!
!  ROMS/TOMS Standard Input parameters.
!
!svn $Id: ocean.in 8 2007-02-06 19:00:29Z arango $
!========================================================= Hernan G. Arango ===
!  Copyright (c) 2002-2007 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.  All comments will ignored during   !
! reading.  Blank lines are also allowed and ignored. Continuation lines in   !
! a parameter specification are allowed and must be 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 a 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 and/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 extremely important.  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.              !
!                                                                             !
!==============================================================================
!

! Application title.

       TITLE = ROMS 3.6 - S800 - Coupled ROMS-CICE

! C-preprocessing Flag.

    MyAppCPP = SA4

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

  VARNAME = /cluster/home/pduarte/models2/metroms/apps/common/include/varinfo.dat

! Number of nested grids.

      Ngrids =  1

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

          Lm == 694       ! Number of I-direction INTERIOR RHO-points
          Mm == 452      ! Number of J-direction INTERIOR RHO-points
           N == 35       ! Number of vertical levels

        Nbed =  0             ! Number of sediment bed layers

         NAT =  2             ! Number of active tracers (usually, 2)
         NPT =  0             ! Number of inactive passive tracers
         NCS =  0             ! Number of cohesive (mud) sediment tracers
         NNS =  0             ! Number of non-cohesive (sand) sediment tracers

! Domain decomposition parameters for serial, distributed-memory or
! shared-memory configurations used to determine tile horizontal range
! indices (Istr,Iend) and (Jstr,Jend), [1:Ngrids].

      NtileI ==  24                               ! I-direction partition
      NtileJ ==  16                          ! 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
!   Cla        Clamped
!   Clo        Closed
!   Fla        Flather                                _____N_____     j=Mm
!   Gra        Gradient                              |     4     |
!   Nes        Nested                                |           |
!   Nud        Nudging                             1 W           E 3
!   Per        Periodic                              |           |
!   Rad        Radiation                             |_____S_____|
!   Red        Reduced Physics                             2          j=1
!                                                   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) ==   Cha     Cha     Cha     Cha         ! free-surface
   LBC(isUbar) ==   Fla     Fla     Fla     Fla         ! 2D U-momentum
   LBC(isVbar) ==   Fla     Fla     Fla     Fla         ! 2D V-momentum
   LBC(isUvel) ==   RadNud     RadNud     RadNud     RadNud         ! 3D U-momentum
   LBC(isVvel) ==   RadNud     RadNud     RadNud     RadNud         ! 3D V-momentum
   LBC(isMtke) ==   Gra     Gra     Gra     Gra         ! mixing TKE

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

! Time-Stepping parameters.

      NTIMES == 2484000.0
          DT == 120 ! 120
     NDTFAST == 60 !

! 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 == 1
   LcycleRST == T
        NRST == 120 !720 !2160 !10800 !2160 !10800
        NSTA == 10800
        NFLT == 299970
       NINFO == 1

! Output history, average, diagnostic files parameters.

     LDEFOUT == T
        NHIS == 10800 !64800
     NDEFHIS == 10800 !64800
      NTSAVG == 0
        NAVG == 720 ! 2160
     NDEFAVG == 720 !10800
      NTSDIA == 1
        NDIA == 10800
!     NDIA == 720        
     NDEFDIA == 0

! Output tangent linear and adjoint models parameters.

   LcycleTLM == F
        NTLM == 72
     NDEFTLM == 0
   LcycleADJ == F
        NADJ == 72
     NDEFADJ == 0

! Output check pointing GST restart parameters.

     LrstGST =  F                               ! GST restart switch
  MaxIterGST =  500                             ! maximun number of iterations
        NGST =  10                              ! check pointing interval

! Relative accuracy of the Ritz values computed in the GST analysis.

    Ritz_tol =  1.0d-15

! Harmonic/biharmonic horizontal diffusion of tracer: [1:NAT+NPT,Ngrids].

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

! Harmononic/biharmonic, horizontal viscosity coefficient: [Ngrids].

       VISC2 == 0.0d0                           ! m2/s
       VISC4 == 1.0d+12                         ! m4/s

! Vertical mixing coefficients for active tracers: [1:NAT+NPT,Ngrids]

     AKT_BAK == 1.0d-6 1.0d-6                   ! m2/s

! Vertical mixing coefficient for momentum: [Ngrids].

     AKV_BAK == 1.0d-5                     ! m2/s

! Turbulent closure parameters.

     AKK_BAK == 5.0d-6                          ! m2/s
     AKP_BAK == 5.0d-6                          ! m2/s
      TKENU2 == 0.0d0                           ! m2/s
      TKENU4 == 0.0d0                           ! m4/s

! Generic length-scale turbulence closure parameters.

       GLS_P == 0.0d0                           ! Mellor-Yamada 2.5
       GLS_M == 1.0d0
       GLS_N == 1.0d0
    GLS_Kmin == 5.0d-6
    GLS_Pmin == 5.0d-6

    GLS_CMU0 == 0.5544d0
      GLS_C1 == 0.9d0
      GLS_C2 == 0.5d0
     GLS_C3M == 0.9d0
     GLS_C3P == 0.9d0
    GLS_SIGK == 1.96d0
    GLS_SIGP == 1.96d0

! Constants used in momentum stress computation.
                                     
        RDRG == 0.0d-04                    ! m/s
       RDRG2 == 3.0d-03                    ! nondimensional
         Zob == 0.0d0                      ! m
         Zos == 0.02d0                     ! m

! Bulk flux measurement heights for atmospheric variables
      BLK_ZQ == 2.0d0                     ! m
      BLK_ZT == 2.0d0                     ! m
      BLK_ZW == 10.0d0                     ! m

! Various parameters.

       WTYPE == 1
     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 == 2                          ! stretching function

! Vertical S-coordinates parameters, [1:Ngrids].

     THETA_S == 8.0d0                      ! 0 < THETA_S < 20
     THETA_B == 0.1d0                      ! 0 < THETA_B < 1
      TCLINE == 20.0d0                     ! m

! Mean Density and Brunt-Vaisala frequency.

        RHO0 =  1025.0d0                   ! kg/m3
     BVF_BAK =  1.0d-4                     ! 1/s2

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

      DSTART =  21550.0d0                  ! Use start time equal to tidal reference date
   TIDE_START = 21550.0d0                  ! Tides reference
    TIME_REF =  19480101.00                    ! yyyymmdd.dd

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

       TNUDG == 5.0d0 5.0d0                ! days
       ZNUDG == 0.0d0                      ! days
      M2NUDG == 5.0d0                      ! days
      M3NUDG == 15.0d0                      ! days

! Factor between passive (outflow) and active (inflow) open boundary
! conditions, [1:Ngrids]. If OBCFAC > 1, nudging on inflow is stronger
! than on outflow (recommended).

      OBCFAC == 360.0d0                    ! 120 .0d0 nondimensional

! Width of nudgingzone.
      
      IWRK == 50                         ! 15 no. of gridpoints

! Logical switches (TRUE/FALSE) to specify which variables to process for
! tracers climatology: [1:NAT+NPT,Ngrids]. See glossary below for details.

  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

! Linear equation of State parameters:

          R0 == 1027.0d0                   ! kg/m3
          T0 == 10.0d0                     ! Celsius
          S0 == 35.0d0                     ! PSU
       TCOEF == 1.7d-4                     ! 1/Celsius
       SCOEF == 7.6d-4                     ! 1/PSU

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

      GAMMA2 ==  1.0d0

! Starting (DstrS) and ending (DendS) day for adjoint sensitivity forcing.
! DstrS must be less or equal to DendS. If both values are zero, their
! values are reset internally to the full range of the adjoint integration.

       DstrS == 0.0d0                      ! starting day
       DendS == 0.0d0                      ! ending day

! Starting and ending vertical levels of the 3D adjoint state variables
! whose sensitivity is required.

       KstrS == 1                          ! starting level
       KendS == 1                          ! ending level

! Logical switches (TRUE/FALSE) to specify the adjoint state variables
! whose sensitivity is required.

Lstate(isFsur) == F                        ! free-surface
Lstate(isUbar) == F                        ! 2D U-momentum
Lstate(isVbar) == F                        ! 2D V-momentum
Lstate(isUvel) == F                        ! 3D U-momentum
Lstate(isVvel) == F                        ! 3D V-momentum

! Logical switches (TRUE/FALSE) to specify the adjoint state tracer
! variables whose sensitivity is required (NT values are expected).

Lstate(isTvar) == F F                      ! tracers

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

    SO_decay == 2.0d0                      ! days

! Logical switches (TRUE/FALSE) to specify the state surface forcing
! variable whose stochastic optimals is required.

SOstate(isUstr) == T                       ! surface u-stress
SOstate(isVstr) == T                       ! surface v-stress

! Logical switches (TRUE/FALSE) to specify the surface tracer forcing
! variable whose stochastic optimals is required (NT values are expected).

SOstate(isTsur) == F F                     ! surface tracer flux

! Stochastic optimals surface forcing standard deviation for
! dimensionalization.

SO_sdev(isUstr) == 1.0d0                   ! surface u-stress
SO_sdev(isVstr) == 1.0d0                   ! surface v-stress
SO_sdev(isTsur) == 1.0d0 1.0d0             ! NT surface tracer flux

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

  LtracerSrc == F F                        ! mitya temperature, salinity, inert

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

Hout(idUvel) == T                          ! 3D U-velocity
Hout(idVvel) == T                          ! 3D V-velocity
Hout(idWvel) == T                          ! 3D W-velocity
Hout(idOvel) == T                          ! omega vertical velocity
Hout(idUbar) == T                          ! 2D U-velocity
Hout(idVbar) == T                          ! 2D V-velocity
Hout(idFsur) == T                          ! free-surface

Hout(idTvar) == T T                        ! temperature and salinity

Hout(idUsms) == T                          ! surface U-stress
Hout(idVsms) == T                          ! surface V-stress
Hout(idUbms) == F                          ! bottom U-stress
Hout(idVbms) == F                          ! bottom V-stress

Hout(idUbrs) == F                          ! bottom U-current stress
Hout(idVbrs) == F                          ! bottom V-current stress
Hout(idUbws) == F                          ! bottom U-wave stress
Hout(idVbws) == F                          ! bottom V-wave stress
Hout(idUbcs) == F                          ! bottom max wave-current U-stress
Hout(idVbcs) == F                          ! bottom max wave-current V-stress

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

Hout(idTsur) == T T                        ! surface net heat and salt flux
Hout(idLhea) == F                          ! latent heat flux
Hout(idShea) == F                          ! sensible heat flux
Hout(idLrad) == F                          ! longwave radiation flux
Hout(idSrad) == T                          ! shortwave radiation flux
Hout(idevap) == F                          ! evaporation rate
Hout(idrain) == F                          ! precipitation rate

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

Hout(idSSSf) == F                          ! sea surface salinity corr. flux


! Logical switches (TRUE/FALSE) to activate writing of extra inert passive
! tracers other than biological and sediment tracers. An inert passive tracer
! is one that it is only advected and diffused. Other processes are ignored.
! These tracers include, for example, dyes, pollutants, oil spills, etc.
! NPT values are expected. However, these switches can be activated using
! compact parameter specification.

 Hout(inert) == F                          ! inert passive tracers

! Logical switches (TRUE/FALSE) to activate writing of exposed sediment
! layer properties into HISTORY output file.  Currently, MBOTP properties
! are expected for the bottom boundary layer and/or sediment models:
!
!   Hout(idBott(isd50)),  isd50 = 1        ! mean grain diameter
!   Hout(idBott(idens)),  idens = 2        ! mean grain density
!   Hout(idBott(iwsed)),  iwsed = 3        ! mean settling velocity
!   Hout(idBott(itauc)),  itauc = 4        ! critical erosion stress
!   Hout(idBott(irlen)),  irlen = 5        ! ripple length
!   Hout(idBott(irhgt)),  irhgt = 6        ! ripple height
!   Hout(idBott(ibwav)),  ibwav = 7        ! wave excursion amplitude
!   Hout(idBott(izdef)),  izdef = 8        ! default bottom roughness
!   Hout(idBott(izapp)),  izapp = 9        ! apparent bottom roughness
!   Hout(idBott(izNik)),  izNik = 10       ! Nikuradse bottom roughness
!   Hout(idBott(izbio)),  izbio = 11       ! biological bottom roughness
!   Hout(idBott(izbfm)),  izbfm = 12       ! bed form bottom roughness
!   Hout(idBott(izbld)),  izbld = 13       ! bed load bottom roughness
!   Hout(idBott(izwbl)),  izwbl = 14       ! wave bottom roughness
!   Hout(idBott(iactv)),  iactv = 15       ! active layer thickness
!   Hout(idBott(ishgt)),  ishgt = 16       ! saltation height
!
!                                 1 1 1 1 1 1 1
!               1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6

Hout(idBott) == 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                          ! 3D U-velocity
Aout(idVvel) == T                          ! 3D V-velocity
Aout(idWvel) == T                          ! 3D W-velocity
Aout(idOvel) == T                          ! omega vertical velocity
Aout(idUbar) == T                          ! 2D U-velocity
Aout(idVbar) == T                          ! 2D V-velocity
Aout(idFsur) == T                          ! free-surface

Aout(idTvar) == T T                        ! temperature and salinity

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

Aout(idW2xx) == F                          ! 2D radiation stress, Sxx component
Aout(idW2xy) == F                          ! 2D radiation stress, Sxy component
Aout(idW2yy) == F                          ! 2D radiation stress, Syy component
Aout(idU2rs) == F                          ! 2D radiation U-stress
Aout(idV2rs) == F                          ! 2D radiation V-stress
Aout(idU2Sd) == F                          ! 2D U-Stokes velocity
Aout(idV2Sd) == F                          ! 2D V-Stokes velocity

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

Aout(idTsur) == T T                        ! surface net heat and salt flux
Aout(idLhea) == F                          ! latent heat flux
Aout(idShea) == F                          ! sensible heat flux
Aout(idLrad) == F                          ! longwave radiation flux
Aout(idSrad) == F                          ! shortwave radiation flux
Aout(idevap) == F                          ! evaporation rate
Aout(idrain) == F                          ! precipitation rate

Aout(idPair) == F                          ! Pair- surface air pressure

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

Aout(id2dRV) == T                          ! 2D relative vorticity
Aout(id3dRV) == T                          ! 3D relative vorticity
Aout(id2dPV) == T                          ! 2D potential vorticity
Aout(id3dPV) == T                          ! 3D potential vorticity

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

Aout(idTrcD) == F F                        ! detided temperature and salinity

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

Aout(idTTav) == F F                        ! quadratic <t*t> T/S terms
Aout(idUTav) == F F                        ! quadratic <u*t> T/S terms
Aout(idVTav) == F F                        ! quadratic <v*t> T/S terms
Aout(iHUTav) == F F                        ! T/S volume flux, <Huon*t>
Aout(iHVTav) == F F                        ! T/S 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) == F                          ! 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                          ! acceleration
Dout(M2pgrd) == F                          ! pressure gradient
Dout(M2fcor) == F                          ! Coriolis force
Dout(M2hadv) == F                          ! horizontal total advection
Dout(M2xadv) == F                          ! horizontal XI-advection
Dout(M2yadv) == F                          ! horizontal ETA-advection
Dout(M2hrad) == F                          ! horizontal total radiation stress
Dout(M2hvis) == F                          ! horizontal total viscosity
Dout(M2xvis) == F                          ! horizontal XI-viscosity
Dout(M2yvis) == F                          ! horizontal ETA-viscosity
Dout(M2sstr) == F                          ! surface stress
Dout(M2bstr) == F                          ! 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                          ! acceleration
Dout(M3pgrd) == F                          ! pressure gradient
Dout(M3fcor) == F                          ! Coriolis force
Dout(M3hadv) == F                          ! horizontal total advection
Dout(M3xadv) == F                          ! horizontal XI-advection
Dout(M3yadv) == F                          ! horizontal ETA-advection
Dout(M3vadv) == F                          ! vertical advection
Dout(M3hrad) == F                          ! horizontal total radiation stress
Dout(M3vrad) == F                          ! vertical radiation stress
Dout(M3hvis) == F                          ! horizontal total viscosity
Dout(M3xvis) == F                          ! horizontal XI-viscosity
Dout(M3yvis) == F                          ! horizontal ETA-viscosity
Dout(M3vvis) == F                          ! 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) == F T                        ! time rate of change
Dout(iThadv) == F F                        ! horizontal total advection
Dout(iTxadv) == F F                        ! horizontal XI-advection
Dout(iTyadv) == F F                        ! horizontal ETA-advection
Dout(iTvadv) == F F                        ! vertical advection
Dout(iThdif) == F F                        ! horizontal total diffusion
Dout(iTxdif) == F F                        ! horizontal XI-diffusion
Dout(iTydif) == F F                        ! horizontal ETA-diffusion
Dout(iTsdif) == F F                        ! horizontal S-diffusion
Dout(iTvdif) == F F                        ! vertical diffusion

! Generic User parameters, [1:NUSER].

       NUSER =  0
        USER =  0.d0

! Input NetCDF file names, [1:Ngrids].
     GRDNAME == /cluster/shared/arcticfjord/input_data/s800_cice_processed_a4_mod/arctic4km_grd_svalbard.nc
!     ININAME == /cluster/shared/arcticfjord/input_data/rst/ocean_rst.nc
!     ININAME == /cluster/shared/arcticfjord/input_data/rst/ocean_rst_2014-10-01_with_bgc_Betzy_corr_AW_with_Zoop_test_values.nc
     ININAME == /cluster/shared/arcticfjord/input_data/rst/ocean_rst_2014-10-01_with_bgc_Betzy_corr_AW.nc
     CLMNAME ==  /cluster/shared/arcticfjord/input_data/A4_S4K/clima_2014.nc  |
                 /cluster/shared/arcticfjord/input_data/A4_S4K/clima_2015.nc
!                CLMFILE2 |
!                CLMFILE3 |
!                CLMFILE4
!     BRYNAME == /cluster/shared/arcticfjord/input_data/s800_cice_processed_a4_mod/svalbard_a4_bry_2014.nc  |
!                /cluster/shared/arcticfjord/input_data/s800_cice_processed_a4_mod/svalbard_a4_bry_2015.nc 
!      BRYNAME == /cluster/shared/arcticfjord/OBC/data/bry_2015.nc
     BRYNAME == /cluster/shared/arcticfjord/OBC/data/bry_2014.nc |
                /cluster/shared/arcticfjord/OBC/data/bry_2015.nc
!      BRYNAME == /cluster/shared/arcticfjord/OBC/data/bry_2014_with_Zoop_test.nc |
!                 /cluster/shared/arcticfjord/OBC/data/bry_2015_with_Zoop_test.nc
!                BRYFILE2 |
!                BRYFILE3 |
!                BRYFILE4 


! Input climatology nudging coefficients file name.

     NUDNAME ==  /cluster/shared/arcticfjord/input_data/s800_cice_processed/ocean_nud.nc

! Input forcing NetCDF file name(s).  The USER has the option to enter
! several files names per each nested grid.  For example, the USER may
! have a different files for wind products, heat fluxes, rivers, tides,
! etc.  The model will scan the file list and will read the needed data
! from the first file in the list containing the forcing field. Therefore,
! the order of the file names is very important.  If multiple forcing
! files per grid, enter first all the file names for grid 1, then grid 2,
! and so on.  Use a single line per entry with a continuation (\) symbol
! at the each entry, except the last one.

    NFFILES == 5                         ! number of forcing files

    FRCNAME ==  /cluster/shared/arcticfjord/input_data/s800_cice_processed_a4_mod/era5_a4_svalbard_2014.nc |
                /cluster/shared/arcticfjord/input_data/s800_cice_processed_a4_mod/era5_a4_svalbard_2015.nc \
!                FORCEFILE3 |
!                FORCEFILE4 |
!                FORCEFILE5 |
!                FORCEFILE6 \
                /cluster/shared/arcticfjord/input_data/s800_cice_processed_a4_mod/era5_a4_svalbard_prec_2014.nc |
                /cluster/shared/arcticfjord/input_data/s800_cice_processed_a4_mod/era5_a4_svalbard_prec_2015.nc \
!                FORCEFILE9 |
!                FORCEFIL10 |
!                FORCEFIL11 |
!                FORCEFIL12 \
!                /cluster/shared/arcticfjord/input_data/s800_cice_processed/svalbard_800m_river.nc \
                /cluster/shared/arcticfjord/input_data/s800_cice_processed_a4_mod/tide_svalbard.nc  
 

                
!                /cluster/work/users/mitya/tmproms/run/S800/AN_1998_unlim.nc |
!                /cluster/work/users/mitya/tmproms/run/S800/AN_1999_unlim.nc |
!                /cluster/work/users/mitya/tmproms/run/S800/AN_2000_unlim.nc |
!                /cluster/work/users/mitya/tmproms/run/S800/AN_2001_unlim.nc  \
!                /cluster/work/users/mitya/tmproms/run/S800/FC_2001_unlim.nc \
!                /cluster/work/users/mitya/tmproms/run/S800/FC_1998_unlim.nc |
!                /cluster/work/users/mitya/tmproms/run/S800/FC_1999_unlim.nc |
!                /cluster/work/users/mitya/tmproms/run/S800/FC_2000_unlim.nc |
!                /cluster/work/users/mitya/tmproms/run/S800/FC_2001_unlim.nc \
!                RIVERFILE



!    FRCNAME ==  /cluster/work/users/mitya/tmproms/run/S800/tide.nc \
!                /cluster/work/users/mitya/tmproms/run/S800/AN_2001_unlim.nc  \
!                /cluster/work/users/mitya/tmproms/run/S800/FC_2001_unlim.nc  \
!                /cluster/work/users/mitya/tmproms/run/S800/AN_2002_unlim.nc  \
!                /cluster/work/users/mitya/tmproms/run/S800/FC_2002_unlim.nc  \
!                RIVERFILE
!
!                /work/hdj002/tmproms/run/arctic-4km_orginal_big/AN_2001_unlim.nc
!                /work/hdj002/tmproms/run/arctic-4km_orginal_big/FC_2001_unlim.nc
!                /work/hdj002/tmproms/run/arctic-4km_orginal_big/AN_2002_unlim.nc
!                /work/hdj002/tmproms/run/arctic-4km_orginal_big/FC_2002_unlim.nc


! Output NetCDF file names, [1:Ngrids].
     RSTNAME == /cluster/work/users/pduarte/tmproms/run/SA4_for_tests/ocean_rst.nc
     HISNAME == /cluster/shared/arcticfjord/A4_S4K/ocean_his.nc
     AVGNAME == /cluster/work/users/pduarte/tmproms/run/SA4_for_tests/ocean_avg.nc
     STANAME == /cluster/work/users/pduarte/tmproms/run/SA4_for_tests/ocean_sta.nc
     DIANAME == /cluster/work/users/pduarte/tmproms/run/SA4_for_tests/ocean_dia.nc

! Input ASCII parameter filenames.
     BPARNAM = /cluster/home/pduarte/models/metroms/apps/common/include/ecodynamo.in
!     SPOSNAM =  /prod/forecast/sea/ROMS/trunk/Apps/Arctic-20km/Include/stations_arctic20km.in
!     IPARNAM =  /cluster/work/users/mitya/tmproms/run/S800/ice.in

!
!  GLOSSARY:
!  =========
!
!------------------------------------------------------------------------------
! Application title (string with a maximum of eighty characters) and
! C-preprocessing flag.
!------------------------------------------------------------------------------
!
!  TITLE       Application title.
!
!  MyAppCPP    Application C-preprocession option.
!
!------------------------------------------------------------------------------
! Variable information file name (string with a maximum of eighty characters).
!------------------------------------------------------------------------------
!
!  VARNAME     Input/Output variable information file name.  This file need to
!              be processed first so all information arrays and indices can be
!              initialized properly in "mod_ncparam.F".
!
!------------------------------------------------------------------------------
! Grid dimension parameters.
!------------------------------------------------------------------------------+!
! These parameters are very important since it 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 posible 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 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 or greater than one.
!
!  NtileJ      Number of domain partitions in the J-direction (ETA-coordinate).
!              It must be equal 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.
!
!------------------------------------------------------------------------------
! Time-Stepping parameters.
!------------------------------------------------------------------------------
!
!  NTIMES      Total number time-steps in current run.  If 3D configuration,
!              NTIMES is the total of baroclinic time-steps.  If only 2D
!              configuration, NTIMES is the total of barotropic time-steps.
!
!  DT          Time-Step size in seconds.  If 3D configuration, DT is the
!              size of baroclinic time-step.  If only 2D configuration, DT
!              is the size of the barotropic time-step.
!
!  NDTFAST     Number of barotropic time-steps between each baroclinic time
!              step. If only 2D configuration, NDTFAST should be unity since
!              there is not need to splitting time-stepping.
!
!------------------------------------------------------------------------------
! 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 in 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 a-priori analysis to guide the selection of NCV
!  relative to NEV.  The only formal requirement is that NCV > NEV. However
!  in optimal perturbations, it is recommended to have NCV 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 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 (said 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 files.  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
!              re-start file.  If TRUE,  only the latest two re-start time
!              records are maintained.  If FALSE, all re-start fields are
!              saved every NRST time-steps without recycling.  The re-start
!              fields are written at all levels in double precision.
!
!  NRST        Number of time-steps between writing of re-start fields.
!
!  NSTA        Number of time-steps between writing data into stations file.
!              Station data is written at all levels.
!
!  NFLT        Number of time-steps between writing data into floats file.
!
!  NINFO       Number of time-steps between print of single line information
!              to standard output.  If also determines the interval between
!              computation of global energy diagnostics.
!
!------------------------------------------------------------------------------
!  Output history and average files parameters.
!------------------------------------------------------------------------------
!
!  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, average, diagnostic and
!              station files are created during the initialization stage.
!              If FALSE and applicable, data is appended to an existing
!              history, average, diagnostic and station files.  See also
!              parameters NDEFHIS, NDEFAVG and NDEFDIA below.
!
!  NHIS        Number of time-steps between writing fields into history file.
!
!  NDEFHIS     Number of time-steps between the creation of new history file.
!              If NDEFHIS=0, the model will only process one history file.
!              This feature is useful for long simulations when history files
!              get too large; it creates a new file every NDEFHIS time-steps.
!
!  NTSAVG      Starting time-step for the accumulation of output time-averaged
!              data.
!
!  NAVG        Number of time-steps between writing time-averaged data
!              into averages file.  Averaged date is written for all fields.
!
!  NDEFAVG     Number of time-steps between the creation of new average
!              file.  If NDEFAVG=0, the model will only process one average
!              file.  This feature is useful for long simulations when
!              average files get too large; it creates a new file every
!              NDEFAVG time-steps.
!
!  NTSDIA      Starting time-step for the accumulation of output time-averaged
!              diagnostics data.
!
!  NDIA        Number of time-steps between writing time-averaged diagnostics
!              data into diagnostics file.  Averaged date is written for all
!              fields.
!
!  NDEFDIA     Number of time-steps 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 diagnostics files get too large; it creates a new file
!              every NDEFDIA time-steps.
!
!------------------------------------------------------------------------------
!  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 time-steps without recycling.
!
!  NTLM        Number of time-steps between writing fields into tangent linear
!              model file.
!
!  NDEFTLM     Number of time-steps 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 long simulations when
!              output NetCDF files get too large; it creates a new file every
!              NDEFTLM time-steps.
!
!  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 re saved
!              every NADJ time-steps without recycling.
!
!  NADJ        Number of time-steps between writing fields into adjoint model
!              file.
!
!  NDEFADJ     Number of time-steps between the creation of new adjoint file.
!              If NDEFADJ=0, the model will only process one adjoint file.
!              This feature is useful for long simulations when output NetCDF
!              files get too large; it creates a new file every NDEFADJ
!              time-steps.
!
!------------------------------------------------------------------------------
!  Generalized Stability Theory (GST) analysis parameters.
!------------------------------------------------------------------------------
!
!  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 check pointing 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 check pointing data at regular intervals so there
!              is a mechanism to recover from an unexpected interruption
!              in this very expensive 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.
!------------------------------------------------------------------------------
!
!  TNU2        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        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.
!
!------------------------------------------------------------------------------
! Harmonic/biharmonic horizontal viscosity coefficients.
!------------------------------------------------------------------------------
!
!  VISC2       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       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.
!
!------------------------------------------------------------------------------
! Vertical mixing coefficients for active tracers.
!------------------------------------------------------------------------------
!
!  AKT_BAK     Background vertical mixing coefficient (m2/s) for active
!              (NAT) and inert (NPT) tracer variables.
!
!------------------------------------------------------------------------------
! Vertical mixing coefficient for momentum.
!------------------------------------------------------------------------------
!
!  AKV_BAK     Background vertical mixing coefficient (m2/s) for momentum.
!
!------------------------------------------------------------------------------
! 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 (non-dimensional).
!
!  GLS_M       Turbulent kinetic energy exponent (non-dimensional).
!
!  GLS_N       Turbulent length scale exponent (non-dimensional).
!
!  GLS_Kmin    Minimum value of specific turbulent kinetic energy
!
!  GLS_Pmin    Minimum Value of dissipation.
!
! Closure independent constraint parameters (non-dimensional):
!
!  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 (non-dimensional) for turbulent
!              kinetic energy diffusivity.
!
!  GLS_SIGP    Constant Schmidt number (non-dimensional) for turbulent
!              generic statistical field, "psi".
!
! Suggested values for various parameterizations:
!
!              MY2.5         K-epsilon    K-omega      K-omega      K-tao
!
!      GLS_P = 0.d0          3.0d0       -1.0d0       -1.0d0       -3.0d0
!      GLS_M = 1.d0          1.5d0        0.5d0        0.5d0        0.5d0
!      GLS_N = 1.d0         -1.0d0       -1.0d0       -1.0d0        1.0d0
!   GLS_Kmin = 5.0d-6        7.6d-6       7.6d-6       7.6d-6       7.6d-6
!   GLS_Pmin = 5.0d-6        1.0d-12      1.0d-12      1.0d-12      1.0d-12
!
!   GLS_CMU0 = 0.5544d0      0.5477d0     0.5477d0     0.5477d0     0.5477d0
!     GLS_C1 = 0.9d0         1.44d0       0.555d0      0.52d0       0.173d0
!     GLS_C2 = 0.5d0         1.92d0       0.833d0      0.8d0        0.225d0
!    GLS_C3M = 0.9d0        -0.4d0       -0.6d0       -0.6d0        0.0d0
!    GLS_C3P = 0.9d0         1.0d0        1.0d0        1.0d0        0.0d0
!   GLS_SIGK = 1.96d0        1.0d0        2.0d0        2.0d0        1.46d0
!   GLS_SIGP = 1.96d0        1.30d0       2.0d0        2.0d0       10.8d0
!
!------------------------------------------------------------------------------
! 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).
!
!------------------------------------------------------------------------------
! Jerlow Water type.
!------------------------------------------------------------------------------
!
!  WTYPE       Jerlov water type: an integer value from 1 to 5.
!
!------------------------------------------------------------------------------
! 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.
!------------------------------------------------------------------------------
!
!  THETA_S     S-coordinate surface control parameter, [0 < theta_s < 20].
!
!  THETA_B     S-coordinate bottom  control parameter, [0 < theta_b < 1].
!
!  TCLINE      Width (m) of surface or bottom boundary layer in which
!              higher vertical resolution is required during stretching.
!
!              WARNING:  Users need to experiment with these parameters. We
!                        have found out that the model goes unstable with
!                        high values of THETA_S.  In steep and very tall
!                        topography, it is recommended to use THETA_S < 3.0.
!
!------------------------------------------------------------------------------
! 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, 0:0:0 4713 BCE
!              modified Julian Day = 1  for  May 24, 0:0:0 1968  CE GMT
!
!              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'
!
!              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 0000-01-01 00:00:00'
!
!              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 0000-01-01 00:00:00'
!
!              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'
!
!------------------------------------------------------------------------------
! 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    PSU
!                               TCOEF = 1.7d-4  1/Celsius
!                               SCOEF = 7.6d-4  1/PSU
!
!  R0          Background density value (Kg/m3) used in Linear Equation of
!              State.
!
!  T0          Background potential temperature (Celsius) constant.
!
!  S0          Background salinity (PSU) 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).
!
!------------------------------------------------------------------------------
!  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 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(isTvar):   Traces (NT values expected)
!
!------------------------------------------------------------------------------
!  Stochastic optimals parameters.
!------------------------------------------------------------------------------
!
!  SO_decay    Stochastic optimals time decorrelation scale (days) assumed
!                for red noise processes.
!
!  SOstate     Logical switches (TRUE/FALSE) to specify the state surface
!                forcing variable whose stochastic optimals is required.
!
!                SOstate(isustr):  surface u-stress
!                SOstate(isvstr):  surface v-stress
!                SOstate(isTsur):  surface tracer flux (NT values expected)
!
!  SO_sdev     Stochastic optimals surface forcing standard deviation for
!                dimensionalization.
!
!                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 fields into HISTORY file.
!------------------------------------------------------------------------------
!
!  Hout(idUvel)  Write out 3D U-velocity component.
!  Hout(idVvel)  Write out 3D V-velocity component.
!  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(idFsur)  Write out free-surface.
!
!  Hout(idTvar)  Write out active (NAT) tracers: temperature and salinity.
!
!  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(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(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.
!
!------------------------------------------------------------------------------
! 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] Firt 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.
!
!------------------------------------------------------------------------------
! Input/output NetCDF file names (string with a maximum of eighty characters).
!------------------------------------------------------------------------------
!
!  GRDNAME     Input grid file name.
!  ININAME     Input nonlinear initial conditions file name. It can be a
!                re-start file.
!  IRPNAME     Input representer model initial conditions file name.
!  ITLNAME     Input tangent linear model initial conditions file name.
!  IADNAME     Input adjoint model initial conditions file name.
!  FRCNAME     Input forcing fields file name.
!  CLMNAME     Input climatology fields file name.
!  BRYNAME     Input open boundary data file name.
!  FWDNAME     Input forward solution fields file name.
!  ADSNAME     Input adjoint sensitivity functional file name.
!
!  GSTNAME     Output GST analysis re-start file name.
!  RSTNAME     Output re-start file name.
!  HISNAME     Output history 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.
!  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.
!






!
!  *************** COUPLING ************
!
!
! Logical switch to report verbose information about import/export field
! ranges.

        Lreport = T

! Number of models to couple.

        Nmodels = 2

! Coupled models order label used to process information arrays, [1:Nmodels]
! string values are expected. The order is arbitrary, the indices below are
! ordered from bottom to top grids.
!
!     OrderLabel = ocean \
!                  waves \
!                  atmos \
!                  cice

     OrderLabel = ocean \
                  cice

! Number of parallel threads assigned to each model in the coupled system,
! [1:Nmodels] KEYWORD entries are expected with the order label (OrderLabel)
! in parenthesis. The sum of all entries must be equal to the total number
! of processors.

Nthreads(ocean) = 384
Nthreads(cice) = 96

! Time interval (seconds) between coupling of models, [1:Nmodels] real
! values are expected corresponding to the entries of a lower triangular
! matrix Aij for i>j.  For example, for three model components ordered
! as ocean, waves, and atmos, the time interval is read as:
!
!      Aij     1      2     3
!      i\j   ocean  waves atmos
!  1  ocean    -      -     -          v(1): ocean-waves coupling interval
!  2  waves   v(1)    -     -          v(2): ocean-atmos coupling interval
!  3  atmos   v(2)   v(3)   -          v(3): waves-atmos coupling interval
!
!  TimeInterval = v(1) v(2) v(3)

!   TimeInterval = 60.0d0 10.0d0  10.0d0

TimeInterval = 360

! Coupled model standard input file name, [1:Nmodels] KEYWORD entries are
! expected with the label code in parenthesis.

 INPname(ocean) = /cluster/work/users/pduarte/tmproms/run/SA4_for_tests/roms.in
 INPname(cice)  = /cluster/work/users/pduarte/tmproms/run/SA4/ice_in

! Coupled models variables information file name.
! This file gets copied to the bin dir by the build script

        CPLname = /cluster/shared/arcticfjord/input_data/A4_S4K/coupling.dat

! Export/Import fields: Use the following string codes to set the fields
!                       to export/import for each coupled model.
!
!   Field   Export    Import
!
!   NONE    -         -                 No field to import or export
!   Pair    atmos     ocean             surface air pressure
!   Tair    atmos     ocean             surface air temperature
!   Hair    atmos     ocean             surface air relative humidity
!   cloud   atmos     ocean             cloud fraction
!   SWrad   atmos     ocean             shortwave radiation flux
!   LWrad   atmos     ocean             longwave radiation flux
!   rain    atmos     ocean             rain fall rate
!   Uwind   atmos     ocean, waves      surface U-wind component
!   Vwind   atmos     ocean, waves      surface V-wind component
!   heat    atmos     ocean             surface net heat flux
!   Ustr    atmos     ocean             surface U-momentum stress
!   Vstr    atmos     ocean             surface V-momentum stress
!   SST     ocean     atmos             sea surface temperature
!   bath    ocean     waves             bathymetry
!   SSH     ocean     waves             free-surface
!   Ubar    ocean     waves             vertically integrated U-momentum
!   Vbar    ocean     waves             vertically integrated V-momentum
!   ZO      ocean     waves             bottom roughness
!   Wdir    waves     ocean             wave direction
!   Wamp    waves     ocean             significant wave height
!   Wlen    waves     ocean             average wave length
!   Wptop   waves     ocean             surface wave relative peak period
!   Wpbot   waves     ocean             bottom wave period
!   Wdiss   waves     ocean             wave energy dissipation
!   Wbrk    waves     ocean             percent wave breaking
!   Wubot   waves     ocean             wave bottom orbital velocity
!
! Export fields per model, [1:Nexport(...)] string values are expected per
! coupled model. The string inside parenthesis must be the same as the one
! given in "OrderLabel". If there is no field to export, set
!
!      Nexport(...) = 0
!       Export(...) = NONE

 Nexport(ocean) = 9
 Nexport(cice)  = 11

  Export(ocean) = SST  \
                  SSS  \
                  FRZMLT \
                  u  \
                  v  \
                  SSH  \
                  NO3 \
                  NH4 \
                  SiOH

!  Export(ocean) = SST   \
!                  bath  \
!                  SSH   \
!                  Ubar  \
!                  Vbar

!  Export(waves) = Wdir  \
!                  Wamp  \
!                  Wlen  \
!                  Wptop \
!                  Wpbot
!
!  Export(atmos) = Pair  \
!                  Tair  \
!                  Hair  \
!                  cloud \
!                  SWrad \
!                  LWrad \
!                  rain  \
!                  Uwind \
!                 Vwind

  Export(cice) =  AICE  \
                  freshAI \
                  fsaltAI \
                  fhocnAI \
                  fswthruAI \
                  strocnx \
                  strocny \
                  fNit \
                  fAm \
                  fN001 \
                  fSil


! Import fields per model, [1:Nimport(...)] string values are expected per
! coupled model. If there is no field to import, set
!
!      Nimport(...) = 0
!       Import(...) = NONE

 Nimport(ocean) = 11
 Nimport(cice)  = 9

  Import(ocean) = AICE \
                  freshAI \
                  fsaltAI \
                  fhocnAI \
                  fswthruAI \
                  strocnx \
                  strocny \
                  fNit \
                  fAm \
                  fN001 \
                  fSil


!  Import(waves) = Uwind \
!                  Vwind \
!                  bath  \
!                  SSH   \
!                  Ubar  \
!                  Vbar
!
!  Import(atmos) = SST

  Import(cice) = SST  \
                 SSS  \
                 FRZMLT \
                 u    \
                 v    \
                 SSH \
                 NO3 \
                 NH4 \
                 SiOH

  

!
!  GLOSSARY:
!  =========
!
!------------------------------------------------------------------------------
! Coupled model parameters.
!------------------------------------------------------------------------------
!
! Lreport       Logical switch (T/F) to report verbose information about
!                 import/export field ranges.
!
! Nmodels       Number of models to couple.
!
! OrderLabel    Coupled models label code, [1:Nmodels] string values are
!                 expected. Enter one string per line and use the continuation
!                 backlash for each entry, except last. The order of the
!                 strings determines how information arrays are processed
!                 and DO loops executed. Currently, the following labels
!                 and associated indices are used:
!
!                    ocean =>  Iocean           Ocean model label
!                    waves =>  Iwaves           Wave model label
!                    atmos =>  Iatmos           Atmosphere model label
!
!                 These labels and indices are defined in "mod_coupler.F"
!                 and processed in "inp_par.F" (routine read_CouplePar).
!
!                 Use the same label code in  other KEYWORD entries set
!                 in this input file. It is highly recommended to use
!                 "ocean" first since all coupled models use ROMS framework
!                 to build the program driver.  This allows ROMS to own
!                 the master thread (node 0 in MPI).
!
! Nthreads(...) Number of parallel threads assigned to each model in the
!                 coupled system, [1:Nmodels] KEYWORD entries are expected
!                 with label code in parenthesis:
!
!                 Nthreads(ocean) = ?           Ocean model
!                 Nthreads(waves) = ?           Wave model
!                 Nthreads(atmos) = ?           Atmosphere model
!                 ...
!
!                 The sum of all entries must be equal to the total number
!                 of processors.
!
! TimeInterval  Time interval (seconds) between coupling of models,
!                 [1:Nmodels] real values are expected corresponding to
!                 the entries of a lower triangular matrix Aij for i>j.
!                 For example, for three model components ordered
!                 as ocean, waves, and atmos, the time interval is
!                 assigned as follows:
!
!                     Aij     1      2     3
!                     i\j   ocean  waves atmos  ...
!                 1  ocean    -      -     -
!                 2  waves   v(1)    -     -
!                 3  atmos   v(2)   v(3)   -
!                     ...
!
!                 where:
!
!                   v(1): ocean-waves coupling interval
!                   v(2): ocean-atmos coupling interval
!                   v(3): waves-atmos coupling interval
!                   ...
!
!                 This matrix is read in "inp_par.F" using the following
!                 statements:
!
!                 ic=0
!                 DO j=1,Nmodels
!                   DO i=1,Nmodels
!                     IF (i.gt.j) THEN
!                       ic=ic+1
!                       TimeInterval(i,j)=v(ic)
!                       TimeInterval(j,i)=v(ic)
!                     END IF
!                   END DO
!                 END DO
!
!------------------------------------------------------------------------------
! Coupled models standard input file names.
!------------------------------------------------------------------------------
!
! INPname(...)  Coupled model standard input file names, [1:Nmodels] KEYWORD
!                 entries are expected with the label code in parenthesis:
!
!                 INPname(ocean) = ?            Ocean model
!                 INPname(waves) = ?            Wave model
!                 INPname(atmos) = ?            Atmosphere model
!
! CPL_name      Coupled models variables information file name.
!
!------------------------------------------------------------------------------
! Export/Import fields to process.
!------------------------------------------------------------------------------
!
! Export/Import fields names (abbreviated string codes). Currently, the
! following fields below are processed. However, the list can be expanded
! easly.
!
!               NONE      No import or export field
!               Pair      surface air pressure
!               Tair      surface air temperature
!               Hair      surface air relative humidity
!               cloud     cloud fraction
!               SWrad     shortwave radiation flux
!               LWrad     longwave radiation flux
!               rain      rain fall rate
!               Uwind     surface U-wind component
!               Vwind     surface V-wind component
!               heat      surface net heat flux
!               Ustr      surface U-momentum stress
!               Vstr      surface V-momentum stress
!               SST       sea surface temperature
!               bath      bathymetry
!               SSH       free-surface
!               Ubar      vertically integrated U-momentum
!               Vbar      vertically integrated V-momentum
!               ZO        bottom roughness
!               Wdir      wave direction
!               Wamp      significant wave height
!               Wlen      average wave length
!               Wptop     surface wave relative peak period
!               Wpbot     bottom wave period
!               Wdiss     wave energy dissipation
!               Wbrk      percent wave breaking
!               Wubot     wave bottom orbital velocity
!
!  Nexport(...) Number of export fields per model, [1:Nmodels] KEYWORD
!                 entries are expected with the label code in parenthesis.
!                 Set to zero if no fields to export by a particular model.
!
!                 Nexport(ocean) = ?            Ocean model
!                 Nexport(waves) = ?            Wave model
!                 Nexport(atmos) = ?            Atmosphere model
!
!  Export(...)  Export fields codes per model, Nexport(...) string codes
!                 are expected. If Nexport(...) = 0, set Export = NONE.
!
!  Nimport(...) Number of import fields per model, [1:Nmodels] KEYWORD
!                 entries are expected with the label code in parenthesis.
!                 Set to zero if no fields to import by a particular model.
!
!                 Nimport(ocean) = ?            Ocean model
!                 Nimport(waves) = ?            Wave model
!                 Nimport(atmos) = ?            Atmosphere model
!
!  Import(...)  Import fields codes per model, Nimport(...) string codes
!                 are expected. If Nimport(...) = 0, set Import = NONE.
!





