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.

• Options associated with momentum equations: The default horizontal and

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

UV_ADV	use to activate advection terms
UV_COR	use to activate Coriolis term
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_LOGDRAG	use to activate logarithmic bottom friction
UV_LDRAG	use to activate linear bottom friction
UV_QDRAG	use to activate quadratic bottom friction
UV_PSOURCE	use to activate point Sources/Sinks

• 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_A4HADVECTION	use if 4th-order Akima horizontal advection
TS_C2HADVECTION	use if 2nd-order centered horizontal advection
TS_C4HADVECTION	use if 4th-order centered horizontal advection
TS_MPDATA	use if recursive MPDATA 3D advection
TS_U3HADVECTION	use if 3rd-order upstream horiz. advection
TS_A4VADVECTION	use if 4th-order Akima vertical advection
TS_C2VADVECTION	use if 2nd-order centered vertical advection
TS_C4VADVECTION	use if 4th-order centered vertical advection
TS_SVADVECTION	use if splines vertical advection
TS_DIF2	use to turn ON or OFF harmonic horizontal mixing
TS_DIF4	use to turn ON or OFF biharmonic horizontal mixing
TS_FIXED	use if diagnostic run, no evolution of tracers
T_PASSIVE	use if inert passive tracers (dyes, etc)
SALINITY	use if having salinity
NONLIN_EOS	use if using nonlinear equation of state
QCORRECTION	use if net heat flux correction
SCORRECTION	use if freshwater flux correction
SOLAR_SOURCE	use if solar radiation source term
SRELAXATION	use if salinity relaxation as a freshwater flux
TS_PSOURCE	use to turn ON or OFF point Sources/Sinks

• Pressure gradient algorithm options: 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 reconsicliation 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

• Model coupling options:

SWAN_COUPLING	use if two-way coupling to SWAN
WRF_COUPLING	use if two-way coupling to WRF

• Options for surface fluxes formutalion using atmospheric boundary layer

(Fairall et al, 1996): There are three ways to provide longwave radiation in the atmospheric boundary layer: (1) 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; (2) provide (read) longwave downwelling radiation only and then add outgoing longwave radiation (LONGWAVE_OUT) as a function of the model sea surface temperature; (3) provide net longwave radiation (default).

BULK_FLUXES	use if bulk fluxes computation
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

• 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 day-of-year.

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

• Model configuration options:

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 bodyforces
PROFILE	use if time profiling
AVERAGES	use if writing out time-averaged data
AVERAGES_AKV	use if writing out time-averaged AKv
AVERAGES_AKT	use if writing out time-averaged AKt
AVERAGES_AKS	use if writing out time-averaged AKs
AVERAGES_BEDLOAD	use if writing out time-averaged bed load
AVERAGES_FLUXES	use if writing out time-averaged fluxes
AVERAGES_NEARSHORE	use if writing out time-averaged nearshore stresses
AVERAGES_QUADRATIC	use if writing out quadratic terms
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_VWALK	use if vertical random walk

• Option to activate conservative, parabolic spline reconstruction of

vertical derivatives. Notice that there also options (see above) for vertical advection of momentum and tracers using splines.

SPLINES	use to activate parabolic splines reconstruction

• Options for analytical fields configuration:

Any of the analytical expressions are coded in analytical.F.

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_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_PAIR	use if analytical surface air pressure
ANA_PASSIVE	use if analytical initial condtions 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_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 on 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 on geopotential (constant Z) surfaces
MIX_ISO_TS	use if mixing on epineutral (constant RHO) surfaces

• Options for vertical turbulent mixing scheme of momentum and tracers:

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) interior closure

• Options for the Generic Length-Scale closure (Warner et al., 2005):

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
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:

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

• Options for the Large et al. (1994) K-profile parameterization mixing:

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

• Options to activate smoothing of Richardson number, if 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

• Lateral boundary conditions options:

Select ONE option at each boundary edge for free-surface, 2D momentum, 3D momentum, and tracers. The turbulent kineric energy (TKE) conditions are only activated for the Generic length scale or Mellor-Yamada 2.5 vertical mixing closures. If open boundary radiation conditions, an additional option can be activated at each boundary edge to include a passive (active) nudging term with weak (strong) values for outflow (inflow).

• Option to impose a sponge layer near the lateral boundary:

SPONGE	use if enhanced viscosity/diffusion areas

• Options to impose mass conservation at the open boundary:

EAST_VOLCONS	use if Eastern edge mass conservation enforcement
WEST_VOLCONS	use if Western edge mass conservation enforcement
NORTH_VOLCONS	use if Northern edge mass conservation enforcement
SOUTH_VOLCONS	use if Southern edge mass conservation enforcement

• Options for periodic boundary conditions:

EW_PERIODIC	use if East-West periodic boundaries
NS_PERIODIC	use if North-South periodic boundaries

• Options for closed boundary conditions:

EASTERN_WALL	use if Eastern edge, closed wall condition
WESTERN_WALL	use if Western edge, closed wall condition
NORTHERN_WALL	use if Northern edge, closed wall condition
SOUTHERN_WALL	use if Southern edge, closed wall condition

• Additional option for radiation open boundary conditions:

RADIATION_2D	use if tangential phase speed in radiation conditions

• Eastern edge open boundary condtions options:

EAST_FSCHAPMAN	use if free-surface Chapman condition
EAST_FSGRADIENT	use if free-surface gradient condition
EAST_FSRADIATION	use if free-surface radiation condition
EAST_FSNUDGING	use if free-surface passive/active nudging term
EAST_FSCLAMPED	use if free-surface clamped condition
EAST_M2FLATHER	use if 2D momentum Flather condition
EAST_M2GRADIENT	use if 2D momentum gradient condition
EAST_M2RADIATION	use if 2D momentum radiation condition
EAST_M2REDUCED	use if 2D momentum reduced-physics
EAST_M2NUDGING	use if 2D momentum passive/active nudging term
EAST_M2CLAMPED	use if 2D momentum clamped condition
EAST_M3GRADIENT	use if 3D momentum gradient condition
EAST_M3RADIATION	use if 3D momentum radiation condition
EAST_M3NUDGING	use if 3D momentum passive/active nudging term
EAST_M3CLAMPED	use if 3D momentum clamped condition
EAST_KGRADIENT	use if TKE fields gradient condition
EAST_KRADIATION	use if TKE fields radiation condition
EAST_TGRADIENT	use if tracers gradient condition
EAST_TRADIATION	use if tracers radiation condition
EAST_TNUDGING	use if tracers passive/active nudging term
EAST_TCLAMPED	use if tracers clamped condition

• Western edge open boundary conditions options:

WEST_FSCHAPMAN	use if free-surface Chapman condition
WEST_FSGRADIENT	use if free-surface gradient condition
WEST_FSRADIATION	use if free-surface radiation condition
WEST_FSNUDGING	use if free-surface passive/active nudging term
WEST_FSCLAMPED	use if free-surface clamped condition
WEST_M2FLATHER	use if 2D momentum Flather condition
WEST_M2GRADIENT	use if 2D momentum gradient condition
WEST_M2RADIATION	use if 2D momentum radiation condition
WEST_M2REDUCED	use if 2D momentum reduced-physics
WEST_M2NUDGING	use if 2D momentum passive/active nudging term
WEST_M2CLAMPED	use if 2D momentum clamped condition
WEST_M3GRADIENT	use if 3D momentum gradient condition
WEST_M3RADIATION	use if 3D momentum radiation condition
WEST_M3NUDGING	use if 3D momentum passive/active nudging term
WEST_M3CLAMPED	use if 3D momentum clamped condition
WEST_KGRADIENT	use if TKE fields gradient condition
WEST_KRADIATION	use if TKE fields radiation condition
WEST_TGRADIENT	use if tracers gradient condition
WEST_TRADIATION	use if tracers radiation condition
WEST_TNUDGING	use if tracers passive/active nudging term
WEST_TCLAMPED	use if tracers clamped condition

• Northern edge open boundary condtions options:

NORTH_FSCHAPMAN	use if free-surface Chapman condition
NORTH_FSGRADIENT	use if free-surface gradient condition
NORTH_FSRADIATION	use if free-surface radiation condition
NORTH_FSNUDGING	use if free-surface passive/active nudging term
NORTH_FSCLAMPED	use if free-surface clamped condition
NORTH_M2FLATHER	use if 2D momentum Flather condition
NORTH_M2GRADIENT	use if 2D momentum gradient condition
NORTH_M2RADIATION	use if 2D momentum radiation condition
NORTH_M2REDUCED	use if 2D momentum reduced-physics
NORTH_M2NUDGING	use if 2D momentum passive/active nudging term
NORTH_M2CLAMPED	use if 2D momentum clamped condition
NORTH_M3GRADIENT	use if 3D momentum gradient condition
NORTH_M3RADIATION	use if 3D momentum radiation condition
NORTH_M3NUDGING	use if 3D momentum passive/active nudging term
NORTH_M3CLAMPED	use if 3D momentum clamped condition
NORTH_KGRADIENT	use if TKE fields gradient condition
NORTH_KRADIATION	use if TKE fields radiation condition
NORTH_TGRADIENT	use if tracers gradient condition
NORTH_TRADIATION	use if tracers radiation condition
NORTH_TNUDGING	use if tracers passive/active nudging term
NORTH_TCLAMPED	use if tracers clamped condition

• Southern edge open boundary condtions options:

SOUTH_FSCHAPMAN	use if free-surface Chapman condition
SOUTH_FSGRADIENT	use if free-surface gradient condition
SOUTH_FSRADIATION	use if free-surface radiation condition
SOUTH_FSNUDGING	use if free-surface passive/active nudging term
SOUTH_FSCLAMPED	use if free-surface clamped condition
SOUTH_M2FLATHER	use if 2D momentum Flather condition
SOUTH_M2GRADIENT	use if 2D momentum gradient condition
SOUTH_M2RADIATION	use if 2D momentum radiation condition
SOUTH_M2REDUCED	use if 2D momentum reduced-physics
SOUTH_M2NUDGING	use if 2D momentum passive/active nudging term
SOUTH_M2CLAMPED	use if 2D momentum clamped condition
SOUTH_M3GRADIENT	use if 3D momentum gradient condition
SOUTH_M3RADIATION	use if 3D momentum radiation condition
SOUTH_M3NUDGING	use if 3D momentum passive/active nudging term
SOUTH_M3CLAMPED	use if 3D momentum clamped condition
SOUTH_KGRADIENT	use if TKE fields gradient condition
SOUTH_KRADIATION	use if TKE fields radiation condition
SOUTH_TGRADIENT	use if tracers gradient condition
SOUTH_TRADIATION	use if tracers radiation condition
SOUTH_TNUDGING	use if tracers passive/active nudging term
SOUTH_TCLAMPED	use if tracers clamped condition

• 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 by reduced physics. 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 OBC data
ADD_M2OBC	use to add tidal currents to processed OBC data

• Options for reading and processing of climatological fields:

M2CLIMATOLOGY	use if processing 2D momentum climatology
M3CLIMATOLOGY	use if processing 3D momentum climatology
TCLIMATOLOGY	use if processing tracers climatology
ZCLIMATOLOGY	use if processing SSH climatology

• Options to nudge climatology data: Used primarily in sponge areas.

M2CLM_NUDGING	use if nudging 2D momentum climatology
M3CLM_NUDGING	use if nudging 3D momentum climatology
TCLM_NUDGING	use if nudging tracers climatology
ZCLM_NUDGING	use if nudging SSH climatology

• Optimal Interpolation (OI) or nudging data assimilation options:

The OI assimilation is intermittent whereas nudging is continuous (observations are time interpolated). If applicable, choose only one option for each field to update: either OI assimilation or nudging.

ASSIMILATION_SSH	use if assimilating SSH observations
ASSIMILATION_SST	use if assimilating SST observations
ASSIMILATION_T	use if assimilating tracers observations
ASSIMILATION_UVsur	use if assimilating surface current observations
ASSIMILATION_UV	use if assimilating horizontal current observations
UV_BAROCLINIC	use if assimilating baroclinic currents only
NUDGING_SSH	use if nudging SSH observations
NUDGING_SST	use if nudging SST observations
NUDGING_T	use if nudging tracers observations
NUDGING_UVsur	use if nudging surface current observations
NUDGING_UV	use if nudging horizontal currents observations

• ROMS/TOMS driver options:

ADM_DRIVER	use if generic adjoint model driver
AD_SENSITIVITY	use if adjoint sensitivity driver
AFT_EIGENMODES	use if adjoint finite time eingenmodes driver
CONVOLUTION	use if adjoint convolution driver
CORRELATION	use if background-error correlation model driver
ENSEMBLE	use if ensemble prediction driver
FORCING_SV	use if forcing singular vectors driver
FT_EIGENMODES	use if finite time eingenmodes driver: normal modes
GRADIENT_CHECK	use if tangent linear and adjoint codes gradient test
INNER_PRODUCT	use if tangent linear and adjoint inner product check
IS4DVAR	use if incremental 4DVar data assimilation
IS4DVAR_OLD	use if old incremental 4DVar data assimilation
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
R_SYMMETRY	use if representer matrix symmetry test
RPM_DRIVER	use if generic representers model driver
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
STOCHASTIC_OPT	use if stochastic optimals
S4DVAR	use if Strong constraint 4DVar data assimilation
TLM_CHECK	use if tangent linear model linearization check
TLM_DRIVER	use if generic tangent linear model driver
W4DPSAS	use if weak constraint 4D-PSAS data assimilation
W4DVAR	use if Weak constraint 4DVar data assimilation

• Options associated with tangent linear, representer and adjoint models:

ADJUST_STFLUX	use if including surface tracer flux in 4DVar state
ADJUST_WSTRESS	use if including wind-stress in 4DVar state	**	use if error covariance multivariate balance term
CELERITY_WRITE	use if writing radiation celerity in forward file
CONVOLVE	use if convolving solution with diffusion operators
ENERGY1_NORM	use if cost function scaled with the energy norm, 1
ENERGY2_NORM	use if cost function scaled with the energy norm, 2
ENERGY3_NORM	use if cost function scaled with the energy norm, 3
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
IMPLICIT_VCONV	use if implicit vertical convolution algorithm
IMPULSE	use if processing adjoint impulse forcing
IOM	use to activate IOM multiple executables
LANCZOS	use to activate Lanczos conjugate gradient algorithm
MULTIPLE_TLM	use if multiple TLM history files in 4DVAR
N2NORM_PROFILE	use if N2(z) profile for energy normalization
NLM_OUTER	use if nonlinear model as basic state in outer loop
RPM_RELAXATION	use if Picard iterations, Diffusive Relaxation of RPM
SO_SEMI_WHITE	use to activate white/red noise processes
VCONVOLUTION	use to add vertical correlation to 3D convolution
VERIFICATION	use if writing out solution at observation locations

• Option for processing the full grid range: (interior and boundary points)

of the state vector in variational data assimilation and generalized stability theory analysis. Otherwise, only interior points are processed.

FULL_GRID	use to consider both interior and boundary points

• Fasham-type biology model options:

BIO_FASHAM	use if Fasham type 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)
RIVER_BIOLOGY	use to process river biology point-sources
TALK_PROGNOSTIC	use if prognostic/diagnotic alkalinity

• NPZD biology model options:

NPZD_FRANKS	use if NPZD Biology model, Franks et al. (1986)
NPZD_POWELL	use if NPZD Biology model, Powell et al. (2006)

• Bio-optical EcoSim model options:

ECOSIM	use if bio-optical EcoSim model

• Sediment transport model options:

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
RIVER_SEDIMENT	use to process river sediment point-sources
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 two-way coupling to other models:

REFDIF_COUPLING	use if coupling to REFDIT wave model
SWAN_COUPLING	use if coupling to SWAN wave model
WRF_COUPLING	use if coupling to WRF atmospheric model

• Nearshore and shallow water model options:

WET_DRY	use to activate wetting and drying
NEARSHORE_MELLOR	use to activate radiation stress terms.

• NetCDF input/output options:

NO_WRITE_GRID	use if not writing grid arrays
PERFECT_RESTART	use to include perfect restart variables
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

• Option to process 3D data by levels (2D slabs) to reduce memory needs in

distributed-memory configurations. This option is convinient for large problems on nodes with limited memory.

INLINE_2DIO	use if processing 3D IO level by level

• Idealized Test Problems:

A4DVAR_TOY	4DVAR Data Assimilation Toy
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_A	Canyon_A Example
CANYON_B	Canyon_B Example
CHANNEL_NECK	Channel with a Constriction
COUPLING_TEST	Two-way Atmosphere-Ocean Coupling 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_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

• Climatological Applications: (See www.myroms.org/Datasets)

DAMEE_4	North Atlantic DAMEE Application, 3/4 degree

• Selected Realistic Applications:

ADRIA02	Adriatic Sea Application
NJ_BIGHT	New Jersey Bight Application