! ! ROMS/TOMS Standard Input parameters. ! !svn $Id$ !========================================================= Hernan G. Arango === ! Copyright (c) 2002-2013 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 will be 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. ! ! ! ! Multiple NetCDF files are allowed for input field(s). This is useful when ! ! splitting input data (climatology, boundary, forcing) time records into ! ! several files (say monthly, annual, etc). In this case, each multiple file ! ! entry line needs to be ended by the vertical bar (|) symbol. For example: ! ! ! ! NFFILES == 8 ! number of forcing files ! ! ! ! FRCNAME == my_rivers.nc \ ! ! my_tides.nc \ ! ! 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 8 and not 14. There are 8 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 = Wind-Driven Upwelling/Downwelling over a Periodic Channel ! C-preprocessing Flag. MyAppCPP = ROSS ! Input variable information file name. This file needs to be processed ! first so all information arrays can be initialized properly. VARNAME = /nv/hp5/fzhang76/data/RMOS/roms-ice/roms/ROMS/External/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 == 304 ! Number of I-direction INTERIOR RHO-points Mm == 240 ! Number of J-direction INTERIOR RHO-points N == 24 ! 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 == 8 ! 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) == 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) == RadNud RadNud RadNud RadNud ! mixing TKE LBC(isTvar) == RadNud RadNud RadNud RadNud \ ! temperature RadNud RadNud RadNud RadNud ! salinity ! Ice boundary conditions LBC(isAice) == Clo Per Clo Clo ! ice concentration LBC(isHice) == Clo Per Clo Clo ! ice thickness LBC(isHsno) == Clo Per Clo Clo ! snow thickness LBC(isTice) == Clo Per Clo Clo ! ice temperature LBC(isSfwat)== Clo Per Clo Clo ! surface water LBC(isSig11)== Clo Per Clo Clo ! sigma-11 LBC(isSig12)== Clo Per Clo Clo ! sigma-12 LBC(isSig22)== Clo Per Clo Clo ! sigma-22 LBC(isUice) == Clo Per Clo Clo ! ice U-momentum LBC(isVice) == Clo Per Clo Clo ! ice V-momentum ! Adjoint-based algorithms can have different lateral boundary ! conditions keywords. ad_LBC(isFsur) == Clo Clo Clo Clo ! free-surface ad_LBC(isUbar) == Clo Clo Clo Clo ! 2D U-momentum ad_LBC(isVbar) == Clo Clo Clo Clo ! 2D U-momentum ad_LBC(isUvel) == Clo Clo Clo Clo ! 3D U-momentum ad_LBC(isVvel) == Clo Clo Clo Clo ! 3D V-momentum ad_LBC(isMtke) == Clo Clo Clo Clo ! mixing TKE ad_LBC(isTvar) == Clo Clo Clo Clo \ ! temperature Clo Clo Clo 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 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 == 1576800 DT == 200.0d0 NDTFAST == 30 ! Model iteration loops parameters. ERstr = 1 ERend = 1 Nouter = 1 Ninner = 1 Nintervals = 1 ! Number of eigenvalues (NEV) and eigenvectors (NCV) to compute for the ! Lanczos/Arnoldi problem in the Generalized Stability Theory (GST) ! analysis. NCV must be greater than NEV (see documentation below). NEV = 2 ! Number of eigenvalues NCV = 10 ! Number of eigenvectors ! Input/Output parameters. NRREC == 0 LcycleRST == T NRST == 288 NSTA == 1 NFLT == 1 NINFO == 1 ! Output history, average, diagnostic files parameters. ! EDIT LDEFOUT == T NHIS == 1296 NDEFHIS == 0!155520 NTSAVG == 1 NAVG == 1296 NDEFAVG == 0!155520 NTSDIA == 1 NDIA == 72 NDEFDIA == 0 ! Output tangent linear and adjoint models parameters. LcycleTLM == F NTLM == 72 NDEFTLM == 0 LcycleADJ == F NADJ == 72 NDEFADJ == 0 NSFF == 72 NOBC == 72 ! 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 == 2*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 == 5.0d0 ! m2/s VISC4 == 0.0d0 ! m4/s ad_VISC2 == 0.0d0 ! m2/s ad_VISC4 == 0.0d0 ! m4/s ! Vertical mixing coefficients for tracers in nonlinear model and ! basic state scale factor in adjoint-based algorithms: [1:NAT+NPT,Ngrids] AKT_BAK == 1.0d-6 1.0d-6 ! m2/s 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 ad_AKV_fac == 1.0d0 ! nondimensional ! 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 == 3.0d0 ! K-epsilon GLS_M == 1.5d0 GLS_N == -1.0d0 GLS_Kmin == 7.6d-6 GLS_Pmin == 1.0d-12 GLS_CMU0 == 0.5477d0 GLS_C1 == 1.44d0 GLS_C2 == 1.92d0 GLS_C3M == -0.4d0 GLS_C3P == 1.0d0 GLS_SIGK == 1.0d0 GLS_SIGP == 1.30d0 ! Constants used in surface turbulent kinetic energy flux computation. CHARNOK_ALPHA == 1400.0d0 ! Charnok surface roughness ZOS_HSIG_ALPHA == 0.5d0 ! roughness from wave amplitude SZ_ALPHA == 0.25d0 ! roughness from wave dissipation CRGBAN_CW == 100.0d0 ! Craig and Banner wave breaking ! Constants used in momentum stress computation. RDRG == 3.0d-04 ! m/s RDRG2 == 3.0d-03 ! nondimensional Zob == 0.02d0 ! m Zos == 0.02d0 ! m ! Height (m) of atmospheric measurements for Bulk fluxes parameterization. BLK_ZQ == 10.0d0 ! air humidity BLK_ZT == 10.0d0 ! air temperature BLK_ZW == 10.0d0 ! winds ! Minimum depth for wetting and drying. DCRIT == 0.10d0 ! 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 == 4 ! stretching function ! Vertical S-coordinates parameters (see below for details), [1:Ngrids]. THETA_S == 3.0d0 ! surface stretching parameter THETA_B == 0.4d0 ! bottom stretching parameter TCLINE == 200.0d0 ! 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 = 0.0d0 ! days TIDE_START = 0.0d0 ! days TIME_REF = 0.0d0 ! yyyymmdd.dd ! Nudging/relaxation time scales, inverse scales will be computed ! internally, [1:Ngrids]. TNUDG == 2*0.0d0 ! days ZNUDG == 0.0d0 ! days M2NUDG == 0.0d0 ! days M3NUDG == 0.0d0 ! days ! Factor between passive (outflow) and active (inflow) open boundary ! conditions, [1:Ngrids]. If OBCFAC > 1, nudging on inflow is stronger ! than on outflow (recommended). OBCFAC == 0.0d0 ! nondimensional ! Linear equation of State parameters: R0 == 1027.0d0 ! kg/m3 T0 == 14.0d0 ! Celsius S0 == 35.0d0 ! PSU TCOEF == 1.7d-4 ! 1/Celsius SCOEF == 0.0d0 ! 1/PSU ! Slipperiness parameter: 1.0 (free slip) or -1.0 (no slip) GAMMA2 == 1.0d0 ! Logical switches (TRUE/FALSE) to specify which variables to process for ! tracers climatology: [1:NAT+NPT,Ngrids]. See glossary below for details. LtracerCLM == T T ! temperature, salinity, inert ! 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 == T T ! 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(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) == T ! w 3D W-velocity Hout(idOvel) == T ! 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) == T ! bath time-dependent bathymetry Hout(idTvar) == T T ! temp, salt temperature and salinity 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) == F F ! shflux, ssflux surface net heat and salt flux Hout(idLhea) == F ! latent latent heat flux Hout(idShea) == F ! sensible sensible heat flux Hout(idLrad) == F ! lwrad longwave radiation flux Hout(idSrad) == F ! swrad shortwave radiation flux Hout(idEmPf) == F ! EminusP E-P flux Hout(idevap) == F ! evaporation evaporation rate Hout(idrain) == F ! 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. 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 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_stres 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) == T T T T T T T T T 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) == T ! 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) == F ! sustr surface U-stress Aout(idVsms) == F ! 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) == F F ! shflux, ssflux surface net heat and salt flux Aout(idLhea) == F ! latent latent heat flux Aout(idShea) == F ! sensible sensible heat flux Aout(idLrad) == F ! lwrad longwave radiation flux Aout(idSrad) == F ! swrad shortwave radiation flux Aout(idevap) == F ! evaporation evaporation rate Aout(idrain) == F ! rain precipitation rate Aout(idDano) == F ! rho density anomaly Aout(idVvis) == F ! AKv vertical viscosity Aout(idTdif) == F ! AKt vertical T-diffusion Aout(idSdif) == F ! AKs vertical Salinity diffusion Aout(idHsbl) == F ! Hsbl depth of surface boundary layer Aout(idHbbl) == F ! 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) == F ! Huon u-volume flux, Huon Aout(idHVav) == F ! Hvom v-volume flux, Hvom Aout(idUUav) == F ! uu quadratic term Aout(idUVav) == F ! uv quadratic term Aout(idVVav) == F ! vv quadratic term Aout(idU2av) == F ! ubar2 quadratic term Aout(idV2av) == F ! vbar2 quadratic term Aout(idZZav) == F ! zeta2 quadratic term Aout(idTTav) == F F ! temp2, ... quadratic tracer terms Aout(idUTav) == F F ! utemp, ... quadratic tracer terms Aout(idVTav) == F F ! vtemp, ... quadratic tracer terms Aout(iHUTav) == F F ! Huontemp, ... tracer volume flux, Aout(iHVTav) == F F ! Hvomtemp, ... tracer volume flux, ! 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) == T ! ubar_accel, ... acceleration Dout(M2pgrd) == T ! ubar_prsgrd, ... pressure gradient Dout(M2fcor) == T ! ubar_cor, ... Coriolis force Dout(M2hadv) == T ! ubar_hadv, ... horizontal total advection Dout(M2xadv) == T ! ubar_xadv, ... horizontal XI-advection Dout(M2yadv) == T ! ubar_yadv, ... horizontal ETA-advection Dout(M2hrad) == T ! ubar_hrad, ... horizontal total radiation stress Dout(M2hvis) == T ! ubar_hvisc, ... horizontal total viscosity Dout(M2xvis) == T ! ubar_xvisc, ... horizontal XI-viscosity Dout(M2yvis) == T ! ubar_yvisc, ... horizontal ETA-viscosity Dout(M2sstr) == T ! ubar_sstr, ... surface stress Dout(M2bstr) == T ! 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) == T ! u_accel, ... acceleration Dout(M3pgrd) == T ! u_prsgrd, ... pressure gradient Dout(M3fcor) == T ! u_cor, ... Coriolis force Dout(M3hadv) == T ! u_hadv, ... horizontal total advection Dout(M3xadv) == T ! u_xadv, ... horizontal XI-advection Dout(M3yadv) == T ! u_yadv, ... horizontal ETA-advection Dout(M3vadv) == T ! u_vadv, ... vertical advection Dout(M3hrad) == T ! u_hrad, ... horizontal total radiation stress Dout(M3vrad) == T ! u_vrad, ... vertical radiation stress Dout(M3hvis) == T ! u_hvisc, ... horizontal total viscosity Dout(M3xvis) == T ! u_xvisc, ... horizontal XI-viscosity Dout(M3yvis) == T ! u_yvisc, ... horizontal ETA-viscosity Dout(M3vvis) == T ! 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) == T T ! temp_xadv, ... horizontal XI-advection Dout(iTyadv) == T T ! temp_yadv, ... horizontal ETA-advection Dout(iTvadv) == T T ! temp_vadv, ... vertical advection Dout(iThdif) == T T ! temp_hdiff, ... horizontal total diffusion Dout(iTxdif) == T T ! temp_xdiff, ... horizontal XI-diffusion Dout(iTydif) == T T ! temp_ydiff, ... horizontal ETA-diffusion Dout(iTsdif) == T T ! 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]. ! EDIT GRDNAME == /nv/pe7/fzhang76/ross/input/ross-iceshelf-grid-update.nc ININAME == /nv/pe7/fzhang76/ross/input/ross-init.nc ITLNAME == ocean_itl.nc IRPNAME == ocean_irp.nc IADNAME == ocean_iad.nc FWDNAME == ocean_fwd.nc ADSNAME == ocean_ads.nc ! Input lateral boundary and climatology file names. The USER has the ! option to enter several files names per each nested grid. For example, ! the USER may have a different files for velocity, ice, etc. ! The model will scan the file list and will read the needed data ! from the first file in the list containing the boundary field. Therefore, ! the order of the file names is very important. If multiple boundary ! 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. ! 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. ! EDIT NCLMFILES == 1 ! number of climate files CLMNAME == /nv/pe7/fzhang76/ross/input/ross-clim.nc NBCFILES == 1 ! number of boundary files BRYNAME == /nv/pe7/fzhang76/ross/input/ross-bry.nc ! Input forcing NetCDF file name(s). The USER has the option to enter ! several file names for each nested grid. For example, the USER may ! have 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 using multiple forcing ! files per grid, first enter all the file names for grid 1, then grid 2, ! and so on. It is also possible to split input data time records into ! several NetCDF files (see prologue instructions above). Use a single line ! per entry with a continuation (\) or vertical bar (|) symbol after each ! entry, except the last one. ! EDIT NFFILES == 1 ! number of unique forcing files FRCNAME == /nv/pe7/fzhang76/ross/input/ross-forc-other-mean2008-2009.nc ! forcing file 1, grid 1 ! Output NetCDF file names, [1:Ngrids]. ! EDIT GSTNAME == ocean_gst.nc RSTNAME == ocean_zice_rst.nc HISNAME == /nv/pe7/fzhang76/ross/out/ross_nud_open_zice_new_200_his.nc TLMNAME == ocean_tlm.nc TLFNAME == ocean_tlf.nc ADJNAME == ocean_adj.nc AVGNAME == /nv/pe7/fzhang76/ross/out/ross_nud_open_zice_new_200_avg.nc DIANAME == ocean_dia.nc STANAME == ocean_sta.nc FLTNAME == ocean_flt.nc ! Input ASCII parameter filenames. APARNAM = ROMS/External/s4dvar.in SPOSNAM = ROMS/External/stations.in FPOSNAM = ROMS/External/floats.in BPARNAM = ROMS/External/bio_Fennel.in SPARNAM = ROMS/External/sediment.in USRNAME = ROMS/External/MyFile.dat ! ! GLOSSARY: ! ========= ! !------------------------------------------------------------------------------ ! Application title (string with a maximum of eighty 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. !------------------------------------------------------------------------------ ! ! Ngrids Number of nested grids. It needs to be read at the top of all ! other parameters in order to allocate all model variables. ! !------------------------------------------------------------------------------ ! 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 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. ! ! Ice boundary conditions ! ! LBC(isAice) Ice concentration, [1:4, Ngrids] values are expected. ! LBC(isHice) Ice thickness, [1:4, Ngrids] values are expected. ! LBC(isHsno) Snow thickness, [1:4, Ngrids] values are expected. ! LBC(isTice) Ice temperature, [1:4, Ngrids] values are expected. ! LBC(isSfwat)Surface water, [1:4, Ngrids] values are expected. ! LBC(isSig11)Sigma-11, [1:4, Ngrids] values are expected. ! LBC(isSig12)Sigma-12, [1:4, Ngrids] values are expected. ! LBC(isSig22)Sigma-22, [1:4, Ngrids] values are expected. ! LBC(isUice) Ice U-momentum, [1:4, Ngrids] values are expected. ! LBC(isVice) Ice V-momentum, [1:4, 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 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. ! !------------------------------------------------------------------------------ ! 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 the 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 no need to split 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 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 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 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 ! 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. It 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 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. ! ! NSFF Number of time-steps 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 time-steps 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 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 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. ! !------------------------------------------------------------------------------ ! Harmonic/biharmonic horizontal viscosity coefficients. !------------------------------------------------------------------------------ ! ! 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. ! !------------------------------------------------------------------------------ ! Vertical mixing coefficients for active tracers. !------------------------------------------------------------------------------ ! ! AKT_BAK Background vertical mixing coefficient (m2/s) for active ! (NAT) and inert (NPT) tracer variables. ! ! ad_AKT_fac Adjoint-based algorithms vertical mixing, basic state, scale ! factor (nondimensional) for active (NAT) and inert (NPT) ! tracer variables. In some applications, a 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. ! ! ad_AKV_fac Adjoint-based algorithms vertical mixing, basic state, scale ! factor (nondimensional) for momentum. In some applications, ! a 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 (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: ! ! 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. ! !------------------------------------------------------------------------------ ! 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. !------------------------------------------------------------------------------ ! ! 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 ! ! Many other stretching functions (Vstretching>4) 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, 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 0001-01-01 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 0001-01-01 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). ! !------------------------------------------------------------------------------ ! Tracer climatology processing switches. !------------------------------------------------------------------------------ ! ! LtracerCLM Logical switches (T/F) to specify which tracer variables ! to consider when the option TCLIMATOLOGY is activated. 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. ! ! Recall that TCLIMATOLOGY is usually activated to nudge to ! tracer climatology (TLCM_NUDGING). The purpose of these ! switches is to control which climatology tracer fields ! (specially passive tracers) needs to be processed. So we ! may reduce the memory allocation for such array. ! !------------------------------------------------------------------------------ ! Tracer point Sources/Sink sources switches. !------------------------------------------------------------------------------ ! ! LtracerSrc Logical switches (T/F) to specify which tracer variables ! to consider when the option TS_PSOURCE is activated. Only ! NAT active tracers (temperature, salinity) and NPT inert ! tracers need to be specified 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 specified in ! their respective input scripts. ! ! Recall that TS_PSOURCE is 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" ! ! This logic 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. ! !------------------------------------------------------------------------------ ! 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(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(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 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 term. ! Aout(idUVav) Write out quadratic term. ! Aout(idVVav) Write out quadratic term. ! Aout(idU2av) Write out quadratic term. ! Aout(idV2av) Write out quadratic term. ! Aout(idZZav) Write out quadratic term. ! ! Aout(idTTav) Write out quadratic active and inert tracers terms. ! Aout(idUTav) Write out quadratic active and inert tracers terms. ! Aout(idVTav) Write out quadratic active and inert tracers terms. ! Aout(iHUTav) Write out active and inert tracer u-volume flux, . ! Aout(iHVTav) Write out active and inert tracer v-volume flux, . ! ! 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. ! ! 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 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, 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. 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 == 8 ! number of unique forcing files ! ! FRCNAME == my_rivers.nc \ ! river forcing ! my_tides.nc \ ! tidal forcing ! 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: ! ! 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. !