
  ADJNAME == ocean_adj.nc  ! ADM history
  AVGNAME == ocean_avg.nc  ! Averages
  DIANAME == ocean_dia.nc  ! Diagnostics
  STANAME == ocean_sta.nc  ! Stations
  FLTNAME == ocean_flt.nc  ! Floats

Additional Input Scripts

• Input ASCII parameter filenames.
  APARNAM = ROMS/External/s4dvar.in
  SPOSNAM = ROMS/External/stations.in
  FPOSNAM = ROMS/External/floats.in
  BPARNAM = ROMS/External/biology.in
  SPARNAM = ROMS/External/sediment.in
  USRNAME = ROMS/External/MyFile.dat