ocean_ECB.in

!
!  ROMS/TOMS Standard Input parameters.
!
!svn $Id: ocean.in 889 2018-02-10 03:32:52Z arango $
!========================================================= Hernan G. Arango ===
!  Copyright (c) 2002-2018 The ROMS/TOMS Group                                !
!    Licensed under a MIT/X style license                                     !
!    See License_ROMS.txt                                                     !
!==============================================================================
!                                                                             !
! Input parameters can be entered in ANY order, provided that the parameter   !
! KEYWORD (usually, upper case) is typed correctly followed by "="  or "=="   !
! symbols. Any comment lines are allowed and must begin with an exclamation   !
! mark (!) in column one.  Comments may appear to the right of a parameter    !
! specification to improve documentation.  Comments are ignored during        !
! reading.  Blank lines are also allowed and ignored. Continuation lines in   !
! a parameter specification are allowed if preceded by a backslash (\).  In   !
! some instances, more than one value is required for a parameter.  If fewer  !
! values are provided, the last value is assigned for the entire parameter    !
! array.  The multiplication symbol (*),  without blank spaces in between,    !
! is allowed for a parameter specification. For example, in two grids nested  !
! application:                                                                !
!                                                                             !
!    AKT_BAK == 2*1.0d-6  2*5.0d-6              ! m2/s                        !
!                                                                             !
! indicates that the first two entries of array AKT_BAK,  in fortran column-  !
! major order, will have the same value of "1.0d-6" for grid 1,  whereas the  !
! next two entries will have the same value of "5.0d-6" for grid 2.           !
!                                                                             !
! In multiple levels of nesting or multiple connected domains step-ups,       !
! "Ngrids" entries are expected for some of these parameters. In such case,   !
! the order of the entries for a parameter is critical. It must follow the    !
! same order (1:Ngrids) as in the state variable declaration. The USER may    !
! follow the above guidelines for specifying his/her values. These parameters !
! are marked by "==" plural symbol after the KEYWORD.                         !
!                                                                             !
! Multiple NetCDF files are allowed for input field(s). It is useful when     !
! splitting input data (climatology,  boundary,  forcing) time records into   !
! several files (say monthly, annual, etc.). In this case, each multiple      !
! filename entry lines need to end with the vertical bar (|) symbol. For      !
! example:                                                                    !
!                                                                             !
!    NFFILES == 6                          ! number of forcing files          !
!                                                                             !
!    FRCNAME == my_lwrad_year1.nc |                                           !
!               my_lwrad_year2.nc \                                           !
!               my_swrad_year1.nc |                                           !
!               my_swrad_year2.nc \                                           !
!               my_winds_year1.nc |                                           !
!               my_winds_year2.nc \                                           !
!               my_Pair_year1.nc  |                                           !
!               my_Pair_year2.nc  \                                           !
!               my_Qair_year1.nc  |                                           !
!               my_Qair_year2.nc  \                                           !
!               my_Tair_year1.nc  |                                           !
!               my_Tair_year2.nc                                              !
!                                                                             !
! Notice that NFFILES is 6 and not 12. There are 6 uniquely different fields  !
! in the file list,  we  DO NOT  count file entries followed by the vertical  !
! bar symbol.  This is because  multiple file  entries are processed in ROMS  !
! with derived type structures.                                               !
!                                                                             !
!==============================================================================
!
! Application title.

       TITLE = ChesROMS ECB Coupled Physical-Biogeochemical Model

! C-preprocessing Flag.

    MyAppCPP = ChesROMS_ECB

! Input variable information file name.  This file needs to be processed
! first so all information arrays can be initialized properly.

     VARNAME = varinfo.dat

! Number of nested grids.

      Ngrids =  1

! Number of grid nesting layers.  This parameter is used to allow refinement
! and composite grid combinations.

  NestLayers =  1

! Number of grids in each nesting layer [1:NestLayers].

GridsInLayer =  1

! Grid dimension parameters. See notes below in the Glossary for how to set
! these parameters correctly.

          Lm == 98            ! Number of I-direction INTERIOR RHO-points
          Mm == 148           ! Number of J-direction INTERIOR RHO-points
           N == 20            ! Number of vertical levels

        Nbed =  0             ! Number of sediment bed layers

         NAT =  2             ! Number of active tracers (usually, 2)
         NPT =  1             ! 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].

      NtileI ==  6            ! I-direction partition
      NtileJ ==  8            ! J-direction partition

! Set lateral boundary conditions keyword. Notice that a value is expected
! for each boundary segment per nested grid for each state variable.
!
! Each tracer variable requires [1:4,1:NAT+NPT,Ngrids] values. Otherwise,
! [1:4,1:Ngrids] values are expected for other variables. The boundary
! order is: 1=west, 2=south, 3=east, and 4=north. That is, anticlockwise
! starting at the western boundary.
!
! The keyword is case insensitive and usually has three characters. However,
! it is possible to have compound keywords, if applicable. For example, the
! keyword "RadNud" implies radiation boundary condition with nudging. This
! combination is usually used in active/passive radiation conditions.
!
!   Keyword    Lateral Boundary Condition Type
!
!   Cha        Chapman_implicit (free-surface)
!   Che        Chapman_explicit (free-surface)
!   Cla        Clamped
!   Clo        Closed
!   Fla        Flather (2D momentum)                  _____N_____     j=Mm
!   Gra        Gradient                              |     4     |
!   Nes        Nested (refinement)                   |           |
!   Nud        Nudging                             1 W           E 3
!   Per        Periodic                              |           |
!   Rad        Radiation                             |_____S_____|
!   Red        Reduced Physics (2D momentum)               2          j=1
!   Shc        Shchepetkin (2D momentum)            i=1         i=Lm
!
!                   W       S       E       N
!                   e       o       a       o
!                   s       u       s       r
!                   t       t       t       t
!                           h               h
!
!                   1       2       3       4

   LBC(isFsur) ==   Clo     Clo     Cha     Clo         ! free-surface
   LBC(isUbar) ==   Clo     Clo     Fla     Clo         ! 2D U-momentum
   LBC(isVbar) ==   Clo     Clo     Fla     Clo         ! 2D V-momentum
   LBC(isUvel) ==   Clo     Clo     Rad     Clo         ! 3D U-momentum
   LBC(isVvel) ==   Clo     Clo     Rad     Clo         ! 3D V-momentum
   LBC(isMtke) ==   Clo     Clo     Rad     Clo         !mixing TKE

   LBC(isTvar) ==   Clo     Clo     RadNud  Clo \       !temperature
                    Clo     Clo     RadNud  Clo         !salinity

! Adjoint-based algorithms can have different lateral boundary
! conditions keywords.

ad_LBC(isFsur) ==   Per     Clo     Per     Clo         ! free-surface
ad_LBC(isUbar) ==   Per     Clo     Per     Clo         ! 2D U-momentum
ad_LBC(isVbar) ==   Per     Clo     Per     Clo         ! 2D U-momentum
ad_LBC(isUvel) ==   Per     Clo     Per     Clo         ! 3D U-momentum
ad_LBC(isVvel) ==   Per     Clo     Per     Clo         ! 3D V-momentum
ad_LBC(isMtke) ==   Per     Clo     Per     Clo         ! mixing TKE

ad_LBC(isTvar) ==   Per     Clo     Per     Clo \       ! temperature
                    Per     Clo     Per     Clo         ! salinity

! Set lateral open boundary edge volume conservation switch for
! nonlinear model and adjoint-based algorithms. Usually activated
! with radiation boundary conditions to enforce global mass
! conservation, except if tidal forcing is enabled. [1:Ngrids].

   VolCons(west)  ==  F                            ! western  boundary
   VolCons(east)  ==  F                            ! eastern  boundary
   VolCons(south) ==  F                            ! southern boundary
   VolCons(north) ==  F                            ! northern boundary

ad_VolCons(west)  ==  F                            ! western  boundary
ad_VolCons(east)  ==  F                            ! eastern  boundary
ad_VolCons(south) ==  F                            ! southern boundary
ad_VolCons(north) ==  F                            ! northern boundary

! Time-Stepping parameters.

     NTIMES ==  1049760 ! (timesteps) <=> Jan.1,2017 to Dec.31,2018.
          DT == 60.0d0
     NDTFAST == 15

! 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 == 1440 ! 24 hours.
        NSTA == 60
        NFLT == 12
       NINFO == 1

! Output history, quicksave, average, and diagnostic files parameters.

     LDEFOUT == T
        NHIS == 43200 ! 30 days.
     NDEFHIS == 43200 ! 30 days.
        NQCK ==   180 !  3 hours.
     NDEFQCK == 43200 ! 30 days.
      NTSAVG == 1
        NAVG ==  1440 ! 24 hours.
     NDEFAVG == 43200 ! 30 days.
      NTSDIA == 1
        NDIA ==  1440 ! 24 hours.
     NDEFDIA == 43200 ! 30 days.

! Output tangent linear and adjoint models parameters.

   LcycleTLM == F
        NTLM == 1440
     NDEFTLM == 0
   LcycleADJ == F
        NADJ == 1440
     NDEFADJ == 0
        NSFF == 80
        NOBC == 80

! GST output and check pointing restart parameters.

   LmultiGST =  F                               ! one eigenvector per file
     LrstGST =  F                               ! GST restart switch
  MaxIterGST =  500                             ! maximum 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 tracer for nonlinear model
! and adjoint-based algorithms: [1:NAT+NPT,Ngrids].

        TNU2 == 0.0d0  0.0d0                    ! m2/s
        TNU4 == 0.0d0  0.0d0                    ! m4/s

     ad_TNU2 == 0.0d0  0.0d0                    ! m2/s
     ad_TNU4 == 0.0d0  0.0d0                    ! m4/s

! Harmonic/biharmonic, horizontal viscosity coefficient for nonlinear model
! and adjoint-based algorithms: [Ngrids].

       VISC2 == 0.0d0                           ! m2/s
       VISC4 == 0.0d0                           ! m4/s

    ad_VISC2 == 0.0d0                           ! m2/s
    ad_VISC4 == 0.0d0                           ! m4/s

! Logical switches (TRUE/FALSE) to increase/decrease horizontal viscosity
! and/or diffusivity in specific areas of the application domain (like
! sponge areas) for the desired application grid.

    LuvSponge == F                              ! horizontal momentum
LtracerSponge == F F                            ! temperature, salinity, inert

! Vertical mixing coefficients for tracers in nonlinear model and
! basic state scale factor in adjoint-based algorithms: [1:NAT+NPT,Ngrids]

     AKT_BAK == 2*1.0d-5                        ! m2/s Malcolm's number

  ad_AKT_fac == 1.0d0  1.0d0                    ! nondimensional

! Vertical mixing coefficient for momentum for nonlinear model and
! basic state scale factor in adjoint-based algorithms: [Ngrids].

        AKV_BAK == 1.0d-5                       ! m2/s Malcolm's number

  ad_AKV_fac == 1.0d0                           ! nondimensional

! Upper threshold values to limit vertical mixing coefficients computed
! from vertical mixing parameterizations. Although this is an engineering
! fix, the vertical mixing values inferred from ocean observations are
! rarely higher than this upper limit value.

   AKT_LIMIT == 1.0d-3 1.0d-3                   ! m2/s

   AKV_LIMIT == 1.0d-3                          ! m2/s

! Turbulent closure parameters.

     AKK_BAK == 1.0d-5                          ! m2/s Malcolm's number
     AKP_BAK == 1.0d-5                          ! m2/s Malcolm's number
      TKENU2 == 0.0d0                           ! m2/s
      TKENU4 == 0.0d0                           ! m4/s

! Generic length-scale turbulence closure parameters.

       GLS_P == -1.0d0                           ! K-epsilon
       GLS_M == 0.5d0
       GLS_N == -1.0d0
    GLS_Kmin == 1.0d-10                          ! Malcolm's number
    GLS_Pmin == 1.0d-12

    GLS_CMU0 == 0.5477d0
      GLS_C1 == 0.555d0
      GLS_C2 == 0.833d0
     GLS_C3M == -0.6d0
     GLS_C3P == 1.0d0
    GLS_SIGK == 2.0d0
    GLS_SIGP == 2.0d0

! 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-4                    ! m/s
       RDRG2 == 3.0d-3                    ! nondimensional
         Zob == 5.0d-4                     ! m
         Zos == 5.0d-3                     ! 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 ! Use NARR wind
!psl20161117 BLK_ZW == 18.0d0              ! winds ! Use Malcolm's TPL wind

! Minimum depth for wetting and drying.

       DCRIT == 0.10d0                     ! m

! Various parameters.

       WTYPE == 7                          ! psl20180104, from Fei Da (201712).
     LEVSFRC == 15
     LEVBFRC == 1

! Set vertical, terrain-following coordinates transformation equation and
! stretching function (see below for details), [1:Ngrids].

  Vtransform == 2                          ! transformation equation
 Vstretching == 4                          ! stretching function

! Vertical S-coordinates parameters (see below for details), [1:Ngrids].

     THETA_S == 6.0d0                      ! surface stretching parameter
     THETA_B == 4.0d0                      ! bottom  stretching parameter
      TCLINE == 10.0d0                     ! critical depth (m)

! Mean Density and Brunt-Vaisala frequency.

        RHO0 =  1025.0d0                   ! kg/m3
     BVF_BAK =  1.0d-5                     ! 1/s2

! Time-stamp assigned for model initialization, reference time
! origin for tidal forcing, and model reference time for output
! NetCDF units attribute.

      DSTART = 15341.d0                   ! (Days since TREF) <=> Jan.1, 2017.
  TIDE_START =  2557.d0                   ! Jan.1, 1982 (an "average" year).
    TIME_REF =  19750101.0d0              ! yyyymmdd.dd

! Nudging/relaxation time scales, inverse scales will be computed
! internally, [1:Ngrids].

       TNUDG == 2*0.08333d0                  ! days: Not used in present NENA
       ZNUDG == 0.001d0                      ! days
      M2NUDG == 0.001d0                      ! days
      M3NUDG == 0.001d0                      ! 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 ==  24.0d0                    ! nondimensional: modified from previous NENA

! Linear equation of State parameters:

          R0 == 1027.0d0                   ! kg/m3
          T0 == 14.0d0                     ! Celsius
          S0 == 35.0d0                     ! nondimensional
       TCOEF == 1.7d-4                     ! 1/Celsius
       SCOEF == 7.6d-4                     ! 1/PSU ! Cathy ChesNENA value !nondimensional

! Slipperiness parameter: 1.0 (free slip) or -1.0 (no slip)

      GAMMA2 == 1.0d0

! Logical switches (TRUE/FALSE) to activate horizontal momentum transport
! point Sources/Sinks (like river runoff transport) and mass point
! Sources/Sinks (like volume vertical influx), [1:Ngrids].

      LuvSrc == T                          ! horizontal momentum transport
       LwSrc == F                          ! volume vertical influx

! Logical switches (TRUE/FALSE) to activate tracers point Sources/Sinks
! (like river runoff) and to specify which tracer variables to consider:
! [1:NAT+NPT,Ngrids].  See glossary below for details.

  LtracerSrc == T T                        ! temperature, salinity, inert

! Logical switches (TRUE/FALSE) to read and process climatology fields.
! See glossary below for details.

     LsshCLM == F                          ! sea-surface height
      Lm2CLM == F                          ! 2D momentum
      Lm3CLM == F                          ! 3D momentum

  LtracerCLM == F F                        ! temperature, salinity, inert

! Logical switches (TRUE/FALSE) to nudge the desired climatology field(s).
! If not analytical climatology fields, users need to turn ON the logical
! switches above to process the fields from the climatology NetCDF file
! that are needed for nudging. See glossary below for details.

 LnudgeM2CLM == F                          ! 2D momentum
 LnudgeM3CLM == F                          ! 3D momentum

  LnudgeTCLM == F F                        ! temperature, salinity, inert

! 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
Lstate(isWvel) == F                        ! 3D W-momentum

Lstate(isTvar) == F F                      ! NT tracers

! Logical switches (TRUE/FALSE) to specify the state variables for
! which Forcing Singular Vectors or Stochastic Optimals is required.

Fstate(isFsur) == F                        ! free-surface
Fstate(isUbar) == F                        ! 2D U-momentum
Fstate(isVbar) == F                        ! 2D V-momentum
Fstate(isUvel) == F                        ! 3D U-momentum
Fstate(isVvel) == F                        ! 3D V-momentum
Fstate(isTvar) == F F                      ! NT tracers

Fstate(isUstr) == T                        ! surface U-stress
Fstate(isVstr) == T                        ! surface V-stress
Fstate(isTsur) == F F                      ! NT surface tracers flux

! Stochastic Optimals time decorrelation scale (days) assumed for
! red noise processes.

      SO_decay == 2.0d0                    ! days

! Stochastic Optimals surface forcing standard deviation for
! dimensionalization.

SO_sdev(isFsur) == 1.0d0                   ! free-surface
SO_sdev(isUbar) == 1.0d0                   ! 2D U-momentum
SO_sdev(isVbar) == 1.0d0                   ! 2D V-momentum
SO_sdev(isUvel) == 1.0d0                   ! 3D U-momentum
SO_sdev(isVvel) == 1.0d0                   ! 3D V-momentum
SO_sdev(isTvar) == 1.0d0 1.0d0             ! NT tracers

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 tracers flux

! Logical switches (TRUE/FALSE) to activate writing of fields into
! HISTORY output file.

Hout(idUvel) == T       ! u                  3D U-velocity
Hout(idVvel) == T       ! v                  3D V-velocity
Hout(idu3dE) == F       ! u_eastward         3D U-eastward  at RHO-points
Hout(idv3dN) == F       ! v_northward        3D V-northward at RHO-points
Hout(idWvel) == F       ! w                  3D W-velocity
Hout(idOvel) == F       ! omega              omega vertical velocity
Hout(idUbar) == T       ! ubar               2D U-velocity
Hout(idVbar) == T       ! vbar               2D V-velocity
Hout(idu2dE) == F       ! ubar_eastward      2D U-eastward  at RHO-points
Hout(idv2dN) == F       ! vbar_northward     2D V-northward at RHO-points
Hout(idFsur) == T       ! zeta               free-surface
Hout(idBath) == F       ! bath               time-dependent bathymetry

Hout(idTvar) == T T     ! temp, salt         temperature and salinity

Hout(idpthR) == F       ! z_rho              time-varying depths of RHO-points
Hout(idpthU) == F       ! z_u                time-varying depths of U-points
Hout(idpthV) == F       ! z_v                time-varying depths of V-points
Hout(idpthW) == F       ! z_w                time-varying depths of W-points

Hout(idUsms) == F       ! sustr              surface U-stress
Hout(idVsms) == F       ! svstr              surface V-stress
Hout(idUbms) == F       ! bustr              bottom U-stress
Hout(idVbms) == F       ! bvstr              bottom V-stress

Hout(idUbrs) == F       ! bustrc             bottom U-current stress
Hout(idVbrs) == F       ! bvstrc             bottom V-current stress
Hout(idUbws) == F       ! bustrw             bottom U-wave stress
Hout(idVbws) == F       ! bvstrw             bottom V-wave stress
Hout(idUbcs) == F       ! bustrcwmax         bottom max wave-current U-stress
Hout(idVbcs) == F       ! bvstrcwmax         bottom max wave-current V-stress

Hout(idUbot) == F       ! Ubot               bed wave orbital U-velocity
Hout(idVbot) == F       ! Vbot               bed wave orbital V-velocity
Hout(idUbur) == F       ! Ur                 bottom U-velocity above bed
Hout(idVbvr) == F       ! Vr                 bottom V-velocity above bed

Hout(idW2xx) == F       ! Sxx_bar            2D radiation stress, Sxx component
Hout(idW2xy) == F       ! Sxy_bar            2D radiation stress, Sxy component
Hout(idW2yy) == F       ! Syy_bar            2D radiation stress, Syy component
Hout(idU2rs) == F       ! Ubar_Rstress       2D radiation U-stress
Hout(idV2rs) == F       ! Vbar_Rstress       2D radiation V-stress
Hout(idU2Sd) == F       ! ubar_stokes        2D U-Stokes velocity
Hout(idV2Sd) == F       ! vbar_stokes        2D V-Stokes velocity

Hout(idW3xx) == F       ! Sxx                3D radiation stress, Sxx component
Hout(idW3xy) == F       ! Sxy                3D radiation stress, Sxy component
Hout(idW3yy) == F       ! Syy                3D radiation stress, Syy component
Hout(idW3zx) == F       ! Szx                3D radiation stress, Szx component
Hout(idW3zy) == F       ! Szy                3D radiation stress, Szy component
Hout(idU3rs) == F       ! u_Rstress          3D U-radiation stress
Hout(idV3rs) == F       ! v_Rstress          3D V-radiation stress
Hout(idU3Sd) == F       ! u_stokes           3D U-Stokes velocity
Hout(idV3Sd) == F       ! v_stokes           3D V-Stokes velocity

Hout(idWamp) == F       ! Hwave              wave height
Hout(idWlen) == F       ! Lwave              wave length
Hout(idWdir) == F       ! Dwave              wave direction
Hout(idWptp) == F       ! Pwave_top          wave surface period
Hout(idWpbt) == F       ! Pwave_bot          wave bottom period
Hout(idWorb) == F       ! Ub_swan            wave bottom orbital velocity
Hout(idWdis) == F       ! Wave_dissip        wave dissipation

Hout(idPair) == F       ! Pair               surface air pressure
Hout(idUair) == F       ! Uair               surface U-wind component
Hout(idVair) == F       ! Vair               surface V-wind component

Hout(idTsur) == T T     ! shflux, ssflux     surface net heat and salt flux
Hout(idLhea) == T       ! latent             latent heat flux
Hout(idShea) == T       ! sensible           sensible heat flux
Hout(idLrad) == T       ! lwrad              longwave radiation flux
Hout(idSrad) == T       ! swrad              shortwave radiation flux
Hout(idEmPf) == T       ! EminusP            E-P flux
Hout(idevap) == T       ! evaporation        evaporation rate
Hout(idrain) == T       ! rain               precipitation rate

Hout(idDano) == F       ! rho                density anomaly
Hout(idVvis) == F       ! AKv                vertical viscosity
Hout(idTdif) == F       ! AKt                vertical T-diffusion
Hout(idSdif) == F       ! AKs                vertical Salinity diffusion
Hout(idHsbl) == F       ! Hsbl               depth of surface boundary layer
Hout(idHbbl) == F       ! Hbbl               depth of bottom boundary layer
Hout(idMtke) == F       ! tke                turbulent kinetic energy
Hout(idMtls) == F       ! gls                turbulent length scale

! Logical switches (TRUE/FALSE) to activate writing of extra inert passive
! tracers other than biological and sediment tracers into the HISTORY
! output file. 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       ! dye_01, ...        inert passive tracers

! Logical switches (TRUE/FALSE) to activate writing of fields into
! QUICKSAVE output file.

Qout(idUvel) == F       ! u                  3D U-velocity
Qout(idVvel) == F       ! v                  3D V-velocity
Qout(idu3dE) == F       ! u_eastward         3D U-eastward  at RHO-points
Qout(idv3dN) == F       ! v_northward        3D V-northward at RHO-points
Qout(idWvel) == F       ! w                  3D W-velocity
Qout(idOvel) == F       ! omega              omega vertical velocity
Qout(idUbar) == T       ! ubar               2D U-velocity
Qout(idVbar) == T       ! vbar               2D V-velocity
Qout(idu2dE) == F       ! ubar_eastward      2D U-eastward  at RHO-points
Qout(idv2dN) == F       ! vbar_northward     2D V-northward at RHO-points
Qout(idFsur) == T       ! zeta               free-surface
Qout(idBath) == F       ! bath               time-dependent bathymetry

Qout(idTvar) == F F     ! temp, salt         temperature and salinity

Qout(idUsur) == T       ! u_sur              surface U-velocity
Qout(idVsur) == T       ! v_sur              surface V-velocity
Qout(idUsuE) == F       ! u_sur_eastward     surface U-eastward  velocity
Qout(idVsuN) == F       ! v_sur_northward    surface V-northward velocity

Qout(idsurT) == T T     ! temp_sur, salt_sur surface temperature and salinity

Qout(idpthR) == F       ! z_rho              time-varying depths of RHO-points
Qout(idpthU) == F       ! z_u                time-varying depths of U-points
Qout(idpthV) == F       ! z_v                time-varying depths of V-points
Qout(idpthW) == F       ! z_w                time-varying depths of W-points

Qout(idUsms) == T       ! sustr              surface U-stress
Qout(idVsms) == T       ! svstr              surface V-stress
Qout(idUbms) == T       ! bustr              bottom U-stress
Qout(idVbms) == T       ! bvstr              bottom V-stress

Qout(idUbrs) == T       ! bustrc             bottom U-current stress
Qout(idVbrs) == T       ! bvstrc             bottom V-current stress
Qout(idUbws) == F       ! bustrw             bottom U-wave stress
Qout(idVbws) == F       ! bvstrw             bottom V-wave stress
Qout(idUbcs) == F       ! bustrcwmax         bottom max wave-current U-stress
Qout(idVbcs) == F       ! bvstrcwmax         bottom max wave-current V-stress

Qout(idUbot) == F       ! Ubot               bed wave orbital U-velocity
Qout(idVbot) == F       ! Vbot               bed wave orbital V-velocity
Qout(idUbur) == F       ! Ur                 bottom U-velocity above bed
Qout(idVbvr) == F       ! Vr                 bottom V-velocity above bed

Qout(idW2xx) == F       ! Sxx_bar            2D radiation stress, Sxx component
Qout(idW2xy) == F       ! Sxy_bar            2D radiation stress, Sxy component
Qout(idW2yy) == F       ! Syy_bar            2D radiation stress, Syy component
Qout(idU2rs) == F       ! Ubar_Rstress       2D radiation U-stress
Qout(idV2rs) == F       ! Vbar_Rstress       2D radiation V-stress
Qout(idU2Sd) == F       ! ubar_stokes        2D U-Stokes velocity
Qout(idV2Sd) == F       ! vbar_stokes        2D V-Stokes velocity

Qout(idW3xx) == F       ! Sxx                3D radiation stress, Sxx component
Qout(idW3xy) == F       ! Sxy                3D radiation stress, Sxy component
Qout(idW3yy) == F       ! Syy                3D radiation stress, Syy component
Qout(idW3zx) == F       ! Szx                3D radiation stress, Szx component
Qout(idW3zy) == F       ! Szy                3D radiation stress, Szy component
Qout(idU3rs) == F       ! u_Rstress          3D U-radiation stress
Qout(idV3rs) == F       ! v_Rstress          3D V-radiation stress
Qout(idU3Sd) == F       ! u_stokes           3D U-Stokes velocity
Qout(idV3Sd) == F       ! v_stokes           3D V-Stokes velocity

Qout(idWamp) == F       ! Hwave              wave height
Qout(idWlen) == F       ! Lwave              wave length
Qout(idWdir) == F       ! Dwave              wave direction
Qout(idWptp) == F       ! Pwave_top          wave surface period
Qout(idWpbt) == F       ! Pwave_bot          wave bottom period
Qout(idWorb) == F       ! Ub_swan            wave bottom orbital velocity
Qout(idWdis) == F       ! Wave_dissip        wave dissipation

Qout(idPair) == F       ! Pair               surface air pressure
Qout(idUair) == F       ! Uair               surface U-wind component
Qout(idVair) == F       ! Vair               surface V-wind component

Qout(idTsur) == T T     ! shflux, ssflux     surface net heat and salt flux
Qout(idLhea) == T       ! latent             latent heat flux
Qout(idShea) == T       ! sensible           sensible heat flux
Qout(idLrad) == T       ! lwrad              longwave radiation flux
Qout(idSrad) == T       ! swrad              shortwave radiation flux
Qout(idEmPf) == F       ! EminusP            E-P flux
Qout(idevap) == F       ! evaporation        evaporation rate
Qout(idrain) == F       ! rain               precipitation rate

Qout(idDano) == F       ! rho                density anomaly
Qout(idVvis) == F       ! AKv                vertical viscosity
Qout(idTdif) == F       ! AKt                vertical T-diffusion
Qout(idSdif) == F       ! AKs                vertical Salinity diffusion
Qout(idHsbl) == T       ! Hsbl               depth of surface boundary layer
Qout(idHbbl) == T       ! Hbbl               depth of bottom boundary layer
Qout(idMtke) == F       ! tke                turbulent kinetic energy
Qout(idMtls) == F       ! gls                turbulent length scale

! Logical switches (TRUE/FALSE) to activate writing of extra inert passive
! tracers other than biological and sediment tracers into the QUICKSAVE
! output file. 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.

 Qout(inert) == F       ! dye_01, ...        inert passive tracers
 Qout(Snert) == F       ! dye_01_sur, ..     surface 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:
!
! idBott( 1=isd50)   grain_diameter          mean grain diameter
! idBott( 2=idens)   grain_density           mean grain density
! idBott( 3=iwsed)   settling_vel            mean settling velocity
! idBott( 4=itauc)   erosion_stress          critical erosion stress
! idBott( 5=irlen)   ripple_length           ripple length
! idBott( 6=irhgt)   ripple_height           ripple height
! idBott( 7=ibwav)   bed_wave_amp            wave excursion amplitude
! idBott( 8=izdef)   Zo_def                  default bottom roughness
! idBott( 9=izapp)   Zo_app                  apparent bottom roughness
! idBott(10=izNik)   Zo_Nik                  Nikuradse bottom roughness
! idBott(11=izbio)   Zo_bio                  biological bottom roughness
! idBott(12=izbfm)   Zo_bedform              bed form bottom roughness
! idBott(13=izbld)   Zo_bedload              bed load bottom roughness
! idBott(14=izwbl)   Zo_wbl                  wave bottom roughness
! idBott(15=iactv)   active_layer_thickness  active layer thickness
! idBott(16=ishgt)   saltation               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) == F F F F F F F F F F F F F F F F

! Logical switches (TRUE/FALSE) to activate writing of time-averaged
! fields into AVERAGE output file.

Aout(idUvel) == T       ! u                  3D U-velocity
Aout(idVvel) == T       ! v                  3D V-velocity
Aout(idu3dE) == F       ! u_eastward         3D U-eastward  at RHO-points
Aout(idv3dN) == F       ! v_northward        3D V-northward at RHO-points
Aout(idWvel) == T       ! w                  3D W-velocity
Aout(idOvel) == F       ! omega              omega vertical velocity
Aout(idUbar) == T       ! ubar               2D U-velocity
Aout(idVbar) == T       ! vbar               2D V-velocity
Aout(idu2dE) == F       ! ubar_eastward      2D U-eastward  at RHO-points
Aout(idv2dN) == F       ! vbar_northward     2D V-northward at RHO-points
Aout(idFsur) == T       ! zeta               free-surface

Aout(idTvar) == T T     ! temp, salt         temperature and salinity

Aout(idUsms) == T       ! sustr              surface U-stress
Aout(idVsms) == T       ! svstr              surface V-stress
Aout(idUbms) == F       ! bustr              bottom U-stress
Aout(idVbms) == F       ! bvstr              bottom V-stress

Aout(idW2xx) == F       ! Sxx_bar            2D radiation stress, Sxx component
Aout(idW2xy) == F       ! Sxy_bar            2D radiation stress, Sxy component
Aout(idW2yy) == F       ! Syy_bar            2D radiation stress, Syy component
Aout(idU2rs) == F       ! Ubar_Rstress       2D radiation U-stress
Aout(idV2rs) == F       ! Vbar_Rstress       2D radiation V-stress
Aout(idU2Sd) == F       ! ubar_stokes        2D U-Stokes velocity
Aout(idV2Sd) == F       ! vbar_stokes        2D V-Stokes velocity

Aout(idW3xx) == F       ! Sxx                3D radiation stress, Sxx component
Aout(idW3xy) == F       ! Sxy                3D radiation stress, Sxy component
Aout(idW3yy) == F       ! Syy                3D radiation stress, Syy component
Aout(idW3zx) == F       ! Szx                3D radiation stress, Szx component
Aout(idW3zy) == F       ! Szy                3D radiation stress, Szy component
Aout(idU3rs) == F       ! u_Rstress          3D U-radiation stress
Aout(idV3rs) == F       ! v_Rstress          3D V-radiation stress
Aout(idU3Sd) == F       ! u_stokes           3D U-Stokes velocity
Aout(idV3Sd) == F       ! v_stokes           3D V-Stokes velocity

Aout(idPair) == F       ! Pair               surface air pressure
Aout(idUair) == F       ! Uair               surface U-wind component
Aout(idVair) == F       ! Vair               surface V-wind component

Aout(idTsur) == T T     ! shflux, ssflux     surface net heat and salt flux
Aout(idLhea) == T       ! latent             latent heat flux
Aout(idShea) == T       ! sensible           sensible heat flux
Aout(idLrad) == T       ! lwrad              longwave radiation flux
Aout(idSrad) == T       ! swrad              shortwave radiation flux
Aout(idevap) == T       ! evaporation        evaporation rate
Aout(idrain) == T       ! rain               precipitation rate

Aout(idDano) == F       ! rho                density anomaly
Aout(idVvis) == T       ! AKv                vertical viscosity
Aout(idTdif) == T       ! AKt                vertical T-diffusion
Aout(idSdif) == F       ! AKs                vertical Salinity diffusion
Aout(idHsbl) == T       ! Hsbl               depth of surface boundary layer
Aout(idHbbl) == T       ! Hbbl               depth of bottom boundary layer

Aout(id2dRV) == F       ! pvorticity_bar     2D relative vorticity
Aout(id3dRV) == F       ! pvorticity         3D relative vorticity
Aout(id2dPV) == F       ! rvorticity_bar     2D potential vorticity
Aout(id3dPV) == F       ! rvorticity         3D potential vorticity

Aout(idu3dD) == F       ! u_detided          detided 3D U-velocity
Aout(idv3dD) == F       ! v_detided          detided 3D V-velocity
Aout(idu2dD) == F       ! ubar_detided       detided 2D U-velocity
Aout(idv2dD) == F       ! vbar_detided       detided 2D V-velocity
Aout(idFsuD) == F       ! zeta_detided       detided free-surface

Aout(idTrcD) == F F     ! temp_detided, ...  detided temperature and salinity

Aout(idHUav) == T       ! Huon               u-volume flux, Huon
Aout(idHVav) == T       ! Hvom               v-volume flux, Hvom
Aout(idUUav) == F       ! uu                 quadratic <u*u> term
Aout(idUVav) == F       ! uv                 quadratic <u*v> term
Aout(idVVav) == F       ! vv                 quadratic <v*v> term
Aout(idU2av) == F       ! ubar2              quadratic <ubar*ubar> term
Aout(idV2av) == F       ! vbar2              quadratic <vbar*vbar> term
Aout(idZZav) == F       ! zeta2              quadratic <zeta*zeta> term

Aout(idTTav) == F F     ! temp_2, ...        quadratic <t*t> tracer terms
Aout(idUTav) == F F     ! u_temp, ...        quadratic <u*t> tracer terms
Aout(idVTav) == F F     ! v_temp, ...        quadratic <v*t> tracer terms
Aout(iHUTav) == T T     ! Huon_temp, ...     tracer volume flux, <Huon*t>
Aout(iHVTav) == T T     ! Hvom_temp, ...     tracer volume flux, <Hvom*t>

! Logical switches (TRUE/FALSE) to activate writing of extra inert passive
! tracers other than biological and sediment tracers into the AVERAGE file.

 Aout(inert) == T       ! dye_01, ...        inert passive tracers

! Logical switches (TRUE/FALSE) to activate writing of time-averaged,
! 2D momentum (ubar,vbar) diagnostic terms into DIAGNOSTIC output file.

Dout(M2rate) == F       ! ubar_accel, ...    acceleration
Dout(M2pgrd) == F       ! ubar_prsgrd, ...   pressure gradient
Dout(M2fcor) == F       ! ubar_cor, ...      Coriolis force
Dout(M2hadv) == F       ! ubar_hadv, ...     horizontal total advection
Dout(M2xadv) == F       ! ubar_xadv, ...     horizontal XI-advection
Dout(M2yadv) == F       ! ubar_yadv, ...     horizontal ETA-advection
Dout(M2hrad) == F       ! ubar_hrad, ...     horizontal total radiation stress
Dout(M2hvis) == F       ! ubar_hvisc, ...    horizontal total viscosity
Dout(M2xvis) == F       ! ubar_xvisc, ...    horizontal XI-viscosity
Dout(M2yvis) == F       ! ubar_yvisc, ...    horizontal ETA-viscosity
Dout(M2sstr) == F       ! ubar_sstr, ...     surface stress
Dout(M2bstr) == F       ! ubar_bstr, ...     bottom stress

! Logical switches (TRUE/FALSE) to activate writing of time-averaged,
! 3D momentum (u,v) diagnostic terms into DIAGNOSTIC output file.

Dout(M3rate) == F       ! u_accel, ...       acceleration
Dout(M3pgrd) == F       ! u_prsgrd, ...      pressure gradient
Dout(M3fcor) == F       ! u_cor, ...         Coriolis force
Dout(M3hadv) == F       ! u_hadv, ...        horizontal total advection
Dout(M3xadv) == F       ! u_xadv, ...        horizontal XI-advection
Dout(M3yadv) == F       ! u_yadv, ...        horizontal ETA-advection
Dout(M3vadv) == F       ! u_vadv, ...        vertical advection
Dout(M3hrad) == F       ! u_hrad, ...        horizontal total radiation stress
Dout(M3vrad) == F       ! u_vrad, ...        vertical radiation stress
Dout(M3hvis) == F       ! u_hvisc, ...       horizontal total viscosity
Dout(M3xvis) == F       ! u_xvisc, ...       horizontal XI-viscosity
Dout(M3yvis) == F       ! u_yvisc, ...       horizontal ETA-viscosity
Dout(M3vvis) == F       ! u_vvisc, ...       vertical viscosity

! Logical switches (TRUE/FALSE) to activate writing of time-averaged,
! active (temperature and salinity) and passive (inert) tracer diagnostic
! terms into DIAGNOSTIC output file: [1:NAT+NPT,Ngrids].

Dout(iTrate) == T T     ! temp_rate, ...     time rate of change
Dout(iThadv) == T T     ! temp_hadv, ...     horizontal total advection
Dout(iTxadv) == F F     ! temp_xadv, ...     horizontal XI-advection
Dout(iTyadv) == F F     ! temp_yadv, ...     horizontal ETA-advection
Dout(iTvadv) == T T     ! temp_vadv, ...     vertical advection
Dout(iThdif) == T T     ! temp_hdiff, ...    horizontal total diffusion
Dout(iTxdif) == F F     ! temp_xdiff, ...    horizontal XI-diffusion
Dout(iTydif) == F F     ! temp_ydiff, ...    horizontal ETA-diffusion
Dout(iTsdif) == F F     ! temp_sdiff, ...    horizontal S-diffusion
Dout(iTvdif) == T T     ! temp_vdiff, ...    vertical diffusion

! Generic User parameters, [1:NUSER].

       NUSER =  0
        USER =  0.d0

! NetCDF-4/HDF5 compression parameters for output files.

  NC_SHUFFLE =  1                 ! if non-zero, turn on shuffle filter
  NC_DEFLATE =  1                 ! if non-zero, turn on deflate filter
   NC_DLEVEL =  1                 ! deflate level [0-9]

! Input NetCDF file names, [1:Ngrids].

     GRDNAME == /home/rjin4/scr16_agnanad1/inputs_ecb/grd/chesroms_grd_smoother_msl_mes.nc
     ININAME == /home/rjin4/scr16_agnanad1/inputs_ecb/ini/DOP_111420/ocean_ini20170101.nc
     ITLNAME == ocean_itl.nc
     IRPNAME == ocean_irp.nc
     IADNAME == ocean_iad.nc
     FWDNAME == ocean_fwd.nc
     ADSNAME == ocean_ads.nc

! Nesting grids connectivity data: contact points information. This
! NetCDF file is special and complex. It is currently generated using
! the script "matlab/grid/contact.m" from the Matlab repository.

     NGCNAME =  ocean_ngc.nc

! Input lateral boundary conditions and climatology file names.  The
! USER has the option to split input data time records into several
! NetCDF files (see prologue instructions above). If so, use a single
! line per entry with a vertical bar (|) symbol after each entry,
! except the last one.

     BRYNAME == /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1979_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1980_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1981_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1982_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1983_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1984_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1985_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1986_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1987_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1988_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1989_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1990_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1991_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1992_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1993_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1994_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1995_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1996_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1997_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1998_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_1999_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2000_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2001_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2002_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2003_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2004_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2005_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2006_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2007_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2008_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2009_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2010_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2011_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2012_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2013_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2014_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2015_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2016_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2017_20190813.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/bry/Ches_OBC_2018_20190813.nc

     CLMNAME == ocean_clm.nc

! Input climatology nudging coefficients file name.

     NUDNAME == ocean_nud.nc

! Input Sources/Sinks forcing (like river runoff) file name.

     SSFNAME == /home/rjin4/scr16_agnanad1/inputs_ecb/rivers/121720/riv_ches_dlem1900_2014_usgs2015_2018.nc

! Input tidal forcing file name.

    TIDENAME == /home/rjin4/scr16_agnanad1/inputs_ecb/tides/chesroms_tides_adcirc7_1982.nc

! Input forcing NetCDF file name(s).
!
! The USER has the option to enter several sets of file names for each
! nested grid. For example, the USER may have different data for the
! wind products, heat fluxes, etc. Alternatively, if the all the forcing
! files are the same for nesting and the data is in its native resolution,
! we could enter only one set of files names and ROMS will replicate those
! files internally to the remaining grids using the plural KEYWORD protocol.
!
! The model will scan the files and will read the needed data from the first
! file in the list containing the forcing field. Therefore, the order of the
! filenames is critical. If using multiple forcing files per grid, first
! enter all the file names for grid one followed by two, and so on.  It is
! also possible to split input data time records into several NetCDF files
! (see Prolog instructions above). Use a single line per entry with a
! continuation (\) or a vertical bar (|) symbol after each entry, except
! the last one.

     NFFILES == 2                          ! number of unique forcing files

     FRCNAME == /home/rjin4/scr16_agnanad1/inputs_ecb/frc/frc_ches_era5_with_downwelling_longwave1979.nc      |
                /home/rjin4/scr16_agnanad1/inputs_ecb/frc/frc_ches_era5_with_downwelling_longwave1980_1984.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/frc/frc_ches_era5_with_downwelling_longwave1985_1989.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/frc/frc_ches_era5_with_downwelling_longwave1990_1994.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/frc/frc_ches_era5_with_downwelling_longwave1995_1999.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/frc/frc_ches_era5_with_downwelling_longwave2000_2004.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/frc/frc_ches_era5_with_downwelling_longwave2005_2009.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/frc/frc_ches_era5_with_downwelling_longwave2010_2014.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/frc/frc_ches_era5_with_downwelling_longwave2015.nc      |
                /home/rjin4/scr16_agnanad1/inputs_ecb/frc/frc_ches_era5_with_downwelling_longwave2016.nc      |
                /home/rjin4/scr16_agnanad1/inputs_ecb/frc/frc_ches_era5_with_downwelling_longwave2017.nc      |
                /home/rjin4/scr16_agnanad1/inputs_ecb/frc/frc_ches_era5_with_downwelling_longwave2018.nc      \
                /home/rjin4/scr16_agnanad1/inputs_ecb/atmos_nitrogen_depos/ChesROMS_atmo_nit_dep_forcing_1979_wetdep_from_WQSTM_1985_drydep_from_CMAQ_2002.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/atmos_nitrogen_depos/ChesROMS_atmo_nit_dep_forcing_1980_1984_wetdep_from_WQSTM_1985_drydep_from_CMAQ_2002_on_a_loop.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/atmos_nitrogen_depos/ChesROMS_atmo_nit_dep_forcing_1985_1989_wetdep_from_WQSTM_drydep_from_CMAQ_2002_on_a_loop.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/atmos_nitrogen_depos/ChesROMS_atmo_nit_dep_forcing_1990_1994_wetdep_from_WQSTM_drydep_from_CMAQ_2002_on_a_loop.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/atmos_nitrogen_depos/ChesROMS_atmo_nit_dep_forcing_1995_1999_wetdep_from_WQSTM_drydep_from_CMAQ_2002_on_a_loop.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/atmos_nitrogen_depos/ChesROMS_atmo_nit_dep_forcing_2000_2004_wetdep_from_WQSTM_drydep_from_CMAQ_2002_2012.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/atmos_nitrogen_depos/ChesROMS_atmo_nit_dep_forcing_2005_2009_wetdep_from_WQSTM_drydep_from_CMAQ_2002_2012.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/atmos_nitrogen_depos/ChesROMS_atmo_nit_dep_forcing_2010_2014_wetdep_from_WQSTM_drydep_from_CMAQ_2002_2012.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/atmos_nitrogen_depos/ChesROMS_atmo_nit_dep_forcing_2015_wetdep_from_WQSTM_drydep_from_CMAQ_2002_2012.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/atmos_nitrogen_depos/ChesROMS_atmo_nit_dep_forcing_2016_wetdep_from_WQSTM_drydep_from_CMAQ_2002_2012.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/atmos_nitrogen_depos/ChesROMS_atmo_nit_dep_forcing_2017_wetdep_from_WQSTM_drydep_from_CMAQ_2002_2012.nc |
                /home/rjin4/scr16_agnanad1/inputs_ecb/atmos_nitrogen_depos/ChesROMS_atmo_nit_dep_forcing_2018_wetdep_from_WQSTM_drydep_from_CMAQ_2002_2012.nc

! Output NetCDF file names, [1:Ngrids].

     DAINAME == ocean_dai.nc
     GSTNAME == ocean_gst.nc
     RSTNAME == ocean_rst.nc
     HISNAME == ocean_his.nc
     QCKNAME == ocean_qck.nc
     TLMNAME == ocean_tlm.nc
     TLFNAME == ocean_tlf.nc
     ADJNAME == ocean_adj.nc
     HARNAME == ocean_har.nc
     AVGNAME == ocean_avg.nc
     DIANAME == ocean_dia.nc
     STANAME == ocean_sta.nc
     FLTNAME == ocean_flt.nc

! Input ASCII parameter filenames.

     APARNAM =  ROMS/External/s4dvar.in
     SPOSNAM =  stations.in
     FPOSNAM =  ROMS/External/floats.in
     BPARNAM =  bio_ECB.in
     SPARNAM =  ROMS/External/sediment.in
     USRNAME =  ROMS/External/MyFile.dat

!
!  GLOSSARY:
!  =========
!
!------------------------------------------------------------------------------
! Application title (string with a maximum of 80 characters) and
! C-preprocessing flag.
!------------------------------------------------------------------------------
!
! TITLE        Application title.
!
! MyAppCPP     Application C-preprocessing option.
!
!------------------------------------------------------------------------------
! Variable information file name (string with a maximum of 256 characters).
!------------------------------------------------------------------------------
!
! VARNAME      Input/Output variable information file name.  This file needs to
!                be processed first so all information arrays and indices can
!                be initialized properly in "mod_ncparam.F".
!
!------------------------------------------------------------------------------
! Nested grid parameters (processing order of these parameters is important).
!------------------------------------------------------------------------------
!
! Ngrids       Number of nested grids. It needs to be read before all other
!                parameters in order to allocate all model variables.
!
! NestLayers   Number of grid nesting layers. It is used to allow applications
!                with both composite and refinement grid combinations, as shown
!                in WikiROMS diagrams for the Refinement and Partial Boundary
!                Composite Sub-Classes. See,
!
!                https://www.myroms.org/wiki/index.php/Nested_Grids
!
!                In non-nesting applications, set NestLayers = 1.
!
! GridsInLayer Number of grids in each nested layer, a vector of size
!                [1:NestLayers]. Notice that,
!
!                SUM(GridsInLayer)    = Ngrids
!                LENGHT(GridsInLayer) = NestLayers
!
!                The order of grids and nesting layers is extremely important.
!                It determines the order of the sequential solution at every
!                sub-timestep.  See WikiROMS nesting Sub-Classes diagrams.
!
!                In non-nesting applications, set GridsInLayer = 1.
!
!                NOTE:  In main3d, we use these parameters to determine which
!                ====   grid index, ng, to solve when calling the routines of
!                       the computational kernel:
!
!                  NEST_LAYER : DO nl=1,NestLayers
!                    ...
!                    STEP_LOOP : DO istep=1,Nsteps
!                      ...
!                      DO ig=1,GridsInLayer(nl)
!                        ng=GridNumber(ig,nl)
!                        ...
!                      END DO
!                      ...
!                    END DO STEP_LOOP
!                  END DO NEST_LAYER
!
!                Here, the grid order "ng" for the computations is determined
!                from array "GridNumber", which is computed at initialization
!                in "read_phypar.F". It can be computed on the fly as:
!
!                  ng=Ngrids+1
!                  DO j=NestLayers,nl,-1
!                    DO i=GridsInLayer(j),1,-1
!                      ng=ng-1
!                      IF ((j.eq.nl).and.(i.eq.ig)) EXIT
!                    END DO
!                  END DO
!
!                but it is too inefficient. This information is provided here
!                to help you configure the order of nested grids.
!
!------------------------------------------------------------------------------
! Grid dimension parameters.
!------------------------------------------------------------------------------
!
! These parameters are very important since they determine the grid of the
! application to solve. They need to be read first in order to dynamically
! allocate all model variables.
!
! WARNING: It is trivial and possible to change these dimension parameters in
! -------  idealized applications via analytical expressions.  However, in
! realistic applications any change to these parameters requires redoing all
! input NetCDF files.
!
! Lm           Number of INTERIOR grid RHO-points in the XI-direction for
!                each nested grid, [1:Ngrids]. If using NetCDF files as
!                input, Lm=xi_rho-2 where "xi_rho" is the NetCDF file
!                dimension of RHO-points. Recall that all RHO-point
!                variables have a computational I-range of [0:Lm+1].
!
! Mm           Number of INTERIOR grid RHO-points in the ETA-direction for
!                each nested grid, [1:Ngrids]. If using NetCDF files as
!                input, Mm=eta_rho-2 where "eta_rho" is the NetCDF file
!                dimension of RHO-points. Recall that all RHO-point
!                variables have a computational J-range of [0:Mm+1].
!
! N            Number of vertical terrain-following levels at RHO-points,
!                [1:Ngrids].
!
! Nbed         Number of sediment bed layers, [1:Ngrids]. This parameter
!                is only relevant if CPP option SEDIMENT is activated.
!
!                Mm+1  ___________________                _______  Kw = N
!                     |                   |              |       |
!                  Mm |   _____________   |              |       | Kr = N
!                     |  |             |  |              |_______|
!                     |  |             |  |              |       |
!                  Jr |  |             |  |              |       |
!                     |  |             |  |              |_______|
!                     |  |             |  |              |       |
!                   1 |  |_____________|  |              |       |
!                     |                   |              |_______|
!                   0 |___________________|              |       |
!                              Ir                        |       | 1
!                     0  1            Lm  Lm+1    h(i,j) |_______|
!                                                        ::::::::: 0
!                                                        :::::::::
!                                                        ::::::::: Nbed-1
!                                                        ::::::::: Nbed
!
! NAT          Number of active tracer type variables. Usually, NAT=2 for
!                potential temperature and salinity.
!
! NPT          Number of inert (dyes, age, etc) passive tracer type variables
!                to advect and diffuse only. This parameter is only relevant
!                if CPP option T_PASSIVE is activated.
!
! NCS          Number of cohesive (mud) sediment tracer type variables. This
!                parameter is only relevant if CPP option SEDIMENT is
!                activated.
!
! NNS          Number of non-cohesive (sand) sediment tracer type variables.
!                This parameter is only relevant if CPP option SEDIMENT is
!                activated.
!
!                The total number of sediment tracers is NST=NCS+NNS.  Notice
!                that NST must be greater than zero (NST>0).
!
!------------------------------------------------------------------------------
! Domain tile partition parameters.
!------------------------------------------------------------------------------
!
! Model tile decomposition parameters for serial and parallel configurations
! which are used to determine tile horizontal range indices (Istr,Iend and
! Jstr,Jend). In some computers, it is advantageous to have tile partitions
! in serial applications.
!
! NtileI       Number of domain partitions in the I-direction (XI-coordinate).
!                It must be equal to or greater than one.
!
! NtileJ       Number of domain partitions in the J-direction (ETA-coordinate).
!                It must be equal to or greater than one.
!
! WARNING:     In shared-memory (OpenMP), the product of NtileI and NtileJ must
!              be a MULTIPLE of the number of parallel threads specified with
!              the OpenMP environmental variable OMP_NUM_THREADS.
!
!              In distributed-memory (MPI), the product of NtileI and NtileJ
!              must be EQUAL to the number of parallel nodes specified during
!              execution with the "mprun" or "mpirun" command.
!
!------------------------------------------------------------------------------
! Lateral boundary conditions parameters.
!------------------------------------------------------------------------------
!
! The lateral boundary conditions are now specified with logical switches
! instead of CPP flags to allow nested grid configurations. Their values are
! loaded into structured array:
!
!    LBC(1:4, nLBCvar, Ngrids)
!
! where 1:4 are the number of boundary edges, nLBCvar are the number of LBC
! state variables, and Ngrids is the number of nested grids. For Example, to
! apply gradient boundary conditions we use:
!
!    LBC(iwest,  isFsur, ng) % gradient
!    LBC(ieast,  ...   , ng) % gradient
!    LBC(isouth, ...   , ng) % gradient
!    LBC(inorth, ...   , ng) % gradient
!
! The lateral boundary conditions are entered with a keyword. This keyword
! is case insensitive and usually has three characters. However, it is
! possible to have compound keywords, if applicable. For example, the
! keyword "RadNud" implies radiation boundary condition with nudging. This
! combination is usually used in active/passive radiation conditions.
!
!   Keyword    Lateral Boundary Condition Type
!
!   Cha        Chapman_implicit (free-surface only)
!   Che        Chapman_explicit (free-surface only)
!   Cla        Clamped
!   Clo        Closed
!   Fla        Flather (2D momentum only)             _____N_____     j=Mm
!   Gra        Gradient                              |     4     |
!   Nes        Nested (refinement only)              |           |
!   Nud        Nudging                             1 W           E 3
!   Per        Periodic                              |           |
!   Rad        Radiation                             |_____S_____|
!   Red        Reduced Physics (2D momentum only)          2          j=1
!   Shc        Shchepetkin (2D momentum only)       i=1         i=Lm
!
! LBC(isFsur) Free-surface,  [1:4, Ngrids] values are expected.
! LBC(isUbar) 2D U-momentum, [1:4, Ngrids] values are expected.
! LBC(isVbar) 2D V-momentum, [1:4, Ngrids] values are expected.
! LBC(isUvel) 3D U-momentum, [1:4, Ngrids] values are expected.
! LBC(isVvel) 3D V-momentum, [1:4, Ngrids] values are expected.
! LBC(isMtke) Mixing TKE,    [1:4, Ngrids] values are expected.
! LBC(isTvar) Tracers,       [1:4, 1:NAT+NPT, Ngrids] values are expected.
!
! Similarly, the adjoint-based algorithms (ADM, TLM, RPM) can have different
! lateral boundary conditions keywords:
!
! ad_LBC(isFsur) Free-surface,  [1:4, Ngrids] values are expected.
! ad_LBC(isUbar) 2D U-momentum, [1:4, Ngrids] values are expected.
! ad_LBC(isVbar) 2D V-momentum, [1:4, Ngrids] values are expected.
! ad_LBC(isUvel) 3D U-momentum, [1:4, Ngrids] values are expected.
! ad_LBC(isVvel) 3D V-momentum, [1:4, Ngrids] values are expected.
! ad_LBC(isMtke) Mixing TKE,    [1:4, Ngrids] values are expected.
! ad_LBC(isTvar) Tracers,       [1:4, 1:NAT+NPT, Ngrids] values are expected.
!
! Lateral open boundary edge volume conservation switch for nonlinear model
! and adjoint-based algorithm. Usually activated with radiation boundary
! conditions to enforce global mass conservation. Notice that these switches
! should not be activated if tidal forcing is enabled, [1:Ngrids] values are
! expected.
!
! VolCons(west)       Western  boundary volume conservation switch.
! VolCons(east)       Eastern  boundary volume conservation switch.
! VolCons(south)      Southern boundary volume conservation switch.
! VolCons(north)      Northern boundary volume conservation switch.
!
! ad_VolCons(west)    Western  boundary volume conservation switch.
! ad_VolCons(east)    Eastern  boundary volume conservation switch.
! ad_VolCons(south)   Southern boundary volume conservation switch.
! ad_VolCons(north)   Northern boundary volume conservation switch.
!
!------------------------------------------------------------------------------
! Timestepping parameters.
!------------------------------------------------------------------------------
!
! NTIMES       Total number timesteps in current run.  If 3D configuration,
!                NTIMES is the total of baroclinic timesteps.  If only 2D
!                configuration, NTIMES is the total of barotropic timesteps.
!
! DT           TimeStep size in seconds.  If 3D configuration, DT is the
!                size of the baroclinic timestep.  If only 2D configuration,
!                DT is the size of the barotropic timestep.
!
! NDTFAST      Number of barotropic timesteps between each baroclinic time
!                step. If only 2D configuration, NDTFAST should be unity since
!                there is no need to split timestepping.
!
!------------------------------------------------------------------------------
! Model iteration loops parameters.
!------------------------------------------------------------------------------
!
! ERstr        Starting ensemble run (perturbation or iteration) number.
!
! ERend        Ending   ensemble run (perturbation or iteration) number.
!
! Nouter       Maximum number of 4DVAR outer loop iterations.
!
! Ninner       Maximum number of 4DVAR inner loop iterations.
!
! Nintervals   Number of time interval divisions for Stochastic Optimals
!                computations. It must be a multiple of NTIMES. The tangent
!                linear model (TLM) and the adjoint model (ADM) are integrated
!                forward and backward at different intervals.  For example,
!                if Nintervals=3,
!
!              1               NTIMES/3         2*NTIMES/3           NTIMES
!              +..................+..................+..................+
!              <========================================================> (1)
!                                 <=====================================> (2)
!                                                    <==================> (3)
!
!              In the first iteration (1), the TLM is integrated forward from
!              1 to NTIMES and the ADM is integrated backward from NTIMES to 1.
!              In the second iteration (2), the TLM is integrated forward from
!              NTIMES/3 to NTIMES and the ADM is integrated backward from
!              NTIMES to NTIMES/3. And so on.
!
!------------------------------------------------------------------------------
! Eigenproblem parameters.
!------------------------------------------------------------------------------
!
! NEV          Number of eigenvalues to compute for the Lanczos/Arnoldi
!                problem.  Notice that the model memory requirement increases
!                substantially as NEV increases.  The GST requires NEV+1
!                copies of the model state vector.  The memory requirements
!                are decreased in distributed-memory applications.
!
! NCV          Number of eigenvectors to compute for the Lanczos/Arnoldi
!                problem. NCV must be greater than NEV.
!
!  At present, there is no apriori 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 greater than or
!  equal to 2*NEV. In Finite Time Eigenmodes (FTE) and Adjoint Finite Time
!  Eigenmodes (AFTE) the requirement is to have NCV greater than or equal to
!  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 a very long time.
!
!------------------------------------------------------------------------------
! Input/Output parameters.
!------------------------------------------------------------------------------
!
! NRREC        Switch to indicate re-start from a previous solution.  Use
!                NRREC=0 for new solutions. In a re-start solution, NRREC
!                is the time index of the re-start NetCDF file assigned for
!                initialization.  If NRREC is negative (say NRREC=-1), the
!                model will re-start from the most recent time record. That
!                is, the initialization record is assigned internally.
!                Notice that it is also possible to re-start from a history
!                or time-averaged NetCDF file.  If a history file is used
!                for re-start, it must contains all the necessary primitive
!                variables at all levels.
!
! LcycleRST    Logical switch (T/F) used to recycle time records in output
!                restart file.  If TRUE,  only the latest two re-start time
!                records are maintained.  If FALSE, all re-start fields are
!                saved every NRST timesteps without recycling.  The restart
!                fields are written at all levels in double precision.
!
! NRST         Number of timesteps between the writing of re-start fields.
!                Set NRST=0 to suppress writing of RESTART file.
!
! NSTA         Number of timesteps between writing data into STATIONS file.
!                Station data is written at all levels.
!
! NFLT         Number of timesteps between writing data into FLOATS file.
!
! NINFO        Number of timesteps between the print of single line information
!                to standard output.  It also determines the interval between
!                computation of global energy diagnostics.
!
!------------------------------------------------------------------------------
!  Output HISTORY, QUICKSAVE, AVERAGE and DIAGNOSTIC files parameters.
!------------------------------------------------------------------------------
!
!  Notice that it is possible to have two types of output NetCDF files for
!  instantaneous fields: HISTORY and QUICKSAVE. The QUICKSAVE file can be used
!  for writing fewer fields at shorter time intervals. For example, the User
!  may just write 2D and surface fields frequently (hourly) to reduce file
!  size and to time resolve fast dynamics. In conjunction, the User may write
!  full HISTORY fields infrequently (daily, weekly, etc) to avoid creating
!  large output files. This gives a lot of flexibility to manage ROMS output.
!
!
! LDEFOUT      Logical switch (T/F) used to create new output files when
!                initializing from a re-start file, abs(NRREC) > 0.  If TRUE
!                and applicable, a new HISTORY, QUICKSAVE, AVERAGE, DIAGNOSTIC
!                and STATIONS files are created during the initialization
!                stage. If FALSE and applicable, data is appended to existing
!                HISTORY, QUICKSAVE, AVERAGE, DIAGNOSTIC and STATIONS files.
!                See also parameters NDEFHIS, NDEFQCK, NDEFAVG and NDEFDIA
!                below.
!
! NHIS         Number of timesteps between writing fields into the HISTORY
!                 file. Set NHIS=0 to suppress writing of HISTORY file.
!
! NDEFHIS      Number of timesteps between the creation of new HISTORY file.
!                If NDEFHIS=0, the model will only process one HISTORY file.
!                This feature is useful for extended simulations when HISTORY
!                file get too large; it creates a new file every NDEFHIS
!                timesteps.
!
! NQCK         Number of timesteps between writing fields into QUICKSAVE file.
!                Set NQCK=0 to suppress writing of QUICKSAVE file.
!
! NDEFQCK      Number of timesteps between the creation of new QUICKSAVE file.
!                If NDEFQCK=0, the model will only process one QUICKSAVE file.
!                This feature is useful for extended simulations when QUICKSAVE
!                file get too large; it creates a new file every NDEFQCK
!                timesteps.
!
! NTSAVG       Starting timestep for the accumulation of output time-averaged
!                data.
!
! NAVG         Number of timesteps between writing time-averaged data
!                into AVERAGE file.  Averaged date is written for all fields.
!                Set NAVG=0 to suppress writing of AVERAGE file.
!
! NDEFAVG      Number of timesteps between the creation of new AVERAGE
!                file.  If NDEFAVG=0, the model will only process one AVERAGE
!                file.  This feature is useful for extended simulations when
!                AVERAGE file get too large; it creates a new file every
!                NDEFAVG timesteps.
!
! NTSDIA       Starting timestep for the accumulation of output time-averaged
!                diagnostics data.
!
! NDIA         Number of timesteps between writing time-averaged diagnostics
!                data into DIAGNOSTIC file.  Averaged date is written for all
!                fields. Set NDIA=0 to suppress writing of DIAGNOSTIC file.
!
! NDEFDIA      Number of timesteps between the creation of new time-averaged
!                diagnostics file.  If NDEFDIA=0, the model will only process
!                one DIAGNOSTICS file.  This feature is useful for long
!                simulations when DIAGNOSTIC file get too large; it creates
!                a new file every NDEFDIA timesteps.
!
!------------------------------------------------------------------------------
!  Output tangent linear and adjoint model parameters.
!------------------------------------------------------------------------------
!
! LcycleTLM    Logical switch (T/F) used to recycle time records in output
!                tangent linear file.  If TRUE, only the latest two time
!                records are maintained.  If FALSE, all tangent linear fields
!                are saved every NTLM timesteps without recycling.
!
! NTLM         Number of timesteps between writing fields into tangent linear
!                model file.
!
! NDEFTLM      Number of timesteps between the creation of new tangent linear
!                file. If NDEFTLM=0, the model will only process one tangent
!                linear file. This feature is useful for extended simulations
!                when output NetCDF files get too large; it creates a new file
!                every NDEFTLM timesteps.
!
! LcycleADJ    Logical switch (T/F) used to recycle time records in output
!                adjoint file.  If TRUE, only the latest two time records are
!                maintained.  If FALSE, all tangent linear fields are saved
!                every NADJ timesteps without recycling.
!
! NADJ         Number of timesteps between writing fields into the adjoint
!                 model file.
!
! NDEFADJ      Number of timesteps between the creation of the new adjoint
!                file. If NDEFADJ=0, the model will only process one adjoint
!                file. This feature is useful for extensive simulations when
!                the output NetCDF files get too large; it creates a new file
!                every NDEFADJ timesteps.
!
! NSFF         Number of timesteps between 4DVAR adjustment of surface forcing
!                fluxes. In strong constraint 4DVAR, it is possible to adjust
!                surface forcing at other time intervals in addition to initial
!                time.  This parameter is used to store the appropriate number
!                of surface forcing records in the output history NetCDF files:
!                1+NTIMES/NSFF records. NSFF must be a factor of NTIMES or
!                greater than NTIMES. If NSFF > NTIMES, only one record is
!                stored in the NetCDF files and the adjustment is for constant
!                forcing with constant correction. This parameter is only
!                relevant in 4DVAR when activating either ADJUST_STFLUX or
!                ADJUST_WSTRESS.
!
! NOBC         Number of timesteps between 4DVAR adjustment of open boundary
!                fields. In strong constraint 4DVAR, it is possible to adjust
!                open boundaries at other time intervals in addition to initial
!                time.  This parameter is used to store the appropriate number
!                of open boundary records in the output history NetCDF files:
!                1+NTIMES/NOBC records. NOBC must be a factor of NTIMES or
!                greater than NTIMES. If NOBC > NTIMES, only one record is
!                stored in the NetCDF files and the adjustment is for constant
!                forcing with constant correction. This parameter is only
!                relevant in 4DVAR when activating ADJUST_BOUNDARY.
!
!------------------------------------------------------------------------------
!  Generalized Stability Theory (GST) analysis parameters.
!------------------------------------------------------------------------------
!
! LmultiGST    Logical switch (TRUE/FALSE) to write out one GST analysis
!                eigenvector per history file.
!
! LrstGST      Logical switch (TRUE/FALSE) to restart GST analysis. If TRUE,
!                the check pointing data is read in from the GST restart NetCDF
!                file.  If FALSE and applicable, the checkpointing GST data is
!                saved and overwritten every NGST iterations of the algorithm.
!
! MaxIterGST   Maximum number of GST algorithm iterations.
!
! NGST         Number of GST iterations between storing of check pointing
!                data into NetCDF file. The restart data is always saved if
!                MaxIterGST is reached without convergence. It is also saved
!                when convergence is achieved. It is always a good idea to
!                save the checkpointing data at regular intervals so there
!                is a mechanism to recover from an unexpected interruption
!                in this costly computation. The check pointing data can
!                be used also to recompute the Ritz vectors by changing some
!                of the parameters, like convergence criteria (Ritz_tol)
!                and number of Arnoldi iterations (iparam(3)).
!
! Ritz_tol     Relative accuracy of the Ritz values computed in the GST
!                analysis.
!
!------------------------------------------------------------------------------
! Harmonic/Biharmonic horizontal diffusion for active tracers and viscosity
! for momentum.
!------------------------------------------------------------------------------
!
! TNU2         Nonlinear model lateral, harmonic, constant, mixing
!                coefficient (m2/s) for active (NAT) and inert (NPT) tracer
!                variables. If variable horizontal diffusion is activated,
!                TNU2 is the mixing coefficient for the largest grid-cell
!                in the domain.
!
! TNU4         Nonlinear model lateral, biharmonic, constant, mixing
!                coefficient (m4/s) for active (NAT) and inert (NPT) tracer
!                variables. If variable horizontal diffusion is activated,
!                TNU4 is the mixing coefficient for the largest grid-cell
!                in the domain.
!
! ad_TNU2      Adjoint-based algorithms lateral, harmonic, constant, mixing
!                coefficient (m2/s) for active (NAT) and inert (NPT) tracer
!                variables. If variable horizontal diffusion is activated,
!                ad_TNU2 is the mixing coefficient for the largest grid-cell
!                in the domain. In some applications, a larger value than
!                that used in the nonlinear model (basic state) is necessary
!                for stability.
!
! ad_TNU4      Adjoint-based algorithms lateral, biharmonic, constant, mixing
!                coefficient (m4/s) for active (NAT) and inert (NPT) tracer
!                variables. If variable horizontal diffusion is activated,
!                ad_TNU4 is the mixing coefficient for the largest grid-cell
!                in the domain. In some applications, a larger value than
!                that used in the nonlinear model (basic state) is necessary
!                for stability.
!
! VISC2        Nonlinear model lateral, harmonic, constant, mixing
!                coefficient (m2/s) for momentum. If variable horizontal
!                viscosity is activated, UVNU2 is the mixing coefficient
!                for the largest grid-cell in the domain.
!
! VISC4        Nonlinear model lateral, biharmonic, constant mixing
!                coefficient (m4/s) for momentum. If variable horizontal
!                viscosity is activated, UVNU4 is the mixing coefficient
!                for the largest grid-cell in the domain.
!
! ad_VISC2     Adjoint-based algorithms lateral, harmonic, constant, mixing
!                coefficient (m2/s) for momentum. If variable horizontal
!                viscosity is activated, ad_UVNU2 is the mixing coefficient
!                for the largest grid-cell in the domain. In some applications,
!                a larger value than that used in the nonlinear model (basic
!                state) is necessary for stability.
!
! ad_VISC4     Adjoint-based algorithms lateral, biharmonic, constant mixing
!                coefficient (m4/s) for momentum. If variable horizontal
!                viscosity is activated, ad_UVNU4 is the mixing coefficient
!                for the largest grid-cell in the domain. In some applications,
!                a larger value than that used in the nonlinear model (basic
!                state) is necessary for stability.
!
!------------------------------------------------------------------------------
! Switches to activate sponge areas with enhanced horizontal mixing.
!------------------------------------------------------------------------------
!
! LuvSponge     Logical switch (TRUE/FALSE) to increase/decrease horizontal
!                 viscosity in specific areas of the domain. It can be used
!                 to specify sponge areas with larger horizontal mixing
!                 coefficients for damping of high frequency noise due to
!                 open boundary conditions or nesting. The CPP option SPONGE
!                 is now deprecated and replaced with this switch to facilitate
!                 or not sponge areas over a particular nested grid.
!
!                 The horizontal mixing distribution is specified in
!                 "ini_hmixcoef.F" as:
!
!                   visc2_r(i,j) = visc_factor(i,j) * visc2_r(i,j)
!                   visc4_r(i,j) = visc_factor(i,j) * visc4_r(i,j)
!
!                 The variable "visc_factor" can be read from the grid
!                 NetCDF file. Alternately, the horizontal viscosity in the
!                 sponge area can be set-up with analytical functions in
!                 "ana_sponge.h" using CPP ANA_SPONGE when the switch
!                 "LuvSponge" is turned ON for a particular grid.
!
! LtracerSponge Logical switch (TRUE/FALSE) to increase/decrease horizontal
!                 diffusivity in specific areas of the domain. It can be used
!                 to specify sponge areas with larger horizontal mixing
!                 coefficients for damping of high frequency noise due to
!                 open boundary conditions or nesting. The CPP option SPONGE
!                 is now deprecated and replaced with this switch to facilitate
!                 or not sponge areas over a particular nested grid.
!
!                 The horizontal mixing distribution is specified in
!                 "ini_hmixcoef.F" as:
!
!                   diff2(i,j,itrc) = diff_factor(i,j) * diff2(i,j,itrc)
!                   diff4(i,j,itrc) = diff_factor(i,j) * diff4(i,j,itrc)
!
!                 The variable "diff_factor" can be read from the grid
!                 NetCDF file. Alternately, the horizontal viscosity in the
!                 sponge area can be set-up with analytical functions in
!                 "ana_sponge.h" using CPP ANA_SPONGE when the switch
!                 "LuvSponge" is turned ON for a particular grid.
!
!------------------------------------------------------------------------------
! Vertical mixing coefficients for active tracers.
!------------------------------------------------------------------------------
!
! AKT_BAK      Background vertical mixing coefficient (m2/s) for active
!                (NAT) and inert (NPT) tracer variables.
!
! AKT_LIMIT    Upper threshold values to limit vertical diffusion coefficients
!                computed from vertical mixing parameterizations (GLS_MIXING,
!                LMD_MIXING, MY25_MIXING). Sometimes, these parameterizations
!                yield high mixing values and the threshold values are used as
!                upper limiter when LIMIT_VDIFF is activated.
!
! ad_AKT_fac   Adjoint-based algorithms vertical mixing, basic state, scale
!                factor (nondimensional) for active (NAT) and inert (NPT)
!                tracer variables. In some applications, smaller/larger
!                values of vertical mixing are necessary for stability. It
!                is only used when FORWARD_MIXING is activated.
!
!------------------------------------------------------------------------------
! Vertical mixing coefficient for momentum.
!------------------------------------------------------------------------------
!
! AKV_BAK      Background vertical mixing coefficient (m2/s) for momentum.
!
! AKV_LIMIT    Upper threshold value to limit vertical viscosity coefficient
!                computed from vertical mixing parameterizations (GLS_MIXING,
!                LMD_MIXING, MY25_MIXING). Sometimes, these parameterizations
!                yield a high mixing value and the threshold value is used as
!                upper limiter when LIMIT_VVISC is activated.
!
! ad_AKV_fac   Adjoint-based algorithms vertical mixing, basic state, scale
!                factor (nondimensional) for momentum. In some applications,
!                smaller/larger values of vertical mixing are necessary for
!                stability. It is only used when FORWARD_MIXING is activated.
!
!------------------------------------------------------------------------------
! Turbulent closure parameters.
!------------------------------------------------------------------------------
!
! AKK_BAK      Background vertical mixing coefficient (m2/s) for turbulent
!                kinetic energy.
!
! AKP_BAK      Background vertical mixing coefficient (m2/s) for turbulent
!                generic statistical field, "psi".
!
! TKENU2       Lateral, harmonic, constant, mixing coefficient (m2/s) for
!                turbulent closure variables.
!
! TKENU4       Lateral, biharmonic, constant mixing coefficient (m4/s) for
!                turbulent closure variables.
!
!------------------------------------------------------------------------------
! Generic length-scale turbulence closure parameters.
!------------------------------------------------------------------------------
!
! GLS_P        Stability exponent (nondimensional).
!
! GLS_M        Turbulent kinetic energy exponent (nondimensional).
!
! GLS_N        Turbulent length scale exponent (nondimensional).
!
! GLS_Kmin     Minimum value of specific turbulent kinetic energy
!
! GLS_Pmin     Minimum Value of dissipation.
!
! Closure independent constraint parameters (nondimensional):
!
! GLS_CMU0     Stability coefficient.
!
! GLS_C1       Shear production coefficient.
!
! GLS_C2       Dissipation coefficient.
!
! GLS_C3M      Buoyancy production coefficient (minus).
!
! GLS_C3P      Buoyancy production coefficient (plus).
!
! GLS_SIGK     Constant Schmidt number (nondimensional) for turbulent
!                kinetic energy diffusivity.
!
! GLS_SIGP     Constant Schmidt number (nondimensional) for turbulent
!                generic statistical field, "psi".
!
! Suggested values for various parameterizations:
!
!              k-kl         k-epsilon    k-omega      gen
!
!      GLS_P = 0.d0          3.0d0       -1.0d0        2.0d0
!      GLS_M = 1.d0          1.5d0        0.5d0        1.0d0
!      GLS_N = 1.d0         -1.0d0       -1.0d0       -0.67d0
!   GLS_Kmin = 5.0d-6        7.6d-6       7.6d-6       1.0d-8
!   GLS_Pmin = 5.0d-6        1.0d-12      1.0d-12      1.0d-8
!
!   GLS_CMU0 = 0.5544d0      0.5477d0     0.5477d0     0.5544d0
!     GLS_C1 = 0.9d0         1.44d0       0.555d0      1.00d0
!     GLS_C2 = 0.52d0        1.92d0       0.833d0      1.22d0
!    GLS_C3M = 2.5d0        -0.4d0       -0.6d0        0.1d0
!    GLS_C3P = 1.0d0         1.0d0        1.0d0        1.0d0
!   GLS_SIGK = 1.96d0        1.0d0        2.0d0        0.8d0
!   GLS_SIGP = 1.96d0        1.30d0       2.0d0        1.07d0
!
!------------------------------------------------------------------------------
! Constants used in the various formulations of surface turbulent kinetic
! energy flux in the GLS.
!------------------------------------------------------------------------------
!
! CHARNOK_ALPHA    Charnok surface roughness,
!                    Zos:   (charnok_alpha * u_star**2) / g
!
! ZOS_HSIG_ALPHA   Roughness from wave amplitude,
!                    Zos:   zos_hsig_alpha * Hsig
!
! SZ_ALPHA         Surface flux from wave dissipation,
!                    flux:  dt * sz_alpha * Wave_dissip
!
! CRGBAN_CW        Surface flux due to Craig and Banner wave breaking,
!                    flux:  dt * crgban_cw * u_star**3
!
!------------------------------------------------------------------------------
! Constants used in the computation of momentum stress.
!------------------------------------------------------------------------------
!
! RDRG         Linear bottom drag coefficient (m/s).
!
! RDRG2        Quadratic bottom drag coefficient.
!
! Zob          Bottom roughness (m).
!
! Zos          Surface roughness (m).
!
!------------------------------------------------------------------------------
! Height of atmospheric measurements for bulk fluxes parameterization.
!------------------------------------------------------------------------------
!
! BLK_ZQ       Height (m) of surface air humidity measurement. Usually,
!                recorded at 10 m.
!
! BLK_ZT       Height (m) of surface air temperature measurement. Usually,
!                recorded at 2 or 10 m.
!
! BLK_ZW       Height (m) of surface winds measurement. Usually, recorded
!                at 10 m.
!
!------------------------------------------------------------------------------
! Wetting and drying parameters.
!------------------------------------------------------------------------------
!
! DCRIT        Minimum depth (m) for wetting and drying.
!
!------------------------------------------------------------------------------
! Jerlov Water type.
!------------------------------------------------------------------------------
!
! WTYPE        Jerlov water type array index used to model the light absorption
!                with a double exponential function (Paulson and Simpson,
!                1977).  The classification ranges from clear open ocean
!                waters (type I) to dark turbulent coastal waters (type 7).
!
!              Array     Jerlov
!              Index   Water Type   Examples
!              -----   ----------   --------
!
!                1         I        Open Pacific
!                2         IA       Eastern Mediterranean, Indian Ocean
!                3         IB       Western Mediterranean, Open Atlantic
!                4         II       Coastal waters, Azores
!                5         III      Coastal waters, North Sea
!                6         1        Skagerrak Strait
!                7         3        Baltic
!                8         5        Black Sea
!                9         7        Dark coastal water
!
!------------------------------------------------------------------------------
! Body-force parameters. Used when CPP option BODYFORCE is activated.
!------------------------------------------------------------------------------
!
! LEVSFRC      Deepest level to apply surface momentum stress as a body-force.
!
! LEVBFRC      Shallowest level to apply bottom momentum stress as a body-force.
!
!------------------------------------------------------------------------------
! Vertical S-coordinates parameters.
!------------------------------------------------------------------------------
!
! The parameters below must be consistent in all input fields associated with
! the vertical grid.  The same vertical grid transformation (depths) needs to
! be used when preparing initial conditions, boundary conditions, climatology,
! observations, and so on. Please check:
!
!   https://www.myroms.org/wiki/index.php/Vertical_S-coordinate
!
! for details, rules and examples.
!
!
! Vtransform   Vertical transformation equation:
!
!                (1) Original formulation (Shchepetkin and McWilliams, 2005),
!                    Vtransform=1 (In ROMS since 1999)
!
!                      z(x,y,s,t)=Zo(x,y,s)+zeta(x,y,t)*[1+Zo(x,y,s)/h(x,y)]
!
!                    where
!
!                      Zo(x,y,s)=hc*s+[h(x,y)-hc]*C(s)
!
!                (2) Improved formulation (A. Shchepetkin, 2005),
!                    Vtransform=2
!
!                      z(x,y,s,t)=zeta(x,y,t)*[zeta(x,y,t)+h(x,y)]*Zo(x,y,s)
!
!                    where
!
!                      Zo(x,y,s)=[hc*s(k)+h(x,y)*C(k)]/[hc+h(x,y)]
!
!                    The true sigma-coordinate system is recovered as hc goes
!                    to INFINITY. This is useful when configuring applications
!                    with flat bathymetry and uniform level thickness.
!                    Practically, you can achieve this by setting:
!
!                      THETA_S = 0.0d0
!                      THETA_B = 0.0d0
!                      TCLINE  = 1.0d+17       (a large number)
!
!
! Vstretching  Vertical stretching function, C(s):
!
!                (1) Original function (Song and Haidvogel, 1994),
!                    Vstretching=1
!
!                    C(s)=(1-theta_b)*[SINH(s*theta_s)/SINH(theta_s)]+
!                         theta_b*[-0.5+0.5*TANH(theta_s*(s+0.5))/
!                                           TANH(0.5*theta_s)]
!
!                (2) A. Shchepetkin (2005) function,
!                    Vstretching=2
!
!                      C(s)=Cweight*Csur(s)+(1-Cweight)*Cbot(s)
!
!                    where
!
!                      Csur(s)=[1-COSH(theta_s*s)]/[COSH(theta_s)-1]
!
!                      Cbot(s)=-1+[1-SINH(theta_b*(s+1))]/SINH(theta_b)
!
!                      Cweight=(s+1)**alpha*
!                              (1+(alpha/beta)*(1-(s+1)**beta))
!
!                (3) R. Geyer function for shallow sediment applications,
!                    Vstretching=3
!
!                      C(s)=Cweight*Cbot(s)+(1-Cweight)*Csur(s)
!
!                    where
!
!                      Csur(s)=-LOG(COSH(Hscale*ABS(s)** alpha))/
!                               LOG(COSH(Hscale))
!
!                      Cbot(s)= LOG(COSH(Hscale*(s+1)** beta))/
!                               LOG(COSH(Hscale))-1
!
!                      Cweight=0.5*(1-TANH(Hscale*(s+0.5))
!
!                (4) A. Shchepetkin (2010) improved double stretching function,
!                    Vstretching=4
!
!                      C(s)=[1-COSH(theta_s*s)]/[COSH(theta_s)-1]
!
!                    with bottom refinement
!
!                      C(s)=[EXP(theta_b*C(s))-1]/[1-EXP(-theta_b)]
!
!                    The resulting double transformation is continuous with
!                    respect control parameters theta_s and theta_b with a
!                    meaningful range of:
!
!                      0 <  theta_s <= 10.0
!                      0 <= theta_b <=  4.0
!
!                 (5) Souza et al. (2015) quadratic Legendre polynomial function
!                     that allows higher resolution near the surface,
!                     Vstretching=5. It is similar to Vstretching=4, but the
!                     fractional stretched vertical coordinate (s) is re-defined
!                     as:
!
!                       s(k)=- [(k*k - 2*k*N + k + N*N - N) / (N*N - N)]
!                            - weight * [(k*k - k*N) / (1 - N)]
!
!                     at vertical W-points, k=0,...,N and weight=0.01. To get
!                     the equation at vertical RHO-points, replace k with k-0.5.
!
!              Many other stretching functions (Vstretching>5) are possible
!              provided that:
!
!                * C(s) is a dimensionless, nonlinear, monotonic function.
!                * C(s) is a continuous differentiable function, or
!                  a differentiable piecewise function with smooth transition.
!                * The stretching vertical coordinate ,s, is constrained
!                  between -1 <= s <= 0, with s=0 corresponding to the
!                  free-surface and s=-1 corresponding to the bathymetry.
!                * Similarly, the stretching function, C(s), is constrained
!                  between -1 <= C(s) <= 0, with C(0)=0 corresponding to the
!                  free-surface and C(-1)=-1 corresponding to the bathymetry.
!
!              These functions are coded in routine "Utility/set_scoord.F".
!
! Due to its functionality and properties, the default and recommended vertical
! coordinates transformation is:
!
!              Vtransform  = 2
!              Vstretching = 4
!
!
! THETA_S      S-coordinate surface control parameter. The range of optimal
!                values depends on the vertical stretching function, C(s).
!
! THETA_B      S-coordinate bottom  control parameter. The range of optimal
!                values depends on the vertical stretching function, C(s).
!
! TCLINE       Critical depth (hc) in meters (positive) controlling the
!                stretching. It can be interpreted as the width of surface or
!                bottom boundary layer in which higher vertical resolution
!                (levels) is required during stretching.
!
!------------------------------------------------------------------------------
! Mean Density and background Brunt-Vaisala frequency.
!------------------------------------------------------------------------------
!
!  RHO0        Mean density (Kg/m3) used when the Boussinesq approximation
!              is inferred.
!
!  BVF_BAK     Background Brunt-Vaisala frequency squared (1/s2). Typical
!              values for the ocean range (as a function of depth) from
!              1.0E-4 to 1.0E-6.
!
!------------------------------------------------------------------------------
! Time Stamps.
!------------------------------------------------------------------------------
!
! DSTART       Time stamp assigned to model initialization (days).  Usually
!                a Calendar linear coordinate, like modified Julian Day.  For
!                Example:
!
!                         Julian Day    = 1      for  Nov 25, 00:00:00 4713 BCE
!                modified Julian Day    = 1      for  May 24, 00:00:00 1968 GMT
!                Days since Jan 1, 2000 = 988.5  for  Sep 15, 12:00:00 2002
!
!                It is called truncated or modified Julian day because an
!                offset of 2440000 needs to be added.
!
! TIDE_START   Reference time origin for tidal forcing (days). This is the
!                time used when processing input tidal model data. It is needed
!                in routine "set_tides" to compute the correct phase lag with
!                respect ROMS/TOMS initialization time.
!
! TIME_REF     Reference time (yyyymmdd.f) used to compute relative time:
!                elapsed time interval since reference-time.  The "units"
!                attribute takes the form "time-unit since reference-time".
!                This parameter also provides information about the calendar
!                used:
!
!                If TIME_REF = -2, model time and DSTART are in modified Julian
!                days units.  The "units" attribute is:
!
!                  'time-units since 1968-05-23 00:00:00 GMT'    (May 23, 1968)
!
!                If TIME_REF = -1, model time and DSTART are in a calendar
!                with 360 days in every year (30 days each month).  The "units"
!                attribute is:
!
!                  'time-units since 0000-12-30 00:00:00'        (Dec 30, 0000)
!
!                If TIME_REF = 0, model time and DSTART are in a common year
!                calendar with 365.25 days.  The "units" attribute is:
!
!                  'time-units since 0001-01-01 00:00:00'        (Jan  1, 0001)
!
!                If TIME_REF > 0, model time and DSTART are the elapsed time
!                units since specified reference time.  For example,
!                TIME_REF=20020115.5 will yield the following attribute:
!
!                  'time-units since 2002-01-15 12:00:00'        (Jan 15, 2002)
!
!------------------------------------------------------------------------------
! Nudging/relaxation time scales, inverse scales will be computed internally.
!------------------------------------------------------------------------------
!
! When passive/active open boundary conditions are activated, these nudging
! values correspond to the passive (outflow) nudging time scales.
!
! TNUDG        Nudging time scale (days) for active tracer variables.
!                (1:NAT+NPT,1:Ngrids) values are expected.
!
! ZNUDG        Nudging time scale (days) for free-surface.
!
! M2NUDG       Nudging time scale (days) for 2D momentum.
!
! M3NUDG       Nudging time scale (days) for 3D momentum.
!
! OBCFAC       Factor between passive (outflow) and active (inflow) open
!                boundary conditions.  The nudging time scales for the
!                active (inflow) conditions are obtained by multiplying
!                the passive values by OBCFAC. If OBCFAC > 1, nudging on
!                inflow is stronger than on outflow (recommended).
!
!------------------------------------------------------------------------------
! Linear equation of State parameters.
!------------------------------------------------------------------------------
!
! Ignoring pressure, the linear equation of state is:
!
!              rho(:,:,:) = R0 - R0 * TCOEF * (t(:,:,:,:,itemp) - T0)
!                              + R0 * SCOEF * (t(:,:,:,:,isalt) - S0)
!
!              Typical values:     R0 = 1027.0  kg/m3
!                                  T0 = 10.0    Celsius
!                                  S0 = 35.0    nondimensional
!                               TCOEF = 1.7d-4  1/Celsius
!                               SCOEF = 7.6d-4  1/nondimensional
!
!              Notice that salinity has NO UNITS, it is nondimensional. Many
!              people use PSU (Practical Salinity Unit).  However, salinity
!              has always been defined as a conductivity ratio and does not
!              have physical units. For details, check the following forum
!              post:  www.myroms.org/forum/viewtopic.php?f=30&t=294
!
! R0           Background density value (Kg/m3) used in Linear Equation of
!                State.
!
! T0           Background potential temperature (Celsius) constant.
!
! S0           Background salinity (nondimensional) constant.
!
! TCOEF        Thermal expansion coefficient in Linear Equation of State.
!
! SCOEF        Saline contraction coefficient in Linear Equation of State.
!
!------------------------------------------------------------------------------
! Slipperiness parameter.
!------------------------------------------------------------------------------
!
! GAMMA2       Slipperiness variable, either 1.0 (free slip) or -1.0 (no slip).
!
!------------------------------------------------------------------------------
! Point Sources/Sink sources activation switches.
!------------------------------------------------------------------------------
!
! LuvSrc       Logical switches (T/F) to activate momentum horizontal transport
!                points Sources/Sinks. Usually it is used to turn on/off river
!                runoff transport (u or v variables) in an application,
!                [1:Ngrids].
!
!                In nesting applications, turn on only the grids that require
!                activation and processing of momentum point Sources/Sinks.
!
! LwSrc        Logical switches (T/F) to activate mass points Sources/Sinks.
!                Usually, it is used to turn on/off volume vertical influx (w)
!                in an application.
!
!                In nesting applications, turn on only the grids that require
!                activation and processing of mass influx point Sources/Sinks.
!
! LtracerSrc   Logical switches (T/F) to activate tracer variables point
!                Sources/Sinks. Only NAT active tracers (temperature, salinity)
!                and NPT inert tracers are activated here:
!
!                 LtracerSrc(itemp,ng)     for temperature (itemp=1)
!                 LtracerSrc(isalt,ng)     for salinity    (isalt=2)
!                 LtracerSrc(NAT+1,ng)     for inert tracer 1
!                 ...                      ...
!                 LtracerSrc(NAT+NPT,ng)   for inert tracer NPT
!
!                Other biological and sediment tracers switches are activated
!                in their respective input scripts.
!
!                In nesting applications, turn on only the grids that require
!                activation and processing of tracers point Sources/Sinks.
!
!                Recall that switches are usually activated to add river runoff
!                as a point source. At minimum, it is necessary to specify both
!                temperature and salinity for all rivers.  The other tracers are
!                optional.
!
!                This logical switch REPLACES and ELIMINATES the need to have
!                or read the variable "river_flag(river)" in the input rivers
!                forcing NetCDF file:
!
!                 double river_flag(river)
!                        river_flag:long_name = "river runoff tracer flag"
!                        river_flag:option_0 = "all tracers are off"
!                        river_flag:option_1 = "only temperature"
!                        river_flag:option_2 = "only salinity"
!                        river_flag:option_3 = "both temperature and salinity"
!                        river_flag:units = "nondimensional"
!
!                The above variable was too cumbersome and complicated when
!                additional tracers are considered. However, this change is
!                backward compatible.
!
!                The LtracerSrc switch will be used to activate the reading of
!                respective tracer variable from input river forcing NetCDF
!                file. If you want to add other tracer variables (other than
!                temperature and salinity) as a source for a particular
!                river(s), you just need to specify such values on those
!                river(s). Then, set the values to ZERO on the other river(s)
!                that do NOT require such river forcing for that tracer.
!                Recall that you need to specify the tracer values for all
!                rivers, even if their values are zero.
!
!------------------------------------------------------------------------------
! Logical switches to process climatology fields. The climatology fields are
! either read from a NetCDF file or set with analytical CPP options.
!------------------------------------------------------------------------------
!
! LsshCLM      Logical switch (T/F) to process sea-surface height climatology.
!                The CPP option ZCLIMATOLOGY is now obsolete and replaced with
!                this switch to facilitate nesting applications. Currently,
!                the sea-surface height climatology, CLIMA(ng)%ssh, is NOT
!                used but it is kept for future use.
!
!                The nudging of SSH on the free-surface governing equation
!                (vertically integrated continuity equation) is NOT allowed
!                because it violates mass/volume conservation. Recall that
!                the time rate of change of free-surface is computed from the
!                divergence of "ubar" and "vbar".  If such nudging term is
!                required, it needs to be specified on the momentum equations
!                for (u,v) and/or (ubar,vbar). If done on (u,v) only, its
!                effects enter the 2D momentum equations via the residual
!                vertically integrated forcing term.
!
! Lm2CLM       Logical switch (T/F) to process 2D momentum (ubar, vbar)
!                climatology. The CPP option M2CLIMATOLOGY is now obsolete
!                and replaced with this switch to facilitate nesting
!                applications. Currently, the CLIMA(ng)%ubarclm and
!                CLIMA(ng)%vbarclm are used for sponges and nudging. If
!                tidal forcing, the climatological values are adjusted to
!                include tides.
!
! Lm3CLM       Logical switch (T/F) to process 3D momentum climatology (u,v)
!                The CPP option M3CLIMATOLOGY is now obsolete and replaced
!                with this switch to facilitate nesting applications.
!                Currently, the CLIMA(ng)%uclm and CLIMA(ng)%vclm are used
!                for sponges and nudging.
!
! LtracerCLM   Logical switches (T/F) to process active and inert tracer
!                variables climatology.  The CPP option TCLIMATOLOGY is now
!                obsolete and replaced with these switches to facilitate
!                nesting applications. Currently, the CLIMA(ng)%tclm is
!                used for horizontal mixing, sponges, and nudging.
!
!                Only NAT active tracers (temperature, salinity) and NPT inert
!                tracers need to be specified here:
!
!                 LtracerCLM(itemp,ng)     for temperature (itemp=1)
!                 LtracerCLM(isalt,ng)     for salinity    (isalt=2)
!                 LtracerCLM(NAT+1,ng)     for inert tracer 1
!                 ...                      ...
!                 LtracerCLM(NAT+NPT,ng)   for inert tracer NPT
!
!                Other biological and sediment tracers switches are specified
!                in their respective input scripts.
!
!                These switches also controls which climatology tracer fields
!                (specially passive tracers) needs to be processed.  So we
!                may reduce the memory allocation for the CLIMA(ng)%tclm array.
!
!------------------------------------------------------------------------------
! Logical switches for nudging to climatology fields.
!------------------------------------------------------------------------------
!
! LnudgeM2CLM   Logical switch (T/F) to activate the nudging of 2D momentum
!                 climatology.  The CPP option M2CLM_NUDGING is now obsolete
!                 and replaced with this switch to facilitate nesting
!                 applications.  Users also need to TURN ON the logical
!                 switch "Lm2CLM", described above, to process the required
!                 2D momentum climatology data.  This data can be set with
!                 analytical functions (ANA_M2CLIMA) or read from input
!                 climatology NetCDF file(s).
!
!                 The nudging coefficients CLIMA(ng)%M2nudgcof can be set
!                 with analytical functions in "ana_nudgcoef.h" using CPP
!                 option ANA_NUDGCOEF.  Otherwise, it will be read from
!                 NetCDF file NUDNAME.
!
! LnudgeM3CLM   Logical switch (T/F) to activate the nudging of 3D momentum
!                 climatology.  The CPP option M3CLM_NUDGING is now obsolete
!                 and replaced with this switch to facilitate nesting
!                 applications.
!
!                 Users also need to TURN ON the logical switch "Lm3CLM",
!                 described above, to process the required 3D momentum
!                 climatology data.  This data can be set with analytical
!                 functions (ANA_M3CLIMA) or read from input climatology
!                 NetCDF file(s).
!
!                 The nudging coefficients CLIMA(ng)%M3nudgcof can be set
!                 with analytical functions in "ana_nudgcoef.h"  using CPP
!                 option ANA_NUDGCOEF.  Otherwise, it will be read from
!                 NetCDF file NUDNAME.
!
! LnudgeTCLM    Logical switches (T/F) to activate the nudging of active and
!                 inert tracer variables climatology. These switches also
!                 control which tracer variables to nudge.  The CPP option
!                 TCLM_NUDGING is now obsolete and replaced with these
!                 switches to facilitate nesting applications.
!
!                 Only NAT active tracers (temperature, salinity) and NPT
!                 inert tracers need to be specified here:
!
!                   LnudgeTCLM(itemp,ng)     for temperature (itemp=1)
!                   LnudgeTCLM(isalt,ng)     for salinity    (isalt=2)
!                   LnudgeTCLM(NAT+1,ng)     for inert tracer 1
!                   ...                      ...
!                   LnudgeTCLM(NAT+NPT,ng)   for inert tracer NPT
!
!                 Other biological and sediment tracers switches are specified
!                 in their respective input scripts.
!
!                 User also needs to TURN ON the respective logical switches
!                 "LtracerCLM", described above, to process the required 3D
!                 tracer climatology data. This data can be set with analytical
!                 functions (ANA_TCLIMA) or read from input climatology
!                 NetCDF file(s).
!
!                 The nudging coefficients CLIMA(ng)%Tnudgcof can be set
!                 with analytical functions in "ana_nudgcoef.h"  using CPP
!                 option ANA_NUDGCOEF.  Otherwise, it will be read from
!                 NetCDF file NUDNAME.
!
!------------------------------------------------------------------------------
! Adjoint sensitivity parameters.
!------------------------------------------------------------------------------
!
! DstrS        Starting day for adjoint sensitivity forcing.
!
! DendS        Ending   day for adjoint sensitivity forcing.
!
!                The adjoint forcing is applied at every time step according
!                to desired state functional stored in the adjoint sensitivity
!                NetCDF file. DstrS must be less than or equal to DendS. If
!                both values are zero, their values are reset internally to
!                the full range of the adjoint integration.
!
!  KstrS       Starting vertical level of the 3D adjoint state variables whose
!                sensitivity is required.
!
!  KendS       Ending   vertical level of the 3D adjoint state variables whose
!                sensitivity is required.
!
!  Lstate      Logical switches (TRUE/FALSE) to specify the adjoint state
!                variables whose sensitivity is required.
!
!                Lstate(isFsur):   Free-surface
!                Lstate(isUbar):   2D U-momentum
!                Lstate(isVbar):   2D V-momentum
!                Lstate(isUvel):   3D U-momentum
!                Lstate(isVvel):   3D V-momentum
!                Lstate(isWvel):   3D W-momentum
!                Lstate(isTvar):   Traces (NT values expected)
!
!------------------------------------------------------------------------------
! Forcing Singular Vectors or Stochastic Optimals parameters.
!------------------------------------------------------------------------------
!
! Fstate       Logical switches (TRUE/FALSE) to specify state variables for
!                which Forcing Singular Vectors or Stochastic Optimals is
!                required.
!
!                Fstate(isFsur):   Free-surface
!                Fstate(isUbar):   2D U-momentum
!                Fstate(isVbar):   2D V-momentum
!                Fstate(isUvel):   3D U-momentum
!                Fstate(isVvel):   3D V-momentum
!                Fstate(isTvar):   Traces (NT values expected)
!
!                Fstate(isUstr):   surface U-stress
!                Fstate(isVstr):   surface V-stress
!                Fstate(isTsur):   surface tracers flux (NT values expected)
!
! SO_decay     Stochastic Optimals time decorrelation scale (days) assumed
!                for red noise processes.
!
! SO_sdev      Stochastic Optimals surface forcing standard deviation for
!                dimensionalization.
!
!                SO_sdev(isFsur):  Free-surface
!                SO_sdev(isUbar):  2D U-momentum
!                SO_sdev(isVbar):  2D V-momentum
!                SO_sdev(isUvel):  3D U-momentum
!                SO_sdev(isVvel):  3D V-momentum
!                SO_sdev(isTvar):  Traces (NT values expected)
!
!                SO_sdev(isUstr):  surface U-stress
!                SO_sdev(isVstr):  surface V-stress
!                SO_sdev(isTsur):  surface tracer flux (NT values expected)
!
!------------------------------------------------------------------------------
! Logical switches (T/F) to activate writing of instantaneous fields into
! HISTORY file.
!------------------------------------------------------------------------------
!
! Hout(idUvel)   Write out 3D U-velocity component.
! Hout(idVvel)   Write out 3D V-velocity component.
! Hout(idu3dE)   Write out 3D Eastward  velocity component at RHO-points.
! Hout(idv3dN)   Write out 3D Northward velocity component at RHO-points.
! Hout(idWvel)   Write out 3D W-velocity component.
! Hout(idOvel)   Write out 3D omega vertical velocity.
! Hout(idUbar)   Write out 2D U-velocity component.
! Hout(idVbar)   Write out 2D V-velocity component.
! Hout(idu2dE)   Write out 2D Eastward  velocity component at RHO-points.
! Hout(idv2dN)   Write out 2D Northward velocity component at RHO-points.
! Hout(idFsur)   Write out free-surface.
! Hout(idBath)   Write out time-dependent bathymetry.
!
! Hout(idTvar)   Write out active (NAT) tracers: temperature and salinity.
!
! Hout(idpthR)   Write out time-varying depths of RHO-points.
! Hout(idpthU)   Write out time-varying depths of U-points.
! Hout(idpthV)   Write out time-varying depths of V-points.
! Hout(idpthW)   Write out time-varying depths of W-points.
!
! Hout(idUsms)   Write out surface U-momentum stress.
! Hout(idVsms)   Write out surface V-momentum stress.
! Hout(idUbms)   Write out bottom  U-momentum stress.
! Hout(idVbms)   Write out bottom  V-momentum stress.
!
! Hout(idUbrs)   Write out current-induced, U-momentum stress.
! Hout(idVbrs)   Write out current-induced, V-momentum stress.
! Hout(idUbws)   Write out wind-induced, bottom U-wave stress.
! Hout(idVbws)   Write out wind-induced, bottom V-wave stress.
! Hout(idUbcs)   Write out bottom maximum wave and current U-stress.
! Hout(idVbcs)   Write out bottom maximum wave and current V-stress.
!
! Hout(idUbot)   Write out wind-induced, bed wave orbital U-velocity.
! Hout(idVbot)   Write out wind-induced, bed wave orbital V-velocity.
! Hout(idUbur)   Write out bottom U-velocity above bed.
! Hout(idVbvr)   Write out bottom V-velocity above bed.
!
! Hout(idW2xx)   Write out 2D radiation stress, Sxx component.
! Hout(idW2xy)   Write out 2D radiation stress, Sxy component.
! Hout(idW2yy)   Write out 2D radiation stress, Syy component.
! Hout(idU2rs)   Write out 2D U-radiation stress.
! Hout(idV2rs)   Write out 2D V-radiation stress.
! Hout(idU2Sd)   Write out 2D U-Stokes velocity.
! Hout(idV2Sd)   Write out 2D V-Stokes velocity.
!
! Hout(idW3xx)   Write out 3D radiation stress, Sxx component.
! Hout(idW3xy)   Write out 3D radiation stress, Sxy component.
! Hout(idW3yy)   Write out 3D radiation stress, Syy component.
! Hout(idW3zx)   Write out 3D radiation stress, Szx component.
! Hout(idW3zy)   Write out 3D radiation stress, Szy component.
! Hout(idU3rs)   Write out 3D U-radiation stress.
! Hout(idV3rs)   Write out 3D V-radiation stress.
! Hout(idU3Sd)   Write out 3D U-Stokes velocity.
! Hout(idV3Sd)   Write out 3D V-Stokes velocity.
!
! Hout(idWamp)   Write out wave height.
! Hout(idWlen)   Write out wave length.
! Hout(idWdir)   Write out wave direction.
! Hout(idWptp)   Write out wave surface period.
! Hout(idWpbt)   Write out wave bottom period.
! Hout(idWorb)   Write out wave bottom orbital velocity.
! Hout(idWdis)   Write out wave dissipation.
!
! Hout(idPair)   Write out surface air pressure.
! Hout(idUair)   Write out surface U-wind component.
! Hout(idVair)   Write out surface V-wind component.
!
! Hout(idTsur)   Write out surface net heat and salt flux
! Hout(idLhea)   Write out latent heat flux.
! Hout(idShea)   Write out sensible heat flux.
! Hout(idLrad)   Write out long-wave radiation flux.
! Hout(idSrad)   Write out short-wave radiation flux.
! Hout(idEmPf)   Write out E-P flux.
! Hout(idevap)   Write out evaporation rate.
! Hout(idrain)   Write out precipitation rate.
!
! Hout(idDano)   Write out density anomaly.
! Hout(idVvis)   Write out vertical viscosity coefficient.
! Hout(idTdif)   Write out vertical diffusion coefficient of temperature.
! Hout(idSdif)   Write out vertical diffusion coefficient of salinity.
! Hout(idHsbl)   Write out depth of oceanic surface boundary layer.
! Hout(idHbbl)   Write out depth of oceanic bottom boundary layer.
! Hout(idMtke)   Write out turbulent kinetic energy.
! Hout(idMtls)   Write out turbulent kinetic energy times length scale.
!
! Hout(inert)    Write out extra inert passive tracers.
! Hout(idBott)   Write out exposed sediment layer properties, 1:MBOTP.
!
!------------------------------------------------------------------------------
! Logical switches (T/F) to activate writing of instantaneous fields into
! QUICKSAVE file.
!------------------------------------------------------------------------------
!
! Qout(idUvel)   Write out 3D U-velocity component.
! Qout(idVvel)   Write out 3D V-velocity component.
! Qout(idu3dE)   Write out 3D Eastward  velocity component at RHO-points.
! Qout(idv3dN)   Write out 3D Northward velocity component at RHO-points.
! Qout(idWvel)   Write out 3D W-velocity component.
! Qout(idOvel)   Write out 3D omega vertical velocity.
! Qout(idUbar)   Write out 2D U-velocity component.
! Qout(idVbar)   Write out 2D V-velocity component.
! Qout(idu2dE)   Write out 2D Eastward  velocity component at RHO-points.
! Qout(idv2dN)   Write out 2D Northward velocity component at RHO-points.
! Qout(idFsur)   Write out free-surface.
! Qout(idBath)   Write out time-dependent bathymetry.
!
! Qout(idTvar)   Write out active (NAT) tracers: temperature and salinity.
!
! Qout(idUsur)   Write out surface U-velocity component.
! Qout(idVsur)   Write out surface V-velocity component.
! Qout(idUsuE)   Write out surface Eastward  velocity component at RHO-points.
! Qout(idVsuN)   Write out surface Northward velocity component at RHO-points.
!
! Qout(idsurT)   Write out surface temperature and salinity
!
! Qout(idpthR)   Write out time-varying depths of RHO-points.
! Qout(idpthU)   Write out time-varying depths of U-points.
! Qout(idpthV)   Write out time-varying depths of V-points.
! Qout(idpthW)   Write out time-varying depths of W-points.
!
! Qout(idUsms)   Write out surface U-momentum stress.
! Qout(idVsms)   Write out surface V-momentum stress.
! Qout(idUbms)   Write out bottom  U-momentum stress.
! Qout(idVbms)   Write out bottom  V-momentum stress.
!
! Qout(idUbrs)   Write out current-induced, U-momentum stress.
! Qout(idVbrs)   Write out current-induced, V-momentum stress.
! Qout(idUbws)   Write out wind-induced, bottom U-wave stress.
! Qout(idVbws)   Write out wind-induced, bottom V-wave stress.
! Qout(idUbcs)   Write out bottom maximum wave and current U-stress.
! Qout(idVbcs)   Write out bottom maximum wave and current V-stress.
!
! Qout(idUbot)   Write out wind-induced, bed wave orbital U-velocity.
! Qout(idVbot)   Write out wind-induced, bed wave orbital V-velocity.
! Qout(idUbur)   Write out bottom U-velocity above bed.
! Qout(idVbvr)   Write out bottom V-velocity above bed.
!
! Qout(idW2xx)   Write out 2D radiation stress, Sxx component.
! Qout(idW2xy)   Write out 2D radiation stress, Sxy component.
! Qout(idW2yy)   Write out 2D radiation stress, Syy component.
! Qout(idU2rs)   Write out 2D U-radiation stress.
! Qout(idV2rs)   Write out 2D V-radiation stress.
! Qout(idU2Sd)   Write out 2D U-Stokes velocity.
! Qout(idV2Sd)   Write out 2D V-Stokes velocity.
!
! Qout(idW3xx)   Write out 3D radiation stress, Sxx component.
! Qout(idW3xy)   Write out 3D radiation stress, Sxy component.
! Qout(idW3yy)   Write out 3D radiation stress, Syy component.
! Qout(idW3zx)   Write out 3D radiation stress, Szx component.
! Qout(idW3zy)   Write out 3D radiation stress, Szy component.
! Qout(idU3rs)   Write out 3D U-radiation stress.
! Qout(idV3rs)   Write out 3D V-radiation stress.
! Qout(idU3Sd)   Write out 3D U-Stokes velocity.
! Qout(idV3Sd)   Write out 3D V-Stokes velocity.
!
! Qout(idWamp)   Write out wave height.
! Qout(idWlen)   Write out wave length.
! Qout(idWdir)   Write out wave direction.
! Qout(idWptp)   Write out wave surface period.
! Qout(idWpbt)   Write out wave bottom period.
! Qout(idWorb)   Write out wave bottom orbital velocity.
! Qout(idWdis)   Write out wave dissipation.
!
! Qout(idPair)   Write out surface air pressure.
! Qout(idUair)   Write out surface U-wind component.
! Qout(idVair)   Write out surface V-wind component.
!
! Qout(idTsur)   Write out surface net heat and salt flux
! Qout(idLhea)   Write out latent heat flux.
! Qout(idShea)   Write out sensible heat flux.
! Qout(idLrad)   Write out long-wave radiation flux.
! Qout(idSrad)   Write out short-wave radiation flux.
! Qout(idEmPf)   Write out E-P flux.
! Qout(idevap)   Write out evaporation rate.
! Qout(idrain)   Write out precipitation rate.
!
! Qout(idDano)   Write out density anomaly.
! Qout(idVvis)   Write out vertical viscosity coefficient.
! Qout(idTdif)   Write out vertical diffusion coefficient of temperature.
! Qout(idSdif)   Write out vertical diffusion coefficient of salinity.
! Qout(idHsbl)   Write out depth of oceanic surface boundary layer.
! Qout(idHbbl)   Write out depth of oceanic bottom boundary layer.
! Qout(idMtke)   Write out turbulent kinetic energy.
! Qout(idMtls)   Write out turbulent kinetic energy times length scale.
!
! Qout(inert)    Write out inert passive tracers.
! Qout(Snert)    Write out surface inert passive tracers.
!
!------------------------------------------------------------------------------
! Logical switches (T/F) to activate writing of time-averaged fields into
! AVERAGE file.
!------------------------------------------------------------------------------
!
! Aout(idUvel)   Write out 3D U-velocity component.
! Aout(idVvel)   Write out 3D V-velocity component.
! Aout(idu3dE)   Write out 3D Eastward  velocity component at RHO-points.
! Aout(idv3dN)   Write out 3D Northward velocity component at RHO-points.
! Aout(idWvel)   Write out 3D W-velocity component.
! Aout(idOvel)   Write out 3D omega vertical velocity.
! Aout(idUbar)   Write out 2D U-velocity component.
! Aout(idVbar)   Write out 2D V-velocity component.
! Aout(idu2dE)   Write out 2D Eastward  velocity component at RHO-points.
! Aout(idv2dN)   Write out 2D Northward velocity component at RHO-points.
! Aout(idFsur)   Write out free-surface.
!
! Aout(idTvar)   Write out active (NAT) tracers: temperature and salinity.
!
! Aout(idUsms)   Write out surface U-momentum stress.
! Aout(idVsms)   Write out surface V-momentum stress.
! Aout(idUbms)   Write out bottom  U-momentum stress.
! Aout(idVbms)   Write out bottom  V-momentum stress.
!
! Aout(idW2xx)   Write out 2D radiation stress, Sxx component.
! Aout(idW2xy)   Write out 2D radiation stress, Sxy component.
! Aout(idW2yy)   Write out 2D radiation stress, Syy component.
! Aout(idU2rs)   Write out 2D U-radiation stress.
! Aout(idV2rs)   Write out 2D V-radiation stress.
! Aout(idU2Sd)   Write out 2D U-Stokes velocity.
! Aout(idV2Sd)   Write out 2D V-Stokes velocity.
!
! Aout(idW3xx)   Write out 3D radiation stress, Sxx component.
! Aout(idW3xy)   Write out 3D radiation stress, Sxy component.
! Aout(idW3yy)   Write out 3D radiation stress, Syy component.
! Aout(idW3zx)   Write out 3D radiation stress, Szx component.
! Aout(idW3zy)   Write out 3D radiation stress, Szy component.
! Aout(idU3rs)   Write out 3D U-radiation stress.
! Aout(idV3rs)   Write out 3D V-radiation stress.
! Aout(idU3Sd)   Write out 3D U-Stokes velocity.
! Aout(idV3Sd)   Write out 3D V-Stokes velocity.
!
! Aout(idPair)   Write out surface air pressure.
! Aout(idUair)   Write out surface U-wind component.
! Aout(idVair)   Write out surface V-wind component.
!
! Aout(idTsur)   Write out surface net heat and salt flux
! Aout(idLhea)   Write out latent heat flux.
! Aout(idShea)   Write out sensible heat flux.
! Aout(idLrad)   Write out long-wave radiation flux.
! Aout(idSrad)   Write out short-wave radiation flux.
! Aout(idevap)   Write out evaporation rate.
! Aout(idrain)   Write out precipitation rate.
!
! Aout(idDano)   Write out density anomaly.
! Aout(idVvis)   Write out vertical viscosity coefficient.
! Aout(idTdif)   Write out vertical diffusion coefficient of temperature.
! Aout(idSdif)   Write out vertical diffusion coefficient of salinity.
! Aout(idHsbl)   Write out depth of oceanic surface boundary layer.
! Aout(idHbbl)   Write out depth of oceanic bottom boundary layer.
!
! Aout(id2dRV)   Write out 2D relative vorticity (vertically integrated).
! Aout(id3dRV)   Write out 3D relative vorticity.
! Aout(id2dPV)   Write out 2D potential vorticity (shallow water).
! Aout(id3dPV)   Write out 3D potential vorticity.
!
! Aout(idu3dD)   Write out detided 3D U-velocity.
! Aout(idv3dD)   Write out detided 3D V-velocity.
! Aout(idu2dD)   Write out detided 2D U-velocity.
! Aout(idv2dD)   Write out detided 2D V-velocity.
! Aout(idFsuD)   Write out detided free-surface
!
! Aout(idTrcD)   Write out detided temperature and salinity.
!
! Aout(idHUav)   Write out u-volume flux, Huon.
! Aout(idHVav)   Write out v-volume flux, Hvom.
! Aout(idUUav)   Write out quadratic <u*u> term.
! Aout(idUVav)   Write out quadratic <u*v> term.
! Aout(idVVav)   Write out quadratic <v*v> term.
! Aout(idU2av)   Write out quadratic <ubar*ubar> term.
! Aout(idV2av)   Write out quadratic <vbar*vbar> term.
! Aout(idZZav)   Write out quadratic <zeta*zeta> term.
!
! Aout(idTTav)   Write out quadratic <t*t> active and inert tracers terms.
! Aout(idUTav)   Write out quadratic <u*t> active and inert tracers terms.
! Aout(idVTav)   Write out quadratic <v*t> active and inert tracers terms.
! Aout(iHUTav)   Write out active and inert tracer u-volume flux, <Huon*t>.
! Aout(iHVTav)   Write out active and inert tracer v-volume flux, <Hvom*t>.
!
! Aout(inert)    Write out extra inert passive tracers.
!
!------------------------------------------------------------------------------
! Logical switches (T/F) to activate writing of time-averaged fields into
! DIAGNOSTIC file.
!------------------------------------------------------------------------------
!
! Time-averaged, 2D momentum (ubar,vbar) diagnostic terms:
! (if DIAGNOSTICS_UV)
!
! Dout(M2rate)   Write out acceleration.
! Dout(M2pgrd)   Write out pressure gradient.
! Dout(M2fcor)   Write out Coriolis force, if UV_COR.
! Dout(M2hadv)   Write out horizontal total advection, if UV_ADV.
! Dout(M2xadv)   Write out horizontal  XI-advection, if UV_ADV.
! Dout(M2yadv)   Write out horizontal ETA-advection, if UV_ADV.
! Dout(M2hrad)   Write out horizontal total radiation stress, NEARSHORE_MELLOR.
! Dout(M2hvis)   Write out horizontal total viscosity, if UV_VIS2 or UV_VIS4.
! Dout(M2xvis)   Write out horizontal  XI-viscosity, if UV_VIS2 or UV_VIS4.
! Dout(M2yvis)   Write out horizontal ETA-viscosity, if UV_VIS2 or UV_VIS4.
! Dout(M2sstr)   Write out surface stress.
! Dout(M2bstr)   Write out bottom stress
!
! Time-averaged, 3D momentum (u,v) diagnostic terms:
! (if SOLVE3D and DIAGNOSTICS_UV)
!
! Dout(M3rate)   Write out acceleration.
! Dout(M3pgrd)   Write out pressure gradient.
! Dout(M3fcor)   Write out Coriolis force, if UV_COR.
! Dout(M3hadv)   Write out horizontal total advection, if UV_ADV.
! Dout(M3xadv)   Write out horizontal  XI-advection, if UV_ADV.
! Dout(M3yadv)   Write out horizontal ETA-advection, if UV_ADV.
! Dout(M3hrad)   Write out horizontal total radiation stress, NEARSHORE_MELLOR.
! Dout(M3vrad)   Write out vertical radiation stress, if NEARSHORE_MELLOR.
! Dout(M3hvis)   Write out horizontal total viscosity, if UV_VIS2 or UV_VIS4.
! Dout(M3xvis)   Write out horizontal  XI-viscosity, if UV_VIS2 or UV_VIS4.
! Dout(M3yvis)   Write out horizontal ETA-viscosity, if UV_VIS2 or UV_VIS4.
! Dout(M3yvis)   Write out horizontal ETA-viscosity, if UV_VIS2 or UV_VIS4.
! Dout(M3vvis)   Write out vertical viscosity.
!
! Time-averaged, active (temperature and salinity) and passive (inert) tracer
! diagnostic terms, [1:NAT+NPT,Ngrids] values expected:
! (if SOLVE3D and DIAGNOSTICS_TS)
!
! Dout(iTrate)   Write out time rate of change.
! Dout(iThadv)   Write out horizontal total advection.
! Dout(iTxadv)   Write out horizontal  XI-advection.
! Dout(iTyadv)   Write out horizontal ETA-advection.
! Dout(iTvadv)   Write out vertical advection.
! Dout(iThdif)   Write out horizontal total diffusion, if TS_DIF2 or TS_DIF4.
! Dout(iTxdif)   Write out horizonta1  XI-diffusion, if TS_DIF2 or TS_DIF4.
! Dout(iTydif)   Write out horizontal ETA-diffusion, if TS_DIF2 or TS_DIF4.
! Dout(iTsdif)   Write out horizontal   S-diffusion, if TS_DIF2 or TS_DIF4 and
!                  rotated tensor (MIX_GEO_TS or MIX_ISO_TS).
! Dout(iTvdif)   Write out vertical diffusion.
!
!------------------------------------------------------------------------------
! Generic User parameters.
!------------------------------------------------------------------------------
!
! NUSER        Number of User parameters to consider (integer).
!
! USER         Vector containing user parameters (real array). This array
!                is used with the SANITY_CHECK to test the correctness of
!                the tangent linear adjoint models.  It contains information
!                of the model variable and grid point to perturb:
!
!                INT(user(1)):  tangent state variable to perturb
!                INT(user(2)):  adjoint state variable to perturb
!                               [isFsur=1] free-surface
!                               [isUbar=2] 2D U-momentum
!                               [isVbar=3] 2D V-momentum
!                               [isUvel=4] 3D U-momentum
!                               [isVvel=5] 3D V-momentum
!                               [isTvar=6] First tracer (temperature)
!                               [   ...  ]
!                               [isTvar=?] Last tracer
!
!                INT(user(3)):  I-index of tangent variable to perturb
!                INT(user(4)):  I-index of adjoint variable to perturb
!                INT(user(5)):  J-index of tangent variable to perturb
!                INT(user(6)):  J-index of adjoint variable to perturb
!                INT(user(7)):  K-index of tangent variable to perturb, if 3D
!                INT(user(8)):  K-index of adjoint variable to perturb, if 3D
!
!                Set tangent and adjoint parameters to the same values
!                if perturbing and reporting the same variable.
!
!------------------------------------------------------------------------------
! I/O NetCDF files parameters.
!------------------------------------------------------------------------------
!
! NetCDF-4/HDF5 compression parameters for output files. This capability
! is used when both HDF5 and DEFLATE C-preprocessing options are
! activated. The user needs to compile with the NetCDF-4/HDF5 and MPI
! libraries. File deflation cannot be used in parallel I/O for writing
! because the compression makes it impossible for the HDF5 library
! to exactly map the data to the disk location.  For more information,
! check NetCDF official website: www.unidata.ucar.edu/software/netcdf.
!
! NC_SHUFFLE   Shuffle filter integer flag. If non-zero, turn on shuffle
!                filter.
!
! NC_DEFLATE   Deflate filter integer flag, If non-zero, turn on deflate
!                filter at the level specified by the NC_DLEVEL parameter.
!
! NC_DLEVEL    Deflate filter level parameter (integer). If NC_DEFLATE is
!                non-zero, set the deflate level to this value. Must be
!                between 0 and 9.
!
!------------------------------------------------------------------------------
! Input/output NetCDF file names (string with a maximum of 256 characters).
!------------------------------------------------------------------------------
!
! Input file names:
!
!  GRDNAME     Input grid file name.
!
!  ININAME     Input nonlinear initial conditions file name. It can be a
!                re-start file.
!
!  ITLNAME     Input tangent linear model initial conditions file name.
!
!  IRPNAME     Input representer model initial conditions file name.
!
!  IADNAME     Input adjoint model initial conditions file name.
!
!  FWDNAME     Input forward solution fields file name.
!
!  ADSNAME     Input adjoint sensitivity functional file name.
!
!
! Nesting grids connectivity data:
!
!  NGCNAME     Input nested grids contact points information file name. This
!                NetCDF file is currently generated using script:
!
!                matlab/grid/contact.m
!
!                from the ROMS Matlab repository.  The nesting information
!                is not trivial and this Matlab scripts is quite complex. See
!
!                https://www.myroms.org/wiki/index.php/Nested_Grids
!                https://www.myroms.org/wiki/index.php/Grid_Processing_Scripts
!
!                for more information.
!
!
! Input lateral boundary conditions and climatology file names:
!
! BRYNAME      Input open boundary data file name(s) per nested grid.
!
! CLMNAME      Input climatology fields file name(s) per nested grid
!
!  The USER has the option to split input data time records into several
!  NetCDF files, as many as required. If so, use a single line per entry
!  with a vertical bar (|) symbol after each entry, except the last one:
!
!    BRYNAME == my_bry_year1.nc |
!               my_bry_year2.nc
!
!    CLMNAME == my_clm_year1.nc |
!               my_clm_year2.nc
!
!
! Input nudging coefficients file name:
!
! NUDNAME      Input nudging coefficients file name.
!
!
! Input Sources/Sinks forcing file name:
!
! SSFNAME      River runoff data. This file is now separated from the
!                regular forcing files to allow manipulations over nested
!                grids.  A particular nesting grid may or may not have
!                Sources/Sinks forcing.
!
!                For example, in an application with 3 nested grids but
!                with river forcing in grids 1 and 3 we would have:
!
!                    LuvSrc == T F T
!                LtracerSrc == 2*T 2*F 2*T
!
!                   SSFNAME == my_rivers_grid1.nc \
!                              my_rivers_grid2.nc \
!                              my_rivers_grid3.nc
!
!                Here, "my_rivers_grid2.nc" is a dummy name that will never
!                be processed in ROMS because of the logical switches are
!                FALSE the second grid.
!
! Input/output tidal forcing file name:
!
! TIDENAME     Tidal constituents period, phase, elevation, and current data.
!                This data is needed when SSH_TIDES, UV_TIDES, or both are
!                activated to force tides at the open boundaries. Currently,
!                in nested applications, the tidal forcing is used in the
!                coarser/larger grid (ng=1). If AVERAGES_DETIDE is activated,
!                several least-squares time-accumulated harmonic variables
!                are written into this NetCDF file to facilitate restart for
!                during long fitting simulations.
!
! Input forcing file(s) name:
!
! NFFILES      Number of unique forcing files per nested grid.
!
! FRCNAME      Input forcing fields file name per nested grid.
!
!  The USER has the option to enter several file names for forcing fields
!  and/or split input data time records for each nested grid. For example,
!  the USER may have different files for wind products, heat fluxes, 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. It is also possible to
!  split input data time records into several NetCDF files.
!
!  Use a single line per entry with a continuation (\) or vertical bar (|)
!  symbol after each entry, except the last one:
!
!    NFFILES == 6                          ! number of unique forcing files
!
!    FRCNAME == my_lwrad_year1.nc |        ! net longwave radiation flux
!               my_lwrad_year2.nc \
!               my_swrad_year1.nc |        ! solar shortwave radiation flux
!               my_swrad_year2.nc \
!               my_winds_year1.nc |        ! surface winds
!               my_winds_year2.nc \
!               my_Pair_year1.nc  |        ! surface air pressure
!               my_Pair_year2.nc  \
!               my_Qair_year1.nc  |        ! surface air relative humidity
!               my_Qair_year2.nc  \
!               my_Tair_year1.nc  |        ! surface air temperature
!               my_Tair_year2.nc
!
!
! Output file names:
!
! DAINAME      Output data assimilation next cycle initial conditions (4D-Var
!                analysis) or restart (Ensemble Kalman Filter, EnKF) file name.
! GSTNAME      Output GST analysis re-start file name.
! RSTNAME      Output re-start file name.
! HISNAME      Output history file name.
! QCKNAME      Output quicksave file name.
! TLFNAME      Output impulse forcing for tangent linear (TLM and RPM) models.
! TLMNAME      Output tangent linear file name.
! ADJNAME      Output adjoint file name.
! AVGNAME      Output averages file name.
! HARNAME      Output least-squares detiding harmonics file name.
! DIANAME      Output diagnostics file name.
! STANAME      Output stations file name.
! FLTNAME      Output floats file name.
!
!------------------------------------------------------------------------------
! Input ASCII parameters file names.
!------------------------------------------------------------------------------
!
! APARNAM      Input assimilation parameters file name.
! SPOSNAM      Input stations positions file name.
! FPOSNAM      Input initial drifters positions file name.
! BPARNAM      Input biological parameters file name.
! SPARNAM      Input sediment transport parameters file name.
! USRNAME      USER's input generic file name.
!