roms.in

Standard Input Script - roms.in

Notice: In SVN revision 933 (January 26, 2019), all "ocean_*.in" files were renamed to roms_*.in and all ocean* ROMS executables were renamed to roms* in order to facilitate and clarify model coupling efforts. More information can be found in the ROMS repository Trac ticket #794.

File roms.in is the ROMS standard input file to any model run. This file sets the application spatial dimensions and many of the parameters that are not specified at compile time, including parallel tile decomposition, timestepping, physical coefficients and constants, vertical coordinate set-up, logical switches and flags to control the frequency of output, the names of input and output NetCDF files, and additional input scripts names for data assimilation, stations, floats trajectories, ecosystem models, and sediment model.

This standard input ASCII file is organized in several sections as shown below, with links to more detailed explanation where required.

Notice: A detailed information about ROMS input script file syntax can be found here.

Notice: A default roms.in input script is provided in the User/External subdirectory. Also there are several standard input scripts in the ROMS/External subdirectory which are used in the distributed test cases. They are usually named roms_app.in where app is the lowercase of the test case cpp option.

Configuration Parameters

• Application title. This string will be saved in the output NetCDF files.
  TITLE = Wind-Driven Upwelling/Downwelling over a Periodic Channel

• C-preprocessing Flag to define the specific configuration.
  MyAppCPP = UPWELLING
  Though this is set by ROMS_APPLICATION in the makefile or build Script, ROMS is also compiled with -D$(ROMS_APPLICATION), which allows the use of
  #ifdef UPWELLING
  for instance. The net result of both
  -D$(ROMS_APPLICATION)=UPWELLING -DUPWELLING
  is that ROMS_APPLICATION becomes 1 in the source code. ROMS therefore needs to be told the application name here as well in order to report it to the output file.

• Input variable information file name. This file needs to be processed first so all information arrays can be initialized properly. Notice that we need an absolute or relative path for input metadata file varinfo.dat. There are many posts in the ROMS Forum of new users that fail to specify the correct location of this file. Expert users usually have the own modified copy of this file for a particular application.
  VARNAME = ROMS/External/varinfo.dat

NOTE: Starting with revision 460 file names can be up to 256 characters long. Previously only 80 characters were allowed.

• Number of nested grids.
  Ngrids = 1

• Number of grid nesting layers. This parameter is used to allow refinement and composite grid combinations.
  NestLayers = 1

• Number of grids in each nesting layer, [1:NestLayers] values are expected.
  GridsInLayer = 1

• Grid dimension parameters. These are used to dynamically allocate all model state variables upon execution.
  Lm == 41  ! Number of I-direction INTERIOR RHO-points
  Mm == 80  ! Number of J-direction INTERIOR RHO-points
  N == 16  ! Number of vertical levels
  
  Nbed = 0  ! Number of sediment bed layers
  
  NAT = 2  ! Number of active tracers (usually, 2)
  NPT = 0  ! Number of inactive passive tracers
  NCS = 0  ! Number of cohesive (mud) sediment tracers
  NNS = 0  ! Number of non-cohesive (sand) sediment tracers

• Domain decomposition parameters for serial, distributed-memory or shared-memory configurations used to determine tile horizontal range indices (Istr,Iend) and (Jstr,Jend), [1:Ngrids] values are expected.
  NtileI == 1  ! I-direction partition
  NtileJ == 1  ! J-direction partition

Tracer Advection Schemes

Set horizontal and vertical advection schemes for active and inert tracers. A different advection scheme is allowed for each tracer. For example, a positive-definite (monotonic) algorithm can be activated for salinity and inert tracers, while a different one is set for temperature.

It is more advantageous to set the horizontal and vertical advection schemes for each tracer with switches instead of a single CPP flag for all of them. Positive-definite and monotonic algorithms (i.e., MPDATA and HSIMT) are appropriate and useful for positive fields like salinity, inert, biological, and sediment tracers. However, since the temperature has a dynamic range with negative and positive values in the ocean, other advection schemes are more appropriate.

Currently, the following tracer advection schemes are available and are activated using the associated Keyword:

Keyword Advection Algorithm

A4 4th-order Akima (horizontal/vertical)
C2 2nd-order centered differences (horizontal/vertical)
C4 4th-order centered differences (horizontal/vertical)
HSIMT 3th-order HSIMT with TVD limiter (horizontal/vertical)
MPDATA recursive flux corrected MPDATA (horizontal/vertical)
SPLINES parabolic splines reconstruction (only vertical)
SU3 split third-order upstream (horizontal/vertical)
U3 3rd-order upstresm-bias (only horizontal)

The user has the option of specifying the full Keyword or the first two letters, regardless if using uppercase or lowercase.

If using either HSIMT (Wu and Zhu, 2010) or MPDATA (Smolarkiewicz and Margolin, 1998) options, the user needs to set the same scheme for both horizontal and vertical advection to preserve monotonicity.

• Horizontal and vertical advection for each active (temperature and salinity) and inert tracer, [1:NAT+NPT,Ngrids] values are expected.
  Hadvection == U3 \  ! temperature
  U3 \  ! salinity
  HSIMT \  ! dye_01, inert(1)
  HSIMT  ! dy2_02, inert(2)
  
  Vadvection == C4 \  ! temperature
  C4 \  ! salinity
  HSIMT \  ! dye_01, inert(1)
  HSIMT  ! dy2_02, inert(2)

• Horizontal and vertical advection for each active (temperature and salinity) and inert tracer for adjoint-based algorithms can have different horizontal schemes, [1:NAT+NPT,Ngrids] values are expected.
  ad_Hadvection == U3 \  ! temperature
  U3 \  ! salinity
  HSIMT \  ! dye_01, inert(1)
  HSIMT  ! dy2_02, inert(2)
  
  ad_Vadvection == C4 \  ! temperature
  C4 \  ! salinity
  HSIMT \  ! dye_01, inert(1)
  HSIMT  ! dy2_02, inert(2)

Lateral Open 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 the structured array:
  LBC(1:4, nLBCvar, Ngrids)
  where 1:4 are the numbered boundary edges, nLBCvar are the number LBC state variables, and Ngrids is the number of nested grids. For example, to apply gradient boundary conditions for free-surface 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. 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. [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) == Per Clo Per Clo  ! free-surface
  LBC(isUbar) == Per Clo Per Clo  ! 2D U-momentum
  LBC(isVbar) == Per Clo Per Clo  ! 2D V-momentum
  LBC(isUvel) == Per Clo Per Clo  ! 3D U-momentum
  LBC(isVvel) == Per Clo Per Clo  ! 3D V-momentum
  LBC(isMtke) == Per Clo Per Clo  ! mixing TKE
  
  LBC(isTvar) == Per Clo Per Clo \  ! temperature
  Per Clo Per Clo  ! salinity

• Adjoint-based algorithms can have different lateral boundary conditions keywords.
  ad_LBC(isFsur) == Per Clo Per Clo  ! free-surface
  ad_LBC(isUbar) == Per Clo Per Clo  ! 2D U-momentum
  ad_LBC(isVbar) == Per Clo Per Clo  ! 2D U-momentum
  ad_LBC(isUvel) == Per Clo Per Clo  ! 3D U-momentum
  ad_LBC(isVvel) == Per Clo Per Clo  ! 3D V-momentum
  ad_LBC(isMtke) == Per Clo Per Clo  ! mixing TKE
  
  ad_LBC(isTvar) == Per Clo Per Clo \  ! temperature
  Per Clo Per Clo  ! salinity

• Lateral open boundary edge volume conservation switch for nonlinear model and adjoint-based algorithm. This is usually activated with radiation boundary conditions to enforce global mass conservation. Notice that these switches should not be activated if tidal forcing, [1:Ngrids] values are expected.
  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

Timestepping and Iterations Parameters

• Timestepping parameters.
  NTIMES = 1440  ! Number of timesteps
  DT == 300.0d0  ! Timestep size (seconds)
  NDTFAST == 30  ! Number of barotropic steps

• Total number of timesteps for computing observations impacts interval during the analysis (NTIMES_ANA) or forecast (NTIMES_FCT) cycle.
  NTIMES_ANA = 1440  ! analysis interval
  NTIMES_FCT = 1440  ! forecast interval

• Model iteration loops parameters.
  ERstr = 1  ! Starting perturbation or iteration
  ERend = 1  ! Ending perturbation or iteration
  Nouter = 1  ! Maximum number of 4DVar outer loop iterations
  Ninner = 1  ! Maximum number of 4DVar inner loop iterations
  Nintervals = 1  ! Number of stochastic optimals interval divisions

• Number of eigenvalues (NEV) and eigenvectors (NCV) to compute for the Lanczos/Arnoldi problem in the Generalized Stability Theory (GST) analysis. NCV must be greater than NEV.
  NEV = 2  ! Number of eigenvalues
  NCV = 10  ! Number of eigenvectors
  Notice: At present, there is no apriori analysis to guide the selection of NCV relative to NEV. The only formal requirement is that NCV > NEV. However in optimal perturbations, it is recommended to have NCV ≥ 2*NEV. In Finite Time Eigenmodes (FTE) and Adjoint Finite Time Eigenmodes (AFTE) the requirement is to have NCV ≥ 2*NEV+1. The efficiency of calculations depends critically on the combination of NEV and NCV. If NEV is large (greater than 10 say), you can use NCV=2*NEV+1 but for NEV small (less than 6) it will be inefficient to use NCV=2*NEV+1. In complicated applications, you can start with NEV=2 and NCV=10. Otherwise, it will iterate for very long time.

Output Frequency Parameters

• Flags controlling the frequency of output.
  NRREC = 0  ! Model restart flag
  LcycleRST == T  ! Switch to recycle restart time records
  NRST == 288  ! Number of timesteps between writing restart records
  NSTA == 1  ! Number of timesteps between stations records
  NFLT == 1  ! Number of timesteps between floats records
  NINFO == 1  ! Number of timesteps between printing information diagnostics

• Output history, average, diagnostic files parameters.
  LDEFOUT == T  ! File creation/append switch
  NHIS == 72  ! Number of timesteps between writing history records
  NDEFHIS == 0  ! Number of timesteps between creation of new history file
  NQCK == 0  ! Number of timesteps between writing quicksave records
  NDEFQCK == 0  ! Number of timesteps between creation of new quicksave file
  NTSAVG == 1  ! Starting averages timestep
  NAVG == 72  ! Number of timesteps between writing averages records
  NDEFAVG == 0  ! Number of timesteps between creation of new averages file
  NTSDIA == 1  ! Starting diagnostics timestep
  NDIA == 72  ! Number of timesteps between writing diagnostics records
  NDEFDIA == 0  ! Number of timesteps between creation of new diagnostics file

• Output tangent linear and adjoint models parameters.
  LcycleTLM == F  ! Switch to recycle TLM time records
  NTLM == 72  ! Number of timesteps writing between TLM records
  NDEFTLM == 0  ! Number of timesteps between creation of new TLM file
  LcycleADJ == F  ! Switch to recycle ADM time records
  NADJ == 72  ! Number of timesteps between writing ADM records
  NDEFADJ == 0  ! Number of timesteps between creation of new ADM file
  NSFF == 72  ! Number of timesteps between 4DVAR adjustment of
   ! surface forcing fluxes
  NOBC == 72  ! Number of timesteps between 4DVAR adjustment of
   ! open boundary fields

• Output check pointing GST restart parameters.
  LmultiGST = F  ! one eigenvector per history file
  LrstGST = F  ! GST restart switch
  MaxIterGST = 500  ! maximum number of iterations
  NGST = 10  ! check pointing interval

Physical and Numerical Parameters

• Relative accuracy of the Ritz values computed in the GST analysis.
  Ritz_tol = 1.0d-15

• Harmonic/biharmonic horizontal diffusion of all active and passive (dye) tracers for the nonlinear model and adjoint-based algorithms: [1:NAT+NPT,Ngrids] values are expected. Diffusion coefficients for biology and sediment tracers are set in their respective input scripts.
  TNU2 == 0.0d0 0.0d0  ! m2/s
  TNU4 == 2*0.0d0  ! m4/s
  
  ad_TNU2 == 0.0d0 0.0d0  ! m2/s
  ad_TNU4 == 0.0d0 0.0d0  ! m4/s

• Harmonic/biharmonic, horizontal viscosity coefficient for the nonlinear model and adjoint-based algorithms: [1:Ngrids values are expected. Only used if the appropriate CPP options are defined.
  VISC2 == 0.0d0  ! m2/s
  VISC4 == 0.0d0  ! m4/s
  
  ad_VISC2 == 0.0d0  ! m2/s
  ad_VISC4 == 0.0d0  ! m4/s

• Logical switches (TRUE/FALSE) to increase/decrease horizontal viscosity and/or diffusivity in specific areas of the application domain (like sponge areas) for the desired application grid.
  LuvSponge == F  ! horizontal momentum
  LtracerSponge == F F  ! temperature, salinity, inert

• Background vertical mixing coefficients for active (NAT) and inert (NPT) tracers for the nonlinear model and basic state scale factor in adjoint-based algorithms: [1:NAT+NPT,Ngrids] values are expected.
  AKT_BAK == 1.0d-6 1.0d-6  ! m2/s
  
  ad_AKT_fac == 1.0d0 1.0d0 !nondimensional

• Background vertical mixing coefficient for momentum for the nonlinear model and basic state scale factor in the adjoint-based algorithms: [1:Ngrids] values are expected.
  AKV_BAK == 1.0d-5  ! m2/s
  
  ad_AKV_fac == 1.0d0 !nondimensional

• Upper threshold values to limit vertical mixing coefficients computed from vertical mixing parameterizations. Although this is an engineering fix, the vertical mixing values inferred from ocean observations are rarely higher than this upper limit value.
  AKT_LIMIT == 1.0d-3 1.0d-3  ! m2/s
  
  AKV_LIMIT == 1.0d-3  ! m2/s

• Turbulent closures parameters.
  AKK_BAK == 5.0d-6  ! m2/s
  AKP_BAK == 5.0d-6  ! m2/s
  TKENU2 == 0.0d0  ! m2/s
  TKENU4 == 0.0d0  ! m4/s

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

• Constants used in surface turbulent kinetic energy flux computation.
  CHARNOK_ALPHA == 1400.0d0  ! Charnok surface roughness
  ZOS_HSIG_ALPHA == 0.5d0  ! Roughness from wave amplitude
  SZ_ALPHA == 0.25d0  ! roughness from wave dissipation
  CRGBAN_CW == 100.0d0  ! Craig and Banner wave breaking

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

• Height (m) of atmospheric measurements for Bulk fluxes parameterization.
  BLK_ZQ == 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

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

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

• Mean Density and Brunt-Vaisala frequency.
  RHO0 = 1025.0d0  ! kg/m3
  BVF_BAK = 1.0d-4  ! 1/s2

• Timestamp assigned for model initialization, reference time origin for tidal forcing, and model reference time for output NetCDF units attribute.
  DSTART = 0.0d0  ! days
  TIDE_START = 0.0d0  ! days
  TIME_REF = 0.0d0  ! yyyymmdd.dd

• Nudging/relaxation time scales, inverse scales will be computed internally, [1:Ngrids] values are expected. These values are used for two purposes.

1. When climatology nudging is active throughout the domain because the logical flags LtracerCLM, Lm3CLM, Lm2CLM etc. are TRUE, these values are the default nudging time scales set in Functionals/ana_nudgcoef.h. Since the user can choose to customize ana_nudgcoef.h, or provide 3-D climatology nudging time scales in an external file, these parameters might not be used
2. When nudging is applied in the lateral open boundary conditions because the LBC logical flags are set to "RadNud" the values here set the nudging time scale when the Orlanski radiation scheme detects outflow conditions. When the Orlanski scheme detects inflow conditions, the nudging time scale is TNUDG/OBCFAC (see OBCFAC below).

TNUDG == 2*0.0d0  ! days
ZNUDG == 0.0d0  ! days
M2NUDG == 0.0d0  ! days
M3NUDG == 0.0d0  ! days

• Factor between passive (outflow) and active (inflow) (in the Orlanksi radiation sense) open boundary condition nudging time scales, [1:Ngrids]. If OBCFAC > 1, nudging on inflow is stronger than on outflow (recommended) because the inflow time scale TNUDG/OBCFAC is less than the outflow timescale TNUDG (see above). The passive/active radiation conditions in ROMS follow the method proposed by Marchesiello et al. (2001):
  $${\frac {\partial \phi }{\partial t}}+C_{x}{\frac {\partial \phi }{\partial x}}+C_{y}{\frac {\partial \phi }{\partial y}}=-{\frac {1}{\tau }}(\phi -\phi ^{ext})$$
  with
  $${\begin{aligned}\tau &=\tau _{out}&{\text{if}}\;\;\;&C_{x}>0,\\\tau &=\tau _{in}&{\text{if}}\;\;\;&C_{x}<0\;\;\;{\text{and}}\;\;\;C_{y}=0\end{aligned}}$$
  where $\phi ^{ext}$ represents the external boundary data and $\tau$ is the nudging time scale with $\tau _{out}$ for outflow, $\tau _{in}$ for inflow, and $\tau _{out}\ll \tau _{in}$. At outflow, a weak nudging is used to prevent a numerical drift in the solution while avoiding over-specification of the boundary data. During inflow, a strong nudging is applied to avoid data-shock in the solution. The nudging time scales provided above are for the outflow (passive) conditions, $\tau _{out}$, in days. The inflow nudging factor in the above equation is ${\frac {1}{\tau _{in}}}={\frac {\text{obcfac}}{\tau _{out}}}$.
  OBCFAC == 10.0d0  ! nondimensional

• Linear equation of State parameters, [1:Ngrids] values are expected.
  R0 == 1027.0d0  ! kg/m3
  T0 == 10.0d0  ! Celsius
  S0 == 35.0d0  ! nondimensional
  TCOEF == 1.7d-4  ! 1/Celsius
  SCOEF == 7.6d-4  ! 1/nondimensional

• Slipperiness parameter: 1.0 (free slip) or -1.0 (no slip).
  GAMMA2 = 1.0d0

• Logical switches (TRUE/FALSE) to activate horizontal momentum transport point Sources/Sinks (like river runoff) and mass point Sources/Sinks (like volume vertical influx): [1:Ngrids] values are expected. These switches replace obsolete CPP options UV_PSOURCE and Q_PSOURCE, respectively. In nesting, a particular grid may or may not have Sources/Sinks forcing.
  LuvSrc == F  ! horizontal momentum transport
  LwSrc == F  ! volume vertical influx

• Logical switches (TRUE/FALSE) to activate tracers point Sources/Sinks (like river runoff) and to specify which tracer variables to consider: [1:NAT+NPT,Ngrids] values are expected. Other biological and sediment tracer switches are activated in their respective input scripts. This switch replaces obsolete CPP option TS_PSOURCE. In nesting, a particular grid may or may not have tracers Sources/Sinks forcing.
  LtracerSrc == F F  ! temperature, salinity, inert

• Logical switches (TRUE/FALSE) to read and process climatology fields.
  LsshCLM == F  ! sea-surface height
  Lm2CLM == F  ! 2D momentum
  Lm3CLM == F  ! 3D momentum
  
  LtracerCLM == F F  ! temperature, salinity, inert

• Logical switches (TRUE/FALSE) to nudge the desired climatology field(s). If not analytical climatology fields, users need to turn ON the logical switches above to process the fields from the climatology NetCDF file that are needed for nudging.
  LnudgeM2CLM == F  ! 2D momentum
  LnudgeM3CLM == F  ! 3D momentum
  
  LnudgeTCLM == F F  ! temperature, salinity, inert

Vertical Coordinates Parameters

• Set vertical, terrain-following coordinates transformation equation and stretching function (see Vertical S-coordinate for more details).
  Vtransform == 2  ! transformation equation
  Vstretching == 4  ! stretching function

• S-coordinate surface control parameter, [1:Ngrids] values are expected. The range of optimal values depends on the vertical stretching function.
  THETA_S == 3.0d0  ! surface stretching parameter

• S-coordinate bottom control parameter, [1:Ngrids] values are expected. The range of optimal values depends on the vertical stretching function.
  THETA_B == 0.0d0  ! bottom stretching parameter

• 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.
  TCLINE == 25.0d0  ! critical depth (m)

Adjoint Sensitivity Parameters

• Starting (DstrS) and ending (DendS) day for adjoint sensitivity forcing. DstrS must be less or equal to DendS. If both values are zero, their values are reset internally to the full range of the adjoint integration.
  DstrS == 0.0d0  ! starting day
  DendS == 0.0d0  ! ending day

• Starting and ending vertical levels of the 3D adjoint state variables whose sensitivity is required.
  KstrS == 1  ! starting level
  KendS == 1  ! ending level

• Logical switches (TRUE/FALSE) to specify the adjoint state variables whose sensitivity is required.
  Lstate(isFsur) == F  ! free-surface
  Lstate(isUbar) == F  ! 2D U-momentum
  Lstate(isVbar) == F  ! 2D V-momentum
  Lstate(isUvel) == F  ! 3D U-momentum
  Lstate(isVvel) == F  ! 3D V-momentum
  Lstate(isWvel) == F  ! 3D W-momentum

• Logical switches (TRUE/FALSE) to specify the adjoint state tracer variables whose sensitivity is required, [1:NT,1:Ngrids] values are expected.
  Lstate(isTvar) == F F  ! NT tracers

Stochastic Optimals Parameters

• Logical switches (TRUE/FALSE) to specify the state variables required by Forcing Singular Vectors or Stochastic Optimals.
  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) == F  ! surface U-stress
  Fstate(isVstr) == F  ! 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
  
  SOstate(isUstr) == 1.0d0  ! surface u-stress
  SOstate(isVstr) == 1.0d0  ! surface v-stress
  SO_sdev(isTsur) == 1.0d0 1.0d0  ! NT surface tracer flux

History Output Variables Switches

• 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(idpthR) == F  ! z_rho time-varying depths of RHO-points
  Hout(idpthU) == F  ! z_u time-varying depths of U-points
  Hout(idpthV) == F  ! z_v time-varying depths of V-points
  Hout(idpthW) == F  ! z_w time-varying depths of W-points
  
  Hout(idUsms) == F  ! sustr surface U-stress
  Hout(idVsms) == F  ! svstr surface V-stress
  Hout(idUbms) == F  ! bustr bottom U-stress
  Hout(idVbms) == F  ! bvstr bottom V-stress
  
  Hout(idUbrs) == F  ! bustrc bottom U-current stress
  Hout(idVbrs) == F  ! bvstrc bottom V-current stress
  Hout(idUbws) == F  ! bustrw bottom U-wave stress
  Hout(idVbws) == F  ! bvstrw bottom V-wave stress
  Hout(idUbcs) == F  ! bustrcwmax bottom max wave-current U-stress
  Hout(idVbcs) == F  ! bvstrcwmax bottom max wave-current V-stress
  
  Hout(idUbot) == F  ! Ubot bed wave orbital U-velocity
  Hout(idVbot) == F  ! Vbot bed wave orbital V-velocity
  Hout(idUbur) == F  ! Ur bottom U-velocity above bed
  Hout(idVbvr) == F  ! Vr bottom V-velocity above bed
  
  Hout(idW2xx) == F  ! Sxx_bar 2D radiation stress, Sxx component
  Hout(idW2xy) == F  ! Sxy_bar 2D radiation stress, Sxy component
  Hout(idW2yy) == F  ! Syy_bar 2D radiation stress, Syy component
  Hout(idU2rs) == F  ! Ubar_Rstress 2D radiation U-stress
  Hout(idV2rs) == F  ! Vbar_Rstress 2D radiation V-stress
  Hout(idU2Sd) == F  ! ubar_stokes 2D U-Stokes velocity
  Hout(idV2Sd) == F  ! vbar_stokes 2D V-Stokes velocity
  
  Hout(idW3xx) == F  ! Sxx 3D radiation stress, Sxx component
  Hout(idW3xy) == F  ! Sxy 3D radiation stress, Sxy component
  Hout(idW3yy) == F  ! Syy 3D radiation stress, Syy component
  Hout(idW3zx) == F  ! Szx 3D radiation stress, Szx component
  Hout(idW3zy) == F  ! Szy 3D radiation stress, Szy component
  Hout(idU3rs) == F  ! u_Rstress 3D U-radiation stress
  Hout(idV3rs) == F  ! v_Rstress 3D V-radiation stress
  Hout(idU3Sd) == F  ! u_stokes 3D U-Stokes velocity
  Hout(idV3Sd) == F  ! v_stokes 3D V-Stokes velocity
  
  Hout(idWamp) == F  ! Hwave wave height
  Hout(idWlen) == F  ! Lwave wave length
  Hout(idWdir) == F  ! Dwave wave direction
  Hout(idWptp) == F  ! Pwave_top wave surface period
  Hout(idWpbt) == F  ! Pwave_bot wave bottom period
  Hout(idWorb) == F  ! Ub_swan wave bottom orbital velocity
  Hout(idWdis) == F  ! Wave_dissip wave dissipation
  
  Hout(idPair) == F  ! Pair surface air pressure
  Hout(idUair) == F  ! Uair surface U-wind component
  Hout(idVair) == F  ! Vair surface V-wind component
  
  Hout(idTsur) == 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. [1:NPT] values are expected. However, these switches can be activated using compact parameter specification.
  Hout(inert) == T  ! dye_01, ... inert passive tracers

Quicksave Output Variables Switches

• Logical switches (TRUE/FALSE) to activate writing of fields into quicksave output file.
  Qout(idUvel) == F  ! u 3D U-velocity
  Qout(idVvel) == F  ! v 3D V-velocity
  Qout(idu3dE) == F  ! u_eastward 3D U-eastward at RHO-points
  Qout(idv3dN) == F  ! v_northward 3D V-northward at RHO-points
  Qout(idWvel) == F  ! w 3D W-velocity
  Qout(idOvel) == F  ! omega omega vertical velocity
  Qout(idUbar) == T  ! ubar 2D U-velocity
  Qout(idVbar) == T  ! vbar 2D V-velocity
  Qout(idu2dE) == T  ! ubar_eastward 2D U-eastward at RHO-points
  Qout(idv2dN) == T  ! vbar_northward 2D V-northward at RHO-points
  Qout(idFsur) == T  ! zeta free-surface
  Qout(idBath) == T  ! bath time-dependent bathymetry
  
  Qout(idTvar) == F F  ! temp, salt temperature and salinity
  
  Qout(idUsur) == T  ! u_sur surface U-velocity
  Qout(idVsur) == T  ! v_sur surface V-velocity
  Qout(idUsuE) == T  ! u_sur_eastward surface U-eastward velocity
  Qout(idVsuN) == T  ! v_sur_northward surface V-northward velocity
  
  Qout(idsurT) == T T  ! temp_sur, salt_sur surface temperature and salinity
  
  Qout(idpthR) == F  ! z_rho time-varying depths of RHO-points
  Qout(idpthU) == F  ! z_u time-varying depths of U-points
  Qout(idpthV) == F  ! z_v time-varying depths of V-points
  Qout(idpthW) == F  ! z_w time-varying depths of W-points
  
  Qout(idUsms) == F  ! sustr surface U-stress
  Qout(idVsms) == F  ! svstr surface V-stress
  Qout(idUbms) == F  ! bustr bottom U-stress
  Qout(idVbms) == F  ! bvstr bottom V-stress
  
  Qout(idUbrs) == F  ! bustrc bottom U-current stress
  Qout(idVbrs) == F  ! bvstrc bottom V-current stress
  Qout(idUbws) == F  ! bustrw bottom U-wave stress
  Qout(idVbws) == F  ! bvstrw bottom V-wave stress
  Qout(idUbcs) == F  ! bustrcwmax bottom max wave-current U-stress
  Qout(idVbcs) == F  ! bvstrcwmax bottom max wave-current V-stress
  
  Qout(idUbot) == F  ! Ubot bed wave orbital U-velocity
  Qout(idVbot) == F  ! Vbot bed wave orbital V-velocity
  Qout(idUbur) == F  ! Ur bottom U-velocity above bed
  Qout(idVbvr) == F  ! Vr bottom V-velocity above bed
  
  Qout(idW2xx) == F  ! Sxx_bar 2D radiation stress, Sxx component
  Qout(idW2xy) == F  ! Sxy_bar 2D radiation stress, Sxy component
  Qout(idW2yy) == F  ! Syy_bar 2D radiation stress, Syy component
  Qout(idU2rs) == F  ! Ubar_Rstress 2D radiation U-stress
  Qout(idV2rs) == F  ! Vbar_Rstress 2D radiation V-stress
  Qout(idU2Sd) == F  ! ubar_stokes 2D U-Stokes velocity
  Qout(idV2Sd) == F  ! vbar_stokes 2D V-Stokes velocity
  
  Qout(idW3xx) == F  ! Sxx 3D radiation stress, Sxx component
  Qout(idW3xy) == F  ! Sxy 3D radiation stress, Sxy component
  Qout(idW3yy) == F  ! Syy 3D radiation stress, Syy component
  Qout(idW3zx) == F  ! Szx 3D radiation stress, Szx component
  Qout(idW3zy) == F  ! Szy 3D radiation stress, Szy component
  Qout(idU3rs) == F  ! u_Rstress 3D U-radiation stress
  Qout(idV3rs) == F  ! v_Rstress 3D V-radiation stress
  Qout(idU3Sd) == F  ! u_stokes 3D U-Stokes velocity
  Qout(idV3Sd) == F  ! v_stokes 3D V-Stokes velocity
  
  Qout(idWamp) == F  ! Hwave wave height
  Qout(idWlen) == F  ! Lwave wave length
  Qout(idWdir) == F  ! Dwave wave direction
  Qout(idWptp) == F  ! Pwave_top wave surface period
  Qout(idWpbt) == F  ! Pwave_bot wave bottom period
  Qout(idWorb) == F  ! Ub_swan wave bottom orbital velocity
  Qout(idWdis) == F  ! Wave_dissip wave dissipation
  
  Qout(idPair) == F  ! Pair surface air pressure
  Qout(idUair) == F  ! Uair surface U-wind component
  Qout(idVair) == F  ! Vair surface V-wind component
  
  Qout(idTsur) == F F  ! shflux, ssflux surface net heat and salt flux
  Qout(idLhea) == F  ! latent latent heat flux
  Qout(idShea) == F  ! sensible sensible heat flux
  Qout(idLrad) == F  ! lwrad longwave radiation flux
  Qout(idSrad) == F  ! swrad shortwave radiation flux
  Qout(idEmPf) == F  ! EminusP E-P flux
  Qout(idevap) == F  ! evaporation evaporation rate
  Qout(idrain) == F  ! rain precipitation rate
  
  Qout(idDano) == F  ! rho density anomaly
  Qout(idVvis) == F  ! AKv vertical viscosity
  Qout(idTdif) == F  ! AKt vertical T-diffusion
  Qout(idSdif) == F  ! AKs vertical Salinity diffusion
  Qout(idHsbl) == F  ! Hsbl depth of surface boundary layer
  Qout(idHbbl) == F  ! Hbbl depth of bottom boundary layer
  Qout(idMtke) == F  ! tke turbulent kinetic energy
  Qout(idMtls) == F  ! gls turbulent length scale

• Logical switches (TRUE/FALSE) to activate writing of extra inert passive tracers other than biological and sediment tracers into the quicksave output file. An inert passive tracer is one that it is only advected and diffused. Other processes are ignored. These tracers include, for example, dyes, pollutants, oil spills, etc. [1:NPT] values are expected. However, these switches can be activated using compact parameter specification.
  Qout(inert) == F  ! dye_01, ... inert passive tracers
  Qout(Snert) == F  ! dye_01, ... surface inert passive tracers

Time-averaged Output Variables Switches

• Logical switches (TRUE/FALSE) to activate writing of fields into time-averaged output file.
  Aout(idUvel) == T  ! u 3D U-velocityy
  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(idu3dD) == 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 <u*u> term
  Aout(idUVav) == F  ! uv quadratic <u*v> term
  Aout(idVVav) == F  ! vv quadratic <v*v> term
  Aout(idU2av) == F  ! ubar2 quadratic <ubar*ubar> term
  Aout(idV2av) == F  ! vbar2 quadratic <vbar*vbar> term
  Aout(idZZav) == F  ! zeta2 quadratic <zeta*zeta> term
  
  Aout(idTTav) == F F  ! temp2, ... quadratic <t*t> tracer terms
  Aout(idUTav) == F F  ! utemp, ... quadratic <u*t> tracer terms
  Aout(idVTav) == F F  ! vtemp, ... quadratic <v*t> tracer terms
  Aout(iHUTav) == F F  ! Huontemp, ... tracer volume flux, <Huon*t>
  Aout(iHVTav) == F F  ! Hvomtemp, ... tracer volume flux, <Hvom*t>

• Logical switches (TRUE/FALSE) to activate writing of extra inert passive tracers other than biological and sediment tracers into the time-averaged output file. An inert passive tracer is one that it is only advected and diffused. Other processes are ignored. These tracers include, for example, dyes, pollutants, oil spills, etc. [1:NPT,1:Ngrids] values are expected. However, these switches can be activated using compact parameter specification.
  Aout(inert) == T  ! dye_01, ... inert passive tracers

Time-averaged Diagnostic Output Variables Switches

• Logical switches (TRUE/FALSE) to activate writing time-averaged. 2D momentum (ubar, vbar) diagnostic terms into the diagnostics 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 the diagnostics 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 the diagnostics output file. [1:NAT+NPT,1:Ngrids] values are expected.
  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

• NUSER is the number (integer) of user parameters to consider. USER is a vector containing NUSER user parameters (real array).
  NUSER = 0
  USER = 0.d0
  This array is primarily used with the SANITY_CHECK to test the correctness of the tangent linear adjoint models. It contains 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.

• This parameter could also be used to adjust constants in analytical functions at run time.

Parallel I/O (PIO) Parameters

• Choose the input and output NetCDF library to use. For example, the user could choose to use the PIO library for writing but still use the standard library for reading. To use this Parallel I/O strategy, the PIO library must be linked to ROMS at compile time and the PIO_LIB CPP option needs to be activated. It is only available in distributed-memory applications since it uses MPI-IO.
  ! [1] Standard NetCDF-3 or NetCDF-4 library
  ! [2] Parallel-IO from the PIO library (MPI, MPI-IO applications)
  
  INP_LIB = 2
  OUT_LIB = 2

• PIO offers several methods for reading/writing NetCDF files. Depending on the build of the PIO libraries, not all the I/O types are available. If the NetCDF library does not support parallel I/O, methods 3 and 4 are not available. Currently, NetCDF4/HDF5 data compression is possible with method 3 during serial write.
  ! [0] parallel read and parallel write of PnetCDF (CDF-5 type files, not recommended because of post-processing)
  ! [1] parallel read and parallel write of NetCDF3 (64-bit offset)
  ! [2] serial read and serial write of NetCDF3 (64-bit offset)
  ! [3] parallel read and serial write of NetCDF4/HDF5
  ! [4] parallel read and parallel write of NETCDF4/HDF5
  
  PIO_METHOD = 2

• Parallel-IO tasks control parameters. Typically, it is advantageous and highly recommended to define the I/O decomposition in smaller number of processes for efficiency and to avoid MPI communications bottlenecks.
  PIO_IOTASKS = 1  ! number of I/O processes to define
  PIO_STRIDE = 1  ! stride in the MPI-rank between I/O processes
  PIO_BASE = 0  ! offset for the first I/O process
  PIO_AGGREG = 1  ! number of MPI-aggregators to use

• Parallel-IO rearranger methods for moving data between computational and I/O processes. It provides the ability to rearrange data between computational and parallel I/O decompositions. Usually the Box rearrangement is more efficient.
  ! [1] Box rearrangement
  ! [2] Subset rearrangement
  
  PIO_REARR = 1
  • In the box method, data is rearranged from computational to I/O processes in a continuous manner to the data ordering in the file. Since the ordering of data between computational and I/O partitions may be different, the rearrangement will require all-to-all MPI communications. Also, notice that each computing tile may transfer data to one or more I/O processes.
  • In the subset method, each I/O process is associated with a subset of computing processes. The computing tile sends its data to a unique I/O process. The data on I/O processes may be more fragmented to the ordering on disk, which may increase the communications to the storage medium. However, the rearrangement scales better since all-to-all MPI communications are not required.

• Parallel-IO rearranger flag for MPI communication between computational and I/O processes. In some systems, the Point-to-Point communications is more efficient.
  ! [0] Point-to-Point communications
  ! [1] Collective communications
  
  PIO_REARRCOM = 0

• Parallel-IO rearranger flow-control direction flag for MPI communications between computational and I/O processes. The flow algorithm controls the rate and volume of messages sent to any destination MPI process. Optimally, the MPI communications should be designed to send a modest number of messages evenly distributed across a number of processes. An excessive number of messages to a single MPI process can exhaust the buffer space which can affect efficiency or failure due to the slowdown in the retransmitting of dropped messages. It only sends messages (Isend) when the receiver is ready and has sufficient resources.
  ! [0] Enable computational to I/O processes, and vice versa
  ! [1] Enable computational to I/O processes only
  ! [2] Enable I/O to computational processes only
  ! [3] Disable flow control
  
  PIO_REARRDIR = 0

• Parallel-IO rearranger options for MPI communications from computational to I/O processes (C2I).
  PIO_C2I_HS = T  ! Enable C2I handshake (T/F)
  PIO_C2I_Send = F  ! Enable C2I Isends (T/F)
  PIO_I2C_HS = 64  ! Maximum pending C2I requests

• Parallel-IO rearranger options for MPI communications from I/O to computational processes (I2C).
  PIO_I2C_HS = F  ! Enable I2C handshake (T/F)
  PIO_I2C_Send = T  ! Enable I2C Isends (T/F)
  PIO_I2C_Preq = 65  ! Maximum pending I2C requests

NetCDF-4/HDF5 Compression 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 libraries. File deflation cannot be used in parallel I/O for writing to exactly map the data to the disk location. For more information, check NetCDF official website.
  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 Files

NOTE: Starting with revision 460 file names can be up to 256 characters long. Previously only 80 characters were allowed.

• Input NetCDF file names, [1:Ngrids] values are expected.
  GRDNAME == roms_grd.nc  ! Grid
  ININAME == roms_ini.nc  ! NLM initial conditions
  ITLNAME == roms_itl.nc  ! TLM initial conditions
  IRPNAME == roms_irp.nc  ! RPM initial conditions
  IADNAME == roms_iad.nc  ! ADM initial conditions
  FWDNAME == roms_fwd.nc  ! Forward trajectory
  ADSNAME == roms_ads.nc  ! Adjoint sensitivity functionals

• Input adjoint forcing NetCDF filenames for computing observations impacts during the analysis-forecast cycle. If the forecast error metric is defined in state-space, then FOInameA and FOInameB should be regular adjoint forcing files just like ADSNAME. If the forecast error metric is defined in observation space (OBS_SPACE is activated) then the forecast is initialized OIFnameA and OIFnameB (specified in s4dvar.in input script) will have the structure of a 4D-Var observation file.
  FOInameA == roms_foi_a.nc
  FOInameB == roms_foi_b.nc

• Input NetCDF filenames for the forecasts initialized from the analysis of the current 4D-Var cycle (FCTnameA) and initialized from the analysis of the previous 4D-Var cycle (FCTnameB).
  FCTnameA == roms_fct_a.nc
  FCTnameB == roms_fct_b.nc

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

• Input lateral boundary conditions and climatology file names. The user has the option to split input data time records into several NetCDF files (see the File Syntax Notes). If so, use a single line per entry with a vertical bar (|) symbol after each entry, except the last one.
  BRYNAME == roms_bry.nc  ! Open boundary conditions
  CLMNAME == roms_clm.nc  ! Climatology

• Input climatology nudging coefficients file name.
  NUDNAME == roms_nud.nc

• Input Sources/Sinks forcing (like river runoff) file name. This file is separated from the regular forcing files to allow manipulations over nested grids. A particular nesting grid may or may not have Sources/Sinks forcing.
  SSFNAME == roms_rivers.nc

• Input tidal forcing file name.
  TIDENAME == roms_tides.nc

• Input forcing NetCDF file name(s). The user has the option to enter several files names for each nested grid. For example, the user may have a different files for wind products, heat fluxes, 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. It is also possible to split input data time records into several NetCDF files (see the File Syntax Notes). Use a single line per entry with a continuation ( \ ) or vertical bar ( | ) symbol after each entry, except the last one.
  NFFILES == 1  ! number of unique forcing files
  
  FRCNAME == roms_frc.nc  ! forcing file 1, grid 1

Output NetCDF Files

NOTE: Starting with revision 460 file names can be up to 256 characters long. Previously only 80 characters were allowed.

• Output NetCDF file names, [1:Ngrids] files are expected.
  DAINAME == roms_dai.nc  ! Data assimilation next cycle initial conditions or restart file
  GSTNAME == roms_gst.nc  ! GST analysis restart
  RSTNAME == roms_rst.nc  ! Restart
  HISNAME == roms_his.nc  ! History
  QCKNAME == roms_qck.nc  ! Quicksave
  TLMNAME == roms_tlm.nc  ! TLM history
  TLFNAME == roms_tlf.nc  ! Impulse TLM forcing
  ADJNAME == roms_adj.nc  ! ADM history
  AVGNAME == roms_avg.nc  ! Averages
  HARNAME == roms_har.nc  ! least-squares detiding harmonics
  DIANAME == roms_dia.nc  ! Diagnostics
  STANAME == roms_sta.nc  ! Stations
  FLTNAME == roms_flt.nc  ! Floats

Additional Input Scripts

NOTE: Starting with revision 460 file names can be up to 256 characters long. Previously only 80 characters were allowed.

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