cppdefs.h

cppdefs.h

Internal header file containing all the C-preprocessing options that defines a particular application. It is included at the top of every ROMS source file. The application CPP option is specified in the makefile definition ROMS_APPLICATION. The application header file is determined during compilation as the lowercase value of ROMS_APPLICATION with the .h extension and loaded into the ROMS_HEADER definition. Then, during C-preprocessing the application header file is included in cppdefs.h using the following directive:

 #if defined ROMS_HEADER
 # include ROMS_HEADER
 #else
   CPPDEFS - Choose an appropriate ROMS application.
 #endif

Options associated with momentum equations

The default horizontal advection is 3rd-order upstream bias for 3D momentum and 4th-order centered for 2D momentum. The default vertical advection is 4th-order centered for 3D momentum. If this is the case, no flags for momentum advection need to be activated.

The 3rd-order upstream split advection (UV_U3ADV_SPLIT) can be used to correct for the spurious mixing of the advection operator in terrain-following coordinates. If this is the case, the advection operator is split in advective and viscosity components and several internal flags are activated in "globaldefs.h". Notice that horizontal and vertical advection of momentum is 4th-order centered plus biharmonic viscosity to correct for spurious mixing. The total time-dependent horizontal mixing coefficient are computed in hmixing.F.

Warning: Use the splines vertical advection option (UV_SADVECTION) only in idealized, high vertical resolution applications.

UV_ADV	use to activate advection terms
UV_COR	use to activate Coriolis term
UV_U3ADV_SPLIT	use if 3rd-order upstream split momentum advection
UV_C2ADVECTION	use to activate 2nd-order centered advection
UV_C4ADVECTION	use to activate 4th-order centered advection
UV_SADVECTION	use to activate splines vertical advection
UV_VIS2	use to activate harmonic horizontal mixing
UV_VIS4	use to activate biharmonic horizontal mixing
UV_SMAGORINSKY	use to turn ON or OFF Smagorinsky-like viscosity
UV_DRAG_GRID	use if spatially varying bottom friction parameters
UV_LOGDRAG	use to activate logarithmic bottom friction
UV_LDRAG	use to activate linear bottom friction
UV_QDRAG	use to activate quadratic bottom friction
SPLINES_VVISC	use if splines reconstruction of vertical viscosity

Option to limit bottom stress

Do not allow the bottom stress components to change the direction of bottom momentum (change sign of velocity components).

LIMIT_BSTRESS	use to limit the magnitude of bottom stress

Options associated with tracers equations

The default horizontal and vertical advection is 4th-order centered. Use the splines vertical advection option is shallow, high vertical resolution applications.

TS_DIF2	use to turn ON or OFF harmonic horizontal mixing
TS_DIF4	use to turn ON or OFF biharmonic horizontal mixing
TS_SMAGORINSKY	use to turn ON or OFF Smagorinsky-like diffusion
TS_FIXED	use if diagnostic run, no evolution of tracers
T_PASSIVE	use if inert passive tracers (dyes, etc)
AGE_MEAN	use if computing Mean Age of inert passive tracers
NONLIN_EOS	use if using nonlinear equation of state
QCORRECTION	use if net heat flux correction
SALINITY	use if having salinity
SCORRECTION	use if freshwater flux correction
SOLAR_SOURCE	use if solar radiation source term
SPLINES_VDIFF	use if splines reconstruction of vertical diffusion
SRELAXATION	use if salinity relaxation as a freshwater flux
WTYPE_GRID	use to turn ON spatially varying Jerlov water type

Option to suppress further surface cooling

Use this option to suppress further surface cooling if the SST is at freezing point or below and the net surface heat flux is cooling:

LIMIT_STFLX_COOLING	use to suppress SST cooling below freezing point

Option for MPDATA 3D Advection

Hadvection(itrc,ng)%MPDATA and Vadvection(itrc,ng)%MPDATA switches.

TS_MPDATA_LIMIT	use to limit upwind corrector fluxes for stability

Options for pressure gradient algorithm

If no option is selected, the pressure gradient term is computed using standard density Jacobian algorithm. Notice that there are two quartic pressure Jacobian options. They differ on how the WENO reconciliation step is done and in the monotonicity constraining algorithms.

DJ_GRADPS	use if splines density Jacobian (Shchepetkin, 2000)
PJ_GRADP	use if finite volume Pressure Jacobian (Lin,1997)
PJ_GRADPQ2	use if quartic 2 Pressure Jacobian (Shchepetkin,2000)
PJ_GRADPQ4	use if quartic 4 Pressure Jacobian (Shchepetkin,2000)
WJ_GRADP	use if weighted density Jacobian (Song,1998)
ATM_PRESS	use to impose atmospheric pressure onto sea surface
PRESS_COMPENSATE	use to compensate for boundary without ATM pressure

Options for atmospheric boundary layer surface fluxes

It is possible to compute surface wind stress and surface net heat and freshwater fluxes form atmospheric fields using the bulk flux parameterization of Fairall et al. (1996). There are three ways to provide longwave radiation in the atmospheric boundary layer: (i) compute the net longwave radiation internally using the Berliand (1952) equation (LONGWAVE) as function of air temperature, sea surface temperature, relative humidity, and cloud fraction; (ii) provide (read) longwave downwelling radiation only and then add outgoing longwave radiation (LONGWAVE_OUT) as a function of the model sea surface temperature; and (iii) provide net longwave radiation (default).

BULK_FLUXES	use if bulk fluxes computation
NL_BULK_FLUXES	use if bulk fluxes computed by nonlinear model
COOL_SKIN	use if cool skin correction
LONGWAVE	use if computing net longwave radiation
LONGWAVE_OUT	use if computing ougoing longwave radiation
EMINUSP	use if computing E-P
WIND_MINUS_CURRENT	use if compute effective wind by removing current

Options for wave roughness formulation in bulk fluxes

COARE_TAYLOR_YELLAND	use Taylor and Yelland (2001) relation
COARE_OOST	use Oost et al (2002) relation
DEEPWATER_WAVES	use Deep water waves approximation

Options for shortwave radiation

The shortwave radiation can be computed using the global albedo equation with a cloud correction. Alternatively, input shortwave radiation data computed from averaged data (with snapshots greater or equal than 24 hours) can be modulated by the local diurnal cycle which is a function longitude, latitude and year day.

ALBEDO	use if albedo equation for shortwave radiation
DIURNAL_SRFLUX	use to impose shortwave radiation local diurnal cycle

Options for model configuration

SOLVE3D	use if solving 3D primitive equations
CURVGRID	use if curvilinear coordinates grid
MASKING	use if land/sea masking
BODYFORCE	use if applying stresses as a body force
PROFILE	use if time profiling
AVERAGES	use if writing out time-averaged data
AVERAGES_DETIDE	use if writing out NLM time-averaged detided fields
AD_AVERAGES	use if writing out ADM time-averaged data
RP_AVERAGES	use if writing out RPM time-averaged data
TL_AVERAGES	use if writing out TLM time-averaged data
DIAGNOSTICS_BIO	use if writing out biological diagnostics
DIAGNOSTICS_UV	use if writing out momentum diagnostics
DIAGNOSTICS_TS	use if writing out tracer diagnostics
ICESHELF	use if including ice shelf cavities
SPHERICAL	use if analytical spherical grid
STATIONS	use if writing out station data
STATIONS_CGRID	use if extracting data at native C-grid

Options for Lagrangian drifters

FLOATS	use to activate simulated Lagrangian drifters
FLOAT_OYSTER	use to activate oyster model behavior in floats
FLOAT_STICKY	ues to reflect/stick floats that hit surface/bottom
FLOAT_VWALK	use if vertical random walk
VWALK_FORWARD	use if forward time stepping vertical random walk

Options for analytical fields configuration

The model may be configured, initialized, and forced with analytical expressions. These analytical expressions are coded in several header files which are included in analytical.F. The analytical header files in the ROMS/Functionals sub-directory correspond to all the distributed idealized test cases. Another set of analytical header files templates are provided in the User/Functionals sub-directory.

ANA_BIOLOGY	use if analytical biology initial conditions
ANA_BPFLUX	use if analytical bottom passive tracers fluxes
ANA_BSFLUX	use if analytical bottom salinity flux
ANA_BTFLUX	use if analytical bottom temperature flux
ANA_CLOUD	use if analytical cloud fraction
ANA_DIAG	use if customized diagnostics
ANA_DQDSST	use if analytical surface heat flux sensitivity to SST
ANA_DRAG	use if analytical spatially varying drag parameters
ANA_FSOBC	use if analytical free-surface boundary conditions
ANA_GRID	use if analytical model grid set-up
ANA_HUMIDITY	use if analytical surface air humidity
ANA_INITIAL	use if analytical initial conditions
ANA_M2CLIMA	use if analytical 2D momentum climatology
ANA_M2OBC	use if analytical 2D momentum boundary conditions
ANA_M3CLIMA	use if analytical 3D momentum climatology
ANA_M3OBC	use if analytical 3D momentum boundary conditions
ANA_MASK	use if analytical Land/Sea masking
ANA_NUDGCOEF	use if analytical climatology nudging coefficients
ANA_PAIR	use if analytical surface air pressure
ANA_PASSIVE	use if analytical initial conditions for inert tracers
ANA_PERTURB	use if analytical perturbation of initial conditions
ANA_PSOURCE	use if analytical point Sources/Sinks
ANA_RAIN	use if analytical rain fall rate
ANA_SEDIMENT	use if analytical sediment initial fields
ANA_SMFLUX	use if analytical surface momentum stress
ANA_SPFLUX	use if analytical surface passive tracers fluxes
ANA_SPINNING	use if analytical time-varying rotation force
ANA_SPONGE	use if analytical enhanced viscosity/diffusion sponge
ANA_SRFLUX	use if analytical surface shortwave radiation flux
ANA_SSFLUX	use if analytical surface salinity flux
ANA_SSH	use if analytical sea surface height
ANA_SSS	use if analytical sea surface salinity
ANA_SST	use if analytical SST and dQdSST
ANA_STFLUX	use if analytical surface temperature flux
ANA_TAIR	use if analytical surface air temperature
ANA_TCLIMA	use if analytical tracers climatology
ANA_TOBC	use if analytical tracers boundary conditions
ANA_VMIX	use if analytical vertical mixing coefficients
ANA_WINDS	use if analytical surface winds
ANA_WWAVE	use if analytical wind induced waves

Options for horizontal mixing of momentum

VISC_GRID	use to scale viscosity coefficient by grid size
MIX_S_UV	use if mixing along constant S-surfaces
MIX_GEO_UV	use if mixing along geopotential (constant Z) surfaces

Options for horizontal mixing of tracers

DIFF_GRID	use to scale diffusion coefficients by grid size
MIX_S_TS	use if mixing along constant S-surfaces
MIX_GEO_TS	use if mixing along geopotential (constant depth) surfaces
MIX_ISO_TS	use if mixing along epineutral (constant density) surfaces
TS_MIX_CLIMA	use if diffusion of tracer perturbation (t-tclm)
TS_MIX_MAX_SLOPE	use if maximum slope in epineutral diffusion
TS_MIX_MIN_STRAT	use if minimum stratification in epineutral diffusion
TS_MIX_STABILITY	use if weighting diffusion between two time levels

Options for vertical mixing of momentum and tracers

There are several vertical mixing parameterizations in ROMS. Activate only one closure.

BVF_MIXING	use if Brunt-Vaisala frequency mixing
GLS_MIXING	use if Generic Length-Scale mixing
MY25_MIXING	use if Mellor/Yamada Level-2.5 closure
LMD_MIXING	use if Large et al. (1994) K-profile vertical parameterization
LIMIT_VDIFF	use to impose an upper limit on vertical diffusion
LIMIT_VVISC	use to impose an upper limit on vertical viscosity

Options for the Generic Length-Scale closure

The Generic Length Scale (GLS) uses two prognostic equations for turbulent kinetic energy (TKE) and length scale (ψ) variables. The GLS may be configured as k-kl, k-ε k-ω by tuning several parameters in roms.in, see Warner et al., 2005 for more details. The default horizontal advection is third-order upstream bias. The default vertical advection is 4th-order centered advection.

CANUTO_A	use if Canuto A-stability function formulation
CANUTO_B	use if Canuto B-stability function formulation
CHARNOK	use if Charnok surface roughness from wind stress
CRAIG_BANNER	use if Craig and Banner wave breaking surface flux
KANTHA_CLAYSON	use if Kantha and Clayson stability function
K_C2ADVECTION	use if 2nd-order centered advection
K_C4ADVECTION	use if 4th-order centered advection
N2S2_HORAVG	use if horizontal smoothing of buoyancy/shear
RI_SPLINES	use if splines reconstruction for vertical sheer
ZOS_HSIG	use if surface roughness from wave amplitude
TKE_WAVEDISS	use if wave breaking surface flux from wave amplitude

Options for the Mellor/Yamada level 2.5 closure

This is the original closure proposed by Mellor and Yamda (1982) and latter modified by Galperin et al. (1994). The default horizontal advection is third-order upstream bias. The default vertical advection is 4th-order centered advection.

N2S2_HORAVG	use if horizontal smoothing of buoyancy/shear
KANTHA_CLAYSON	use if Kantha and Clayson stability function
K_C2ADVECTION	use if 2nd-order centered advection
K_C4ADVECTION	use if 4th-order centered advection
RI_SPLINES	use if splines reconstruction for vertical sheer

Options for K-profile vertical mixing parameterization

LMD_BKPP	use if bottom boundary layer KPP mixing
LMD_CONVEC	use to add convective mixing due to shear instability
LMD_DDMIX	use to add double-diffusive mixing
LMD_NONLOCAL	use if nonlocal transport
LMD_RIMIX	use to add diffusivity due to shear instability
LMD_SHAPIRO	use if Shapiro filtering boundary layer depth
LMD_SKPP	use if surface boundary layer KPP mixing
RI_SPLINES	use if splines reconstruction for vertical sheer

Options for Richardson number smoothing

Mostly all vertical mixing parameterization are based on the Richardson Number (buoyancy/shear ratio). This computation is usually noisy and requires some smoothing. Use the options below if RI_SPLINES is not activated.

RI_HORAVG	use if horizontal Richardson number smoothing
RI_VERAVG	use if vertical Richardson number smoothing

Options for Meinte Blass bottom boundary layer closure

The Options MB_Z0BL and MB_Z0RIP should be activated concurrently.

MB_BBL	use if Meinte Blaas BBL closure
MB_CALC_ZNOT	use if computing bottom roughness internally
MB_CALC_UB	use if computing bottom orbital velocity internally
MB_Z0BIO	use if biogenic bedform roughness for ripples
MB_Z0BL	use if bedload roughness for ripples
MB_Z0RIP	use if bedform roughness for ripples

Options for Styles and Glenn (2000) bottom boundary layer closure

SG_BBL	use if Styles and Glenn (2000) BBL closure
SG_CALC_ZNOT	use if computing bottom roughness internally
SG_CALC_UB	use if computing bottom orbital velocity internally
SG_LOGINT	use if logarithmic interpolation of (Ur,Vr)

Options for the Sherwood/Signell/Warner bottom boundary layer closure

SSW_BBL	use if Sherwood et al. BBL closure
SSW_CALC_ZNOT	use if computing bottom roughness internally
SSW_LOGINT	use if logarithmic interpolation of (Ur,Vr)
SSW_CALC_UB	use if computing bottom orbital velocity internally
SSW_FORM_DRAG_COR	use to activate form drag coefficient
SSW_Z0BIO	use if biogenic bedform roughness from ripples
SSW_Z0BL	use if bedload roughness for ripples
SSW_Z0RIP	use if bedform roughness from ripples

Options for lateral boundary conditions

IMPLICIT_NUDGING	use if implicit nudging term in momentum radiation
RADIATION_2D	use if tangential phase speed in radiation conditions

Options for tidal forcing at open boundaries

The tidal data is processed in terms of tidal components, classified by period. The tidal forcing is computed for the full horizontal grid. If requested, the tidal forcing is added to the processed open boundary data. Both tidal elevation and tidal currents are required to force the model properly. However, if only the tidal elevation is available, the tidal currents at the open boundary can be estimated using reduced physics equations. Only the pressure gradient, Coriolis, and surface and bottom stresses terms are considered at the open boundary. See u2dbc_im.F or v2dbc_im.F for details. Notice that there is an additional option (FSOBC_REDUCED) for the computation of the pressure gradient term in both Flather or reduced physics conditions (*_M2FLATHER, *_M2REDUCED).

SSH_TIDES	use if imposing tidal elevation
UV_TIDES	use if imposing tidal currents
RAMP_TIDES	use if ramping (over one day) tidal forcing
FSOBC_REDUCED	use if SSH data and reduced physics conditions
ADD_FSOBC	use to add tidal elevation to processed open boundary conditions data
ADD_M2OBC	use to add tidal currents to processed open boundary conditions data

Options for ROMS/TOMS driver

Choose only one option.

ADM_DRIVER	use if generic adjoint model driver
AD_SENSITIVITY	use if adjoint sensitivity driver
AFT_EIGENMODES	use if adjoint finite time eingenmodes driver
ARRAY_MODES	use if 4D-Var representer matrix array modes
CLIPPING	use if R4D-Var representer matrix clipping analysis
CORRELATION	use if background-error correlation model driver
ENSEMBLE	use if ensemble prediction driver
EVOLVED_LCZ	use if 4D-Var evolved Hessian singular vectors
FORCING_SV	use if forcing singular vectors driver
FT_EIGENMODES	use if finite time eingenmodes driver: normal modes
HESSIAN_FSV	use if Hessian forcing singular vectors
HESSIAN_SO	use if Hessian stochastic optimals
HESSIAN_SV	use if Hessian singular vectors
INNER_PRODUCT	use if tangent linear and adjoint inner product check
I4DVAR	use if incremental 4DVar data assimilation
I4DVAR_ANA_SENSITIVITY	use if I4D-Var observations sensitivity
LCZ_FINAL	use if computing 4D-Var Hessian singular vectors
OPT_OBSERVATIONS	use if optimal observations driver
OPT_PERTURBATION	use if optimal perturbations driver, singular vectors
PICARD_TEST	use if representer tangent linear model test
PSEUDOSPECTRA	use if pseudospectra of tangent linear resolvant
RBL4DVAR	use if weak constraint RBL4D-Var data assimilation
RBL4DVAR_ANA_SENSITIVITY	use if RBL4D-Var analysis observation sensitivity
RBL4DVAR_FCT_SENSITIVITY	use if RBL4D-Var forecast observation sensitivity
RPM_DRIVER	use if generic representers model driver
R_SYMMETRY	use if representer matrix symmetry test
R4DVAR	use if Strong/Weak constraint dual formulation 4DVar data assimilation (Formerly W4DVAR)
R4DVAR_ANA_SENSITIVITY	use if R4D-Var analysis observation sensitivity
SANITY_CHECK	use if tangent linear and adjoint codes sanity check
SO_SEMI	use if stochastic optimals driver, semi-norm
SO_TRACE	use if stochastic optimals, randomized trace
SPLIT_I4DVAR	use if split I4D-Var data assimilation
SPLIT_RBL4DVAR	use if split RBL4D-Var data assimilation
SPLIT_R4DVAR	use if split R4D-Var data assimilation
SPLIT_SP4DVAR	use if split SP4D-Var data assimilation
SP4DVAR	use if Saddle-Point 4D-Var data assimilation
STOCHASTIC_OPT	use if stochastic optimals
TLM_CHECK	use if tangent linear model linearization check
TLM_DRIVER	use if generic tangent linear model driver

Options associated with tangent linear, representer and adjoint models

AD_IMPULSE	use to force adjoint model with intermittent impulses
ADJUST_BOUNDARY	use if including boundary conditions in 4DVar state
ADJUST_STFLUX	use if including surface tracer flux in 4DVar state
ADJUST_WSTRESS	use if including wind-stress in 4DVar state
ARRAY_MODES_SPLIT	use to separate analysis due to IC, forcing, and OBC
BALANCE_OPERATOR	use if error covariance multivariate balance term
BEOFS_ONLY	use if computing EOFs of background error covariance
BGQC	use if background quality control of observations
BNORM	use if Background norm Hessian singular vectors
CELERITY_WRITE	use if writing radiation celerity in forward file
CLIPPING_SPLIT	use to separate analysis due to IC, forcing, and OBC
DATALESS_LOOPS	use if testing convergence of Picard iterations
ENKF_RESTART	use if writting restart fields for EnKF
FORWARD_MIXING	use if processing forward vertical mixing coefficient
FORWARD_WRITE	use if writing out forward solution, basic state
FORWARD_READ	use if reading in forward solution, basic state
FORWARD_RHS	use if processing forward right-hand-side terms
FULL_GRID	use to consider both interior and boundary points
GEOPOTENTIAL_HCONV	use if horizontal convolutions along geopotentials
IMPACT_INNER	use to write observations impacts for each inner loop
IMPLICIT_VCONV	use if implicit vertical convolution algorithm
IMPULSE	use if processing adjoint impulse forcing
MINRES	use if Minimal Residual Method for 4DVar minimization
MULTIPLE_TLM	use if multiple TLM history files in 4DVAR
NLM_OUTER	use if nonlinear model as basic state in outer loop
OBS_IMPACT	use if observation impact to 4DVAR data assimilation
OBS_IMPACT_SPLIT	use to separate impact due to IC, forcing, and OBC
POSTERIOR_EOFS	use if posterior analysis error covariance EOFS
POSTERIOR_ERROR_F	use if final posterior analysis error covariance
POSTERIOR_ERROR_I	use if initial posterior analysis error covariance
RECOMPUTE_4DVAR	use if recomputing 4DVar in analysis algorithms
RPCG	use if Restricted B-preconditioned Lanczos solver
RPM_RELAXATION	use if Picard iterations, Diffusive Relaxation of RPM
SKIP_NLM	use to skip running NLM, reading NLM trajectory
SO_SEMI_WHITE	use to activate SO semi norm white/red noise processes
STOCH_OPT_WHITE	use to activate SO white/red noise processes
SPLINES_VCONV	use to activate implicit splines vertical convolution
TIME_CONV	use if weak-constraint 4D-Var time convolutions
VCONVOLUTION	use to add vertical correlation to 3D convolution
VERIFICATION	use if writing out solution at observation locations
WEAK_NOINTERP	use if not time interpolation in weak 4D-Var forcing
ZETA_ELLIPTIC	use if SSH elliptic Equation in balance operator

Options for Fennel et. al (2006) biological model

BIO_FENNEL	use if Fennel et al. (2006) nitrogen-based model
BIO_SEDIMENT	use to restore fallen material to the nutrient pool
CARBON	use to add carbon constituents
DENITRIFICATION	use to add denitrification processes
OXYGEN	use to add oxygen dynamics
OCMIP_OXYGEN_SC	use if Schmidt number from Keeling et al. (1998)
TALK_NONCONSERV	use if nonconservative computation of alkalinity

Options for Hypoxia ecosystem model

HYPOXIA_SRM	use if Hypoxia Simple Respiration Model

Options for NPZD biological model

NPZD_FRANKS	use if NPZD Biology model, Franks et al. (1986)
NPZD_IRON	use if NPZD Biology model with iron limitation
NPZD_POWELL	use if NPZD Biology model, Powell et al. (2006)
IRON_LIMIT	use if Fe limitation on phytoplankton growth
IRON_RELAX	use if nudging Fe over the shelf, h <= FeHmin

Options for bio-optical EcoSim model

ECOSIM	use if bio-optical EcoSim model
BIO_OPTICAL	use to compute underwater spectral light properties

Options for Nemuro lower trophic level ecosystem model

Need to choose a zooplankton grazing option (HOLLING_GRAZING or IVLEV_EXPLICIT). The default implicit IVLEV algorithm does not work yet.

NEMURO	use if Nemuro ecosystem model
BIO_SEDIMENT	use to restore fallen material to the nutrient pool
HOLLING_GRAZING	use if Holling-type s-shaped curve grazing (implicit)
IVLEV_EXPLICIT	use if Ivlev explicit grazing algorithm

Options for red tide biological model

RED_TIDE	if red tide biological model

Options for sediment transport model

SEDIMENT	use to activate sediment transport model
BEDLOAD_MPM	use to activate Meyer-Peter-Mueller bed load
BEDLOAD_SOULSBY	use to activate Soulsby wave/current bed load
SED_DENS	use to activate sediment to affect equation of state
SED_MORPH	use to allow bottom model elevation to evolve
SUSPLOAD	use to activate suspended load transport

Options for grid nesting

NESTING	to activate grid nesting: composite/refinement
NESTING_DEBUG	to check mass fluxes conservation in refinement
NO_CORRECT_TRACER	to avoid two-way correction of boundary tracer
ONE_WAY	if one-way nesting in refinement grids
TIME_INTERP_FLUX	time interpolate coarse mass flux instead persist

Options for two-way coupling to other models

These options are for coupling to other Earth System Models (ESM) via the Earth Modeling Framework (ESMF) or Modeling Coupling Toolkit (MCT) libraries. If coupling with ESMF library, it uses the National Unified Operational Prediction Capability (NUOPC) layer "cap" files to facilitate exchanges with other ESM components.

ESMF_LIB	use if coupling with the ESMF/NUOPC library
MCT_LIB	use if Coupling with the MCT library
CICE_COUPLING	use if coupling to CICE sea ice model
COAMPS_COUPLING	use if coupling to COAMPS atmospheric model
DATA_COUPLING	use if coupling to DATA model
EXCLUDE_SPONGE	use if excluding sponge point in export fields
FRC_COUPLING	if forcing from Atmopheric or Data model
REFDIF_COUPLING	use if coupling to REFDIf wave model
REGCM_COUPLING	if coupling to RegCM atmospheric model
SWAN_COUPLING	use if coupling to SWAN wave model
TIME_INTERP	use if importing snapshots for time interpolation
WAM_COUPLING	use if coupling to WAM wave model
WRF_COUPLING	use if coupling to WRF atmospheric model
WRF_TIMEAVG	use if time-averaged fields over coupling interval

Options for nearshore stresses and shallow water configurations

WET_DRY	use to activate wetting and drying
NEARSHORE_MELLOR05	use to activate radiation stress terms (Mellor 2005)
NEARSHORE_MELLOR08	use to activate radiation stress terms (Mellor 2008)

Options for MPI communications

The routines mp_assemble (used in nesting), mp_collect (used in NetCDF I/O and 4D-Var), and mp_reduce (used in global reductions) are coded in distribution.F by either using low-level (mpi_isend and mpi_irecv) or high-level (mpi_allgather and mpi_allreduce) MPI calls. The default is to use the low-level MPI calls. The options for routine mp_boundary (used to process lateral open boundary conditions is either mpi_allgather or mpi_allreduce (default).

The user needs to be aware that the choice of these MPI communication routines it will affect performance issue. In some computers, the low-level are either slower or faster than the high-level MPI library calls. It depends on the computer (cluster) set-up. Some vendors provide native MPI libraries fine-tuned for the computer architecture. The user needs to find which function option performs better by carrying on benchmarks. We provides the following choices:

ASSEMBLE_ALLGATHER	use mpi_allgather in mp_assemble
ASSEMBLE_ALLREDUCE	use mpi_allreduce in mp_assemble
BOUNDARY_ALLGATHER	use mpi_allgather in mp_boundary
COLLECT_ALLGATHER	use mpi_allgather in mp_collect
COLLECT_ALLREDUCE	use mpi_allreduce in mp_collect
REDUCE_ALLGATHER	use mpi_allgather in mp_reduce
REDUCE_ALLREDUCE	use mpi_allreduce in mp_reduce

Options for NetCDF input and output

The CPP option INLINE_2DIO is used to process 3D data by levels (2D slabs) to reduce memory needs in distributed-memory configurations. This option is convenient for large problems on nodes with limited memory.

The CPP option DEUGGING is use to avoid writing current date and CPP options to NetCDF file headers. This is used to compare serial and parallel solutions where the UNIX command "diff" is used between NetCDF files. It will only tell us that the binary files are different or not. Finding the parallel bug is completely different story.

DEBUGGING	use to activate parallel debugging switch
DEFLATE	use to set compression NetCDF-4/HDF5 format files
HDF5	to create NetCDF-4/HDF5 format files
INLINE_2DIO	use if processing 3D IO level by level
NO_LBC_ATT	use to not check NLM_LBC global attribute on restart
NO_READ_GHOST	use to not include ghost points during read/scatter
NO_WRITE_GRID	use if not writing grid arrays
PARALLEL_IO	if parallel I/O via HDF5 or pnetcdf libraries
PERFECT_RESTART	use to include perfect restart variables
PNETCDF	use if parallel I/O with pnetcdf (classic format)
POSITIVE_ZERO	use to impose positive zero in ouput data
READ_WATER	use if only reading water points data
WRITE_WATER	use if only writing water points data
RST_SINGLE	use if writing single precision restart fields
OUT_DOUBLE	use if writing double precision output fields

Options for idealized test problems

These tests are defined using analytical expressions. Choose only one configuration.

BASIN	Big Bad Basin Example
BENCHMARK	Benchmark Tests (small, Medium, big grids)
BIO_TOY	One-dimension (vertical) Biology Toy
BL_TEST	Boundary Layers Test
CANYON	Costal Form Stress Canyon Test
CHANNEL_NECK	Channel with a Constriction
COUPLING_TEST	Two-way Atmosphere-Ocean Coupling Test
DOGBONE	Idealize nesting grids (Composite/Refinement) Test
DOUBLE_GYRE	Idealized Double-gyre Example
ESTUARY_TEST	Test Estuary for Sediment
FLT_TEST	Float Tracking Example
GRAV_ADJ	Graviational Adjustment Example
INLET_TEST	Test Inlet Application
KELVIN	Kelvin wave test
LAB_CANYON	Lab Canyon, Polar Coordinates Example
LAKE_JERSEY	Lake Jersey Nesting Test Case
LAKE_SIGNELL	Lake Signell Sediment Test Case
LMD_TEST	Test for LMD and KPP
OVERFLOW	Graviational/Overflow Example
RIVERPLUME1	River Plume Example 1
RIVERPLUME2	River plume Example 2 (Hyatt and Signell)
SEAMOUNT	Seamount Example
SED_TEST1	Suspended Sediment Test in a Channel
SED_TOY	One-dimension (vertical) Sediment Toy
SHOREFACE	Shore Face Planar Beach Test Case
SOLITON	Equatorial Rossby Wave Example
TEST_CHAN	Sediment Test Channel Case
TEST_HEAD	Sediment Test Headland Case
UPWELLING	Upwelling Example (default)
WEDDELL	Idealized Weddell Sea Shelf Application
WINDBASIN	Linear Wind-driven Constant Coriolis Basin

Options for climatological applications

DAMEE_4	North Atlantic DAMEE Application, 3/4 degree

Options for selected realistic applications

ADRIA02	Adriatic Sea Application
NJ_BIGHT	New Jersey Bight Application
WC13	California Current System, 1/3 degree resolution