Options: Difference between revisions

Latest revision as of 15:32, 20 October 2021

CPP Options

This wikipage includes all ROMS CPP options in alphabetic order. A single long page is built to facilitate printing. Each option also has an individual page and its definition below is loaded using labeled section transclusion syntax. The following attributes have been identified to aid in the description of ROMS CPP options:

conflict: indicates mutually exclusive options.
parameter: important standard input parameter(s) associtated with the option.
parent: indicates association to a main option.
related: indicates other affiliated option(s) that may affect or not its scope.
required: indicates other dependent option(s) that must be activated.
routine: main files associated with the option.
variable: important state array(s) associtated with the option.
input: standard input file for configuring runtime parameters

A

A4DVAR_TOY: Idealized data assimilation example to run 4DVar weak constraint data assimilation algorithms.; parameter = Ninner, Nouter; required = RBL4DVAR or R4DVAR; related = CONVOLVE, RPM_RELAXATION; routine = rbl4dvar_ocean.h, r4dvar_ocean.h; input = roms.in, s4dvar.in

AD_IMPULSE: Option to control the forcing of the adjoint model as an intermittent impulse (on) or continuous force term (off).; parent = ADJOINT; routine = adsen_force.F

AD_SENSITIVITY: Option to run the adjoint sensitivity ocean driver ( Moore et al., 2006).; parent = ADJOINT; routine = adsen_ocean.h, ocean_control.F

ADD_FSOBC: Option to add tidal elevation to sea surface height climatology, if any, and open boundary conditions data.; variable = ssh, zeta_east, zeta_north, zeta_south, zeta_west; required = SSH_TIDES; related = ZCLIMATOLOGY; related = EAST_FSOBC, NORTH_FSOBC, SOUTH_FSOBC, WEST_FSOBC; routine = set_tides.F

ADD_M2OBC: Option to add tidal currents to 2D momentum climatology, if any, and open boundary conditions data.; variable = ubarclm, vbarclm; variable = ubar_east, ubar_north, ubar_south, ubar_west; variable = vbar_east, vbar_north, vbar_south, vbar_west; required = UV_TIDES; related = M2CLIMATOLOGY; related = EAST_M2OBC, NORTH_M2OBC, SOUTH_M2OBC, WEST_M2OBC; routine = set_tides.F

ADJOINT: Internal option to include adjoint model. It primarily declares and allocate all adjoint state variables and activates all adjoint subroutines.; related = TANGENT

ADJUST_STFLUX: Option to include surface tracer flux in 4DVar state with tangent linear, representer and adjoint models.; parameter =; parent =; required =; related = ADJUST_WSTRESS; conflict =; routine =

ADJUST_WSTRESS: Option to include wind stress in 4DVar state with tangent linear, representer and adjoint models.; parameter =; parent =; required =; related = ADJUST_STFLUX; conflict =; routine =

ADM_DRIVER: Option to run the adjoint model as a standalone driver.; related = RPM_DRIVER, TLM_DRIVER; routine = ocean_control.F

ADRIA02: Option to compile and run a realistic Adriatic Sea application.; parameter =; parent =; required =; related =; conflict =; routine =; input = floats.in, roms.in, sediment.in, stations.in

AFT_EIGENMODES: Option to run the adjoint finite time eigenvalues driver ( Moore et al., 2004).; parent = ADJOINT; related = FT_EIGENMODES; routine = aft_ocean.h, ocean_control.F

AIR_OCEAN: Option to activate two-way coupling to an atmospheric model. Currently, the coupling is done with the Model Coupling Toolkit (MCT). The coupling is either sequential or concurrent and it is only available for distributed-memory configurations. If concurrent, the MPI communicator is splited into atmosphere and ocean nodes.; conflict = WAVES_OCEAN; routine = master.F, air_ocean.h; input = coupling.in

ALBEDO: Option to compute net shortwave radiation flux using the Laevastu (1960) cloud correction to the Zillerman (1972) equation for cloudless radiation (Parkinson and Washington, 1979).; variable = srflx; required = ANA_SRFLUX; related = DIURNAL_SRFLUX; routine = analytical.F (ana_srflux)

ANA_BIOLOGY: Option to set biological tracers initial conditions with analytical expressions.; variable = t(:,:,:,:,idbio(1:NBT)); related = BIOLOGY; routine = analytical.F (ana_biology)

ANA_BMFLUX: Option to set spatially varying bottom roughness with an analytical expression.; variable =; required = SEDIMENT; conflict = ANA_SEDIMENT; routine = analytical.F (ana_bmflux)

ANA_BPFLUX: Option to set passive tracers bottom flux with analytical expressions (usually zero, no bottom flux).; variable = btflx(:,:,NAT+1:NT(ng)); required = BIOLOGY, SEDIMENT; related = ANA_BSFLUX, ANA_BTFLUX; routine = analytical.F (ana_btflux)

ANA_BSFLUX: Option to set kinematic bottom salinity flux with an analytical expression (usually zero, no bottom flux).; variable = btflx(:,:,isalt); required = SALINITY, SOLVE3D; related = ANA_BPFLUX, ANA_BTFLUX; routine = analytical.F (ana_btflux)

ANA_BTFLUX: Option to set kinematic bottom heat flux with an analytical expression (usually zero, no bottom flux).; variable = btflx(:,:,itemp); required = SOLVE3D; related = ANA_BPFLUX, ANA_BSFLUX; routine = analytical.F (ana_btflux)

ANA_CLOUD: Option to set cloud fraction with an analytical expression.; variable = cloud; routine = analytical.F (ana_cloud)

ANA_DIAG: Option to activate the computation of any user specified diagnostics.; routine = analytical.F (ana_diag), diag.F

ANA_FSOBC: Option to set free-surface open boundary conditions using analytical expressions.; variable = zeta_east, zeta_north, zeta_south, zeta_west; required = OBC; routine = analytical.F (ana_fsobc)

ANA_GRID: Option to set application grid variables with analytical expressions. Mostly, all the idealized test problems use this option. It sets the following grid-related variables: Coriolis parameter, bathymetry, ξ- and η-direction metrics and its derivates, curvilinear grid angle, ξ- and η-direction coordinates, and spherical coordinates, if applicable.; variable = f, h; variable = angler, dmde , dndx, pm , pn; variable = xp, xr, xu, xv, yp, yr, yu, yv; variable = lonp, lonr, lonu, lonv, latp, latr, latu, latv; routine = analytical.F (ana_grid)

ANA_HUMIDITY: Option to set surface air humidity (moisture) with an analytical expression. There are three types of humidity: i) absolute humidity is the density of water vapor, ii) specific humidity is the ratio of the mass of water vapor to the mass of moist air containing the vapor (g/kg), and iii) relative humidity is the ratio of the actual mixing ratio to saturation mixing ratio of the air at a given temperature and pressure (percentage).; variable = Hair; required = ALBEDO, BULK_FLUXES, ECOSIM; routine = analytical.F (ana_humid)

ANA_INITIAL: Option to set initial conditions for free-surface, momentum, and tracers with analytical expressions. Mostly, all the idealized test problems use this option.; variable = zeta, ubar, vbar; variable = u, v, t; conflict = INI_FILE; routine = analytical.F (ana_initial)

ANA_M2CLIMA: Option to set 2D momentum climatology with analytical expressions.; variable = ubarclm, vbarclm; required = M2CLIMATOLOGY; related = M2CLM_NUDGING, UV_TIDES; routine = analytical.F (ana_m2clima)

ANA_M2OBC: Option to set 2D momentum open boundary conditions using analytical expressions.; variable = ubar_east, ubar_north, ubar_south, ubar_west; variable = vbar_east, vbar_north, vbar_south, vbar_west; required = OBC; routine = analytical.F (ana_m2obc)

ANA_M3CLIMA: Option to set 3D momentum climatology with analytical expressions.; variable = uclm, vclm; parent = SOLVE3D; required = M3CLIMATOLOGY; related = M3CLM_NUDGING; routine = analytical.F (ana_m3clima)

ANA_M3OBC: Option to set 3D momentum open boundary conditions using analytical expressions.; variable = u_east, u_north, u_south, u_west; variable = v_east, v_north, v_south, v_west; required = OBC; routine = analytical.F (ana_m3obc)

ANA_MASK: Option to set land/sea masking using the analytical set-up. It is used in few idealized test problems. The mask has a value of zero over land and unity over water.; variables = pmask, rmask, umask, vmask; routine = analytical.F (ana_mask)

ANA_PAIR: Option to set surface air pressure with an analytical expression.; variable = Pair; required = BULK_FLUXES, ECOSIM; routine = analytical.F (ana_pair)

ANA_PASSIVE: Option to set inert, passive tracers initial conditions with analytical expressions.; variable = t(:,:,:,:,inert(1:NPT)); parent = SOLVE3D; required = T_PASSIVE; routine = analytical.F (ana_passive)

ANA_PERTURB: Option to perturb tangent linear and adjoint state initial conditions at specified spatial (i,j,k) location. This is used to determine the correctness of the tangent linear and adjoint models by computing the inner product at the specified location. This inner product must be symmetric within roundoff (A - A^T = 0).; parameter = user(1:8); parent = ADJOINT, TANGENT; required = SANITY_CHECK; related = INNER_PRODUCT; routine = analytical.F (ana_perturb)

ANA_PSOURCE: Option to set point sources and sinks with analytical expressions. Usually, river runoff are represented as a point source.; variable = Isrc, Jsrc, Lsrc, Dsrc; variable = Qbar, Qshape, Qsrc, Tsrc; required = Q_PSOURCE, TS_PSOURCE, UV_PSOURCE; routine = analytical.F (ana_psource)

ANA_RAIN: Option to set rain fall rate with an analytical expression.; variable = rain; required = BULK_FLUXES; related = EMINUSP; routine = analytical.F (ana_rain)

ANA_SEDIMENT: Option to set cohesive and non-cohesive sediment initial conditions with analytical expressions. It also initializes sediment bed layer properties (thickness, age, porosity), sediment fraction and mass of each size class in each bed layer, and exposed sediment layer properties (mean grain diameter, mean grain density, mean settling velocity, mean critical erosion stress, ripple length and height, bed wave excursion amplitude, and several bottom roughnesses).; variable = t(:,:,:,:,idsed(1:NST)); variable = bed, bed_frac, bed_mass, bottom; parent = SOLVE3D; required = SEDIMENT; related = BBL_MODEL, SED_BIODIFF; routine = analytical.F (ana_sediment)

ANA_SMFLUX: Option to set kinematic, surface momentum flux boundary condition (wind stress) with analytical expressions.; variable = sustr, svstr; routine = analytical.F (ana_smflux)

ANA_SPFLUX: Option to set passive tracers surface flux with analytical expressions (usually zero, no flux).; variable = stflx(:,:,NAT+1:NT(ng)); related = BIOLOGY, SEDIMENT; routine = analytical.F (ana_stflux)

ANA_SPINNING: Option to set time-variable rotation force as the sum of Coriolis and centripetal accelerations. This option is used in polar coordinates (annulus grid) applications.; variable = f, fomn; related = LAB_CANYON; routine = analytical.F (ana_spinning)

ANA_SRFLUX: Option to set kinematic, surface solar shortwave radiation flux with an analytical expression.; variable = srflx; related = ALBEDO, DIURNAL_SRFLUX; routine = analytical.F (ana_srflux)

ANA_SSFLUX: Option to set kinematic surface freshwater flux (E-P) using an analytical expression.; variable = stflx(:,:,isalt); parent = SOLVE3D; related = ANA_SPFLUX, ANA_STFLUX; conflict = EMINUSP; routine = analytical.F (ana_stflux)

ANA_SSH: Option to set sea surface height climatology with an analytical expression.; variable = ssh; required = ZCLIMATOLOGY; routine = analytical.F (ana_ssh)

ANA_SSS: Option to set sea surface salinity with an analytical expression.; variable = sss; required = SALINITY; related = SCORRECTION, SRELAXATION; routine = analytical.F (ana_sss)

ANA_SST: Option to set sea surface temperature with an analytical expression. It also sets surface net heat flux sensitivity to sea surface temperature. Both fields are used for surface net heat flux correction.; variable = dqdt, sst; related = QCORRECTION; routine = analytical.F (ana_sst), set_vbc.F

ANA_STFLUX: Option to set kinematic surface net flux of tracers using analytical expressions.; variable = stflx(:,:,1:NT); parent = SOLVE3D; related = ANA_SPFLUX, ANA_SSFLUX; conflict =; routine = analytical.F (ana_stflux)

ANA_TAIR: Option to set surface air temperature with an analytical expression; variable = Tair; parent = SOLVE3D; required = ALBEDO, BULK_FLUXES, ECOSIM; related = ANA_SRFLUX; routine = analytical.F (ana_tair)

ANA_TCLIMA: Option to set tracer climatology with analytical expressions.; variable = tclm; parent = SOLVE3D; required = TCLIMATOLOGY; related = TCLM_NUDGING; routine = analytical.F (ana_tclima)

ANA_TOBC: Option to set tracers open boundary conditions using analytical expressions.; variable = t_east, t_north, t_south, t_west; required = OBC; routine = analytical.F (ana_tobc)

ANA_VMIX: Option to set vertical mixing coefficients for momentum and tracers with analytical expressions.; variable = Akt(:,:,:,1:NAT), Akv; parent = SOLVE3D; conflict = BVF_MIXING, GLS_MIXING, LMD_MIXING, MY25_MIXING; routine = analytical.F (ana_vmix)

ANA_WINDS: Option to set surface wind vector components with analytical expressions.; variable = Uwind, Vwind; required = BULK_FLUXES, ECOSIM; routine = analytical.F (ana_winds)

ANA_WWAVE: Option to set wind-induced wave fields with analytical expressions. It currently, sets values for wave direction, height, length, top and bottom periods, and dissipation.; variable = Dwave, Hwave, Lwave, Pwave_top, Pwave_bot, wave_dissip; required = BBL_MODEL; related = WAVES_HEIGHT, WAVES_LENGTH, WAVES_TOP_PERIOD, WAVES_BOT_PERIOD; related = TKE_WAVEDISS; routine = analytical.F (ana_wwave)

ASSIMILATION: Internal option defined when any of the optimal interpolation assimilation options is activated.; related = ASSIMILATION_SSH, ASSIMILATION_SST, ASSIMILATION_T, ASSIMILATION_UV, ASSIMILATION_UVsur; conflict = NUDGING, I4DVAR, S4DVAR, RBL4DVAR, R4DVAR; routine = globaldefs.h

ASSIMILATION_SSH: Option to assimilate sea surface height observations (altimetry) using optimal interpolation.; variable = EdatSSH, EobsSSH, SSHdat, SSHobs; parent = ASSIMILATION; related = ASSIMILATION_SST, ASSIMILATION_T, ASSIMILATION_UV, ASSIMILATION_UVsur; conflict = NUDGING_SSH; routine = oi_update.F

ASSIMILATION_SST: Option to assimilate sea surface temperature observations using optimal interpolation.; variable = EdatSST, EobsSST, SSTdat, SSTobs; parent = ASSIMILATION; related = ASSIMILATION_SSH, ASSIMILATION_T, ASSIMILATION_UV, ASSIMILATION_UVsur; conflict = NUDGING_SST; routine = oi_update.F

ASSIMILATION_T: Option to assimilate tracer-type observations (temperature, salinity) using optimal interpolation.; variable = EdatT, EobsT, Tdat, Tobs; parent = ASSIMILATION; related = ASSIMILATION_SSH, ASSIMILATION_SST, ASSIMILATION_UV, ASSIMILATION_UVsur; conflict = NUDGING_T; routine = oi_update.F

ASSIMILATION_UV: Option to assimilate 3D momentum (u,v) observations using optimal interpolation.; variable = EdatUV, EobsUV, UVdat, UVobs; parent = ASSIMILATION; related = ASSIMILATION_SSH, ASSIMILATION_SST, ASSIMILATION_T, ASSIMILATION_UVsur; conflict = NUDGING_UV; routine = oi_update.F

ASSIMILATION_UVsur: Option to assimilate surface momentum (u,v) observations (CODAR) using optimal interpolation.; variable = EdatVsur, EobsVsur, Usurdat, Usur, Vsurdat, Vsur; parent = ASSIMILATION; related = ASSIMILATION_SSH, ASSIMILATION_SST, ASSIMILATION_T, ASSIMILATION_UV; conflict = NUDGING_UVsur; routine = oi_update.F

ASSUMED_SHAPE: Internal option to declare all global arrays as assumed-shape where their size, bounds, and shape are associated with pointers. Imported arrays with dummy arguments that takes the shape of the actual argument passes to it. If not activated, all the arrays are of explicit-shape. In some computers the explicit-shape arrays slow down performance because the arrays are copied when passed as arguments.; routine = globaldefs.h

ATM_PRESS: Option to impose atmospheric pressure onto sea surface. If SOLVE3D is activated the pressure is imposed on the 3D pressure gradient equations (*prsgrd*.h, i.e. prsgrd31.h). Otherwise, it is imposed on the 2D pressure gradient equations found in the step2d_LF_AM3.h routines.; parameter =; parent =; required = SOLVE3D; related = DJ_GRADPS, PJ_GRADP, PJ_GRADPQ2, PJ_GRADPQ4, SOLVE3D, WJ_GRADP; conflict =; routine = ad_prsgrd.F, prsgrd.F, rp_prsgrd.F, tl_prsgrd.F, ad_step2d_LF_AM3.h, step2d_LF_AM3.h, rp_step2d_LF_AM3.h, tl_step2d_LF_AM3.h

AVERAGES: Option to write out time-averaged fields into output NetCDF file.; parameter = nAVG, ndefAVG, ntsAVG; related = AVERAGES_AKS, AVERAGES_AKT, AVERAGES_AKV, AVERAGES_BEDLOAD, AVERAGES_FLUXES, AVERAGES_NEARSHORE, AVERAGES_QUADRATIC; routine = def_avg.F, set_avg.F, wrt_AVG.F

AVERAGES_AKS (REMOVED): This option was removed in revision 462. Option to write out time-averaged vertical diffusion of salinity into output NetCDF file. Use this option when any of the vertical mixing parameterizations is activated.; parameter = nAVG, ndefAVG, ntsAVG; parent = AVERAGES; required = AVERAGES; related = AVERAGES_AKT, AVERAGES_AKV, AVERAGES_BEDLOAD, AVERAGES_FLUXES, AVERAGES_NEARSHORE, AVERAGES_QUADRATIC; routine = def_avg.F, set_avg.F, wrt_AVG.F

AVERAGES_AKT (REMOVED): This option was removed in revision 462. Option to write out time-averaged vertical diffusion of temperature into output NetCDF file. Use this option when any of the vertical mixing parameterizations is activated.; parameter = nAVG, ndefAVG, ntsAVG; parent = AVERAGES; required = AVERAGES; related = AVERAGES_AKS, AVERAGES_AKV, AVERAGES_BEDLOAD, AVERAGES_FLUXES, AVERAGES_NEARSHORE, AVERAGES_QUADRATIC; routine = def_avg.F, set_avg.F, wrt_AVG.F

AVERAGES_AKV (REMOVED): This option was removed in revision 462. Option to write out time-averaged vertical viscosity into output NetCDF file. Use this option when any of the vertical mixing parameterizations is activated.; parameter = nAVG, ndefAVG, ntsAVG; parent = AVERAGES; required = AVERAGES; related = AVERAGES_AKS, AVERAGES_AKT, AVERAGES_BEDLOAD, AVERAGES_FLUXES, AVERAGES_NEARSHORE, AVERAGES_QUADRATIC; routine = def_avg.F, set_avg.F, wrt_AVG.F

AVERAGES_BEDLOAD (REMOVED): This option was removed in revision 462. Option to write out time-averaged bed load components into output NetCDF file.; parameter = nAVG, ndefAVG, ntsAVG; parent = AVERAGES; required = AVERAGES, BEDLOAD, SEDIMENT; related = AVERAGES_AKS, AVERAGES_AKT, AVERAGES_AKV, AVERAGES_FLUXES, AVERAGES_NEARSHORE, AVERAGES_QUADRATIC; routine = def_avg.F, set_avg.F, wrt_AVG.F

AVERAGES_DETIDE: Option to write out time-averaged detided feilds into output NetCDF file.; parameter = nAVG, ndefAVG, ntsAVG; parent = AVERAGES; required = AVERAGES; related =; routine = def_avg.F, set_avg.F, wrt_AVG.F

AVERAGES_FLUXES (REMOVED): This option was removed in revision 462. Option to write out time-averaged surface momentum stress and several fields associated with surface heat and freshwater fluxes.; parameter = nAVG, ndefAVG, ntsAVG; parent = AVERAGES; required = AVERAGES; related = AVERAGES_AKS, AVERAGES_AKT, AVERAGES_AKV, AVERAGES_BEDLOAD, AVERAGES_NEARSHORE, AVERAGES_QUADRATIC, BULK_FLUXES; routine = def_avg.F, set_avg.F, wrt_AVG.F

AVERAGES_NEARSHORE (REMOVED): This option was removed in revision 462. Option to write out time-averaged nearshore stresses variables.; parameter = nAVG, ndefAVG, ntsAVG; parent = AVERAGES; required = AVERAGES, NEARSHORE_MELLOR; related = AVERAGES_AKS, AVERAGES_AKT, AVERAGES_AKV, AVERAGES_BEDLOAD, AVERAGES_FLUXES, AVERAGES_QUADRATIC; routine = def_avg.F, set_avg.F, wrt_AVG.F

AVERAGES_QUADRATIC (REMOVED): This option was removed in revision 462. Option to write out time-averaged variables needed to compute eddy fluxes. These quadratic variables include <H u / n>, <H v / m>, <H u T / n>, <H v T / m>, <T T>, <u T>, <v T>, <u u>, <v v>, <ubar ubar>, <vbar vbar>, and <zeta zeta>.; parameter = nAVG, ndefAVG, ntsAVG; parent = AVERAGES; required = AVERAGES; related = AVERAGES_AKS, AVERAGES_AKT, AVERAGES_AKV, AVERAGES_BEDLOAD, AVERAGES_FLUXES, AVERAGES_NEARSHORE; routine = def_avg.F, set_avg.F, wrt_AVG.F

B

BACKGROUND: Internal option to; parameter =; parent =; required =; related =; conflict =; routine =

BALANCE_OPERATOR: Option to enable error covariance multivariate balance term in the tangent linear, representer and adjoint models.; parameter =; parent =; required = ADJOINT, REPRESENTER, TANGENT; related =; conflict =; routine =

BASIN: Options to compile and run the Big Bad Basin example.; parameter =; parent =; required =; related =; conflict =; routine =; input = roms.in

BEDLOAD: Internal option to; parameter =; parent =; required = SEDIMENT and BEDLOAD_MPM or BEDLOAD_SOULSBY; related = AVERAGES_BEDLOAD], BEDLOAD_MPM, BEDLOAD_SOULSBY; conflict =; routine = sed_bedload.F

BEDLOAD_MPM: Option to activate Meyer-Peter-Mueller bed load in the sediment transport model.; parameter =; parent =; required = SEDIMENT; related = AVERAGES_BEDLOAD], BEDLOAD_SOULSBY; conflict = BEDLOAD_SOULSBY; routine = sed_bedload.F

BEDLOAD_SOULSBY: Option to activate Soulsby wave/current bed load in the sediment transport model.; parameter =; parent =; required =; related = SEDIMENT; related = AVERAGES_BEDLOAD], BEDLOAD_MPM; conflict = BEDLOAD_MPM; routine = sed_bedload.F

BENCHMARK: Option to compile and run the benchmark tests. The benchmark comes in 3 sizes that can be selected at runtime.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine =; input = roms.in (ocean_benchmark1, 2 & 3)

BIO_FENNEL: Option to activate Fennel et al. ecosystem model (Fennel et al., 2009; Fennel et al., 2006). This model is loosely based on the model by Fasham et al. (1990) but it differs in many respects. The detailed equations of the nitrogen cycling component are given in Fennel et al., (2006) Nitrogen is the fundamental elemental currency in this model. This model was adapted from a code written originally by John Moisan and Emanule DiLorenzo.; related = ANA_BIOLOGY, ANA_BPFLUX, ANA_SPFLUX, BIO_SEDIMENT, CARBON, DENITRIFICATION, DIAGNOSTICS_BIO, OXYGEN, TALK_PROGNOSTIC; conflict = ECOSIM, NEMURO, NPZD_FRANKS, NPZD_IRON, NPZD_POWELL; routine = fennel.h; input = bioFennel.in

BIO_SEDIMENT: Option to restore fallen particulate material to the nutrient pool in the Fennel model.; parent = BIO_FENNEL; routine = fennel.h

BIO_TOY: Option to compile and run the one-dimensional (vertical) biology toy.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine =; input = roms.in

BIOLOGY: Internal option defined when any of the biological models is activated.; related = BIO_FENNEL, ECOSIM, NEMURO, NPZD_FRANKS, NPZD_POWELL; routine = biology.F

BL_TEST: Option to compile and run the boundary layers test.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine =; input = roms.in, stations.in

BODYFORCE: Option to apply stresses as body forces.; parameter =; parent =; required =; related =; conflict =; routine =

BULK_FLUXES: Option to use bulk fluxes computation for surface fluxes formulation using atmospheric boundary layer.; parameter =; parent =; required =; related = COOL_SKIN, EMINUSP, LONGWAVE, LONGWAVE_OUT, NL_BULK_FLUXES; conflict =; routine =

BVF_MIXING: Option to use Brunt-Vaisala frequency mixing for vertical turbulent mixing scheme of momentum and tracers.; parameter =; parent =; required =; related =; conflict = GLS_MIXING, LMD_MIXING, MY25_MIXING; routine = bvf_mix.F

C

CANUTO_A: Option to use Canuto A-stability function formulation for the Generic Length Scale closure.; parameter =; parent = GLS_MIXING; required = GLS_MIXING; related = CANUTO_B, KANTHA_CLAYSON; conflict = CANUTO_B, KANTHA_CLAYSON; routine = gls_corstep.F

CANUTO_B: Option to use Canuto B-stability function formulation for the Generic Length Scale closure.; parameter =; parent = GLS_MIXING; required = GLS_MIXING; related = CANUTO_A, KANTHA_CLAYSON; conflict = CANUTO_A, KANTHA_CLAYSON; routine = gls_corstep.F

CANYON: Option to compile and run the coastal form stress canyon test.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine =; input = roms.in (_canyon2d and _canyon3d)

CARBON: Option to include carbon constituents in the Fennel biological model. Currently, four carbon-based tracer are added to include large detritus (iLDeC), small detritus (iSDeC), total inorganic carbon (iTIC_), and total alkalinity (iTAlk).; parent = BIO_FENNEL; required = OXYGEN; routine = fennel.h

CELERITY_WRITE: Option to write radiation celerity in forward file when running tangent linear, representer and adjoint models.; parameter =; parent =; required =; related =; conflict =; routine = mod_boundary.F

CHANNEL_NECK: Option to compile and run the idealized channel with constriction test.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine =; input = roms.in (_channel_neck1 _channel_neck3)

CHARNOK: Option to use Charnok surface roughness from wind stress for the Generic Length Scale closure.; parameter =; parent = GLS_MIXING; required = GLS_MIXING; related =; conflict =; routine = gls_corstep.F

CHECKPOINTING: Internal switch to activate checkpointing switch for generalized stability theory (GST) analysis.; parameter =; parent =; required = PROPAGATOR; related =; conflict =; routine =

CLIMA_TS_MIX: Option to use if diffusion of tracer perturbation (t-tclm) is needed for horizontal mixing of tracers.; parameter =; parent =; required =; related = DIFF_GRID, MIX_S_TS, MIX_GEO_TS, MIX_ISO_TS; conflict =; routine =

CLOUDS: Internal option indicating that cloud data is needed.; required = ALBEDO, ECOSIM, LONGWAVE; related = BULK_FLUXES, ANA_SRFLUX; routine = globaldefs.h

COARE_OOST: Option to use Oost et al. (2002) relation for wave roughness formulation in bulk fluxes.; parameter =; parent =; required =; related =; conflict =; routine =

COARE_TAYLOR_YELLAND: Option to use Taylor and Yelland (2001) relation for wave roughness formulation in bulk fluxes.; parameter =; parent =; required =; related =; conflict =; routine =

CONVOLUTION: Option to use the adjoint convolution driver.; parameter =; parent =; required =; related =; conflict =; routine =

CONVOLVE: Option to use convolving solution with diffusion operators in the tangent linear, representer and adjoint models.; parameter =; parent =; required =; related =; conflict =; routine =

COOL_SKIN: Option to use cool skin correction for surface fluxes formulation using atmospheric boundary layer.; parameter =; parent =; required =; related = BULK_FLUXES; conflict =; routine = ad_bulk_fluxes.F, bulk_fluxes.F, rp_bulk_fluxes.F, tl_bulk_flux.F

CORRELATION: Option to use background-error correlation model driver.; parameter =; parent =; required =; related =; conflict =; routine =

COSINE2: Internal switch to activate the cosine-squared shaped filter.; parameter =; parent =; required =; related =; conflict =; routine =

COUPLING_TEST: Option to compile and run the two-way atmosphere-ocean coupling test.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine =; input = roms.in

CRAIG_BANNER: Option to use Craig and Banner wave breaking surface flux for the Generic Length Scales closure.; parameter =; parent = GLS_MIXING; required = GLS_MIXING; related =; conflict =; routine =

CURVGRID: Option to indicate the ROMS grid coordinates are curvilinear.; parameter =; parent =; required =; related =; conflict =; routine =

D

DAMEE_4: Option to Compile and run the 3/4° north Atlantic DAMEE application; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine =; input = roms.in

DATALESS_LOOPS: Option to test convergence of Picard iterations with the tangent linear, representer and adjoint models.; parameter =; parent =; required =; related =; conflict =; routine =

DEBUGGING: Option 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 whether the binary files are different or not. Finding the parallel bug is a completely different story.; parameter =; parent =; required =; related =; conflict =; routine =

DEEPWATER_WAVES: Option to use deep water waves approximation for wave roughness formulation in bulk fluxes.; parameter =; parent = BULK_FLUXES; required = BULK_FLUXES; related = COARE_TAYLOR_YELLAND, COARE_OOST; conflict = COARE_TAYLOR_YELLAND, COARE_OOST; routine = bulk_flux.F

DEFLATE: Option to set compression for NetCDF-4/HDF5 output files.; parameter =; parent = NETCDF4; required = NETCDF4; related =; conflict =; routine =

DENITRIFICATION: Option to include denitrification processes in the Fennel biological model.; parent = BIO_FENNEL; routine = fennel.h

DIAGNOSTICS: Internal option to compute and write balance term diagnostics for tracers and momentum.; related = DIAGNOSTICS_BIO, DIAGNOSTICS_TS, DIAGNOSTICS_UV; routine = set_diags.F, wrt_diags.F

DIAGNOSTICS_BIO: Option to compute and write biological diagnostic terms in the Fennel model.; parent = BIO_FENNEL; related = DIAGNOSTICS_TS, DIAGNOSTICS_UV; routine = fennel.h, wrt_diags.F

DIAGNOSTICS_TS: Option to compute and write diagnostic terms for tracer equations balances.; related = DIAGNOSTICS_BIO, DIAGNOSTICS_UV; routine = set_diags.F, step3d_t.F, wrt_diags.F

DIAGNOSTICS_UV: Option to compute and write diagnostic terms for momentum equations balances.; related = DIAGNOSTICS_BIO, DIAGNOSTICS_TS; routine = set_diags.F, step2d.F, step3d_t.F, wrt_diags.F

DIFF_GRID: Option to scale diffusion coefficients by grid size for horizontal mixing of tracers.; parameter =; parent =; required =; related = CLIMA_TS_MIX, MIX_S_TS, MIX_GEO_TS, MIX_ISO_TS; conflict =; routine =

DIURNAL_SRFLUX: Option to impose shortwave radiation local diurnal cycle for shortwave radiation. Input shortwave radiation data computed from averaged data (with snapshots greater than or equal to 24 hours) can be modulated by the local diurnal cycle which is a function of longitude, latitude and day of the year.; variable = srflux; parent =; required = ANA_SRFLUX; related = ALBEDO; conflict =; routine = analytical.F (ana_srflux)

DISTRIBUTE: Internal switch for compiling the model to run in parallel using distributed memory (MPI).; variable =; parent =; required =; related =; conflict =; routine =

DJ_GRADPS: Option to use splines density Jacobian (Shchepetkin, 2000) for pressure gradient algorithm.; parameter =; parent =; required = SOLVE3D; related = ATM_PRESS, PJ_GRADP, PJ_GRADPQ2, PJ_GRADPQ4, WJ_GRADP; conflict = PJ_GRADP, PJ_GRADPQ2, PJ_GRADPQ4, WJ_GRADP; routine = ad_prsgrd.F, prsgrd.F, rp_prsgrd.F, tl_prsgrd.F

DOUBLE_GYRE: Option to compile and run the idealized Double-gyre example.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine =; input = roms.in

DOUBLE_PRECISION: Internal switch to enable double precision variables. This switch is on by default.; parameter =; parent =; required =; related =; conflict =; routine = globaldefs.h

E

EAST_FSCLAMPED: Option to use free-surface clamped condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_FSCLAMPED, SOUTH_FSCLAMPED, WEST_FSCLAMPED; conflict = EW_PERIODIC, EAST_FSCHAPMAN, EAST_FSGRADIENT, EAST_FSNUDGING, EAST_FSRADIATION, EASTERN_WALL; routine = zetabc.F

EAST_FSCHAPMAN: Option to use free-surface Chapman condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_FSCHAPMAN, SOUTH_FSCHAPMAN, WEST_FSCHAPMAN; conflict = EW_PERIODIC, EAST_FSCLAMPED, EAST_FSGRADIENT, EAST_FSNUDGING, EAST_FSRADIATION, EASTERN_WALL; routine = zetabc.F

EAST_FSGRADIENT: Option to use free-surface gradient condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_FSGRADIENT, SOUTH_FSGRADIENT, WEST_FSGRADIENT; conflict = EW_PERIODIC, EAST_FSCLAMPED, EAST_FSCHAPMAN, EAST_FSNUDGING, EAST_FSRADIATION, EASTERN_WALL; routine = zetabc.F

EAST_FSNUDGING: Option to use free-surface passive/active nudging term for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_FSNUDGING, SOUTH_FSNUDGING, WEST_FSNUDGING; conflict = EW_PERIODIC, EAST_FSCLAMPED, EAST_FSCHAPMAN, EAST_FSGRADIENT, EASTERN_WALL; routine = zetabc.F

EAST_FSRADIATION: Option to use free-surface radiation condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_FSRADIATION, SOUTH_FSRADIATION, WEST_FSRADIATION; conflict = EW_PERIODIC, EAST_FSCLAMPED, EAST_FSCHAPMAN, EAST_FSGRADIENT, EASTERN_WALL; routine = zetabc.F

EAST_KGRADIENT: Option to use TKE fields gradient condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_KGRADIENT, SOUTH_KGRADIENT, WEST_KGRADIENT; conflict = EW_PERIODIC, EAST_KRADIATION, EASTERN_WALL; routine = tkebc_im.F

EAST_KRADIATION: Option to use TKE fields radiation condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_KRADIATION, SOUTH_KRADIATION, WEST_KRADIATION; conflict = EW_PERIODIC, EAST_KGRADIENT, EASTERN_WALL; routine = tkebc_im.F

EAST_M2CLAMPED: Option to use 2D momentum clamped condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_M2CLAMPED, SOUTH_M2CLAMPED, WEST_M2CLAMPED; conflict = EW_PERIODIC, EAST_M2FLATHER, EAST_M2GRADIENT, EAST_M2NUDGING, EAST_M2RADIATION, EAST_M2REDUCED, EASTERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

EAST_M2FLATHER: Option to use 2D momentum Flather condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_M2FLATHER, SOUTH_M2FLATHER, WEST_M2FLATHER; conflict = EW_PERIODIC, EAST_M2CLAMPED, EAST_M2GRADIENT, EAST_M2NUDGING, EAST_M2RADIATION, EAST_M2REDUCED, EASTERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

EAST_M2GRADIENT: Option to use 2D momentum gradient condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_M2GRADIENT, SOUTH_M2GRADIENT, WEST_M2GRADIENT; conflict = EW_PERIODIC, EAST_M2CLAMPED, EAST_M2FLATHER, EAST_M2NUDGING, EAST_M2RADIATION, EAST_M2REDUCED, EASTERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

EAST_M2NUDGING: Option to use 2D momentum passive/active nudging term for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_M2NUDGING, SOUTH_M2NUDGING, WEST_M2NUDGING; conflict = EW_PERIODIC, EAST_M2CLAMPED, EAST_M2FLATHER, EAST_M2GRADIENT, EAST_M2REDUCED, EASTERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

EAST_M2RADIATION: Option to use 2D momentum radiation condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_M2RADIATION, SOUTH_M2RADIATION, WEST_M2RADIATION; conflict = EW_PERIODIC, EAST_M2CLAMPED, EAST_M2FLATHER, EAST_M2GRADIENT, EAST_M2REDUCED, EASTERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

EAST_M2REDUCED: Option to use 2D momentum reduced-physics for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_M2REDUCED, SOUTH_M2REDUCED, WEST_M2REDUCED; conflict = EW_PERIODIC, EAST_M2CLAMPED, EAST_M2FLATHER, EAST_M2GRADIENT, EAST_M2NUDGING, EAST_M2RADIATION, EASTERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

EAST_M3CLAMPED: Option to use 3D momentum clamped condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_M3CLAMPED, SOUTH_M3CLAMPED, WEST_M3CLAMPED; conflict = EW_PERIODIC, EAST_M3GRADIENT, EAST_M3NUDGING, EAST_M3RADIATION, EASTERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

EAST_M3GRADIENT: Option to use 3D momentum gradient condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_M3GRADIENT, SOUTH_M3GRADIENT, WEST_M3GRADIENT; conflict = EW_PERIODIC, EAST_M3CLAMPED, EAST_M3NUDGING, EAST_M3RADIATION, EASTERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

EAST_M3NUDGING: Option to use 3D momentum passive/active nudging term for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_M3NUDGING, SOUTH_M3NUDGING, WEST_M3NUDGING; conflict = EW_PERIODIC, EAST_M3CLAMPED, EAST_M3GRADIENT, EASTERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

EAST_M3RADIATION: Option to use 3D momentum radiation condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_M3RADIATION, SOUTH_M3RADIATION, WEST_M3RADIATION; conflict = EW_PERIODIC, EAST_M3CLAMPED, EAST_M3GRADIENT, EASTERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

EAST_TCLAMPED: Option to use tracer clamped condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_TCLAMPED, SOUTH_TCLAMPED, WEST_TCLAMPED; conflict = EW_PERIODIC, EAST_TGRADIENT, EAST_TNUDGING, EAST_TRADIATION, EASTERN_WALL; routine = t3dbc_im.F

EAST_TGRADIENT: Option to use tracer gradient condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_TGRADIENT, SOUTH_TGRADIENT, WEST_TGRADIENT; conflict = EW_PERIODIC, EAST_TCLAMPED, EAST_TNUDGING, EAST_TRADIATION, EASTERN_WALL; routine = t3dbc_im.F

EAST_TNUDGING: Option to use tracer passive/active nudging term for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_TNUDGING, SOUTH_TNUDGING, WEST_TNUDGING; conflict = EW_PERIODIC, EAST_TCLAMPED, EAST_TGRADIENT, EASTERN_WALL; routine = t3dbc_im.F

EAST_TRADIATION: Option to use tracer radiation condition for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_TRADIATION, SOUTH_TRADIATION, WEST_TRADIATION; conflict = EW_PERIODIC, EAST_TCLAMPED, EAST_TGRADIENT, EASTERN_WALL; routine = t3dbc_im.F

EAST_VOLCONS: Option to use Southern edge mass conservation enforcement for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_VOLCONS, SOUTH_VOLCONS, WEST_VOLCONS; conflict = EW_PERIODIC, EASTERN_WALL; routine = obc_volcons.F

EASTERN_WALL: Option to use Southern edge closed wall for the eastern open boundary condition.; parameter =; parent =; required =; related = NORTH_WALL, SOUTH_WALL, WEST_WALL; conflict = EW_PERIODIC, EAST_FSCLAMPED, EAST_FSCHAPMAN, EAST_FSGRADIENT, EAST_FSNUDGING, EAST_FSRADIATION, EAST_KGRADIENT, EAST_KRADIATION, EAST_M2CLAMPED, EAST_M2FLATHER, EAST_M2GRADIENT, EAST_M2NUDGING, EAST_M2RADIATION, EAST_M2REDUCED, EAST_M3CLAMPED, EAST_M3GRADIENT, EAST_M3NUDGING, EAST_M3RADIATION, EAST_TCLAMPED, EAST_TGRADIENT, EAST_TNUDGING, EAST_TRADIATION, EAST_VOLCONS; routine = t3dbc_im.F, tkebc_im.F, u2dbc_im.F, u3dbc_im.F, v2dbc_im.F, v3dbc_im.F, zetabc.F

ECOSIM: Option to activate Bio-optical EcoSim (Bissett et al., 1999a, b) model.; related = ANA_BIOLOGY, ANA_BPFLUX, ANA_SPFLUX; conflict = BIO_FENNEL, NEMURO, NPZD_FRANKS, NPZD_IRON, NPZD_POWELL; routine = ecosim.h; input = ecosim.in

EMINUSP: Option to compute E-P for surface fluxes formulation using atmospheric boundary layer.; parameter =; parent =; required =; related = BULK_FLUXES; conflict =; routine = ad_bulk_fluxes.F, bulk_fluxes.F, rp_bulk_fluxes.F, tl_bulk_fluxes.F

ENSEMBLE: Option to use ensemble prediction driver.; parameter =; parent =; required =; related =; conflict =; routine =

ESMF_COUPLING: Internal switch to use Earth System Modeling Framework (ESMF) for coupling.; parameter =; parent =; required =; related = ESMF_LIB, MCT_LIB, MODEL_COUPLING; conflict =; routine = mod_coupler.F

ESMF_LIB: Option to use Earth System Modeling Framework (ESMF) library for coupling.; parameter =; parent =; required =; related = ESMF_COUPLING, MCT_LIB, MODEL_COUPLING; conflict = MCT_LIB; routine = mod_coupler.F

ESTUARY_TEST: Option to compile and run the test estuary for sediment.; parameter = MyAppCPP; parent =; required = SEDIMENT; related = SEDIMENT; conflict =; routine =; input = roms.in, sediment.in

EW_PERIODIC: Option to use East-West periodic boundary conditions.; parameter =; parent =; required =; related =; conflict =; routine =

F

FLOAT_OYSTER: Option to activate oyster model behavior in Langrangian drifters.; parameter =; parent = FLOATS; required = FLOATS; related = FLOATS; conflict =; routine =

FLOAT_STICKY: Option to reflect or stick floats that hit the surface or bottom in Langrangian drifters.; parameter =; parent = FLOATS; required = FLOATS; related = FLOATS; conflict =; routine =

FLOAT_VWALK: Option to use vertical random walk for Langrangian drifters.; parameter =; parent = FLOATS; required = FLOATS; related = FLOATS; conflict =; routine =

FLOATS: Option to activate simulated Lagrangian drifters.; parameter =; parent =; required =; related = FLOAT_VWALK, VWALK_FORWARD; conflict =; routine =

FLT_TEST: Option to compile and run float tracking example.; parameter = MyAppCPP; parent =; required = FLOATS; related = FLOATS; conflict =; routine =; input = floats.in, roms.in (_flt_test2d and _flt_test3d)

FORCING_SV: Option to use forcing singular vectors driver.; parameter =; parent =; required =; related =; conflict =; routine =

FORWARD_MIXING: Option to enable processing forward vertical mixing coefficient for the tangent linear, representer and adjoint models.; parameter =; parent =; required =; related =; conflict =; routine =

FORWARD_READ: Option to enable reading in forward solution, basic state for the tangent linear, representer and adjoint models.; parameter =; parent =; required =; related =; conflict =; routine =

FORWARD_RHS: Option to enable processing forward right-hand-side terms for the tangent linear, representer and adjoint models.; parameter =; parent =; required =; related =; conflict =; routine =

FORWARD_WRITE: Option to enable writing out forward solution, basic state for the tangent linear model.; parameter =; parent =; required =; related =; conflict =; routine =

FSOBC_REDUCED: Option to use SSH data and reduced physics conditions for the computation of the pressure gradient term in Flather or reduced physics boundary conditions (*_M2FLATHER, *_M2REDUCED).; parameter =; parent =; required = SSH_TIDES; related = SSH_TIDES, ADD_FSOBC; conflict =; routine = ad_u2dbc_im.F, ad_v2dbc.im.F, rp_u2dbc_im.F, rp_v2dbc_im.F, tl_u2dbc_im.F, tl_v2dbc_im.F, u2dbc_im.F, v2dbc_im.F

FT_EIGENMODES: Option to use the finite time eigenmodes driver: normal modes.; parameter =; parent =; required =; related =; conflict =; routine = ad_def_his.F, tl_def_his.F

FULL_GRID: Option for processing the full grid range (interior and boundary points) of the state vector in variational data assimilation and generalized stability theory (GST) analysis. Otherwise, only interior points are processed.; parameter =; parent =; required =; related =; conflict =; routine = packing.F

G

GLS_MIXING: Option to activate Generic Length Scale vertical mixing parameterization (Warner et al., 2005) for vertical turbulent mixing of momentum and tracers.; related = CANUTO_A, CANUTO_B, CHARNOK, CRAIG_BANNER, KANTHA_CLAYSON, K_C2ADVECTION, K_C4ADVECTION, N2S2_HORAVG, ZOS_HSIG, TKE_WAVEDISS; conflict = BVF_MIXING, MY25_MIXING, LMD_MIXING; routine = gls_corstep.F, gls_prestep.F, roms.in

GRAV_ADJ: Option to compile and run the gravitational adjustment example.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine =; input = roms.in

H

HDF5 (formerly NETCDF4): Option to create NetCDF-4/HDF5 format files for input/output. This option was named NETCDF4 prior to revision 459.; parameter =; parent =; required =; related = DEFLATE; conflict =; routine = mod_netcdf.F

HOLLING_GRAZING: Option to use Holling-type s-shaped curve grazing (implicit) for the Nemuro lower trophic level ecosystem model.; parameter =; parent = NEMURO; required = NEMURO; related = IVLEV_EXPLICIT; conflict = IVLEV_EXPLICIT; routine = nemuro.h

I

I4DVAR (Formerly IS4DVAR): Option to enable the incremental 4D variational (I4DVar), stong contraint, primal formulation data assimilation driver.; parameter =; parent =; required =; related =; conflict =; routine = i4dvar_ocean.h

I4DVAR_ANA_SENSITIVITY (Formerly IS4DVAR_SENSITIVITY): Option to activate the observation impact and sensitivity driver which quantifies the impact that each observation has on the 4DVAR data assimilation system. By measuring the sensitivity of the data assimilation system to each observation, we can determine the degree to which each observation contributes to the uncertainty in the circulation estimate. This analysis can help us to determine the type of measurements that need to be made, where to observe, and when.; required = ADJOINT, NONLINEAR, TANGENT; related = I4DVAR, LANCZOS; routine = obs_sen_i4dvar_analysis.h

ICESHELF: Option to include ice shelf cavities in the model configuration.; parameter =; parent =; required =; related =; conflict =; routine =

IMPACT_INNER: Option to; parameter =; parent =; required =; related =; conflict =; routine =

IMPLICIT_VCONV: Option to use the implicit vertical convolution algorithm for the tangent linear and adjoint models.; parameter =; parent =; required =; related =; conflict =; routine = ad_conv_3d.F, ad_conv_bry3d.F, conv_3d.F, conv_bry3d.F, tl_conv_3d.F, tl_conv_bry3d.F

IMPULSE: Option to process adjoint impulse forcing for the adjoint model.; parameter =; parent =; required =; related =; conflict =; routine =

INLET_TEST: Option to compile and run the test inlet application.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine =; input = roms.in, sediment.in

INLINE_2DIO: Option 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.; parameter =; parent =; required = SOLVE3D; related =; conflict =; routine = nf_fread3d.F, nf_fwrite3d.F

INNER_PRODUCT: Option to enable tangent linear and adjoint inner product check.; parameter =; parent =; required =; related =; conflict =; routine = pert_ocean.h

IRON_LIMIT: Option to impose iron limitation on phytoplankton growth in the NPZD iron (Fiechter et al. 2009) model.; parameter =; parent = NPZD_IRON; required = NPZD_IRON; related = IRON_RELAX, NPZD_IRON; conflict =; routine = biology.F, npzd_iron.h

IRON_RELAX: Option to allow nudging of iron over the shelf, $h<=FeH_{min}$ in the NPZD iron (Fiechter et al. 2009) model.; parameter =; parent = NPZD_IRON; required = NPZD_IRON; related = IRON_LIMIT, NPZD_IRON; conflict =; routine = biology.F, npzd_iron.h

IS4DVAR OBSOLETE - Renamed to I4DVAR in SVN revision 1022: Option to enable the incremental 4d variational (IS4DVar) data assimilation driver.; parameter =; parent =; required =; related =; conflict =; routine = is4dvar_ocean.h

IS4DVAR_SENSITIVITY OBSOLETE - Renamed to I4DVAR_ANA_SENSITIVITY in SVN revision 1022: Option to activate the observation sensitivity driver which quantifies the impact that each observation has on the 4DVAR data assimilation system. By measuring the sensitivity of the data assimilation system to each observation, we can determine the degree to which each observation contributes to the uncertainty in the circulation estimate. This analysis can help us to determine the type of measurements that need to be made, where to observe, and when.; required = ADJOINT, NONLINEAR, TANGENT; related = IS4DVAR, LANCZOS; routine = obs_sen_is4dvar.h

IVLEV_EXPLICIT: Option to use Ivlev explicit grazing algorithm for the Nemuro lower trophic level ecosystem model.; parameter =; parent = NEMURO; required = NEMURO; related = HOLLING_GRAZING; conflict = HOLLING_GRAZING; routine = nemuro.h

J

K

KANTHA_CLAYSON: Option to use the Kantha and Clayson (1994) stability function for the Generic Length Scale or Mellor/Yamada level 2.5 closure.; parameter =; parent = GLS_MIXING or MY25_MIXING; required = GLS_MIXING or MY25_MIXING; related = CANUTO_A, CANUTO_B; conflict = CANUTO_A, CANUTO_B; routine = gls_corstep.F, my25_corstep.F

KELVIN: Option to compile and run the Kelvin wave test.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine =; input = roms.in

K_C2ADVECTION: Option to use 2^nd-order centered advection for the Generic Length Scale or Mellor/Yamada level 2.5 closure.; parameter =; parent = GLS_MIXING or MY25_MIXING; required = GLS_MIXING or MY25_MIXING; related = [K_C4ADVECTION]]; conflict = [K_C4ADVECTION]]; routine = gls_corstep.F, gls_prestep.F, my25_corstep.F, my25_prestep.F

K_C4ADVECTION: Option to use 4^th-order centered advection for the Generic Length Scale or Mellor/Yamada level 2.5 closure.; parameter =; parent = GLS_MIXING or MY25_MIXING; required = GLS_MIXING or MY25_MIXING; related = K_C2ADVECTION; conflict = K_C2ADVECTION; routine = gls_corstep.F, gls_prestep.F, my25_corstep.F, my25_prestep.F

L

LAB_CANYON: Option to compile and run the lab canyon polar coordinates example.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine =; input = roms.in

LAKE_JERSEY: Option to compile and run the lake Jersey sediment test case. Configurations found on the Nesting Examples page.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine = roms.in, sediment.in

LAKE_SIGNELL: Option to compile and run the lake Signell sediment test case.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine = floats.in, roms.in, sediment.in

LMD_BKPP: Option to use bottom boundary layer KPP mixing for the Large et al. (1994) K-profile parameterization mixing.; parameter =; parent = LMD_MIXING; required = LMD_MIXING; related = LMD_CONVEC, LMD_DDMIX, LMD_NONLOCAL, LMD_RIMIX, LMD_SHAPIRO, LMD_SKPP; conflict =; routine = lmd_bkpp.F, lmd_vmix.F

LMD_CONVEC: Option to add convective mixing due to shear instability for the Large et al. (1994) K-profile parameterization mixing.; parameter =; parent = LMD_MIXING; required = LMD_MIXING; related = LMD_BKPP, LMD_DDMIX, LMD_NONLOCAL, LMD_RIMIX, LMD_SHAPIRO, LMD_SKPP; conflict =; routine = lmd_vmix.F

LMD_DDMIX: Option to add double-diffusive mixing for the Large et al. (1994) K-profile parameterization mixing.; parameter =; parent = LMD_MIXING; required = LMD_MIXING; related = LMD_BKPP, LMD_CONVEC, LMD_NONLOCAL, LMD_RIMIX, LMD_SHAPIRO, LMD_SKPP; conflict =; routine = lmd_vmix.F

LMD_MIXING: Option to activate Large et al. (1994) interior closure for vertical turbulent mixing of momentum and tracers.; parameter =; parent =; required =; related = LMD_BKPP, LMD_CONVEC, LMD_DDMIX, LMD_NONLOCAL, LMD_RIMIX, LMD_SHAPIRO, LMD_SKPP; conflict = BVF_MIXING, GLS_MIXING, MY25_MIXING; routine = ad_main3d.F, lmd_vmix.F, main3d.F, rp_main3d.F, tl_main3d.F

LMD_NONLOCAL: Option to use nonlocal transport for the Large et al. (1994) K-profile parameterization mixing.; parameter =; parent = LMD_MIXING; required = LMD_MIXING; related = LMD_BKPP, LMD_CONVEC, LMD_DDMIX, LMD_RIMIX, LMD_SHAPIRO, LMD_SKPP; conflict =; routine = ad_pre_step3d.F, lmd_skpp.F, rp_pre_step3d.F, tl_pre_step3d.F

LMD_RIMIX: Option to add diffusivity due to shear instability for the Large et al. (1994) K-profile parameterization mixing.; parameter =; parent = LMD_MIXING; required = LMD_MIXING; related = LMD_BKPP, LMD_CONVEC, LMD_DDMIX, LMD_NONLOCAL, LMD_SHAPIRO, LMD_SKPP; conflict =; routine = lmd_vmix.F

LMD_SHAPIRO: Option to use Shapiro filtering boundary layer depth for the Large et al. (1994) K-profile parameterization mixing.; parameter =; parent = LMD_MIXING; required = LMD_MIXING; related = LMD_BKPP, LMD_CONVEC, LMD_DDMIX, LMD_NONLOCAL, LMD_RIMIX, LMD_SKPP; conflict =; routine = lmd_bkpp.F, lmd_skpp.F

LMD_SKPP: Option to use surface boundary layer KPP mixing for the Large et al. (1994) K-profile parameterization mixing.; parameter =; parent = LMD_MIXING; required = LMD_MIXING; related = LMD_BKPP, LMD_CONVEC, LMD_DDMIX, LMD_NONLOCAL, LMD_RIMIX, LMD_SHAPIRO; conflict =; routine = ad_lmd_swfrac.F, lmd_skpp.F, lmd_swfrac.F, rp_lmd_swfrac.F, tl_lmd_swfrac.F

LMD_TEST: Option to compile and run the test for LMD and KPP.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine =; input = roms.in, stations.in

LONGWAVE: Option to compute the net long-wave radiation internally using the Beriland (1952) equation as a function of air temperature, sea surface temperature, relative humidity, and cloud fraction.; parameter =; parent = BULK_FLUXES; required = BULK_FLUXES; related = LOGWAVE_OUT; conflict = LONGWAVE_OUT; routine = ad_bulk_flux.F, bulk_flux.F, rp_bulk_flux.F, tl_bulk_flux.F

LONGWAVE_OUT: Option to provide (read) long-wave downwelling radiation only and then add outgoing long-wave radiation as a function of the model sea surface temperature.; parameter =; parent = BULK_FLUXES; required = BULK_FLUXES; related = LONGWAVE; conflict = LONGWAVE; routine = ad_bulk_flux.F, bulk_flux.F, rp_bulk_flux.F, tl_bulk_flux.F

M

M2CLIMATOLOGY: DEPRICATED in favor of Lm2CLM logical switches to facilitate nesting.

Option to read and process 2D momentum climatology fields.; parameter =; parent =; required =; related = ANA_M2CLIMA, M2CLM_NUDGING, UV_TIDES; conflict =; routine = ad_step2d_LF_AM3.h, set_tides.F, step2d_LF_AM3.h, rp_step2d_LF_AM3.h, tl_step2d_LF_AM3.h

M2CLM_NUDGING: DEPRICATED in favor of LnudgeM2CLM logical switches to facilitate nesting.

Option to use nudging of 2D momentum climatology data (primarily in sponge areas).; parameter =; parent =; required =; related = M2CLIMATOLOGY, ANA_M2CLIMA, UV_TIDES; conflict =; routine = ad_step2d_LF_AM3.h, step2d_LF_AM3.h, rp_step2d_LF_AM3.h, tl_step2d_LF_AM3.h

M3CLIMATOLOGY: DEPRICATED in favor of Lm3CLM logical switches to facilitate nesting.

Option to read and process 3D momentum climatology fields.; parameter =; parent =; required =; related = ANA_M3CLIMA, M3CLM_NUDGING; conflict =; routine =

M3CLM_NUDGING: DEPRICATED in favor of LnudgeM3CLM logical switches to facilitate nesting.

Option to use nudging of 3D momentum climatology data (primarily in sponge areas).; parameter =; parent =; required =; related = M3CLIMATOLOGY, ANA_M3CLIMA; conflict =; routine =

MASKING: Option to use land/sea masking.; parameter =; parent =; required =; related =; conflict =; routine =

MAX_SLOPE: Internal switch to set a maximum density slope in isopycnic diffusion.; parameter =; parent =; required =; related =; conflict =; routine =

MB_BBL: Option to use Meinte Blaas bottom boundary layer closure.; parameter =; parent =; required = BBL_MODEL; related = MB_CALC_UB, MB_CALC_ZNOT, MB_Z0BIO, MB_Z0BL, MB_Z0RIP; conflict = SG_BBL, SSW_BBL; routine =

MB_CALC_UB: Option to use if computing bottom orbital velocity internally for Meinte Blass bottom boundary layer closure; parameter =; parent = MB_BBL; required = BBL_MODEL, MB_BBL; related = MB_CALC_ZNOT, MB_Z0BIO, MB_Z0BL, MB_Z0RIP; conflict =; routine = mb_bbl.h

MB_CALC_ZNOT: Option to use if computing bottom roughness internally for Meinte Blass bottom boundary layer closure.; parameter =; parent = MB_BBL; required = BBL_MODEL, MB_BBL; related = MB_CALC_UB, MB_Z0BIO, MB_Z0BL, MB_Z0RIP; conflict =; routine = mb_bbl.h

MB_ZOBIO: Option to use biogenic bedform roughness for ripples for Meinte Blass bottom boundary layer closure.; parameter =; parent = MB_BBL; required = BBL_MODEL, MB_BBL; related = MB_CALC_UB, MB_CALC_ZNOT, MB_Z0BL, MB_Z0RIP; conflict =; routine = mb_bbl.h

MB_Z0BL: Option to use bedload roughness for ripples for Meinte Blass bottom boundary layer closure.; parameter =; parent = MB_BBL; required = BBL_MODEL, MB_BBL, MB_ZORIP; related = MB_CALC_UB, MB_CALC_ZNOT, MB_Z0BIO, MB_Z0RIP; conflict =; routine = mb_bbl.h

MB_Z0RIP: Option to use bedform roughness for ripples for Meinte Blass bottom boundary layer closure.; parameter =; parent = MB_BBL; required = BBL_MODEL, MB_BBL, MB_ZOBL; related = MB_CALC_UB, MB_CALC_ZNOT, MB_Z0BIO, MB_Z0BL; conflict =; routine = mb_bbl.h

MCT_LIB: Option to use the Model Coupling Toolkit (MCT) library for coupling.; parameter =; parent =; required =; related = ESMF_COUPLING, ESMF_LIB, MODEL_COUPLING; conflict = ESMF_COUPLING, ESMF_LIB; routine = mod_coupler.F

MIN_STRAT: Internal switch to set a minimum density stratification in isopycnic diffusion.; parameter =; parent =; required =; related =; conflict =; routine =

MIX_GEO_TS: Option to use if mixing on geopotential (constant Z) surfaces for horizontal mixing of tracers.; parameter =; parent =; required =; related = MIX_GEO_UV, MIX_ISO_TS, MIX_S_TS, MIX_S_UV; conflict = MIX_ISO_TS, MIX_S_TS; routine = ad_t3dmix.F, hmixing.F, rp_t3dmix.F, t3dmix.F, tl_t3dmix.F

MIX_GEO_UV: Option to use if mixing on geopotential (constant Z) surfaces for horizontal mixing of momentum.; parameter =; parent =; required =; related = MIX_GEO_TS, MIX_ISO_TS, MIX_S_TS, MIX_S_UV; conflict = MIX_S_UV; routine = ad_uv3dmix.F, hmixing.F, rp_uv3dmix.F, tl_uv3dmix.F, uv3dmix.F

MIX_ISO_TS: Option to use if mixing on epineutral (constant RHO) surfaces for horizontal mixing of tracers.; parameter =; parent =; required =; related = MIX_GEO_TS, MIX_GEO_UV, MIX_S_TS, MIX_S_UV; conflict = MIX_GEO_TS, MIX_S_TS; routine = ad_t3dmix.F, rp_t3dmix.F, t3dmix.F, tl_t3dmix.F

MIX_S_TS: Option to use if mixing along constant S-surfaces for horizontal mixing of tracers.; parameter =; parent =; required =; related = MIX_GEO_TS, MIX_GEO_UV, MIX_ISO_TS, MIX_S_UV; conflict = MIX_GEO_TS, MIX_ISO_TS; routine = ad_t3dmix.F, rp_t3dmix.F, t3dmix.F, tl_t3dmix.F

MIX_S_UV: Option to use if mixing along constant S-surfaces for horizontal mixing of momentum.; parameter =; parent =; required =; related = MIX_GEO_TS, MIX_GEO_UV, MIX_ISO_TS, MIX_S_TS; conflict = MIX_GEO_UV; routine = ad_uv3dmix.F, rp_uv3dmix.F, tl_uv3dmix.F, uv3dmix.F

MPI: Internal switch to configure the model to run in distributed memory (MPI).; parameter =; parent =; required =; related =; conflict =; routine =

MULTIPLE_TLM: Option to use multiple TLM (Tangent Linear Model) history files in 4DVAR.; parameter =; parent =; required =; related =; conflict =; routine =

MY25_MIXING: Option to activate Mellor/Yamada Level-2.5 closure for vertical turbulent mixing of momentum and tracers.; parameter =; parent =; required =; related = K_C2ADVECTION, K_C4ADVECTION, KANTHA_CLAYSON, N2S2_HORAVG; conflict = BVF_MIXING, GLS_MIXING, LMD_MIXING; routine = my25_corstep.F, my25_prestep.F

N

N2S2_HORAVG: Option to use horizontal smoothing of buoyancy/shear for the Generic Length Scale of Mellor/Yamada level 2.5 closure; parameter =; parent = GLS_MIXING or MY25_MIXING; required = GLS_MIXING or MY25_MIXING; related =; conflict =; routine = gls_corstep.F, my25_corstep.F

NEARSHORE_MELLOR: Option to activate radiation stress terms for near-shore and shallow water models.; parameter =; parent =; required =; related =; conflict =; routine =

NEMURO: Option to activate NEMURO model.; related = ANA_BIOLOGY, ANA_BPFLUX, ANA_SPFLUX; conflict = BIO_FENNEL, ECOSIM, NPZD_FRANKS, NPZD_IRON, NPZD_POWELL; routine = nemuro.h; input = nemuro.in

NESTING: Option to enable ROMS grid nesting capabilities.; parameter =; parent =; required =; related = ONE_WAY; conflict =; routine = nesting.F

NETCDF4 (RENAMED): Option to create NetCDF-4/HDF5 format files for input/output. This option was renamed to HDF5 in revision 459.; parameter =; parent =; required =; related = DEFLATE; conflict =; routine = mod_netcdf.F

NJ_BIGHT: Option to compile and run NJ_BIGHT realistic application.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine =; input = roms.in

NL_BULK_FLUXES: Option to handle the reading of surface fluxes (E-P) computed by the nonlinear model in the representer model. This option can be also used in the nonlinear model when BULK_FLUXES is not defined to read such surface salinity flux if needed.; parameter =; parent =; required = BULK_FLUXES; related = COOL_SKIN, EMINUS, LONGWAVE, LONGWAVE_OUT; conflict =; routine =

NLM_OUTER: Option to use nonlinear model as basic stat in outer loop with tangent linear, representer and adjoint models.; parameter =; parent =; required =; related =; conflict =; routine =

NO_READ_GHOST: Option to not include ghost points during read/scatter (I/O).; parameter =; parent =; required =; related =; conflict =; routine = nf_fread2d.F, nf_fread3d.F, nf_fread4d.F

NO_WRITE_GRID: Option to not write grid arrays.; parameter =; parent =; required =; related =; conflict =; routine = wrt_info.F

NONLINEAR: Internal switch to include the nonlinear model in compilation.; parameter =; parent =; required =; related = ADJOINT, REPRESENTER, TANGENT; conflict =; routine =

NONLIN_EOS: Option to use the nonlinear equation of state for tracers.; parameter =; parent =; required =; related =; conflict =; routine = ad_rho_eos.F, rho_eos.F, rp_rho_eos.F, tl_rho_eos.F

NORTH_FSCLAMPED: Option to use free-surface clamped condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_FSCLAMPED, SOUTH_FSCLAMPED, WEST_FSCLAMPED; conflict = NS_PERIODIC, NORTH_FSCHAPMAN, NORTH_FSGRADIENT, NORTH_FSNUDGING, NORTH_FSRADIATION, NORTHERN_WALL; routine = zetabc.F

NORTH_FSCHAPMAN: Option to use free-surface Chapman condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_FSCHAPMAN, SOUTH_FSCHAPMAN, WEST_FSCHAPMAN; conflict = NS_PERIODIC, NORTH_FSCLAMPED, NORTH_FSGRADIENT, NORTH_FSNUDGING, NORTH_FSRADIATION, NORTHERN_WALL; routine = zetabc.F

NORTH_FSGRADIENT: Option to use free-surface gradient condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_FSGRADIENT, SOUTH_FSGRADIENT, WEST_FSGRADIENT; conflict = NS_PERIODIC, NORTH_FSCLAMPED, NORTH_FSCHAPMAN, NORTH_FSNUDGING, NORTH_FSRADIATION, NORTHERN_WALL; routine = zetabc.F

NORTH_FSNUDGING: Option to use free-surface passive/active nudging term for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_FSNUDGING, SOUTH_FSNUDGING, WEST_FSNUDGING; conflict = NS_PERIODIC, NORTH_FSCLAMPED, NORTH_FSCHAPMAN, NORTH_FSGRADIENT, NORTHERN_WALL; routine = zetabc.F

NORTH_FSRADIATION: Option to use free-surface radiation condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_FSRADIATION, SOUTH_FSRADIATION, WEST_FSRADIATION; conflict = NS_PERIODIC, NORTH_FSCLAMPED, NORTH_FSCHAPMAN, NORTH_FSGRADIENT, NORTHERN_WALL; routine = zetabc.F

NORTH_KGRADIENT: Option to use TKE fields gradient condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_KGRADIENT, SOUTH_KGRADIENT, WEST_KGRADIENT; conflict = NS_PERIODIC, NORTH_KRADIATION, NORTHERN_WALL; routine = tkebc_im.F

NORTH_KRADIATION: Option to use TKE fields radiation condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_KRADIATION, SOUTH_KRADIATION, WEST_KRADIATION; conflict = NS_PERIODIC, NORTH_KGRADIENT, NORTHERN_WALL; routine = tkebc_im.F

NORTH_M2CLAMPED: Option to use 2D momentum clamped condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_M2CLAMPED, SOUTH_M2CLAMPED, WEST_M2CLAMPED; conflict = NS_PERIODIC, NORTH_M2FLATHER, NORTH_M2GRADIENT, NORTH_M2NUDGING, NORTH_M2RADIATION, NORTH_M2REDUCED, NORTHERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

NORTH_M2FLATHER: Option to use 2D momentum Flather condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_M2FLATHER, SOUTH_M2FLATHER, WEST_M2FLATHER; conflict = NS_PERIODIC, NORTH_M2CLAMPED, NORTH_M2GRADIENT, NORTH_M2NUDGING, NORTH_M2RADIATION, NORTH_M2REDUCED, NORTHERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

NORTH_M2GRADIENT: Option to use 2D momentum gradient condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_M2GRADIENT, SOUTH_M2GRADIENT, WEST_M2GRADIENT; conflict = NS_PERIODIC, NORTH_M2CLAMPED, NORTH_M2FLATHER, NORTH_M2NUDGING, NORTH_M2RADIATION, NORTH_M2REDUCED, NORTHERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

NORTH_M2NUDGING: Option to use 2D momentum passive/active nudging term for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_M2NUDGING, SOUTH_M2NUDGING, WEST_M2NUDGING; conflict = NS_PERIODIC, NORTH_M2CLAMPED, NORTH_M2FLATHER, NORTH_M2GRADIENT, NORTH_M2REDUCED, NORTHERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

NORTH_M2RADIATION: Option to use 2D momentum radiation condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_M2RADIATION, SOUTH_M2RADIATION, WEST_M2RADIATION; conflict = NS_PERIODIC, NORTH_M2CLAMPED, NORTH_M2FLATHER, NORTH_M2GRADIENT, NORTH_M2REDUCED, NORTHERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

NORTH_M2REDUCED: Option to use 2D momentum reduced-physics for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_M2REDUCED, SOUTH_M2REDUCED, WEST_M2REDUCED; conflict = NS_PERIODIC, NORTH_M2CLAMPED, NORTH_M2FLATHER, NORTH_M2GRADIENT, NORTH_M2NUDGING, NORTH_M2RADIATION, NORTHERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

NORTH_M3CLAMPED: Option to use 3D momentum clamped condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_M3CLAMPED, SOUTH_M3CLAMPED, WEST_M3CLAMPED; conflict = NS_PERIODIC, NORTH_M3GRADIENT, NORTH_M3NUDGING, NORTH_M3RADIATION, NORTHERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

NORTH_M3GRADIENT: Option to use 3D momentum gradient condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_M3GRADIENT, SOUTH_M3GRADIENT, WEST_M3GRADIENT; conflict = NS_PERIODIC, NORTH_M3CLAMPED, NORTH_M3NUDGING, NORTH_M3RADIATION, NORTHERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

NORTH_M3NUDGING: Option to use 3D momentum passive/active nudging term for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_M3NUDGING, SOUTH_M3NUDGING, WEST_M3NUDGING; conflict = NS_PERIODIC, NORTH_M3CLAMPED, NORTH_M3GRADIENT, NORTHERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

NORTH_M3RADIATION: Option to use 3D momentum radiation condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_M3RADIATION, SOUTH_M3RADIATION, WEST_M3RADIATION; conflict = NS_PERIODIC, NORTH_M3CLAMPED, NORTH_M3GRADIENT, NORTHERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

NORTH_TCLAMPED: Option to use tracer clamped condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_TCLAMPED, SOUTH_TCLAMPED, WEST_TCLAMPED; conflict = NS_PERIODIC, NORTH_TGRADIENT, NORTH_TNUDGING, NORTH_TRADIATION, NORTHERN_WALL; routine = t3dbc_im.F

NORTH_TGRADIENT: Option to use tracer gradient condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_TGRADIENT, SOUTH_TGRADIENT, WEST_TGRADIENT; conflict = NS_PERIODIC, NORTH_TCLAMPED, NORTH_TNUDGING, NORTH_TRADIATION, NORTHERN_WALL; routine = t3dbc_im.F

NORTH_TNUDGING: Option to use tracer passive/active nudging term for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_TNUDGING, SOUTH_TNUDGING, WEST_TNUDGING; conflict = NS_PERIODIC, NORTH_TCLAMPED, NORTH_TGRADIENT, NORTHERN_WALL; routine = t3dbc_im.F

NORTH_TRADIATION: Option to use tracer radiation condition for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_TRADIATION, SOUTH_TRADIATION, WEST_TRADIATION; conflict = NS_PERIODIC, NORTH_TCLAMPED, NORTH_TGRADIENT, NORTHERN_WALL; routine = t3dbc_im.F

NORTH_VOLCONS: Option to use Southern edge mass conservation enforcement for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_VOLCONS, SOUTH_VOLCONS, WEST_VOLCONS; conflict = NS_PERIODIC, NORTHERN_WALL; routine = obc_volcons.F

NORTHERN_WALL: Option to use Southern edge closed wall for the northern open boundary condition.; parameter =; parent =; required =; related = EAST_WALL, SOUTH_WALL, WEST_WALL; conflict = NS_PERIODIC, NORTH_FSCLAMPED, NORTH_FSCHAPMAN, NORTH_FSGRADIENT, NORTH_FSNUDGING, NORTH_FSRADIATION, NORTH_KGRADIENT, NORTH_KRADIATION, NORTH_M2CLAMPED, NORTH_M2FLATHER, NORTH_M2GRADIENT, NORTH_M2NUDGING, NORTH_M2RADIATION, NORTH_M2REDUCED, NORTH_M3CLAMPED, NORTH_M3GRADIENT, NORTH_M3NUDGING, NORTH_M3RADIATION, NORTH_TCLAMPED, NORTH_TGRADIENT, NORTH_TNUDGING, NORTH_TRADIATION, NORTH_VOLCONS; routine = t3dbc_im.F, tkebc_im.F, u2dbc_im.F, u3dbc_im.F, v2dbc_im.F, v3dbc_im.F, zetabc.F

NPZD_FRANKS: Option to activate Franks et al. (1986) NPZD biological model.; related = ANA_BIOLOGY, ANA_BPFLUX, ANA_SPFLUX; conflict = BIO_FENNEL, ECOSIM, NEMURO, NPZD_IRON, NPZD_POWELL; routine = npzd_Franks.h; input = npzd_Franks.in

NPZD_IRON: Option to activate Fiechter et al. (2009) iron NPZD biological model.; related = ANA_BIOLOGY, ANA_BPFLUX, ANA_SPFLUX; conflict = BIO_FENNEL, ECOSIM, NEMURO, NPZD_FRANKS, NPZD_POWELL; routine = npzd_iron.h; input = npzd_iron.in

NPZD_POWELL: Option to activate Powell et al. (2006) NPZD biological model.; related = ANA_BIOLOGY, ANA_BPFLUX, ANA_SPFLUX; conflict = BIO_FENNEL, ECOSIM, NEMURO, NPZD_FRANKS, NPZD_IRON; routine = npzd_Powell.h; input = npzd_Powell.in

NS_PERIODIC: Option to use North_South periodic boundary conditions.; parameter =; parent =; required =; related =; conflict =; routine =

NUDGING_SSH: Option to nudge sea surface height observations (altimetry).; parameter =; parent =; required =; related = NUDGING_SSH, NUDGING_SST, NUDGING_T, NUDGING_UV, NUDGING_UVsur; conflict = ASSIMILATION_SSH; routine =

NUDGING_SST: Option to nudge sea surface temperature observations.; parameter =; parent =; required =; related = NUDGING_SSH, NUDGING_T, NUDGING_UV, NUDGING_UVsur; conflict = ASSIMILATION_SST; routine =

NUDGING_T: Option to nudge tracer-type observations (temperature and salinity).; parameter =; parent =; required =; related = NUDGING_SSH, NUDGING_SST, NUDGING_UV, NUDGING_UVsur; conflict = ASSIMILATION_T; routine =

NUDGING_UV: Option to nudge horizontal current observations.; parameter =; parent =; required =; related = NUDGING_SSH, NUDGING_SST, NUDGING_T, NUDGING_UVsur; conflict = ASSIMILATION_UV; routine =

NUDGING_UVsur: Option to nudge surface current observations.; parameter =; parent =; required =; related = NUDGING_SSH, NUDGING_SST, NUDGING_T, NUDGING_UV; conflict = ASSIMILATION_UVsur; routine =

O

OBC: Internal option indicating open boundary conditions.; related = EAST_FSOBC, EAST_M2OBC, EAST_M3OBC, EAST_TOBC; related = WEST_FSOBC, WEST_M2OBC, WEST_M3OBC, WEST_TOBC; related = NORTH_FSOBC, NORTH_M2OBC, NORTH_M3OBC, NORTH_TOBC; related = SOUTH_FSOBC, SOUTH_M2OBC, SOUTH_M3OBC, SOUTH_TOBC; routine = globaldefs.h

OBS_IMPACT: Option to to compute the observation impact to RBL4DVAR_ANA_SENSITIVITY, R4DVAR_ANA_SENSITIVITY, and I4DVAR_ANA_SENSITIVITY algorithms.; parameter =; parent =; required = RBL4DVAR_ANA_SENSITIVITY, R4DVAR_ANA_SENSITIVITY, or I4DVAR_ANA_SENSITIVITY; related = OBS_IMPACT_SPLIT; conflict =; routine =

OBS_IMPACT_SPLIT: Option to compute the contributions due to initial conditions, surface forcing, and boundary conditions. This option needs to be used with OBS_IMPACT and RBL4DVAR_ANA_SENSITIVITY or R4DVAR_ANA_SENSITIVITY.; parameter =; parent =; required = OBS_IMPACT and RBL4DVAR_ANA_SENSITIVITY or R4DVAR_ANA_SENSITIVITY; related = OBS_IMPACT; conflict =; routine =

OBS_SPACE: Option to compute the forecast error metrics in observation space.; parameter =; parent =; required =; related =; conflict =; routine = ad_htobs.F, def_info.F, globaldefs.h, mod_fourdvar.F, mod_iounits.F, obs_sen_rbl4dvar_forecast.h, read_asspar.F, read_phypar.F

OBSERVATIONS: Internal switch to process observations in tangent linear, representer and adjoint models.; parameter =; parent =; required =; related =; conflict =; routine =

OCMIP_OXYGEN_SC: Option to use the Keeling et al. (1998) formulae for the Schmit number to model O₂ gas exchange. If deactivated, the formulation of Wanninkhof (1992) is used instead.; parent = BIO_FENNEL; required = OXYGEN; routine = fennel.h

ONE_WAY: Option to activate One-way grid nesting in refinement grids instead of the default two way nesting.; parent = NESTING; required = NESTING; routine = nesting.F

OPT_OBSERVATIONS: Option to use the optimal observations driver.; parameter =; parent =; required =; related =; conflict =; routine =

OPT_PERTURBATION: Option to use the optimal perturbations driver, singular vectors.; parameter =; parent =; required =; related =; conflict =; routine =

OUT_DOUBLE: Option to write double precision output fields to output NetCDF files.; parameter =; parent =; required =; related =; conflict =; routine = mod_netcdf.F

OVERFLOW: Option to compile and run the gravitational/overflow example.; parameter = MyAppCPP; parent =; required =; related =; conflict =; routine = roms.in

OXYGEN: Option to include oxygen dynamics in the Fennel biological model. Currently, an additional tracer is added for dissolved oxygen concentration (iOxyg).; parent = BIO_FENNEL; routine = fennel.h

_OPENMP: Internal switch to activate OpenMP (shared memory) for parallel runs.; parameter =; parent =; required =; related =; conflict =; routine =

P

PERFECT_RESTART: Option to include perfect restart variables in the restart output NetCDF file.; parameter =; parent =; required =; related =; conflict =; routine =

PARALLEL_IO: Option to use parallel I/O via HDF5 or pnetcdf libraries.; parameter =; parent =; required = HDF5 or PNETCDF; related = HDF5, PNETCDF; conflict =; routine = mod_netcdf.F

PICARD_TEST: Option to use representer tangent linear model test driver.; parameter =; parent =; required =; related =; conflict =; routine =

PJ_GRADP: Option to use finite volume pressure Jacobian (Lin, 1997) for pressure gradient algorithm.; parameter =; parent =; required = SOLVE3D; related = ATM_PRESS, DJ_GRADPS, PJ_GRADPQ2, PJ_GRADPQ4, WJ_GRADP; conflict = DJ_GRADPS, PJ_GRADPQ2, PJ_GRADPQ4, WJ_GRADP; routine = ad_prsgrd.F, prsgrd.F, rp_prsgrd.F, tl_prsgrd.F

PJ_GRADPQ2: Option to use quadratic 2 pressure Jacobian (Shchepetkin, 2000) for pressure gradient algorithm.; parameter =; parent =; required = SOLVE3D; related = ATM_PRESS, DJ_GRADPS, PJ_GRADP, PJ_GRADPQ4, WJ_GRADP; conflict = DJ_GRADPS, PJ_GRADP, PJ_GRADPQ4, WJ_GRADP; routine = ad_prsgrd.F, prsgrd.F, rp_prsgrd.F, tl_prsgrd.F

PJ_GRADPQ4: Option to use quadratic 4 pressure Jacobian (Shchepetkin, 2000) for pressure gradient algorithm.; parameter =; parent =; required = SOLVE3D; related = ATM_PRESS, DJ_GRADPS, PJ_GRADP, PJ_GRADPQ2, WJ_GRADP; conflict = DJ_GRADPS, PJ_GRADP, PJ_GRADPQ2, WJ_GRADP; routine = ad_prsgrd.F, prsgrd.F, rp_prsgrd.F, tl_prsgrd.F

PNETCDF: Option to use parallel I/O with pnetcdf (classic format).; parameter =; parent =; required = PARALLEL_IO; related =; conflict = HDF5; routine = mod_netcdf.F

POSTERIOR_EOFS: Option to include the dominant EOFs of the posterior (analysis) error covariance matrix, Ea, for the estimated initial conditions. These EOFs contain information about the patterns of largest uncertainty in the 4DVAR estimate.; parameter =; parent =; required =; related = POSTERIOR_ERROR_F POSTERIOR_ERROR_I; conflict =; routine =

POSTERIOR_ERROR_F: Option to compute the final assimilation time-window posterior error covariance matrix for the RBL4DVAR and R4DVAR algorithms. This represents the diagonal elements of the full error analysis covariance matrix. These should be compared to the background error variances (squared standard deviations) for each variable which are specified in the STDnameI, STDnameI, STDnameB, STDnameF input NetCDF files. The analysis error covariance are written to a new NetCDF file (ERRname) which is specified in s4dvar.in. Currently, the analysis error is only possible for a single outer loop, Nouter=1.

This option must never be run at the same time as POSTERIOR_ERROR_I. If the POSTERIOR_EOFS option is defined, the EOFS of the analysis error covariance matrix are also computed along with the trace estimate. They are saved in the HSSname output NetCDF file.; parameter =; parent =; required =; related = POSTERIOR_EOFS; conflict = POSTERIOR_ERROR_I; routine =

POSTERIOR_ERROR_I: Option to compute the initial assimilation time-window posterior error covariance matrix for the RBL4DVAR and R4DVAR algorithms. This represents the diagonal elements of the full error analysis covariance matrix. These should be compared to the background error variances (squared standard deviations) for each variable which are specified in the STDnameI, STDnameI, STDnameB, STDnameF input NetCDF files. The analysis error covariance are written to a new NetCDF file (ERRname) which is specified in s4dvar.in. Currently, the analysis error is only possible for a single outer loop, Nouter=1.

This option must never be run at the same time as POSTERIOR_ERROR_F. If the POSTERIOR_EOFS option is defined, the EOFS of the analysis error covariance matrix are also computed along with the trace estimate. They are saved in the HSSname output NetCDF file.; parameter =; parent =; required =; related = POSTERIOR_EOFS; conflict = POSTERIOR_ERROR_F; routine =

POWER_LAW: Internal switch to use power law time-averaging filter for barotropic fields.; parameter =; parent =; required = SOLVE3D; related =; conflict =; routine =

PROFILE: Option to use time profiling.; parameter =; parent =; required =; related =; conflict =; routine =

PSEUDOSPECTRA: Option to use pseudospectra of tangent linear resolvant driver.; parameter =; parent =; required =; related =; conflict =; routine =

Q

QCORRECTION: Option to use net heat flux correction for tracers.; parameter =; parent =; required =; related =; conflict =; routine = ad_set_vbc.F, rp_set_vbc.F, set_vbc.F, tl_set_vbc.F

Q_PSOURCE (OBSOLETE as of revision 701): Option to activate/deactivate point sources/sinks of momentum. This option is used to specify the mass transport in the vertical, such as precipitation or groundwater discharge.; variable = Dsrc(1:Nsrc), Qsrc(1:Nsrc,k); related = ANA_PSOURCE, TS_PSOURCE; confict =; routine = step2d.F, step3d_uv.F

R

R_SYMMETRY: Option to; parameter =; parent =; required =; related =; conflict =; routine =

R4DVAR (Formerly W4DVAR): Option to activate indirect Representers 4D-Var; strong/weak constraint, dual formulation. This algorithm is no longer developed due to its instability in multiple outer loops in applications with high Rossby number. It is keep for instructional usage. We do not recommend to be used in realistic applications. Use instead the RBL4D-Var algorithm, which has a more efficient minimization RBLanczos solver.; parameter =; parent =; required =; related =; conflict =; routine = r4dvar_ocean.h

R4DVAR_ANA_SENSITIVITY (Formerly W4DVAR_SENSITIVITY): Option to activate R4D-Var Analysis Observation Impact and Observations Sensitivity.; parameter =; parent =; required =; related =; conflict =; routine = obs_sen_r4dvar_analysis.h

RADIATION_2D: Option to use tangential phase speed in radiation open boundary conditions.; parameter =; parent =; required =; related = EAST_FSRADIATION, EAST_KRADIATION, EAST_M2RADIATION, EAST_M3RADIATION, EAST_TRADIATION, NORTH_FSRADIATION, NORTH_KRADIATION, NORTH_M2RADIATION, NORTH_M3RADIATION, NORTH_TRADIATION SOUTH_FSRADIATION, SOUTH_KRADIATION, SOUTH_M2RADIATION, SOUTH_M3RADIATION, SOUTH_TRADIATION WEST_FSRADIATION, WEST_KRADIATION, WEST_M2RADIATION, WEST_M3RADIATION, WEST_TRADIATION; conflict =; routine =

RAMP_TIDES: Option to ramp (over one day) tidal forcing at open boundaries.; parameter =; parent =; required =; related = SSH_TIDES, UV_TIDES; conflict =; routine =

RBL4DVAR (Formerly W4DPSAS): Option to activate Restricted B-preconditioned Lanczos 4D-Var; strong/weak constraint, dual formulation. This driver has evolved throught the years and it is no longer a PSAS algorithm. See Gürol et al. (2014) for full description of the RBLanczos methodology.; parameter =; parent =; required =; related =; conflict =; routine = rbl4dvar_ocean.h

RBL4DVAR_FCT_SENSITIVITY (Formerly W4DPSAS_FCT_SENSITIVITY): Option to activate RBL4D-Var Forecast Observation Impact and Observations Sensitivity.; parameter =; parent =; required =; related =; conflict =; routine = ad_htobs.F, ad_rpcg_lanczos.F, ceckdefs.F, def_info.F, def_ini.F, def_mod.F, get_state.F, globaldefs.h, mod_iounits.F, mod_fourdvar.F, obs_sen_rbl4dvar_forecast.h, read_asspar.F, read_phypar.F, rpcg_lanczos.F, tl_rpcg_lanczos.F, wrt_info.F

RBL4DVAR_ANA_SENSITIVITY (Formerly W4DPSAS_SENSITIVITY): Option to activate RBL4D-Var analysis observation impact and observations sensitivity.; parameter =; parent =; required =; related =; conflict =; routine = obs_sen_rbl4dvar_analysis.h

READ_WATER: Option to; parameter =; parent =; required =; related =; conflict =; routine =

REFDIF_COUPLING: Option to; parameter =; parent =; required =; related =; conflict =; routine =

RI_HORAVG: Option to; parameter =; parent =; required =; related =; conflict =; routine =

RI_VERAVG: Option to; parameter =; parent =; required =; related =; conflict =; routine =

RIVERPLUME1: Option to; parameter =; parent =; required =; related =; conflict =; routine =

RIVERPLUME2: Option to; parameter =; parent =; required =; related =; conflict =; routine =

RHO_SURF: Option to; parameter =; parent =; required =; related =; conflict =; routine =

RPM_DRIVER: Option to; parameter =; parent =; required =; related =; conflict =; routine =

RPM_RELAXATION: Option to; parameter =; parent =; required =; related =; conflict =; routine =

RST_SINGLE: Option to; parameter =; parent =; required =; related =; conflict =; routine =

S

SALINITY: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SANITY_CHECK: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SCORRECTION: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SEAMOUNT: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SEDIMENT: Option to activate cohesive and non-cohesive sediment model (Warner et al., 2006).; related = ANA_BPFLUX, ANA_SEDIMENT, ANA_SPFLUX; related = BEDLOAD, RIVER_SEDIMENT, SED_DENS, SED_MORPH, SUSPLOAD; routine = sediment.F, sediment.in

SED_DENS: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SED_MORPH: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SED_TEST1: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SED_TOY: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SG_BBL: Option to use Styles and Glenn (2000) bottom boundary layer closure.; parameter =; parent =; required = BBL_MODEL; related = SG_CALC_UB, SG_CALC_ZNOT, SG_LOGINT; conflict =; routine = sg_bbl.h

SG_CALC_UB: Option to use if computing bottom orbital velocity internally for Styles and Glenn (2000) bottom boundary layer closure.; parameter =; parent = SG_BBL; required = BBL_MODEL, SG_BBL; related = SG_CALC_ZNOT, SG_LOGINT; conflict =; routine = sg_bbl.h

SG_CALC_ZNOT: Option to use if computing bottom roughness internally for Styles and Glenn (2000) bottom boundary layer closure.; parameter =; parent = SG_BBL; required = BBL_MODEL, SG_BBL; related = SG_CALC_UB, SG_LOGINT; conflict =; routine = sg_bbl.h

SG_LOGINT: Option to use logarithmic interpolation of (Ur,Vr) for Styles and Glenn (2000) bottom boundary layer closure.; parameter =; parent = SG_BBL; required = BBL_MODEL, SG_BBL; related = SG_CALC_UB, SG_CALC_ZNOT; conflict =; routine = sg_bbl.h

SHOREFACE: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SO_SEMI: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SO_SEMI_WHITE: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SO_TRACE: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SOLAR_SOURCE: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SOLITON: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SOLVE3D: Option to activate/deactivate 3D model configuration. If activated, ROMS solves 3D (baroclinic) primitive equations. If deactivated, ROMS solves vertically-integrated, shallow water (barotropic) equations.; routine = main2d.F, main3d.F

SOUTH_FSCLAMPED: Option to use free-surface clamped condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_FSCLAMPED, NORTH_FSCLAMPED, WEST_FSCLAMPED; conflict = NS_PERIODIC, SOUTH_FSCHAPMAN, SOUTH_FSGRADIENT, SOUTH_FSNUDGING, SOUTH_FSRADIATION, SOUTHERN_WALL; routine = zetabc.F

SOUTH_FSCHAPMAN: Option to use free-surface Chapman condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_FSCHAPMAN, NORTH_FSCHAPMAN, WEST_FSCHAPMAN; conflict = NS_PERIODIC, SOUTH_FSCLAMPED, SOUTH_FSGRADIENT, SOUTH_FSNUDGING, SOUTH_FSRADIATION, SOUTHERN_WALL; routine = zetabc.F

SOUTH_FSGRADIENT: Option to use free-surface gradient condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_FSGRADIENT, NORTH_FSGRADIENT, WEST_FSGRADIENT; conflict = NS_PERIODIC, SOUTH_FSCLAMPED, SOUTH_FSCHAPMAN, SOUTH_FSNUDGING, SOUTH_FSRADIATION, SOUTHERN_WALL; routine = zetabc.F

SOUTH_FSNUDGING: Option to use free-surface passive/active nudging term for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_FSNUDGING, NORTH_FSNUDGING, WEST_FSNUDGING; conflict = NS_PERIODIC, SOUTH_FSCLAMPED, SOUTH_FSCHAPMAN, SOUTH_FSGRADIENT, SOUTHERN_WALL; routine = zetabc.F

SOUTH_FSRADIATION: Option to use free-surface radiation condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_FSRADIATION, NORTH_FSRADIATION, WEST_FSRADIATION; conflict = NS_PERIODIC, SOUTH_FSCLAMPED, SOUTH_FSCHAPMAN, SOUTH_FSGRADIENT, SOUTHERN_WALL; routine = zetabc.F

SOUTH_KGRADIENT: Option to use TKE fields gradient condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_KGRADIENT, NORTH_KGRADIENT, WEST_KGRADIENT; conflict = NS_PERIODIC, SOUTH_KRADIATION, SOUTHERN_WALL; routine = tkebc_im.F

SOUTH_KRADIATION: Option to use TKE fields radiation condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_KRADIATION, NORTH_KRADIATION, WEST_KRADIATION; conflict = NS_PERIODIC, SOUTH_KGRADIENT, SOUTHERN_WALL; routine = tkebc_im.F

SOUTH_M2CLAMPED: Option to use 2D momentum clamped condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_M2CLAMPED, NORTH_M2CLAMPED, WEST_M2CLAMPED; conflict = NS_PERIODIC, SOUTH_M2FLATHER, SOUTH_M2GRADIENT, SOUTH_M2NUDGING, SOUTH_M2RADIATION, SOUTH_M2REDUCED, SOUTHERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

SOUTH_M2FLATHER: Option to use 2D momentum Flather condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_M2FLATHER, NORTH_M2FLATHER, WEST_M2FLATHER; conflict = NS_PERIODIC, SOUTH_M2CLAMPED, SOUTH_M2GRADIENT, SOUTH_M2NUDGING, SOUTH_M2RADIATION, SOUTH_M2REDUCED, SOUTHERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

SOUTH_M2GRADIENT: Option to use 2D momentum gradient condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_M2GRADIENT, NORTH_M2GRADIENT, WEST_M2GRADIENT; conflict = NS_PERIODIC, SOUTH_M2CLAMPED, SOUTH_M2FLATHER, SOUTH_M2NUDGING, SOUTH_M2RADIATION, SOUTH_M2REDUCED, SOUTHERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

SOUTH_M2NUDGING: Option to use 2D momentum passive/active nudging term for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_M2NUDGING, NORTH_M2NUDGING, WEST_M2NUDGING; conflict = NS_PERIODIC, SOUTH_M2CLAMPED, SOUTH_M2FLATHER, SOUTH_M2GRADIENT, SOUTH_M2REDUCED, SOUTHERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

SOUTH_M2RADIATION: Option to use 2D momentum radiation condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_M2RADIATION, NORTH_M2RADIATION, WEST_M2RADIATION; conflict = NS_PERIODIC, SOUTH_M2CLAMPED, SOUTH_M2FLATHER, SOUTH_M2GRADIENT, SOUTH_M2REDUCED, SOUTHERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

SOUTH_M2REDUCED: Option to use 2D momentum reduced-physics for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_M2REDUCED, NORTH_M2REDUCED, WEST_M2REDUCED; conflict = NS_PERIODIC, SOUTH_M2CLAMPED, SOUTH_M2FLATHER, SOUTH_M2GRADIENT, SOUTH_M2NUDGING, SOUTH_M2RADIATION, SOUTHERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

SOUTH_M3CLAMPED: Option to use 3D momentum clamped condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_M3CLAMPED, NORTH_M3CLAMPED, WEST_M3CLAMPED; conflict = NS_PERIODIC, SOUTH_M3GRADIENT, SOUTH_M3NUDGING, SOUTH_M3RADIATION, SOUTHERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

SOUTH_M3GRADIENT: Option to use 3D momentum gradient condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_M3GRADIENT, NORTH_M3GRADIENT, WEST_M3GRADIENT; conflict = NS_PERIODIC, SOUTH_M3CLAMPED, SOUTH_M3NUDGING, SOUTH_M3RADIATION, SOUTHERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

SOUTH_M3NUDGING: Option to use 3D momentum passive/active nudging term for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_M3NUDGING, NORTH_M3NUDGING, WEST_M3NUDGING; conflict = NS_PERIODIC, SOUTH_M3CLAMPED, SOUTH_M3GRADIENT, SOUTHERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

SOUTH_M3RADIATION: Option to use 3D momentum radiation condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_M3RADIATION, NORTH_M3RADIATION, WEST_M3RADIATION; conflict = NS_PERIODIC, SOUTH_M3CLAMPED, SOUTH_M3GRADIENT, SOUTHERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

SOUTH_TCLAMPED: Option to use tracer clamped condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_TCLAMPED, NORTH_TCLAMPED, WEST_TCLAMPED; conflict = NS_PERIODIC, SOUTH_TGRADIENT, SOUTH_TNUDGING, SOUTH_TRADIATION, SOUTHERN_WALL; routine = t3dbc_im.F

SOUTH_TGRADIENT: Option to use tracer gradient condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_TGRADIENT, NORTH_TGRADIENT, WEST_TGRADIENT; conflict = NS_PERIODIC, SOUTH_TCLAMPED, SOUTH_TNUDGING, SOUTH_TRADIATION, SOUTHERN_WALL; routine = t3dbc_im.F

SOUTH_TNUDGING: Option to use tracer passive/active nudging term for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_TNUDGING, NORTH_TNUDGING, WEST_TNUDGING; conflict = NS_PERIODIC, SOUTH_TCLAMPED, SOUTH_TGRADIENT, SOUTHERN_WALL; routine = t3dbc_im.F

SOUTH_TRADIATION: Option to use tracer radiation condition for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_TRADIATION, NORTH_TRADIATION, WEST_TRADIATION; conflict = NS_PERIODIC, SOUTH_TCLAMPED, SOUTH_TGRADIENT, SOUTHERN_WALL; routine = t3dbc_im.F

SOUTH_VOLCONS: Option to use Southern edge mass conservation enforcement for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_VOLCONS, NORTH_VOLCONS, WEST_VOLCONS; conflict = NS_PERIODIC, SOUTHERN_WALL; routine = obc_volcons.F

SOUTHERN_WALL: Option to use Southern edge closed wall for the southern open boundary condition.; parameter =; parent =; required =; related = EAST_WALL, NORTH_WALL, WEST_WALL; conflict = NS_PERIODIC, SOUTH_FSCLAMPED, SOUTH_FSCHAPMAN, SOUTH_FSGRADIENT, SOUTH_FSNUDGING, SOUTH_FSRADIATION, SOUTH_KGRADIENT, SOUTH_KRADIATION, SOUTH_M2CLAMPED, SOUTH_M2FLATHER, SOUTH_M2GRADIENT, SOUTH_M2NUDGING, SOUTH_M2RADIATION, SOUTH_M2REDUCED, SOUTH_M3CLAMPED, SOUTH_M3GRADIENT, SOUTH_M3NUDGING, SOUTH_M3RADIATION, SOUTH_TCLAMPED, SOUTH_TGRADIENT, SOUTH_TNUDGING, SOUTH_TRADIATION, SOUTH_VOLCONS; routine = t3dbc_im.F, tkebc_im.F, u2dbc_im.F, u3dbc_im.F, v2dbc_im.F, v3dbc_im.F, zetabc.F

SPLINES: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SPLINES_VCONV: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SPHERICAL: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SPONGE: DEPRICATED in favor of LuvSponge and LtracerSponge logical switches to facilitate nesting.

Option to impose a sponge layer near the lateral boundary. Used in areas of enhanced viscosity/diffusion.; parameter =; parent =; required =; related =; conflict =; routine =

SRELAXATION: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SSH_TIDES: Option to impose tidal elevation for tidal forcing at the open boundaries.; parameter =; parent =; required =; related = ADD_FSOBC, FSOBC_REDUCED, RAMP_TIDES; conflict =; routine =

SSW_BBL: Option to use the Sherwood/Signell/Warner bottom boundary layer closure.; parameter =; parent =; required = BBL_MODEL; related = SSW_CALC_UB, SSW_CALC_ZNOT, SSW_FORM_DRAG_COR, SSW_LOGINT, SSW_ZOBIO, SSW_ZOBL, SSW_ZORIP; conflict = SG_BBL, MB_BBL; routine = bbl.F, ssw_bbl.h

SSW_CALC_UB: Option to compute bottom orbital velocity internally for the Sherwood/Signell/Warner bottom boundary layer closure.; parameter =; parent = SSW_BBL; required = BBL_MODEL, SSW_BBL; related = SSW_CALC_ZNOT, SSW_FORM_DRAG_COR, SSW_LOGINT, SSW_ZOBIO, SSW_ZOBL, SSW_ZORIP; conflict =; routine = ssw_bbl.h

SSW_CALC_ZNOT: Option to compute bottom roughness internally for the Sherwood/Signell/Warner bottom boundary layer closure.; parameter =; parent = SSW_BBL; required = BBL_MODEL, SSW_BBL; related = SSW_CALC_UB, SSW_FORM_DRAG_COR, SSW_LOGINT, SSW_ZOBIO, SSW_ZOBL, SSW_ZORIP; conflict =; routine = ssw_bbl.h

SSW_FORM_DRAG_COR: Option to activate form drag coefficient for the Sherwood/Signell/Warner bottom boundary layer closure.; parameter =; parent = SSW_BBL; required = BBL_MODEL, SSW_BBL; related = SSW_CALC_UB, SSW_CALC_ZNOT, SSW_LOGINT, SSW_ZOBIO, SSW_ZOBL, SSW_ZORIP; conflict =; routine = ssw_bbl.h

SSW_LOGINT: Option to use logarithmic interpolation of (Ur,Vr) for the Sherwood/Signell/Warner bottom boundary layer closure.; parameter =; parent = SSW_BBL; required = BBL_MODEL, SSW_BBL; related = SSW_CALC_UB, SSW_CALC_ZNOT, SSW_FORM_DRAG_COR, SSW_ZOBIO, SSW_ZOBL, SSW_ZORIP; conflict =; routine = ssw_bbl.h

SSW_ZOBIO: Option to use biogenic bedform roughness from ripples for the Sherwood/Signell/Warner bottom boundary layer closure.; parameter =; parent = SSW_BBL; required = BBL_MODEL, SSW_BBL; related = SSW_CALC_UB, SSW_CALC_ZNOT, SSW_FORM_DRAG_COR, SSW_LOGINT, SSW_ZOBL, SSW_ZORIP; conflict =; routine = ssw_bbl.h

SSW_ZOBL: Option to use bedload roughness for ripples for the Sherwood/Signell/Warner bottom boundary layer closure.; parameter =; parent = SSW_BBL; required = BBL_MODEL, SSW_BBL; related = SSW_CALC_UB, SSW_CALC_ZNOT, SSW_FORM_DRAG_COR, SSW_LOGINT, SSW_ZOBIO, SSW_ZORIP; conflict =; routine = ssw_bbl.h

SSW_ZORIP: Option to use bedform roughness from ripples for the Sherwood/Signell/Warner bottom boundary layer closure.; parameter =; parent = SSW_BBL; required = BBL_MODEL, SSW_BBL; related = SSW_CALC_UB, SSW_CALC_ZNOT, SSW_FORM_DRAG_COR, SSW_LOGINT, SSW_ZOBIO, SSW_ZOBL; conflict =; routine = ssw_bbl.h

STATIONS: Option to activate writing out station data; parameter =; parent =; required =; related =; conflict =; routine = stations.in

STATIONS_CGRID: Option to; parameter =; parent =; required =; related =; conflict =; routine =

STOCHASTIC_OPT: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SUBOBJECT_DEALLOCATION: Option to de-allocate each pointer variable within a structure object individually. This option is mostly to maintain backwards compatibility with older versions of Fortran compilers that don't contain the Fortran 2003 standards. If your compiler is Fortran 2003 capable, we do not recommend activating this option. See Trac ticket #897 for more details.; routines = mod_average.F, mod_bbl.F, mod_boundary.F, mod_clima.F, mod_coupling.F, mod_diags.F, mod_floats.F, mod_forces.F, mod_grid.F, mod_mixing.F, mod_nesting.F, mod_ocean.F, mod_param.F, mod_scalars.F, mod_sedbed_mod.h, mod_sources.F, mod_storage.F, and mod_tides.F

SUSPLOAD: Option to; parameter =; parent =; required =; related =; conflict =; routine =

SWAN_COUPLING: Option to; parameter =; parent =; required =; related =; conflict =; routine =

T

T_PASSIVE: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TALK_NONCONSERV: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TALK_PROGNOSTIC: Option to activate prognostic computation of alkalinity.; parent = BIO_FENNEL; required = CARBON; routine = fennel.h

TANGENT: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TCLIMATOLOGY: DEPRICATED in favor of LtracerCLM logical switches to facilitate nesting.

Option to read and process tracers in climatology fields.; parameter =; parent =; required =; related = ANA_TCLIMA, TCLM_NUDGING; conflict =; routine =

TCLM_NUDGING: Option to use nudging for tracer climatology data (primarily in sponge areas).; parameter =; parent =; required =; related = ANA_TCLIMA, TCLIMATOLOGY; conflict =; routine =

TEST_CHAN: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TEST_HEAD: Option to; parameter =; parent =; required =; related =; conflict =; routine =

THREE_GHOST: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TKE_DIF2: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TKE_DIF4: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TKE_WAVEDISS: Option to use wave breaking surface flux from wave amplitude for the Generic Length-Scale closure (Warner et al., 2005).; parameter =; parent =; required =; related =; conflict =; routine =

TL_R4DVAR (Formerly TL_W4DVAR): Option to activate tangent linearization of the R4D-Var data assimilation system.; parameter =; parent =; required =; related =; conflict =; routine = tl_r4dvar_ocean.h

TL_RBL4DVAR (Formerly TL_W4DPSAS): Option to activate tangent linearization of the RBL4D-Var data assimilation system.; parameter =; parent =; required =; related =; conflict =; routine = tl_rbl4dvar_ocean.h

TL_W4DPSAS OBSOLETE - Renamed to TL_RBL4DVAR in SVN revision 1022: Option to activate tangent linearization of the W4DPSAS data assimilation system.; parameter =; parent =; required =; related =; conflict =; routine = tl_w4dpsas_ocean.h

TL_W4DVAR OBSOLETE - Renamed to TL_R4DVAR in SVN revision 1022: Option to activate tangent linearization of the W4DVAR data assimilation system.; parameter =; parent =; required =; related =; conflict =; routine = tl_w4dvar_ocean.h

TLM_CHECK: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TLM_DRIVER: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TS_A4HADVECTION: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TS_A4VADVECTION: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TS_C2HADVECTION: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TS_C2VADVECTION: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TS_C4HADVECTION: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TS_C4VADVECTION: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TS_DIF2: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TS_DIF4: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TS_FIXED: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TS_MPDATA: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TS_PSOURCE (OBSOLETE as of revision 701): Option to; parameter =; parent =; required =; related =; conflict =; routine =

TS_SMAGORINSKY: Option to; parameter =; parent =; required =; related = UV_SMAGORINSKY; conflict =; routine =

TS_SVADVECTION: Option to; parameter =; parent =; required =; related =; conflict =; routine =

TS_U3ADV_SPLIT: Option to; parameter =; parent =; required =; related = UV_U3ADV_SPLIT; conflict =; routine =

TS_U3HADVECTION: Option to; parameter =; parent =; required =; related =; conflict =; routine =

U

UPWELLING: Option to; parameter =; parent =; required =; related =; conflict =; routine =

UV_ADV: Option to activate/deactivate horizontal and vertical advection of momentum. If no additional options are specified, the default is to discretize the horizontal momentum with a third-order upstream bias advection scheme with velocity dependent hyper-viscosity and the vertical momentum with a fourth-order, centered differences scheme. Since there is some implicit viscosity associated with the default discretization, the user may avoid adding an explicity vicosity to the solution to suppress excisive smoothing.; routine = step2d.F, rhs3d.F

UV_BAROCLINIC: Option to; parameter =; parent =; required =; related =; conflict =; routine =

UV_COR: Option to activate/deactivate Coriolis acceleration term in momentum equations.; routine = step2d.F, rhs3d.F

UV_C2ADVECTION: Option to use second-order, centered, finite differences in advection of momentum.; parent = UV_ADV; conflit = UV_C4ADVECTION

UV_C4ADVECTION: Option to use fourth-order, centered, finite differences in advection of momentum.; parent = UV_ADV; conflit = UV_C2ADVECTION

UV_LDRAG: Option to activate/deactivate linear bottom friction of momentum.; parameter = rdrg(ng); confict = BBL_MODEL, UV_LOGDRAG, UV_QDRAG; routine = set_vbc.F

UV_LOGDRAG: Option to activate/deactivate logarithmic bottom friction of momentum.; parameter = Zob(ng); required = SOLVE3D; confict = BBL_MODEL, UV_LDRAG, UV_QDRAG; routine = set_vbc.F

UV_PSOURCE (OBSOLETE as of revision 701): Option to activate/deactivate point sources/sinks of momentum. This option is used to specify the mass transport in river runoff.; variable = Dsrc(1:Nsrc), Qsrc(1:Nsrc,k); related = ANA_PSOURCE, TS_PSOURCE; confict = BBL_MODEL, UV_LOGDRAG, UV_QDRAG; routine = step2d.F, step3d_uv.F

UV_QDRAG: Option to activate/deactivate quadratic bottom friction of momentum.; parameter = rdrg2(ng); confict = BBL_MODEL, UV_LDRAG, UV_LOGDRAG; routine = set_vbc.F

UV_SADVECTION: Option to use conservative, parabolic splines discretization of momentum vertical advection. This scheme requires high vertical resolution so it is recommended to use this option in shallow, coastal applications.; parent = UV_ADV; conflit = UV_C2ADVECTION, UV_C4ADVECTION

UV_SMAGORINSKY: Option to use Smagorinsky-like viscosity.; related = TS_SMAGORINSKY; routine = hmixing.F

UV_TIDES: Option to impose tidal currents for tidal forcing at open boundaries.; parameter =; parent =; required =; related = ADD_M2OBC, RAMP_TIDES; conflict =; routine =

UV_U3ADV_SPLIT: Option to use 3rd-order upstream split momentum advection. This 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.; related = TS_U3ADV_SPLIT; routine = hmixing.F

UV_U3HADVECTION: Option to; parameter =; parent =; required =; related =; conflict =; routine =

UV_VIS2: Option to activate/deactivate horizontal, harmonic viscosity of momentum. The hamonic mixing of momentum can be applied along terrain-following or geopotential levels. In ROMS, the viscosity is derived from the horizontal divergence of the deviatory stress tensor (Wajsowicz, 1993).; parameter = visc2(ng); variable = visc2_p(:,:), visc2_r(:,:); required = MIX_S_UV, MIX_GEO_UV; related = VISC_GRID; routine = uv3dmix2_s.h, uv3dmix2_geo.h, uv3dmix.F

UV_VIS4: Option to activate/deactivate horizontal, biharmonic viscosity of momentum. The bihamonic mixing of momentum can be applied along terrain-following or geopotential levels. In ROMS, the viscosity is derived from the horizontal divergence of the deviatory stress tensor (Wajsowicz, 1993).; parameter = visc4(ng); variable = visc4_p(:,:), visc4_r(:,:); required = MIX_S_UV, MIX_GEO_UV; related = VISC_GRID; routine = uv3dmix4_s.h, uv3dmix4_geo.h, uv3dmix.F

V

VAR_RHO_2D: Option to; parameter =; parent =; required =; related =; conflict =; routine =

VCONVOLUTION: Option to; parameter =; parent =; required =; related =; conflict =; routine =

VERIFICATION: Option to; parameter =; parent =; required =; related =; conflict =; routine =

VISC_GRID: Option to; parameter =; parent =; required =; related =; conflict =; routine =

VWALK_FORWARD: Option to activate the old forward step vertical random walk computation.; parameter =; parent =; required =; related =; conflict =; routine =

W

W4DPSAS OBSOLETE - Renamed to RBL4DVAR in SVN revision 1022: Option to Option to activate Lanczos 4D-Var, strong/weak constraint, dual formulation.; parameter =; parent =; required =; related =; conflict =; routine = w4dpsas_ocean.h

W4DPSAS_FCT_SENSITIVITY OBSOLETE - Renamed to RBL4DVAR_FCT_SENSITIVITY in SVN revision 1022: Option to activate the observation impact driver for the forecast cycles.; parameter =; parent =; required =; related =; conflict =; routine = ad_htobs.F, ad_rpcg_lanczos.F, ceckdefs.F, def_info.F, def_ini.F, def_mod.F, get_state.F, globaldefs.h, mod_iounits.F, mod_fourdvar.F, obs_sen_w4dpsas_forecast.h, read_asspar.F, read_phypar.F, rpcg_lanczos.F, tl_rpcg_lanczos.F, wrt_info.F

W4DPSAS_SENSITIVITY OBSOLETE - Renamed to RBL4DVAR_ANA_SENSITIVITY in SVN revision 1022: Option to activate Lanczos 4D-Var, strong/weak constraint, dual formulation analysis of observation impact and observations sensitivity.; parameter =; parent =; required =; related =; conflict =; routine = obs_sen_w4dpsas.h

W4DVAR OBSOLETE - Renamed to R4DVAR in SVN revision 1022: Option to activate indirect Representers 4D-Var, strong/weak constraint, dual formulation. This algorithm is no longer developed due to its instability in multiple outer loops in applications with high Rossby number. It is keep for instructional usage. We do not recommend to be used in realistic applications. Use instead the RBL4D-Var algorithm, which has a more efficient minimization RBLanczos solver.; parameter =; parent =; required =; related =; conflict =; routine = w4dvar_ocean.h

W4DVAR_SENSITIVITY OBSOLETE - Renamed to R4DVAR_ANA_SENSITIVITY in SVN revision 1022: Option to activate R4D-Var Analysis Observation Impact and Observations Sensitivity; parameter =; parent =; required =; related =; conflict =; routine = obs_sen_w4dvar.h

WEAK_CONSTRAINT: Option to; parameter =; parent =; required =; related =; conflict =; routine =

WEDDELL: Option to; parameter =; parent =; required =; related =; conflict =; routine =

WEST_FSCLAMPED: Option to use free-surface clamped condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_FSCLAMPED, NORTH_FSCLAMPED, SOUTH_FSCLAMPED; conflict = EW_PERIODIC, WEST_FSCHAPMAN, WEST_FSGRADIENT, WEST_FSNUDGING, WEST_FSRADIATION, WESTERN_WALL; routine = zetabc.F

WEST_FSCHAPMAN: Option to use free-surface Chapman condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_FSCHAPMAN, NORTH_FSCHAPMAN, SOUTH_FSCHAPMAN; conflict = EW_PERIODIC, WEST_FSCLAMPED, WEST_FSGRADIENT, WEST_FSNUDGING, WEST_FSRADIATION, WESTERN_WALL; routine = zetabc.F

WEST_FSGRADIENT: Option to use free-surface gradient condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_FSGRADIENT, NORTH_FSGRADIENT, SOUTH_FSGRADIENT; conflict = EW_PERIODIC, WEST_FSCLAMPED, WEST_FSCHAPMAN, WEST_FSNUDGING, WEST_FSRADIATION, WESTERN_WALL; routine = zetabc.F

WEST_FSNUDGING: Option to use free-surface passive/active nudging term for the western open boundary condition.; parameter =; parent =; required =; related = EAST_FSNUDGING, NORTH_FSNUDGING, SOUTH_FSNUDGING; conflict = EW_PERIODIC, WEST_FSCLAMPED, WEST_FSCHAPMAN, WEST_FSGRADIENT, WESTERN_WALL; routine = zetabc.F

WEST_FSRADIATION: Option to use free-surface radiation condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_FSRADIATION, NORTH_FSRADIATION, SOUTH_FSRADIATION; conflict = EW_PERIODIC, WEST_FSCLAMPED, WEST_FSCHAPMAN, WEST_FSGRADIENT, WESTERN_WALL; routine = zetabc.F

WEST_KGRADIENT: Option to use TKE fields gradient condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_KGRADIENT, NORTH_KGRADIENT, SOUTH_KGRADIENT; conflict = EW_PERIODIC, WEST_KRADIATION, WESTERN_WALL; routine = tkebc_im.F

WEST_KRADIATION: Option to use TKE fields radiation condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_KRADIATION, NORTH_KRADIATION, SOUTH_KRADIATION; conflict = EW_PERIODIC, WEST_KGRADIENT, WESTERN_WALL; routine = tkebc_im.F

WEST_M2CLAMPED: Option to use 2D momentum clamped condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_M2CLAMPED, NORTH_M2CLAMPED, SOUTH_M2CLAMPED; conflict = EW_PERIODIC, WEST_M2FLATHER, WEST_M2GRADIENT, WEST_M2NUDGING, WEST_M2RADIATION, WEST_M2REDUCED, WESTERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

WEST_M2FLATHER: Option to use 2D momentum Flather condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_M2FLATHER, NORTH_M2FLATHER, SOUTH_M2FLATHER; conflict = EW_PERIODIC, WEST_M2CLAMPED, WEST_M2GRADIENT, WEST_M2NUDGING, WEST_M2RADIATION, WEST_M2REDUCED, WESTERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

WEST_M2GRADIENT: Option to use 2D momentum gradient condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_M2GRADIENT, NORTH_M2GRADIENT, SOUTH_M2GRADIENT; conflict = EW_PERIODIC, WEST_M2CLAMPED, WEST_M2FLATHER, WEST_M2NUDGING, WEST_M2RADIATION, WEST_M2REDUCED, WESTERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

WEST_M2NUDGING: Option to use 2D momentum passive/active nudging term for the western open boundary condition.; parameter =; parent =; required =; related = EAST_M2NUDGING, NORTH_M2NUDGING, SOUTH_M2NUDGING; conflict = EW_PERIODIC, WEST_M2CLAMPED, WEST_M2FLATHER, WEST_M2GRADIENT, WEST_M2REDUCED, WESTERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

WEST_M2RADIATION: Option to use 2D momentum radiation condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_M2RADIATION, NORTH_M2RADIATION, SOUTH_M2RADIATION; conflict = EW_PERIODIC, WEST_M2CLAMPED, WEST_M2FLATHER, WEST_M2GRADIENT, WEST_M2REDUCED, WESTERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

WEST_M2REDUCED: Option to use 2D momentum reduced-physics for the western open boundary condition.; parameter =; parent =; required =; related = EAST_M2REDUCED, NORTH_M2REDUCED, SOUTH_M2REDUCED; conflict = EW_PERIODIC, WEST_M2CLAMPED, WEST_M2FLATHER, WEST_M2GRADIENT, WEST_M2NUDGING, WEST_M2RADIATION, WESTERN_WALL; routine = u2dbc_im.F, v2dbc_im.F

WEST_M3CLAMPED: Option to use 3D momentum clamped condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_M3CLAMPED, NORTH_M3CLAMPED, SOUTH_M3CLAMPED; conflict = EW_PERIODIC, WEST_M3GRADIENT, WEST_M3NUDGING, WEST_M3RADIATION, WESTERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

WEST_M3GRADIENT: Option to use 3D momentum gradient condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_M3GRADIENT, NORTH_M3GRADIENT, SOUTH_M3GRADIENT; conflict = EW_PERIODIC, WEST_M3CLAMPED, WEST_M3NUDGING, WEST_M3RADIATION, WESTERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

WEST_M3NUDGING: Option to use 3D momentum passive/active nudging term for the western open boundary condition.; parameter =; parent =; required =; related = EAST_M3NUDGING, NORTH_M3NUDGING, SOUTH_M3NUDGING; conflict = EW_PERIODIC, WEST_M3CLAMPED, WEST_M3GRADIENT, WESTERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

WEST_M3RADIATION: Option to use 3D momentum radiation condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_M3RADIATION, NORTH_M3RADIATION, SOUTH_M3RADIATION; conflict = EW_PERIODIC, WEST_M3CLAMPED, WEST_M3GRADIENT, WESTERN_WALL; routine = u3dbc_im.F, v3dbc_im.F

WEST_TCLAMPED: Option to use tracer clamped condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_TCLAMPED, NORTH_TCLAMPED, SOUTH_TCLAMPED; conflict = EW_PERIODIC, WEST_TGRADIENT, WEST_TNUDGING, WEST_TRADIATION, WESTERN_WALL; routine = t3dbc_im.F

WEST_TGRADIENT: Option to use tracer gradient condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_TGRADIENT, NORTH_TGRADIENT, SOUTH_TGRADIENT; conflict = EW_PERIODIC, WEST_TCLAMPED, WEST_TNUDGING, WEST_TRADIATION, WESTERN_WALL; routine = t3dbc_im.F

WEST_TNUDGING: Option to use tracer passive/active nudging term for the western open boundary condition.; parameter =; parent =; required =; related = EAST_TNUDGING, NORTH_TNUDGING, SOUTH_TNUDGING; conflict = EW_PERIODIC, WEST_TCLAMPED, WEST_TGRADIENT, WESTERN_WALL; routine = t3dbc_im.F

WEST_TRADIATION: Option to use tracer radiation condition for the western open boundary condition.; parameter =; parent =; required =; related = EAST_TRADIATION, NORTH_TRADIATION, SOUTH_TRADIATION; conflict = EW_PERIODIC, WEST_TCLAMPED, WEST_TGRADIENT, WESTERN_WALL; routine = t3dbc_im.F

WEST_VOLCONS: Option to use Southern edge mass conservation enforcement for the western open boundary condition.; parameter =; parent =; required =; related = EAST_VOLCONS, NORTH_VOLCONS, SOUTH_VOLCONS; conflict = EW_PERIODIC, WESTERN_WALL; routine = obc_volcons.F

WESTERN_WALL: Option to use Southern edge closed wall for the western open boundary condition.; parameter =; parent =; required =; related = EAST_WALL, NORTH_WALL, SOUTH_WALL; conflict = EW_PERIODIC, WEST_FSCLAMPED, WEST_FSCHAPMAN, WEST_FSGRADIENT, WEST_FSNUDGING, WEST_FSRADIATION, WEST_KGRADIENT, WEST_KRADIATION, WEST_M2CLAMPED, WEST_M2FLATHER, WEST_M2GRADIENT, WEST_M2NUDGING, WEST_M2RADIATION, WEST_M2REDUCED, WEST_M3CLAMPED, WEST_M3GRADIENT, WEST_M3NUDGING, WEST_M3RADIATION, WEST_TCLAMPED, WEST_TGRADIENT, WEST_TNUDGING, WEST_TRADIATION, WEST_VOLCONS; routine = t3dbc_im.F, tkebc_im.F, u2dbc_im.F, u3dbc_im.F, v2dbc_im.F, v3dbc_im.F, zetabc.F

WET_DRY: Option to activate wetting and drying.; parameter = Dcrit; variable = rmask_wet, umask_wet, vmask_wet; routine = step2d.F

WINDBASIN: Option to; parameter =; parent =; required =; related =; conflict =; routine =

WIND_WAVES: Option to; parameter =; parent =; required =; related =; conflict =; routine =

WJ_GRADP: Option to; parameter =; parent =; required =; related =; conflict =; routine =

WRITE_WATER: Option to; parameter =; parent =; required =; related =; conflict =; routine =

WRF_COUPLING: Option to; parameter =; parent =; required =; related =; conflict =; routine =

X

Y

Z

ZCLIMATOLOGY: DEPRICATED in favor of LsshCLM logical switches to facilitate nesting.

Option to read and process SSH climatology fields.; parameter =; parent =; required =; related = ANA_SSH, SSH_TIDES, ZCLM_NUDGING; conflict =; routine =

ZCLM_NUDGING: Option to nudge SSH climatology data (primarily in sponge areas.; parameter =; parent =; required =; related = ANA_SSH, SSH_TIDES, ZCLIMATOLOGY; conflict =; routine =

ZETA_ELLIPTIC: Option to compute the balanced free-surface increment by solving an elliptical equation as in Fukomuri et al. (1998).; parameter =; parent =; required =; related =; conflict =; routine =

ZOS_HSIG: Option to use horizontal smoothing of buoyancy/shear for the Generic Length-Scale closure (Warner et al., 2005).; parameter =; parent =; required =; related =; conflict =; routine =

Options: Difference between revisions

Latest revision as of 15:32, 20 October 2021

Contents

A

B

C

D

E

F

G

H

I

J

K

L

M

N

O

P

Q

R

S

T

U

V

W

X

Y

Z

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Help

Tools

@@ Line 12: / Line 12: @@
 *'''routine:''' main files associated with the option.
 *'''variable:''' important state array(s) associtated with the option.
+*'''input:''' standard input file for configuring runtime parameters
 <!-- The automatic table of contents is disabled here to allow a simplified table -->
@@ Line 47: / Line 48: @@
 ==<span class="alphabet">A</span>==
+<section begin=A4DVAR_TOY />;<span id="A4DVAR_TOY"></span>[[A4DVAR_TOY]]
+:Idealized data assimilation example to run 4DVar weak constraint data assimilation algorithms.
+:'''parameter = ''' [[Variables#Ninner | Ninner]], [[Variables#Nouter | Nouter]]
+:'''required = ''' [[RBL4DVAR]] or [[R4DVAR]]
+:'''related = ''' [[CONVOLVE]], [[RPM_RELAXATION]]
+:'''routine = ''' [[rbl4dvar_ocean.h]], [[r4dvar_ocean.h]]
+:'''input = ''' [[roms.in]], [[s4dvar.in]]<section end=A4DVAR_TOY />
-<section begin=ADD_FSOBC />;<span id="ADD_FSOBC"></span>'''[[ADD_FSOBC]]'''
+<section begin=AD_IMPULSE />;<span id="AD_IMPULSE"></span>[[AD_IMPULSE]]
+:Option to control the forcing of the adjoint model as an intermittent impulse ('''on''') or continuous force term ('''off''').
+:'''parent = ''' [[ADJOINT]]
+:'''routine = ''' [[adsen_force.F]]<section end=AD_IMPULSE />
+<section begin=AD_SENSITIVITY />;<span id="AD_SENSITIVITY"></span>[[AD_SENSITIVITY]]
+:Option to run the adjoint sensitivity ocean driver ([[Bibliography#MooreAM_20006a | Moore et al., 2006]]).
+:'''parent = ''' [[ADJOINT]]
+:'''routine = ''' [[adsen_ocean.h]], [[ocean_control.F]]<section end=AD_SENSITIVITY />
+<section begin=ADD_FSOBC />;<span id="ADD_FSOBC"></span>[[ADD_FSOBC]]
 :Option to add tidal elevation to sea surface height climatology, if any, and open boundary conditions data.
 :'''variable = '''[[Variables#ssh | ssh]], [[Variables#zeta_east | zeta_east]], [[Variables#zeta_north | zeta_north]], [[Variables#zeta_south | zeta_south]], [[Variables#zeta_west | zeta_west]]
@@ Line 56: / Line 74: @@
 :'''routine = ''' [[set_tides.F]]<section end=ADD_FSOBC />
-<section begin=ADD_M2OBC />;<span id="ADD_M2OBC"></span>'''[[ADD_M2OBC]]'''
+<section begin=ADD_M2OBC />;<span id="ADD_M2OBC"></span>[[ADD_M2OBC]]
 :Option to add tidal currents to 2D momentum climatology, if any, and open boundary conditions data.
 :'''variable = ''' [[Variables#ubarclm | ubarclm]], [[Variables#vbarclm | vbarclm]]
@@ Line 66: / Line 84: @@
 :'''routine = ''' [[set_tides.F]]<section end=ADD_M2OBC />
-<section begin=ADJOINT />;<span id="ADJOINT"></span>'''[[ADJOINT]]'''
+<section begin=ADJOINT />;<span id="ADJOINT"></span>[[ADJOINT]]
 :Internal option to include adjoint model. It primarily declares and allocate all adjoint state variables and activates all adjoint subroutines.
 :'''related = ''' [[TANGENT]]<section end=ADJOINT />
-<section begin=ADM_DRIVER />;<span id="ADM_DRIVER"></span>'''[[ADM_DRIVER]]'''
+<section begin=ADJUST_STFLUX />;<span id="ADJUST_STFLUX"></span>[[ADJUST_STFLUX]]
+:Option to include surface tracer flux in 4DVar state with tangent linear, representer and adjoint models.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[ADJUST_WSTRESS]]
+:'''conflict = '''
+:'''routine = '''  <section end=ADJUST_STFLUX />
+<section begin=ADJUST_WSTRESS />;<span id="ADJUST_WSTRESS"></span>[[ADJUST_WSTRESS]]
+:Option to include wind stress in 4DVar state with tangent linear, representer and adjoint models.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[ADJUST_STFLUX]]
+:'''conflict = '''
+:'''routine = '''  <section end=ADJUST_WSTRESS />
+<section begin=ADM_DRIVER />;<span id="ADM_DRIVER"></span>[[ADM_DRIVER]]
 :Option to run the adjoint model as a standalone driver.
 :'''related = ''' [[RPM_DRIVER]], [[TLM_DRIVER]]
 :'''routine = ''' [[ocean_control.F]]<section end=ADM_DRIVER />
-<section begin=AD_SENSITIVITY />;<span id="AD_SENSITIVITY"></span>'''[[AD_SENSITIVITY]]'''
+<section begin=ADRIA02 />;<span id="ADRIA02"></span>[[ADRIA02]]
-:Option to run the adjoint sensitivity ocean driver ([[Bibliography#MooreAM_20006a | Moore et al., 2006]]).
+:Option to compile and run a realistic Adriatic Sea application.
-:'''parent = ''' [[ADJOINT]]
+:'''parameter = '''
-:'''routine = ''' [[adsen_ocean.h]], [[ocean_control.F]]<section end=AD_SENSITIVITY />
+:'''parent = '''
+:'''required = '''
+:'''related = '''
+:'''conflict = '''
+:'''routine = '''
+:'''input = ''' [[floats.in]], [[roms.in]], [[sediment.in]], [[stations.in]]<section end=ADRIA02 />
-<section begin=AFT_EIGENMODES />;<span id="AFT_EIGENMODES"></span>'''[[AFT_EIGENMODES]]'''
+<section begin=AFT_EIGENMODES />;<span id="AFT_EIGENMODES"></span>[[AFT_EIGENMODES]]
 :Option to run the adjoint finite time eigenvalues driver ([[Bibliography#MooreAM_20004a | Moore et al., 2004]]).
 :'''parent = ''' [[ADJOINT]]
@@ Line 86: / Line 127: @@
 :'''routine = ''' [[aft_ocean.h]], [[ocean_control.F]]<section end=AFT_EIGENMODES />
-<section begin=AIR_OCEAN />;<span id="AIR_OCEAN"></span>'''[[AIR_OCEAN]]'''
+<section begin=AIR_OCEAN />;<span id="AIR_OCEAN"></span>[[AIR_OCEAN]]
 :Option to activate two-way coupling to an atmospheric model. Currently, the coupling is done with the Model Coupling Toolkit ([http://www-unix.mcs.anl.gov/mct MCT]). The coupling is either sequential or concurrent and it is only available for distributed-memory configurations. If concurrent, the MPI communicator is splited into atmosphere and ocean nodes.
 :'''conflict = ''' [[WAVES_OCEAN]]
-:'''routine = '''  [[master.F]], [[air_ocean.h]], [[coupling.in]]<section end=AIR_OCEAN />
+:'''routine = '''  [[master.F]], [[air_ocean.h]]
+:'''input = ''' [[coupling.in]]<section end=AIR_OCEAN />
-<section begin=ALBEDO />;<span id="ALBEDO"></span>'''[[ALBEDO]]'''
+<section begin=ALBEDO />;<span id="ALBEDO"></span>[[ALBEDO]]
 :Option to compute net shortwave radiation flux using the [[Bibliography#LaevastuT_1960a | Laevastu (1960)]] cloud correction to the [[Bibliography#ZillermanJW_1972a | Zillerman (1972)]] equation for cloudless radiation ([[Bibliography#ParkinsonCL_1979a |Parkinson and Washington, 1979]]).
 :'''variable = ''' [[Variables#srflx | srflx]]
@@ Line 98: / Line 140: @@
 :'''routine = '''  [[analytical.F]] (ana_srflux)<section end=ALBEDO />
-<section begin=ANA_BIOLOGY />;<span id="ANA_BIOLOGY"></span>'''[[ANA_BIOLOGY]]'''
+<section begin=ANA_BIOLOGY />;<span id="ANA_BIOLOGY"></span>[[ANA_BIOLOGY]]
 :Option to set biological tracers initial conditions with analytical expressions.
 :'''variable = ''' [[Variables#t | t(:,:,:,:,idbio(1:NBT))]]
@@ Line 104: / Line 146: @@
 :'''routine = ''' [[analytical.F]] (ana_biology)<section end=ANA_BIOLOGY />
-<section begin=ANA_BPFLUX />;<span id="ANA_BPFLUX"></span>'''[[ANA_BPFLUX]]'''
+<section begin=ANA_BMFLUX />;<span id="ANA_BMFLUX"></span>[[ANA_BMFLUX]]
+:Option to set spatially varying bottom roughness with an analytical expression.
+:'''variable = '''
+:'''required = ''' [[SEDIMENT]]
+:'''conflict = ''' [[ANA_SEDIMENT]]
+:'''routine = ''' [[analytical.F]] (ana_bmflux)<section end=ANA_BMFLUX />
+<section begin=ANA_BPFLUX />;<span id="ANA_BPFLUX"></span>[[ANA_BPFLUX]]
 :Option to set passive tracers bottom flux with analytical expressions (usually zero, no bottom flux).
 :'''variable = ''' [[Variables#btflx | btflx(:,:,NAT+1:NT(ng))]]
@@ Line 111: / Line 160: @@
 :'''routine = ''' [[analytical.F]] (ana_btflux)<section end=ANA_BPFLUX />
-<section begin=ANA_BSFLUX />;<span id="ANA_BSFLUX"></span>'''[[ANA_BSFLUX]]'''
+<section begin=ANA_BSFLUX />;<span id="ANA_BSFLUX"></span>[[ANA_BSFLUX]]
 :Option to set kinematic bottom salinity flux with an analytical expression (usually zero, no bottom flux).
 :'''variable = ''' [[Variables#btflx | btflx(:,:,isalt)]]
@@ Line 118: / Line 167: @@
 :'''routine = '''  [[analytical.F]] (ana_btflux)<section end=ANA_BSFLUX />
-<section begin=ANA_BTFLUX />;<span id="ANA_BTFLUX"></span>'''[[ANA_BTFLUX]]'''
+<section begin=ANA_BTFLUX />;<span id="ANA_BTFLUX"></span>[[ANA_BTFLUX]]
 :Option to set kinematic bottom heat flux with an analytical expression (usually zero, no bottom flux).
 :'''variable = ''' [[Variables#btflx | btflx(:,:,itemp)]]
@@ Line 125: / Line 174: @@
 :'''routine = ''' [[analytical.F]] (ana_btflux) <section end=ANA_BTFLUX />
-<section begin=ANA_CLOUD />;<span id="ANA_CLOUD"></span>'''[[ANA_CLOUD]]'''
+<section begin=ANA_CLOUD />;<span id="ANA_CLOUD"></span>[[ANA_CLOUD]]
 :Option to set cloud fraction with an analytical expression.
 :'''variable = ''' [[Variables#cloud | cloud]]
-:'''required = ''' [[CLOUDS]]
+:'''routine = ''' [[analytical.F]] (ana_cloud)<section end=ANA_CLOUD />
-:'''routine = ''' [[analytical.F]] (ana_clouds)<section end=ANA_CLOUD />
-<section begin=ANA_DIAG />;<span id="ANA_DIAG"></span>'''[[ANA_DIAG]]'''
+<section begin=ANA_DIAG />;<span id="ANA_DIAG"></span>[[ANA_DIAG]]
 :Option to activate the computation of any user specified diagnostics.
-:'''routine = '''  [[analytical]] (ana_diag), [[diag.F]]<section end=ANA_DIAG />
+:'''routine = '''  [[analytical.F]] (ana_diag), [[diag.F]]<section end=ANA_DIAG />
-<section begin=ANA_FSOBC />;<span id="ANA_FSOBC"></span>'''[[ANA_FSOBC]]'''
+<section begin=ANA_FSOBC />;<span id="ANA_FSOBC"></span>[[ANA_FSOBC]]
 :Option to set free-surface open boundary conditions using analytical expressions.
 :'''variable = ''' [[Variables#zeta_east | zeta_east]], [[Variables#zeta_north | zeta_north]], [[Variables#zeta_south | zeta_south]], [[Variables#zeta_west | zeta_west]]
@@ Line 141: / Line 189: @@
 :'''routine = ''' [[analytical.F]] (ana_fsobc) <section end=ANA_FSOBC />
-<section begin=ANA_GRID />;<span id="ANA_GRID"></span>'''[[ANA_GRID]]'''
+<section begin=ANA_GRID />;<span id="ANA_GRID"></span>[[ANA_GRID]]
 :Option to set application grid variables with analytical expressions.  Mostly, all the idealized test problems use this option. It sets the following grid-related variables: Coriolis parameter, bathymetry, &xi;- and &eta;-direction metrics and its derivates, curvilinear grid angle, &xi;- and &eta;-direction coordinates,  and spherical coordinates, if applicable.
 :'''variable = ''' [[Variables#f | f]], [[Variables#h | h]]
@@ Line 149: / Line 197: @@
 :'''routine = ''' [[analytical.F]] (ana_grid)<section end=ANA_GRID />
-<section begin=ANA_HUMIDITY />;<span id="ANA_HUMIDITY"></span>'''[[ANA_HUMIDITY]]'''
+<section begin=ANA_HUMIDITY />;<span id="ANA_HUMIDITY"></span>[[ANA_HUMIDITY]]
 :Option to set surface air humidity (moisture) with an analytical expression. There are three types of humidity: '''i)''' ''absolute humidity'' is the density of water vapor, '''ii)''' ''specific humidity'' is the ratio of the mass of water vapor to the mass of moist air containing the vapor (g/kg), and '''iii)''' ''relative humidity'' is the ratio of the actual mixing ratio to saturation mixing ratio of the air at a given temperature and pressure (percentage).
 :'''variable = ''' [[Variables#Hair | Hair]]
@@ Line 155: / Line 203: @@
 :'''routine = ''' [[analytical.F]] (ana_humid)<section end=ANA_HUMIDITY />
-<section begin=ANA_INITIAL />;<span id="ANA_INITIAL"></span>'''[[ANA_INITIAL]]'''
+<section begin=ANA_INITIAL />;<span id="ANA_INITIAL"></span>[[ANA_INITIAL]]
 :Option to set initial conditions for free-surface, momentum, and tracers with analytical expressions. Mostly, all the idealized test problems use this option.
 :'''variable = ''' [[Variables#zeta | zeta]], [[Variables#ubar | ubar]], [[Variables#vbar | vbar]]
@@ Line 162: / Line 210: @@
 :'''routine = ''' [[analytical.F]] (ana_initial)<section end=ANA_INITIAL />
-<section begin=ANA_M2CLIMA />;<span id="ANA_M2CLIMA"></span>'''[[ANA_M2CLIMA]]'''
+<section begin=ANA_M2CLIMA />;<span id="ANA_M2CLIMA"></span>[[ANA_M2CLIMA]]
 :Option to set 2D momentum climatology with analytical expressions.
 :'''variable = ''' [[Variables#ubarclm | ubarclm]], [[Variables#vbarclm | vbarclm]]
@@ Line 169: / Line 217: @@
 :'''routine = ''' [[analytical.F]] (ana_m2clima)<section end=ANA_M2CLIMA />
-<section begin=ANA_M2OBC />;<span id="ANA_M2OBC"></span>'''[[ANA_M2OBC]]'''
+<section begin=ANA_M2OBC />;<span id="ANA_M2OBC"></span>[[ANA_M2OBC]]
 :Option to set 2D momentum open boundary conditions using analytical expressions.
 :'''variable = ''' [[Variables#ubar_east | ubar_east]], [[Variables#ubar_north | ubar_north]], [[Variables#ubar_south | ubar_south]], [[Variables#ubar_west | ubar_west]]
@@ Line 176: / Line 224: @@
 :'''routine = ''' [[analytical.F]] (ana_m2obc) <section end=ANA_M2OBC />
-<section begin=ANA_M3CLIMA />;<span id="ANA_M3CLIMA"></span>'''[[ANA_M3CLIMA]]'''
+<section begin=ANA_M3CLIMA />;<span id="ANA_M3CLIMA"></span>[[ANA_M3CLIMA]]
 :Option to set 3D momentum climatology with analytical expressions.
 :'''variable = ''' [[Variables#uclm | uclm]], [[Variables#vclm | vclm]]
@@ Line 184: / Line 232: @@
 :'''routine = ''' [[analytical.F]] (ana_m3clima)<section end=ANA_M3CLIMA />
-<section begin=ANA_M3OBC />;<span id="ANA_M3OBC"></span>'''[[ANA_M3OBC]]'''
+<section begin=ANA_M3OBC />;<span id="ANA_M3OBC"></span>[[ANA_M3OBC]]
 :Option to set 3D momentum open boundary conditions using analytical expressions.
 :'''variable = ''' [[Variables#u_east | u_east]], [[Variables#u_north | u_north]], [[Variables#u_south | u_south]], [[Variables#u_west | u_west]]
@@ Line 191: / Line 239: @@
 :'''routine = ''' [[analytical.F]] (ana_m3obc) <section end=ANA_M3OBC />
-<section begin=ANA_MASK />;<span id="ANA_MASK"></span>'''[[ANA_MASK]]'''
+<section begin=ANA_MASK />;<span id="ANA_MASK"></span>[[ANA_MASK]]
 :Option to set land/sea masking using the analytical set-up. It is used in few idealized test problems. The mask has a value of ''zero'' over land and ''unity'' over water.
 :'''variables = ''' [[Variables#pmask | pmask]], [[Variables#rmask | rmask]], [[Variables#umask | umask]], [[Variables#vmask | vmask]]
 :'''routine = ''' [[analytical.F]] (ana_mask)<section end=ANA_MASK />
-<section begin=ANA_PAIR />;<span id="ANA_PAIR"></span>'''[[ANA_PAIR]]'''
+<section begin=ANA_PAIR />;<span id="ANA_PAIR"></span>[[ANA_PAIR]]
 :Option to set surface air pressure with an analytical expression.
 :'''variable = ''' [[Variables#Pair | Pair]]
@@ Line 202: / Line 250: @@
 :'''routine = ''' [[analytical.F]] (ana_pair) <section end=ANA_PAIR />
-<section begin=ANA_PASSIVE />;<span id="ANA_PASSIVE"></span>'''[[ANA_PASSIVE]]'''
+<section begin=ANA_PASSIVE />;<span id="ANA_PASSIVE"></span>[[ANA_PASSIVE]]
 :Option to set inert, passive tracers initial conditions with analytical expressions.
 :'''variable = ''' [[Variables#t | t(:,:,:,:,inert(1:NPT))]]
@@ Line 209: / Line 257: @@
 :'''routine = ''' [[analytical.F]] (ana_passive)<section end=ANA_PASSIVE />
-<section begin=ANA_PERTURB />;<span id="ANA_PERTURB"></span>'''[[ANA_PERTURB]]'''
+<section begin=ANA_PERTURB />;<span id="ANA_PERTURB"></span>[[ANA_PERTURB]]
 :Option to perturb tangent linear and adjoint state initial conditions at specified spatial (i,j,k) location. This is used to determine the correctness of the tangent linear and adjoint models by computing the inner product at the specified location. This inner product must be symmetric within roundoff (A - A<sup>T</sup> = 0).
 :'''parameter = ''' [[Variables#user | user(1:8)]]
@@ Line 217: / Line 265: @@
 :'''routine = ''' [[analytical.F]] (ana_perturb)<section end=ANA_PERTURB />
-<section begin=ANA_PSOURCE />;<span id="ANA_PSOURCE"></span>'''[[ANA_PSOURCE]]'''
+<section begin=ANA_PSOURCE />;<span id="ANA_PSOURCE"></span>[[ANA_PSOURCE]]
 :Option to set point sources and sinks with analytical expressions.  Usually, river runoff are represented as a point source.
 :'''variable = ''' [[Variables#Isrc | Isrc]], [[Variables#Jsrc | Jsrc]], [[Variables#Lsrc | Lsrc]], [[Variables#Dsrc | Dsrc]]
@@ Line 224: / Line 272: @@
 :'''routine = ''' [[analytical.F]] (ana_psource) <section end=ANA_PSOURCE />
-<section begin=ANA_RAIN />;<span id="ANA_RAIN"></span>'''[[ANA_RAIN]]'''
+<section begin=ANA_RAIN />;<span id="ANA_RAIN"></span>[[ANA_RAIN]]
 :Option to set rain fall rate with an analytical expression.
 :'''variable = ''' [[Variables#rain | rain]]
@@ Line 231: / Line 279: @@
 :'''routine = ''' [[analytical.F]] (ana_rain) <section end=ANA_RAIN />
-<section begin=ANA_SEDIMENT />;<span id="ANA_SEDIMENT"></span>'''[[ANA_SEDIMENT]]'''
+<section begin=ANA_SEDIMENT />;<span id="ANA_SEDIMENT"></span>[[ANA_SEDIMENT]]
 :Option to set cohesive and non-cohesive sediment initial conditions with analytical expressions. It also initializes sediment bed layer properties (thickness, age, porosity), sediment fraction and mass of each size class in each bed layer, and exposed sediment layer properties (mean grain diameter, mean grain density, mean settling velocity, mean critical erosion stress, ripple length and height, bed wave excursion amplitude, and several bottom roughnesses).
 :'''variable = ''' [[Variables#t | t(:,:,:,:,idsed(1:NST))]]
@@ Line 240: / Line 288: @@
 :'''routine = ''' [[analytical.F]] (ana_sediment)<section end=ANA_SEDIMENT />
-<section begin=ANA_SMFLUX />;<span id="ANA_SMFLUX"></span>'''[[ANA_SMFLUX]]'''
+<section begin=ANA_SMFLUX />;<span id="ANA_SMFLUX"></span>[[ANA_SMFLUX]]
 :Option to set kinematic, surface momentum flux boundary condition (wind stress) with analytical expressions.
 :'''variable = ''' [[Variables#sustr | sustr]], [[Variables#svstr | svstr]]
 :'''routine = ''' [[analytical.F]] (ana_smflux)<section end=ANA_SMFLUX />
-<section begin=ANA_SPFLUX />;<span id="ANA_SPFLUX"></span>'''[[ANA_SPFLUX]]'''
+<section begin=ANA_SPFLUX />;<span id="ANA_SPFLUX"></span>[[ANA_SPFLUX]]
 :Option to set passive tracers surface flux with analytical expressions (usually zero, no flux).
 :'''variable = ''' [[Variables#stflx | stflx(:,:,NAT+1:NT(ng))]]
 :'''related = ''' [[BIOLOGY]], [[SEDIMENT]]
-:'''routine = ''' [[analytical.F]] (ana_spflux)<section end=ANA_SPFLUX />
+:'''routine = ''' [[analytical.F]] (ana_stflux)<section end=ANA_SPFLUX />
-<section begin=ANA_SPINNING />;<span id="ANA_SPINNING"></span>'''[[ANA_SPINNING]]'''
+<section begin=ANA_SPINNING />;<span id="ANA_SPINNING"></span>[[ANA_SPINNING]]
 :Option to set time-variable rotation force as the sum of Coriolis and centripetal accelerations. This option is used in polar coordinates (annulus grid) applications.
 :'''variable = ''' [[Variables#f | f]], [[Variables#fomn | fomn]]
@@ Line 257: / Line 305: @@
 :'''routine = ''' [[analytical.F]] (ana_spinning)<section end=ANA_SPINNING />
-<section begin=ALBEDO />;<span id="ALBEDO"></span>'''[[ALBEDO]]'''
+<section begin=ANA_SRFLUX />;<span id="ANA_SRFLUX"></span>[[ANA_SRFLUX]]
 :Option to set kinematic, surface solar shortwave radiation flux with an analytical expression.
 :'''variable = ''' [[Variables#srflx | srflx]]
 :'''related = ''' [[ALBEDO]], [[DIURNAL_SRFLUX]]
-:'''routine = '''  [[analytical.F]] (ana_srflux)<section end=ALBEDO />
+:'''routine = '''  [[analytical.F]] (ana_srflux)<section end=ANA_SRFLUX />
-<section begin=ANA_SSFLUX />;<span id="ANA_SSFLUX"></span>'''[[ANA_SSFLUX]]'''
+<section begin=ANA_SSFLUX />;<span id="ANA_SSFLUX"></span>[[ANA_SSFLUX]]
 :Option to set kinematic surface freshwater flux (E-P) using an analytical expression.
 :'''variable = ''' [[Variables#stflx | stflx(:,:,isalt)]]
@@ Line 269: / Line 317: @@
 :'''related = ''' [[ANA_SPFLUX]], [[ANA_STFLUX]]
 :'''conflict = ''' [[EMINUSP]]
-:'''routine = '''  <section end=ANA_SSFLUX />
+:'''routine = ''' [[analytical.F]] (ana_stflux)<section end=ANA_SSFLUX />
-<section begin=ANA_SSH />;<span id="ANA_SSH"></span>'''[[ANA_SSH]]'''
+<section begin=ANA_SSH />;<span id="ANA_SSH"></span>[[ANA_SSH]]
 :Option to set sea surface height climatology with an analytical expression.
 :'''variable = ''' [[Variables#ssh | ssh]]
@@ Line 277: / Line 325: @@
 :'''routine = ''' [[analytical.F]] (ana_ssh)<section end=ANA_SSH />
-<section begin=ANA_SSS />;<span id="ANA_SSS"></span>'''[[ANA_SSS]]'''
+<section begin=ANA_SSS />;<span id="ANA_SSS"></span>[[ANA_SSS]]
 :Option to set sea surface salinity with an analytical expression.
 :'''variable = ''' [[Variables#sss | sss]]
@@ Line 284: / Line 332: @@
 :'''routine = ''' [[analytical.F]] (ana_sss)<section end=ANA_SSS />
-<section begin=ANA_SST />;<span id="ANA_SST"></span>'''[[ANA_SST]]'''
+<section begin=ANA_SST />;<span id="ANA_SST"></span>[[ANA_SST]]
 :Option to set sea surface temperature with an analytical expression. It also sets surface net heat flux sensitivity to sea surface temperature. Both fields are used for surface net heat flux correction.
 :'''variable = ''' [[Variables#dqdt | dqdt]], [[Variables#sst | sst]]
@@ Line 290: / Line 338: @@
 :'''routine = ''' [[analytical.F]] (ana_sst), [[set_vbc.F]]<section end=ANA_SST />
-<section begin=ANA_STFLUX />;<span id="ANA_STFLUX"></span>'''[[ANA_STFLUX]]'''
+<section begin=ANA_STFLUX />;<span id="ANA_STFLUX"></span>[[ANA_STFLUX]]
 :Option to set kinematic surface net flux of tracers using analytical expressions.
 :'''variable = ''' [[Variables#stflx | stflx(:,:,1:NT)]]
@@ Line 296: / Line 344: @@
 :'''related = ''' [[ANA_SPFLUX]], [[ANA_SSFLUX]]
 :'''conflict = '''
-:'''routine = '''  <section end=ANA_STFLUX />
+:'''routine = ''' [[analytical.F]] (ana_stflux)<section end=ANA_STFLUX />
-<section begin=ANA_TAIR />;<span id="ANA_TAIR"></span>'''[[ANA_TAIR]]'''
+<section begin=ANA_TAIR />;<span id="ANA_TAIR"></span>[[ANA_TAIR]]
 :Option to set surface air temperature with an analytical expression
 :'''variable = ''' [[Variables#Tair | Tair]]
@@ Line 306: / Line 354: @@
 :'''routine = ''' [[analytical.F]] (ana_tair)<section end=ANA_TAIR />
-<section begin=ANA_TCLIMA />;<span id="ANA_TCLIMA"></span>'''[[ANA_TCLIMA]]'''
+<section begin=ANA_TCLIMA />;<span id="ANA_TCLIMA"></span>[[ANA_TCLIMA]]
 :Option to set tracer climatology with analytical expressions.
 :'''variable = ''' [[Variables#tclm | tclm]]
@@ Line 314: / Line 362: @@
 :'''routine = ''' [[analytical.F]] (ana_tclima)<section end=ANA_TCLIMA />
-<section begin=ANA_TOBC />;<span id="ANA_TOBC"></span>'''[[ANA_TOBC]]'''
+<section begin=ANA_TOBC />;<span id="ANA_TOBC"></span>[[ANA_TOBC]]
 :Option to set tracers open boundary conditions using analytical expressions.
 :'''variable = ''' [[Variables#t_east | t_east]], [[Variables#t_north | t_north]], [[Variables#t_south | t_south]], [[Variables#t_west | t_west]]
@@ Line 320: / Line 368: @@
 :'''routine = ''' [[analytical.F]] (ana_tobc) <section end=ANA_TOBC />
-<section begin=ANA_VMIX />;<span id="ANA_VMIX"></span>'''[[ANA_VMIX]]'''
+<section begin=ANA_VMIX />;<span id="ANA_VMIX"></span>[[ANA_VMIX]]
 :Option to set vertical mixing coefficients for momentum and tracers with analytical expressions.
 :'''variable = ''' [[Variables#Akt | Akt(:,:,:,1:NAT)]], [[Variables#Akv | Akv]]
@@ Line 327: / Line 375: @@
 :'''routine = ''' [[analytical.F]] (ana_vmix)<section end=ANA_VMIX />
-<section begin=ANA_WINDS />;<span id="ANA_WINDS"></span>'''[[ANA_WINDS]]'''
+<section begin=ANA_WINDS />;<span id="ANA_WINDS"></span>[[ANA_WINDS]]
 :Option to set surface wind vector components with analytical expressions.
 :'''variable = ''' [[Variables#Uwind | Uwind]], [[Variables#Vwind | Vwind]]
@@ Line 333: / Line 381: @@
 :'''routine = ''' [[analytical.F]] (ana_winds)<section end=ANA_WINDS />
-<section begin=ANA_WWAVE />;<span id="ANA_WWAVE"></span>'''[[ANA_WWAVE]]'''
+<section begin=ANA_WWAVE />;<span id="ANA_WWAVE"></span>[[ANA_WWAVE]]
 :Option to set wind-induced wave fields with analytical expressions.  It currently, sets values for wave direction, height, length, top and bottom periods, and dissipation.
 :'''variable = ''' [[Variables#Dwave | Dwave]], [[Variables#Hwave | Hwave]], [[Variables#Lwave | Lwave]], [[Variables#Pwave_top | Pwave_top]], [[Variables#Pwave_bot | Pwave_bot]], [[Variables#wave_dissip | wave_dissip]]
@@ Line 341: / Line 389: @@
 :'''routine = ''' [[analytical.F]] (ana_wwave)<section end=ANA_WWAVE />
-<section begin=ASSIMILATION />;<span id="ASSIMILATION"></span>'''[[ASSIMILATION]]'''
+<section begin=ASSIMILATION />;<span id="ASSIMILATION"></span>[[ASSIMILATION]]
 :Internal option defined when any of the optimal interpolation assimilation options is activated.
 :'''related = ''' [[ASSIMILATION_SSH]], [[ASSIMILATION_SST]], [[ASSIMILATION_T]], [[ASSIMILATION_UV]], [[ASSIMILATION_UVsur]]
-:'''conflict = ''' [[NUDGING]], [[IS4DVAR]], [[S4DVAR]], [[W4DPSAS]], [[W4DVAR]]
+:'''conflict = ''' [[NUDGING]], [[I4DVAR]], [[S4DVAR]], [[RBL4DVAR]], [[R4DVAR]]
 :'''routine = ''' [[globaldefs.h]]<section end=ASSIMILATION />
-<section begin=ASSIMILATION_SSH />;<span id="ASSIMILATION_SSH"></span>'''[[ASSIMILATION_SSH]]'''
+<section begin=ASSIMILATION_SSH />;<span id="ASSIMILATION_SSH"></span>[[ASSIMILATION_SSH]]
 :Option to assimilate sea surface height observations (altimetry) using optimal interpolation.
 :'''variable = ''' [[Variables#EdatSSH | EdatSSH]], [[Variables#EobsSSH | EobsSSH]], [[Variables#SSHdat | SSHdat]], [[Variables#SSHobs | SSHobs]]
@@ Line 355: / Line 403: @@
 :'''routine = ''' [[oi_update.F]]<section end=ASSIMILATION_SSH />
-<section begin=ASSIMILATION_SST />;<span id="ASSIMILATION_SST"></span>'''[[ASSIMILATION_SST]]'''
+<section begin=ASSIMILATION_SST />;<span id="ASSIMILATION_SST"></span>[[ASSIMILATION_SST]]
 :Option to assimilate sea surface temperature observations using optimal interpolation.
 :'''variable = ''' [[Variables#EdatSST | EdatSST]], [[Variables#EobsSST | EobsSST]], [[Variables#SSTdat | SSTdat]], [[Variables#SSTobs | SSTobs]]
@@ Line 363: / Line 411: @@
 :'''routine = ''' [[oi_update.F]]<section end=ASSIMILATION_SST />
-<section begin=ASSIMILATION_T />;<span id="ASSIMILATION_T"></span>'''[[ASSIMILATION_T]]'''
+<section begin=ASSIMILATION_T />;<span id="ASSIMILATION_T"></span>[[ASSIMILATION_T]]
 :Option to assimilate tracer-type observations (temperature, salinity) using optimal interpolation.
 :'''variable = ''' [[Variables#EdatT | EdatT]], [[Variables#EobsT | EobsT]], [[Variables#Tdat | Tdat]], [[Variables#Tobs | Tobs]]
@@ Line 371: / Line 419: @@
 :'''routine = ''' [[oi_update.F]]<section end=ASSIMILATION_T />
-<section begin=ASSIMILATION_UV />;<span id="ASSIMILATION_UV"></span>'''[[ASSIMILATION_UV]]'''
+<section begin=ASSIMILATION_UV />;<span id="ASSIMILATION_UV"></span>[[ASSIMILATION_UV]]
 :Option to assimilate 3D momentum (u,v) observations using optimal interpolation.
 :'''variable = ''' [[Variables#EdatUV | EdatUV]], [[Variables#EobsUV | EobsUV]], [[Variables#UVdat | UVdat]], [[Variables#UVobs | UVobs]]
@@ Line 379: / Line 427: @@
 :'''routine = ''' [[oi_update.F]]<section end=ASSIMILATION_UV />
-<section begin=ASSIMILATION_UVsur />;<span id="ASSIMILATION_UVsur"></span>'''[[ASSIMILATION_UVsur]]'''
+<section begin=ASSIMILATION_UVsur />;<span id="ASSIMILATION_UVsur"></span>[[ASSIMILATION_UVsur]]
 :Option to assimilate surface momentum (u,v) observations (CODAR) using optimal interpolation.
 :'''variable = ''' [[Variables#EdatVsur | EdatVsur]], [[Variables#EobsVsur | EobsVsur]], [[Variables#Usurdat | Usurdat]], [[Variables#Usur | Usur]], [[Variables#Vsurdat | Vsurdat]], [[Variables#Vsur | Vsur]]
@@ Line 387: / Line 435: @@
 :'''routine = ''' [[oi_update.F]]<section end=ASSIMILATION_UVsur />
-<section begin=ASSUMED_SHAPE />;<span id="ASSUMED_SHAPE"></span>'''[[ASSUMED_SHAPE]]'''
+<section begin=ASSUMED_SHAPE />;<span id="ASSUMED_SHAPE"></span>[[ASSUMED_SHAPE]]
-:Internal option to declare all global arrays as assumed-shape where their size, bounds, and shape are associated with pointers. Imported arrays with dummy arguments that takes the shape of the actual argument passes to it. If not activated, all the arrays are of explicit-shape. In some computers the explicit-shape arrays slow doen performace because the arrays are copied when passed as argument.
+:Internal option to declare all global arrays as assumed-shape where their size, bounds, and shape are associated with pointers. Imported arrays with dummy arguments that takes the shape of the actual argument passes to it. If not activated, all the arrays are of explicit-shape. In some computers the explicit-shape arrays slow down performance because the arrays are copied when passed as arguments.
 :'''routine = ''' [[globaldefs.h]]<section end=ASSUMED_SHAPE />
-<section begin=AVERAGES />;<span id="AVERAGES"></span>'''[[AVERAGES]]'''
+<section begin=ATM_PRESS />;<span id="ATM_PRESS"></span>[[ATM_PRESS]]
-:Option to write out time-averaged fields into output NetCDF file.
+:Option to impose atmospheric pressure onto sea surface. If [[SOLVE3D]] is activated the pressure is imposed on the 3D pressure gradient equations ('''*prsgrd*.h''', ''i.e.'' [[prsgrd31.h]]). Otherwise, it is imposed on the 2D pressure gradient equations found in the '''step2d_LF_AM3.h''' routines.
-:'''parameter = ''' [[Variables#nAVG | nAVG]], [[Variables#ndefAVG | ndefAVG]], [[Variables#ntsAVG | ntsAVG]]
+:'''parameter = '''
+:'''parent = '''
+:'''required = ''' [[SOLVE3D]]
+:'''related = ''' [[DJ_GRADPS]], [[PJ_GRADP]], [[PJ_GRADPQ2]], [[PJ_GRADPQ4]], [[SOLVE3D]], [[WJ_GRADP]]
+:'''conflict = '''
+:'''routine = ''' [[ad_prsgrd.F]], [[prsgrd.F]], [[rp_prsgrd.F]], [[tl_prsgrd.F]], [[ad_step2d_LF_AM3.h]], [[step2d_LF_AM3.h]], [[rp_step2d_LF_AM3.h]], [[tl_step2d_LF_AM3.h]]<section end=ATM_PRESS />
+<section begin=AVERAGES />;<span id="AVERAGES"></span>[[AVERAGES]]
+:Option to write out time-averaged fields into output NetCDF file.
+:'''parameter = ''' [[Variables#nAVG | nAVG]], [[Variables#ndefAVG | ndefAVG]], [[Variables#ntsAVG | ntsAVG]]
 :'''related = ''' [[AVERAGES_AKS]], [[AVERAGES_AKT]], [[AVERAGES_AKV]], [[AVERAGES_BEDLOAD]], [[AVERAGES_FLUXES]], [[AVERAGES_NEARSHORE]], [[AVERAGES_QUADRATIC]]
 :'''routine = ''' [[def_avg.F]], [[set_avg.F]], [[wrt_AVG.F]]<section end=AVERAGES />
-<section begin=AVERAGES_AKS />;<span id="AVERAGES_AKS"></span>'''[[AVERAGES_AKS]]'''
+<section begin=AVERAGES_AKS />;<span id="AVERAGES_AKS"></span>AVERAGES_AKS (REMOVED)
-:Option to write out time-averaged vertical diffusion of salinity into output NetCDF file. Use this option when any of the vertical mixing parameterizations is activated.
+:This option was removed in '''revision 462'''. Option to write out time-averaged vertical diffusion of salinity into output NetCDF file. Use this option when any of the vertical mixing parameterizations is activated.
 :'''parameter = ''' [[Variables#nAVG | nAVG]], [[Variables#ndefAVG | ndefAVG]], [[Variables#ntsAVG | ntsAVG]]
 :'''parent = ''' [[AVERAGES]]
@@ Line 405: / Line 462: @@
 :'''routine = ''' [[def_avg.F]], [[set_avg.F]], [[wrt_AVG.F]]<section end=AVERAGES_AKS />
-<section begin=AVERAGES_AKT />;<span id="AVERAGES_AKT"></span>'''[[AVERAGES_AKT]]'''
+<section begin=AVERAGES_AKT />;<span id="AVERAGES_AKT"></span>AVERAGES_AKT (REMOVED)
-:Option to write out time-averaged vertical diffusion of temperature into output NetCDF file. Use this option when any of the vertical mixing parameterizations is activated.
+:This option was removed in '''revision 462'''. Option to write out time-averaged vertical diffusion of temperature into output NetCDF file. Use this option when any of the vertical mixing parameterizations is activated.
 :'''parameter = ''' [[Variables#nAVG | nAVG]], [[Variables#ndefAVG | ndefAVG]], [[Variables#ntsAVG | ntsAVG]]
 :'''parent = ''' [[AVERAGES]]
@@ Line 413: / Line 470: @@
 :'''routine = ''' [[def_avg.F]], [[set_avg.F]], [[wrt_AVG.F]]<section end=AVERAGES_AKT />
-<section begin=AVERAGES_AKV />;<span id="AVERAGES_AKV"></span>'''[[AVERAGES_AKV]]'''
+<section begin=AVERAGES_AKV />;<span id="AVERAGES_AKV"></span>AVERAGES_AKV (REMOVED)
-:Option to write out time-averaged vertical viscosity into output NetCDF file. Use this option when any of the vertical mixing parameterizations is activated.
+:This option was removed in '''revision 462'''. Option to write out time-averaged vertical viscosity into output NetCDF file. Use this option when any of the vertical mixing parameterizations is activated.
 :'''parameter = ''' [[Variables#nAVG | nAVG]], [[Variables#ndefAVG | ndefAVG]], [[Variables#ntsAVG | ntsAVG]]
 :'''parent = ''' [[AVERAGES]]
@@ Line 421: / Line 478: @@
 :'''routine = ''' [[def_avg.F]], [[set_avg.F]], [[wrt_AVG.F]]<section end=AVERAGES_AKV />
-<section begin=AVERAGES_BEDLOAD />;<span id="AVERAGES_BEDLOAD"></span>'''[[AVERAGES_BEDLOAD]]'''
+<section begin=AVERAGES_BEDLOAD />;<span id="AVERAGES_BEDLOAD"></span>AVERAGES_BEDLOAD (REMOVED)
-:Option to write out time-averaged bed load components into output NetCDF file.
+:This option was removed in '''revision 462'''. Option to write out time-averaged bed load components into output NetCDF file.
 :'''parameter = ''' [[Variables#nAVG | nAVG]], [[Variables#ndefAVG | ndefAVG]], [[Variables#ntsAVG | ntsAVG]]
 :'''parent = ''' [[AVERAGES]]
@@ Line 429: / Line 486: @@
 :'''routine = ''' [[def_avg.F]], [[set_avg.F]], [[wrt_AVG.F]]<section end=AVERAGES_BEDLOAD />
-<section begin=AVERAGES_FLUXES />;<span id="AVERAGES_FLUXES"></span>'''[[AVERAGES_FLUXES]]'''
+<section begin=AVERAGES_DETIDE />;<span id="AVERAGES_DETIDE"></span>[[AVERAGES_DETIDE]]
-:Option to write out time-averaged surface momentum stress and several fields associated with surface heat and freshwater fluxes.
+:Option to write out time-averaged detided feilds into output NetCDF file.
+:'''parameter = ''' [[Variables#nAVG | nAVG]], [[Variables#ndefAVG | ndefAVG]], [[Variables#ntsAVG | ntsAVG]]
+:'''parent = ''' [[AVERAGES]]
+:'''required = ''' [[AVERAGES]]
+:'''related = '''
+:'''routine = ''' [[def_avg.F]], [[set_avg.F]], [[wrt_AVG.F]]<section end=AVERAGES_DETIDE />
+<section begin=AVERAGES_FLUXES />;<span id="AVERAGES_FLUXES"></span>AVERAGES_FLUXES (REMOVED)
+:This option was removed in '''revision 462'''. Option to write out time-averaged surface momentum stress and several fields associated with surface heat and freshwater fluxes.
 :'''parameter = ''' [[Variables#nAVG | nAVG]], [[Variables#ndefAVG | ndefAVG]], [[Variables#ntsAVG | ntsAVG]]
 :'''parent = ''' [[AVERAGES]]
@@ Line 437: / Line 502: @@
 :'''routine = ''' [[def_avg.F]], [[set_avg.F]], [[wrt_AVG.F]]<section end=AVERAGES_FLUXES />
-<section begin=AVERAGES_NEARSHORE />;<span id="AVERAGES_NEARSHORE"></span>'''[[AVERAGES_NEARSHORE]]'''
+<section begin=AVERAGES_NEARSHORE />;<span id="AVERAGES_NEARSHORE"></span>AVERAGES_NEARSHORE (REMOVED)
-:Option to write out time-averaged nearshore stresses variables.
+:This option was removed in '''revision 462'''. Option to write out time-averaged nearshore stresses variables.
 :'''parameter = ''' [[Variables#nAVG | nAVG]], [[Variables#ndefAVG | ndefAVG]], [[Variables#ntsAVG | ntsAVG]]
 :'''parent = ''' [[AVERAGES]]
@@ Line 445: / Line 510: @@
 :'''routine = ''' [[def_avg.F]], [[set_avg.F]], [[wrt_AVG.F]]<section end=AVERAGES_NEARSHORE />
-<section begin=AVERAGES_QUADRATIC />;<span id="AVERAGES_QUADRATIC"></span>'''[[AVERAGES_QUADRATIC]]'''
+<section begin=AVERAGES_QUADRATIC />;<span id="AVERAGES_QUADRATIC"></span>AVERAGES_QUADRATIC (REMOVED)
-:Option to write out time-averaged variables needed to compute eddy fluxes.  These quadratic variables include &lt;H u / n&gt;, &lt;H v / m&gt;, &lt;H u T / n&gt;, &lt;H v T / m&gt;, &lt;T T&gt;, &lt;u T&gt;, &lt;v T&gt;, &lt;u u&gt;, &lt;v v&gt;, &lt;ubar ubar&gt;, &lt;vbar vbar&gt;, and &lt;zeta zeta&gt;.
+:This option was removed in '''revision 462'''. Option to write out time-averaged variables needed to compute eddy fluxes.  These quadratic variables include &lt;H u / n&gt;, &lt;H v / m&gt;, &lt;H u T / n&gt;, &lt;H v T / m&gt;, &lt;T T&gt;, &lt;u T&gt;, &lt;v T&gt;, &lt;u u&gt;, &lt;v v&gt;, &lt;ubar ubar&gt;, &lt;vbar vbar&gt;, and &lt;zeta zeta&gt;.
 :'''parameter = ''' [[Variables#nAVG | nAVG]], [[Variables#ndefAVG | ndefAVG]], [[Variables#ntsAVG | ntsAVG]]
 :'''parent = ''' [[AVERAGES]]
@@ Line 452: / Line 517: @@
 :'''related = ''' [[AVERAGES_AKS]], [[AVERAGES_AKT]], [[AVERAGES_AKV]], [[AVERAGES_BEDLOAD]], [[AVERAGES_FLUXES]], [[AVERAGES_NEARSHORE]]
 :'''routine = ''' [[def_avg.F]], [[set_avg.F]], [[wrt_AVG.F]]<section end=AVERAGES_QUADRATIC />
-<section begin=A4DVAR_TOY />;<span id="A4DVAR_TOY"></span>'''[[A4DVAR_TOY]]'''
-:Idealized data assimilation example to run 4DVar weak constraint data assimilation algorithms.
-:'''parameter = ''' [[Variables#Ninner | Ninner]], [[Variables#Nouter | Nouter]]
-:'''required = ''' [[W4DPSAS]] or [[W4DVAR]]
-:'''related = ''' [[CONVOLVE]], [[RPM_RELAXATION]]
-:'''routine = ''' [[s4dvar.in]], [[w4dpsas_ocean]], [[w4dvar_ocean.h]] <section end=A4DVAR_TOY />
 ==<span class="alphabet">B</span>==
-<section begin=BACKGROUND />;<span id="BACKGROUND"></span>'''[[BACKGROUND]]'''
+<section begin=BACKGROUND />;<span id="BACKGROUND"></span>[[BACKGROUND]]
-:Option to
+:Internal option to
 :'''parameter = '''
 :'''parent = '''
@@ Line 471: / Line 529: @@
 :'''routine = '''  <section end=BACKGROUND />
-<section begin=BALANCE_OPERATOR />;<span id="BALANCE_OPERATOR"></span>'''[[BALANCE_OPERATOR]]'''
+<section begin=BALANCE_OPERATOR />;<span id="BALANCE_OPERATOR"></span>[[BALANCE_OPERATOR]]
-:Option to
+:Option to enable error covariance multivariate balance term in the tangent linear, representer and adjoint models.
 :'''parameter = '''
 :'''parent = '''
-:'''required = '''
+:'''required = ''' [[ADJOINT]], [[REPRESENTER]], [[TANGENT]]
 :'''related = '''
 :'''conflict = '''
 :'''routine = '''  <section end=BALANCE_OPERATOR />
-<section begin=BASIN />;<span id="BASIN"></span>'''[[BASIN]]'''
+<section begin=BASIN />;<span id="BASIN"></span>[[BASIN]]
-:Option to
+:Options to compile and run the Big Bad Basin example.
 :'''parameter = '''
 :'''parent = '''
@@ Line 487: / Line 545: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=BASIN />
+:'''routine = '''
+:'''input = ''' [[roms.in]]<section end=BASIN />
-<section begin=BEDLOAD />;<span id="BEDLOAD"></span>'''[[BEDLOAD]]'''
+<section begin=BEDLOAD />;<span id="BEDLOAD"></span>[[BEDLOAD]]
-:Option to
+:Internal option to
 :'''parameter = '''
 :'''parent = '''
-:'''required = '''
+:'''required = ''' [[SEDIMENT]] and [[BEDLOAD_MPM]] or [[BEDLOAD_SOULSBY]]
-:'''related = '''
+:'''related = ''' [[AVERAGES_BEDLOAD]]], [[BEDLOAD_MPM]], [[BEDLOAD_SOULSBY]]
 :'''conflict = '''
-:'''routine = '''  <section end=BEDLOAD />
+:'''routine = ''' [[sed_bedload.F]]<section end=BEDLOAD />
-<section begin=BENCHMARK1 />;<span id="BENCHMARK1"></span>'''[[BENCHMARK1]]'''
+<section begin=BEDLOAD_MPM />;<span id="BEDLOAD_MPM"></span>[[BEDLOAD_MPM]]
-:Option to
+:Option to activate Meyer-Peter-Mueller bed load in the sediment transport model.
 :'''parameter = '''
 :'''parent = '''
-:'''required = '''
+:'''required = ''' [[SEDIMENT]]
-:'''related = '''
+:'''related = ''' [[AVERAGES_BEDLOAD]]], [[BEDLOAD_SOULSBY]]
-:'''conflict = '''
+:'''conflict = ''' [[BEDLOAD_SOULSBY]]
-:'''routine = '''  <section end=BENCHMARK1 />
+:'''routine = ''' [[sed_bedload.F]]<section end=BEDLOAD_MPM />
-<section begin=BENCHMARK2 />;<span id="BENCHMARK2"></span>'''[[BENCHMARK2]]'''
+<section begin=BEDLOAD_SOULSBY />;<span id="BEDLOAD_SOULSBY"></span>[[BEDLOAD_SOULSBY]]
-:Option to
+:Option to activate Soulsby wave/current bed load in the sediment transport model.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[SEDIMENT]]
-:'''conflict = '''
+:'''related = ''' [[AVERAGES_BEDLOAD]]], [[BEDLOAD_MPM]]
-:'''routine = '''  <section end=BENCHMARK2 />
+:'''conflict = ''' [[BEDLOAD_MPM]]
+:'''routine = ''' [[sed_bedload.F]]<section end=BEDLOAD_SOULSBY />
-<section begin=BENCHMARK3 />;<span id="BENCHMARK3"></span>'''[[BENCHMARK3]]'''
+<section begin=BENCHMARK />;<span id="BENCHMARK"></span>[[BENCHMARK]]
-:Option to
+:Option to compile and run the benchmark tests. The benchmark comes in 3 sizes that can be selected at runtime.
-:'''parameter = '''
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=BENCHMARK3 />
+:'''routine = '''
+:'''input = ''' [[roms.in]] (ocean_benchmark1, 2 & 3)<section end=BENCHMARK />
-<section begin=BIOLOGY />;<span id="BIOLOGY"></span>'''[[BIOLOGY]]'''
-:Internal option defined when any of the biological models is activated.
-:'''related = ''' [[BIO_FASHAM]], [[ECOSIM]], [[NPZD_FRANKS]], [[NPZD_POWELL]]
-:'''routine = ''' [[biology.F]]<section end=BIOLOGY />
-<section begin=BIO_FASHAM />;<span id="BIO_FASHAM"></span>'''[[BIO_FASHAM]]'''
+<section begin=BIO_FENNEL />;<span id="BIO_FENNEL"></span>[[BIO_FENNEL]]
-:Option to activate Fasham-type, nitrogen-based biological model ([[Bibliography#FashamMJR_1990a |Fasham et al., 1990]]; [[Bibliography#FenellK_2006a | Fennel et al., 2006]])
+:Option to activate Fennel ''et al.'' ecosystem model ([[Bibliography#FennelK_2009a|Fennel et al., 2009]]; [[Bibliography#FenellK_2006a|Fennel et al., 2006]]). This model is loosely based on the model by [[Bibliography#FashamMJR_1990a|Fasham et al. (1990)]] but it differs in many respects.  The detailed equations of the nitrogen cycling component  are given in [[Bibliography#FenellK_2006a|Fennel et al., (2006)]] Nitrogen is the  fundamental elemental  currency in this model. This model was adapted from a code written originally  by  John Moisan and Emanule DiLorenzo.
 :'''related = ''' [[ANA_BIOLOGY]], [[ANA_BPFLUX]], [[ANA_SPFLUX]], [[BIO_SEDIMENT]], [[CARBON]], [[DENITRIFICATION]], [[DIAGNOSTICS_BIO]], [[OXYGEN]], [[TALK_PROGNOSTIC]]
-:'''conflict = ''' [[ECOSIM]], [[NPZD_FRANKS]], [[NPZD_POWELL]]
+:'''conflict = ''' [[ECOSIM]], [[NEMURO]], [[NPZD_FRANKS]], [[NPZD_IRON]], [[NPZD_POWELL]]
-:'''routine = ''' [[fasham.h]], [[bioFasham.in]]<section end=BIO_FASHAM />
+:'''routine = ''' [[fennel.h]]
+:'''input =''' [[bioFennel.in]]<section end=BIO_FENNEL />
-<section begin=BIO_SEDIMENT />;<span id="BIO_SEDIMENT"></span>'''[[BIO_SEDIMENT]]'''
+<section begin=BIO_SEDIMENT />;<span id="BIO_SEDIMENT"></span>[[BIO_SEDIMENT]]
-:Option to restore fallen particulate material to the nutrient pool in Fasham-type model.
+:Option to restore fallen particulate material to the nutrient pool in the Fennel model.
-:'''parent = ''' [[BIO_FASHAM]]
+:'''parent = ''' [[BIO_FENNEL]]
-:'''routine = ''' [[fasham.h]]<section end=BIO_SEDIMENT />
+:'''routine = ''' [[fennel.h]]<section end=BIO_SEDIMENT />
-<section begin=BIO_TOY />;<span id="BIO_TOY"></span>'''[[BIO_TOY]]'''
+<section begin=BIO_TOY />;<span id="BIO_TOY"></span>[[BIO_TOY]]
-:Option to
+:Option to compile and run the one-dimensional (vertical) biology toy.
-:'''parameter = '''
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=BIO_TOY />
+:'''routine = '''
+:'''input = ''' [[roms.in]]<section end=BIO_TOY />
-<section begin=BL_TEST />;<span id="BL_TEST"></span>'''[[BL_TEST]]'''
+<section begin=BIOLOGY />;<span id="BIOLOGY"></span>[[BIOLOGY]]
-:Option to
+:Internal option defined when any of the biological models is activated.
-:'''parameter = '''
+:'''related = ''' [[BIO_FENNEL]], [[ECOSIM]], [[NEMURO]], [[NPZD_FRANKS]], [[NPZD_POWELL]]
+:'''routine = ''' [[biology.F]]<section end=BIOLOGY />
+<section begin=BL_TEST />;<span id="BL_TEST"></span>[[BL_TEST]]
+:Option to compile and run the boundary layers test.
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=BL_TEST />
+:'''routine = '''
+:'''input = ''' [[roms.in]], [[stations.in]]<section end=BL_TEST />
-<section begin=BODYFORCE />;<span id="BODYFORCE"></span>'''[[BODYFORCE]]'''
+<section begin=BODYFORCE />;<span id="BODYFORCE"></span>[[BODYFORCE]]
-:Option to
+:Option to apply stresses as body forces.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=BODYFORCE />
+:'''routine = ''' <section end=BODYFORCE />
-<section begin=BULK_FLUXES />;<span id="BULK_FLUXES"></span>'''[[BULK_FLUXES]]'''
+<section begin=BULK_FLUXES />;<span id="BULK_FLUXES"></span>[[BULK_FLUXES]]
-:Option to
+:Option to use bulk fluxes computation for surface fluxes formulation using atmospheric boundary layer.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[COOL_SKIN]], [[EMINUSP]], [[LONGWAVE]], [[LONGWAVE_OUT]], [[NL_BULK_FLUXES]]
 :'''conflict = '''
 :'''routine = '''  <section end=BULK_FLUXES />
-<section begin=BVF_MIXING />;<span id="BVF_MIXING"></span>'''[[BVF_MIXING]]'''
+<section begin=BVF_MIXING />;<span id="BVF_MIXING"></span>[[BVF_MIXING]]
-:Option to
+:Option to use Brunt-Vaisala frequency mixing for vertical turbulent mixing scheme of momentum and tracers.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
 :'''related = '''
-:'''conflict = '''
+:'''conflict = ''' [[GLS_MIXING]], [[LMD_MIXING]], [[MY25_MIXING]]
-:'''routine = '''  <section end=BVF_MIXING />
+:'''routine = ''' [[bvf_mix.F]]<section end=BVF_MIXING />
 ==<span class="alphabet">C</span>==
-<section begin=CANUTO_A />;<span id="CANUTO_A"></span>'''[[CANUTO_A]]'''
+<section begin=CANUTO_A />;<span id="CANUTO_A"></span>[[CANUTO_A]]
-:Option to
+:Option to use Canuto A-stability function formulation for the [[Generic Length Scale]] closure.
+:'''parameter = '''
+:'''parent = ''' [[GLS_MIXING]]
+:'''required = ''' [[GLS_MIXING]]
+:'''related = ''' [[CANUTO_B]], [[KANTHA_CLAYSON]]
+:'''conflict = ''' [[CANUTO_B]], [[KANTHA_CLAYSON]]
+:'''routine = ''' [[gls_corstep.F]]<section end=CANUTO_A />
+<section begin=CANUTO_B />;<span id="CANUTO_B"></span>[[CANUTO_B]]
+:Option to use Canuto B-stability function formulation for the [[Generic Length Scale]] closure.
 :'''parameter = '''
+:'''parent = ''' [[GLS_MIXING]]
+:'''required = ''' [[GLS_MIXING]]
+:'''related = ''' [[CANUTO_A]], [[KANTHA_CLAYSON]]
+:'''conflict = ''' [[CANUTO_A]], [[KANTHA_CLAYSON]]
+:'''routine = ''' [[gls_corstep.F]]<section end=CANUTO_B />
+<section begin=CANYON />;<span id="CANYON"></span>[[CANYON]]
+:Option to compile and run the coastal form stress canyon test.
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=CANUTO_A />
+:'''routine = '''
+:'''input = ''' [[roms.in]] (_canyon2d and _canyon3d)<section end=CANYON />
+<section begin=CARBON />;<span id="CARBON"></span>[[CARBON]]
+:Option to include carbon constituents in the Fennel biological model. Currently, four carbon-based tracer are added to include large detritus ([[Variables#iLDeC|iLDeC]]), small detritus ([[Variables#iSDeC|iSDeC]]), total inorganic carbon ([[Variables#iTIC_|iTIC_]]), and total alkalinity ([[Variables#iTAlk|iTAlk]]).
+:'''parent = ''' [[BIO_FENNEL]]
+:'''required = ''' [[OXYGEN]]
+:'''routine = ''' [[fennel.h]]<section end=CARBON />
-<section begin=CANUTO_B />;<span id="CANUTO_B"></span>'''[[CANUTO_B]]'''
+<!--section begin=CELERITY_READ />;<span id="CELERITY_READ"></span>[[CELERITY_READ]]
 :Option to
 :'''parameter = '''
 :'''parent = '''
@@ Line 604: / Line 693: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=CANUTO_B />
+:'''routine = '''  <section end=CELERITY_READ /-->
-<section begin=CANYON />;<span id="CANYON"></span>'''[[CANYON]]'''
+<section begin=CELERITY_WRITE />;<span id="CELERITY_WRITE"></span>[[CELERITY_WRITE]]
-:Option to
+:Option to write radiation celerity in forward file when running tangent linear, representer and adjoint models.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' <!--[[CELERITY_READ]]-->
 :'''conflict = '''
-:'''routine = '''  <section end=CANYON />
+:'''routine = ''' [[mod_boundary.F]]<section end=CELERITY_WRITE />
-<section begin=CARBON />;<span id="CARBON"></span>'''[[CARBON]]'''
+<section begin=CHANNEL_NECK />;<span id="CHANNEL_NECK"></span>[[CHANNEL_NECK]]
-:Option to include carbon constituents in Fasham-type biological model. Currently, four carbon-based tracer are added to include large detritus ([[Variables#iLDeC|iLDeC]]), small detritus ([[Variables#iSDeC|iSDeC]]), total inorganic carbon ([[Variables#iTIC_|iTIC_]]), and total alkalinity ([[Variables#iTAlk|iTAlk]]).
+:Option to compile and run the idealized channel with constriction test.
-:'''parent = ''' [[BIO_FASHAM]]
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
-:'''required = ''' [[OXYGEN]]
-:'''routine = ''' [[fasham.h]]<section end=CARBON />
-<section begin=CELERITY_READ />;<span id="CELERITY_READ"></span>'''[[CELERITY_READ]]'''
-:Option to
-:'''parameter = '''
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=CELERITY_READ />
+:'''routine = '''
+:'''input = ''' [[roms.in]] (_channel_neck1 _channel_neck3) <section end=CHANNEL_NECK />
-<section begin=CELERITY_WRITE />;<span id="CELERITY_WRITE"></span>'''[[CELERITY_WRITE]]'''
+<section begin=CHARNOK />;<span id="CHARNOK"></span>[[CHARNOK]]
-:Option to
+:Option to use Charnok surface roughness from wind stress for the [[Generic Length Scale]] closure.
 :'''parameter = '''
-:'''parent = '''
+:'''parent = ''' [[GLS_MIXING]]
-:'''required = '''
+:'''required = ''' [[GLS_MIXING]]
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=CELERITY_WRITE />
+:'''routine = ''' [[gls_corstep.F]]<section end=CHARNOK />
-<section begin=CHARNOK />;<span id="CHARNOK"></span>'''[[CHARNOK]]'''
+<section begin=CHECKPOINTING />;<span id="CHECKPOINTING"></span>[[CHECKPOINTING]]
-:Option to
+:Internal switch to activate checkpointing switch for generalized stability theory (GST) analysis.
 :'''parameter = '''
 :'''parent = '''
-:'''required = '''
+:'''required = ''' [[PROPAGATOR]]
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=CHARNOK />
+:'''routine = '''  <section end=CHECKPOINTING />
-<section begin=CHECKPOINTING />;<span id="CHECKPOINTING"></span>'''[[CHECKPOINTING]]'''
+<section begin=CLIMA_TS_MIX />;<span id="CLIMA_TS_MIX"></span>[[CLIMA_TS_MIX]]
-:Option to
+:Option to use if diffusion of tracer perturbation (t-tclm) is needed for horizontal mixing of tracers.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[DIFF_GRID]], [[MIX_S_TS]], [[MIX_GEO_TS]], [[MIX_ISO_TS]]
 :'''conflict = '''
-:'''routine = '''  <section end=CHECKPOINTING />
+:'''routine = ''' <section end=CLIMA_TS_MIX />
-<section begin=CLOUDS />;<span id="CLOUDS"></span>'''[[CLOUDS]]'''
+<section begin=CLOUDS />;<span id="CLOUDS"></span>[[CLOUDS]]
 :Internal option indicating that cloud data is needed.
 :'''required = ''' [[ALBEDO]], [[ECOSIM]], [[LONGWAVE]]
@@ Line 663: / Line 747: @@
 :'''routine = ''' [[globaldefs.h]]<section end=ANA_CLOUD />
-<section begin=CONVOLUTION />;<span id="CONVOLUTION"></span>'''[[CONVOLUTION]]'''
+<section begin=COARE_OOST />;<span id="COARE_OOST"></span>[[COARE_OOST]]
-:Option to
+:Option to use Oost ''et al.'' (2002) relation for wave roughness formulation in bulk fluxes.
 :'''parameter = '''
 :'''parent = '''
@@ Line 670: / Line 754: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=CONVOLUTION />
+:'''routine = '''  <section end=COARE_OOST />
-<section begin=CONVOLVE />;<span id="CONVOLVE"></span>'''[[CONVOLVE]]'''
+<section begin=COARE_TAYLOR_YELLAND />;<span id="COARE_TAYLOR_YELLAND"></span>[[COARE_TAYLOR_YELLAND]]
-:Option to
+:Option to use Taylor and Yelland (2001) relation for wave roughness formulation in bulk fluxes.
 :'''parameter = '''
 :'''parent = '''
@@ Line 679: / Line 763: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=CONVOLVE />
+:'''routine = '''  <section end=COARE_TAYLOR_YELLAND />
-<section begin=COOL_SKIN />;<span id="COOL_SKIN"></span>'''[[COOL_SKIN]]'''
+<section begin=CONVOLUTION />;<span id="CONVOLUTION"></span>[[CONVOLUTION]]
-:Option to
+:Option to use the adjoint convolution driver.
 :'''parameter = '''
 :'''parent = '''
@@ Line 688: / Line 772: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=COOL_SKIN />
+:'''routine = '''  <section end=CONVOLUTION />
-<section begin=COUPLING_TEST />;<span id="COUPLING_TEST"></span>'''[[COUPLING_TEST]]'''
+<section begin=CONVOLVE />;<span id="CONVOLVE"></span>[[CONVOLVE]]
-:Option to
+:Option to use convolving solution with diffusion operators in the tangent linear, representer and adjoint models.
 :'''parameter = '''
 :'''parent = '''
@@ Line 697: / Line 781: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=COUPLING_TEST />
+:'''routine = '''  <section end=CONVOLVE />
-<section begin=CORRELATION />;<span id="CORRELATION"></span>'''[[CORRELATION]]'''
+<section begin=COOL_SKIN />;<span id="COOL_SKIN"></span>[[COOL_SKIN]]
-:Option to
+:Option to use cool skin correction for surface fluxes formulation using atmospheric boundary layer.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[BULK_FLUXES]]
+:'''conflict = '''
+:'''routine = ''' [[ad_bulk_fluxes.F]], [[bulk_fluxes.F]], [[rp_bulk_fluxes.F]], [[tl_bulk_flux.F]]<section end=COOL_SKIN />
+<section begin=CORRELATION />;<span id="CORRELATION"></span>[[CORRELATION]]
+:Option to use background-error correlation model driver.
 :'''parameter = '''
 :'''parent = '''
@@ Line 708: / Line 801: @@
 :'''routine = '''  <section end=CORRELATION />
-<section begin=COSINE2 />;<span id="COSINE2"></span>'''[[COSINE2]]'''
+<section begin=COSINE2 />;<span id="COSINE2"></span>[[COSINE2]]
-:Option to
+:Internal switch to activate the cosine-squared shaped filter.
 :'''parameter = '''
 :'''parent = '''
@@ Line 717: / Line 810: @@
 :'''routine = '''  <section end=COSINE2 />
-<section begin=CRAIG_BANNER />;<span id="CRAIG_BANNER"></span>'''[[CRAIG_BANNER]]'''
+<section begin=COUPLING_TEST />;<span id="COUPLING_TEST"></span>[[COUPLING_TEST]]
-:Option to
+:Option to compile and run the two-way atmosphere-ocean coupling test.
-:'''parameter = '''
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
 :'''required = '''
+:'''related = '''
+:'''conflict = '''
+:'''routine = '''
+:'''input = ''' [[roms.in]]<section end=COUPLING_TEST />
+<section begin=CRAIG_BANNER />;<span id="CRAIG_BANNER"></span>[[CRAIG_BANNER]]
+:Option to use Craig and Banner wave breaking surface flux for the [[Generic Length Scales]] closure.
+:'''parameter = '''
+:'''parent = ''' [[GLS_MIXING]]
+:'''required = ''' [[GLS_MIXING]]
 :'''related = '''
 :'''conflict = '''
 :'''routine = '''  <section end=CRAIG_BANNER />
-<section begin=CURVGRID />;<span id="CURVGRID"></span>'''[[CURVGRID]]'''
+<section begin=CURVGRID />;<span id="CURVGRID"></span>[[CURVGRID]]
-:Option to
+:Option to indicate the ROMS grid coordinates are curvilinear.
 :'''parameter = '''
 :'''parent = '''
@@ Line 737: / Line 840: @@
 ==<span class="alphabet">D</span>==
-<section begin=DAMEE_4 />;<span id="DAMEE_4"></span>'''[[DAMEE_4]]'''
+<section begin=DAMEE_4 />;<span id="DAMEE_4"></span>[[DAMEE_4]]
-:Option to
+:Option to Compile and run the 3/4&deg; north Atlantic DAMEE application
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
+:'''parent = '''
+:'''required = '''
+:'''related = '''
+:'''conflict = '''
+:'''routine = '''
+:'''input = ''' [[roms.in]]<section end=DAMEE_4 />
+<section begin=DATALESS_LOOPS />;<span id="DATALESS_LOOPS"></span>[[DATALESS_LOOPS]]
+:Option to test convergence of Picard iterations with the tangent linear, representer and adjoint models.
 :'''parameter = '''
 :'''parent = '''
@@ Line 744: / Line 857: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=DAMEE_4 />
+:'''routine = ''' <section end=DATALESS_LOOPS/>
-<section begin=DEBUGGING />;<span id="DEBUGGING"></span>'''[[DEBUGGING]]'''
+<section begin=DEBUGGING />;<span id="DEBUGGING"></span>[[DEBUGGING]]
-:Option to
+:Option 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 whether the binary files are different or not. Finding the parallel bug is a completely different story.
 :'''parameter = '''
 :'''parent = '''
@@ Line 753: / Line 866: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=DEBUGGING />
+:'''routine = ''' <section end=DEBUGGING />
-<section begin=DENITRIFICATION />;<span id="DENITRIFICATION"></span>'''[[DENITRIFICATION]]'''
+<section begin=DEEPWATER_WAVES />;<span id="DEEPWATER_WAVES"></span>[[DEEPWATER_WAVES]]
-:Option to include denitrification processes in Fasham-type biological model.
+:Option to use deep water waves approximation for wave roughness formulation in bulk fluxes.
-:'''parent = ''' [[#BIO_FASHAM | BIO_FASHAM]]
+:'''parameter = '''
-:'''routine = ''' [[fasham.h]]<section end=DENITRIFICATION />
+:'''parent = ''' [[BULK_FLUXES]]
+:'''required = ''' [[BULK_FLUXES]]
+:'''related = ''' [[COARE_TAYLOR_YELLAND]], [[COARE_OOST]]
+:'''conflict = ''' [[COARE_TAYLOR_YELLAND]], [[COARE_OOST]]
+:'''routine = ''' [[bulk_flux.F]]<section end=DEEPWATER_WAVES />
-<section begin=DIAGNOSTICS />;<span id="DIAGNOSTICS"></span>'''[[DIAGNOSTICS]]'''
+<section begin=DEFLATE />;<span id="DEFLATE"></span>[[DEFLATE]]
-:Internal option to compute and write balance term diagnostics for tracers and momentum.
+:Option to set compression for NetCDF-4/HDF5 output files.
+:'''parameter = '''
+:'''parent = ''' [[NETCDF4]]
+:'''required = ''' [[NETCDF4]]
+:'''related = '''
+:'''conflict = '''
+:'''routine = ''' <section end=DEFLATE />
+<section begin=DENITRIFICATION />;<span id="DENITRIFICATION"></span>[[DENITRIFICATION]]
+:Option to include denitrification processes in the Fennel biological model.
+:'''parent = ''' [[#BIO_FENNEL | BIO_FENNEL]]
+:'''routine = ''' [[fennel.h]]<section end=DENITRIFICATION />
+<section begin=DIAGNOSTICS />;<span id="DIAGNOSTICS"></span>[[DIAGNOSTICS]]
+:Internal option to compute and write balance term diagnostics for tracers and momentum.
 :'''related = ''' [[DIAGNOSTICS_BIO]], [[DIAGNOSTICS_TS]], [[DIAGNOSTICS_UV]]
 :'''routine = ''' [[set_diags.F]], [[wrt_diags.F]]<section end=DIAGNOSTICS />
-<section begin=DIAGNOSTICS_BIO />;<span id="DIAGNOSTICS_BIO"></span>'''[[DIAGNOSTICS_BIO]]'''
+<section begin=DIAGNOSTICS_BIO />;<span id="DIAGNOSTICS_BIO"></span>[[DIAGNOSTICS_BIO]]
-:Option to compute and write biological diagnostic terms in Fasham-type model.
+:Option to compute and write biological diagnostic terms in the Fennel model.
-:'''parent = ''' [[BIO_FASHAM]]
+:'''parent = ''' [[BIO_FENNEL]]
 :'''related = ''' [[DIAGNOSTICS_TS]], [[DIAGNOSTICS_UV]]
-:'''routine = ''' [[fasham.h]], [[wrt_diags.F]]<section end=DIAGNOSTICS_BIO />
+:'''routine = ''' [[fennel.h]], [[wrt_diags.F]]<section end=DIAGNOSTICS_BIO />
-<section begin=DIAGNOSTICS_TS />;<span id="DIAGNOSTICS_TS"></span>'''[[DIAGNOSTICS_TS]]'''
+<section begin=DIAGNOSTICS_TS />;<span id="DIAGNOSTICS_TS"></span>[[DIAGNOSTICS_TS]]
 :Option to compute and write diagnostic terms for tracer equations balances.
 :'''related = ''' [[DIAGNOSTICS_BIO]], [[DIAGNOSTICS_UV]]
 :'''routine = ''' [[set_diags.F]], [[step3d_t.F]], [[wrt_diags.F]]<section end=DIAGNOSTICS_TS />
-<section begin=DIAGNOSTICS_UV />;<span id="DIAGNOSTICS_UV"></span>'''[[DIAGNOSTICS_UV]]'''
+<section begin=DIAGNOSTICS_UV />;<span id="DIAGNOSTICS_UV"></span>[[DIAGNOSTICS_UV]]
 :Option to compute and write diagnostic terms for momentum equations balances.
 :'''related = ''' [[DIAGNOSTICS_BIO]], [[DIAGNOSTICS_TS]]
 :'''routine = ''' [[set_diags.F]], [[step2d.F]], [[step3d_t.F]], [[wrt_diags.F]]<section end=DIAGNOSTICS_UV />
-<section begin=DIFF_GRID />;<span id="DIFF_GRID"></span>'''[[DIFF_GRID]]'''
+<section begin=DIFF_GRID />;<span id="DIFF_GRID"></span>[[DIFF_GRID]]
-:Option to
+:Option to scale diffusion coefficients by grid size for horizontal mixing of tracers.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[CLIMA_TS_MIX]], [[MIX_S_TS]], [[MIX_GEO_TS]], [[MIX_ISO_TS]]
 :'''conflict = '''
 :'''routine = '''  <section end=DIFF_GRID />
-<section begin=DIURNAL_SRFLUX />;<span id="DIURNAL_SRFLUX"></span>'''[[DIURNAL_SRFLUX]]'''
+<section begin=DIURNAL_SRFLUX />;<span id="DIURNAL_SRFLUX"></span>[[DIURNAL_SRFLUX]]
-:Option to
+:Option to impose shortwave radiation local diurnal cycle for shortwave radiation. Input shortwave radiation data computed from averaged data (with snapshots greater than or equal to 24 hours) can be modulated by the local diurnal cycle which is a function of longitude, latitude and day of the year.
-:'''parameter = '''
+:'''variable = ''' [[Variables#srflux|srflux]]
 :'''parent = '''
-:'''required = '''
+:'''required = ''' [[ANA_SRFLUX]]
-:'''related = '''
+:'''related = ''' [[ALBEDO]]
 :'''conflict = '''
-:'''routine = '''  <section end=DIURNAL_SRFLUX />
+:'''routine = ''' [[analytical.F]] (ana_srflux)<section end=DIURNAL_SRFLUX />
-<section begin=DJ_GRADPS />;<span id="DJ_GRADPS"></span>'''[[DJ_GRADPS]]'''
+<section begin=DISTRIBUTE />;<span id="DISTRIBUTE"></span>[[DISTRIBUTE]]
-:Option to
+:Internal switch for compiling the model to run in parallel using distributed memory ([[MPI]]).
-:'''parameter = '''
+:'''variable = '''
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=DJ_GRADPS />
+:'''routine = ''' <section end=DISTRIBUTE />
-<section begin=DOUBLE_GYRE />;<span id="DOUBLE_GYRE"></span>'''[[DOUBLE_GYRE]]'''
+<section begin=DJ_GRADPS />;<span id="DJ_GRADPS"></span>[[DJ_GRADPS]]
-:Option to
+:Option to use splines density Jacobian (Shchepetkin, 2000) for pressure gradient algorithm.
 :'''parameter = '''
+:'''parent = '''
+:'''required = ''' [[SOLVE3D]]
+:'''related = ''' [[ATM_PRESS]], [[PJ_GRADP]], [[PJ_GRADPQ2]], [[PJ_GRADPQ4]], [[WJ_GRADP]]
+:'''conflict = ''' [[PJ_GRADP]], [[PJ_GRADPQ2]], [[PJ_GRADPQ4]], [[WJ_GRADP]]
+:'''routine = ''' [[ad_prsgrd.F]], [[prsgrd.F]], [[rp_prsgrd.F]], [[tl_prsgrd.F]]<section end=DJ_GRADPS />
+<section begin=DOUBLE_GYRE />;<span id="DOUBLE_GYRE"></span>[[DOUBLE_GYRE]]
+:Option to compile and run the idealized Double-gyre example.
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=DOUBLE_GYRE />
+:'''routine = '''
+:'''input = ''' [[roms.in]]<section end=DOUBLE_GYRE />
-<section begin=DOUBLE_PRECISION />;<span id="DOUBLE_PRECISION"></span>'''[[DOUBLE_PRECISION]]'''
+<section begin=DOUBLE_PRECISION />;<span id="DOUBLE_PRECISION"></span>[[DOUBLE_PRECISION]]
-:Option to
+:Internal switch to enable double precision variables. This switch is on by default.
 :'''parameter = '''
 :'''parent = '''
@@ Line 824: / Line 965: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=DOUBLE_PRECISION />
+:'''routine = ''' [[globaldefs.h]]<section end=DOUBLE_PRECISION />
 ==<span class="alphabet">E</span>==
-<section begin=EAST_FSCLAMPED />;<span id="EAST_FSCLAMPED"></span>'''[[EAST_FSCLAMPED]]'''
+<section begin=EAST_FSCLAMPED />;<span id="EAST_FSCLAMPED"></span>[[EAST_FSCLAMPED]]
-:Option to
+:Option to use free-surface clamped condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_FSCLAMPED]], [[SOUTH_FSCLAMPED]], [[WEST_FSCLAMPED]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_FSCHAPMAN]], [[EAST_FSGRADIENT]], [[EAST_FSNUDGING]], [[EAST_FSRADIATION]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_FSCLAMPED />
+:'''routine = ''' [[zetabc.F]]<section end=EAST_FSCLAMPED />
-<section begin=EAST_FSCHAPMAN />;<span id="EAST_FSCHAPMAN"></span>'''[[EAST_FSCHAPMAN]]'''
+<section begin=EAST_FSCHAPMAN />;<span id="EAST_FSCHAPMAN"></span>[[EAST_FSCHAPMAN]]
-:Option to
+:Option to use free-surface Chapman condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_FSCHAPMAN]], [[SOUTH_FSCHAPMAN]], [[WEST_FSCHAPMAN]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_FSCLAMPED]], [[EAST_FSGRADIENT]], [[EAST_FSNUDGING]], [[EAST_FSRADIATION]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_FSCHAPMAN />
+:'''routine = ''' [[zetabc.F]]<section end=EAST_FSCHAPMAN />
-<section begin=EAST_FSGRADIENT />;<span id="EAST_FSGRADIENT"></span>'''[[EAST_FSGRADIENT]]'''
+<section begin=EAST_FSGRADIENT />;<span id="EAST_FSGRADIENT"></span>[[EAST_FSGRADIENT]]
-:Option to
+:Option to use free-surface gradient condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_FSGRADIENT]], [[SOUTH_FSGRADIENT]], [[WEST_FSGRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_FSCLAMPED]], [[EAST_FSCHAPMAN]], [[EAST_FSNUDGING]], [[EAST_FSRADIATION]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_FSGRADIENT />
+:'''routine = ''' [[zetabc.F]]<section end=EAST_FSGRADIENT />
-<section begin=EAST_FSNUDGING />;<span id="EAST_FSNUDGING"></span>'''[[EAST_FSNUDGING]]'''
+<section begin=EAST_FSNUDGING />;<span id="EAST_FSNUDGING"></span>[[EAST_FSNUDGING]]
-:Option to
+:Option to use free-surface passive/active nudging term for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_FSNUDGING]], [[SOUTH_FSNUDGING]], [[WEST_FSNUDGING]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_FSCLAMPED]], [[EAST_FSCHAPMAN]], [[EAST_FSGRADIENT]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_FSNUDGING />
+:'''routine = ''' [[zetabc.F]]<section end=EAST_FSNUDGING />
-<section begin=EAST_FSRADIATION />;<span id="EAST_FSRADIATION"></span>'''[[EAST_FSRADIATION]]'''
+<section begin=EAST_FSRADIATION />;<span id="EAST_FSRADIATION"></span>[[EAST_FSRADIATION]]
-:Option to
+:Option to use free-surface radiation condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_FSRADIATION]], [[SOUTH_FSRADIATION]], [[WEST_FSRADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_FSCLAMPED]], [[EAST_FSCHAPMAN]], [[EAST_FSGRADIENT]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_FSRADIATION />
+:'''routine = ''' [[zetabc.F]]<section end=EAST_FSRADIATION />
-<section begin=EAST_M2CLAMPED />;<span id="EAST_M2CLAMPED"></span>'''[[EAST_M2CLAMPED]]'''
+<section begin=EAST_KGRADIENT />;<span id="EAST_KGRADIENT"></span>[[EAST_KGRADIENT]]
-:Option to
+:Option to use TKE fields gradient condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_KGRADIENT]], [[SOUTH_KGRADIENT]], [[WEST_KGRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_KRADIATION]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_M2CLAMPED />
+:'''routine = ''' [[tkebc_im.F]]<section end=EAST_KGRADIENT />
-<section begin=EAST_M2FLATHER />;<span id="EAST_M2FLATHER"></span>'''[[EAST_M2FLATHER]]'''
+<section begin=EAST_KRADIATION />;<span id="EAST_KRADIATION"></span>[[EAST_KRADIATION]]
-:Option to
+:Option to use TKE fields radiation condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_KRADIATION]], [[SOUTH_KRADIATION]], [[WEST_KRADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_KGRADIENT]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_M2FLATHER />
+:'''routine = ''' [[tkebc_im.F]]<section end=EAST_KRADIATION />
-<section begin=EAST_M2GRADIENT />;<span id="EAST_M2GRADIENT"></span>'''[[EAST_M2GRADIENT]]'''
+<section begin=EAST_M2CLAMPED />;<span id="EAST_M2CLAMPED"></span>[[EAST_M2CLAMPED]]
-:Option to
+:Option to use 2D momentum clamped condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_M2CLAMPED]], [[SOUTH_M2CLAMPED]], [[WEST_M2CLAMPED]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_M2FLATHER]], [[EAST_M2GRADIENT]], [[EAST_M2NUDGING]], [[EAST_M2RADIATION]], [[EAST_M2REDUCED]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_M2GRADIENT />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=EAST_M2CLAMPED />
-<section begin=EAST_M2NUDGING />;<span id="EAST_M2NUDGING"></span>'''[[EAST_M2NUDGING]]'''
+<section begin=EAST_M2FLATHER />;<span id="EAST_M2FLATHER"></span>[[EAST_M2FLATHER]]
-:Option to
+:Option to use 2D momentum Flather condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_M2FLATHER]], [[SOUTH_M2FLATHER]], [[WEST_M2FLATHER]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_M2CLAMPED]], [[EAST_M2GRADIENT]], [[EAST_M2NUDGING]], [[EAST_M2RADIATION]], [[EAST_M2REDUCED]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_M2NUDGING />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=EAST_M2FLATHER />
-<section begin=EAST_M2RADIATION />;<span id="EAST_M2RADIATION"></span>'''[[EAST_M2RADIATION]]'''
+<section begin=EAST_M2GRADIENT />;<span id="EAST_M2GRADIENT"></span>[[EAST_M2GRADIENT]]
-:Option to
+:Option to use 2D momentum gradient condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_M2GRADIENT]], [[SOUTH_M2GRADIENT]], [[WEST_M2GRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_M2CLAMPED]], [[EAST_M2FLATHER]], [[EAST_M2NUDGING]], [[EAST_M2RADIATION]], [[EAST_M2REDUCED]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_M2RADIATION />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=EAST_M2GRADIENT />
-<section begin=EAST_M2REDUCED />;<span id="EAST_M2REDUCED"></span>'''[[EAST_M2REDUCED]]'''
+<section begin=EAST_M2NUDGING />;<span id="EAST_M2NUDGING"></span>[[EAST_M2NUDGING]]
-:Option to
+:Option to use 2D momentum passive/active nudging term for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_M2NUDGING]], [[SOUTH_M2NUDGING]], [[WEST_M2NUDGING]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_M2CLAMPED]], [[EAST_M2FLATHER]], [[EAST_M2GRADIENT]], [[EAST_M2REDUCED]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_M2REDUCED />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=EAST_M2NUDGING />
-<section begin=EAST_M3CLAMPED />;<span id="EAST_M3CLAMPED"></span>'''[[EAST_M3CLAMPED]]'''
+<section begin=EAST_M2RADIATION />;<span id="EAST_M2RADIATION"></span>[[EAST_M2RADIATION]]
-:Option to
+:Option to use 2D momentum radiation condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_M2RADIATION]], [[SOUTH_M2RADIATION]], [[WEST_M2RADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_M2CLAMPED]], [[EAST_M2FLATHER]], [[EAST_M2GRADIENT]], [[EAST_M2REDUCED]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_M3CLAMPED />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=EAST_M2RADIATION />
-<section begin=EAST_M3GRADIENT />;<span id="EAST_M3GRADIENT"></span>'''[[EAST_M3GRADIENT]]'''
+<section begin=EAST_M2REDUCED />;<span id="EAST_M2REDUCED"></span>[[EAST_M2REDUCED]]
-:Option to
+:Option to use 2D momentum reduced-physics for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_M2REDUCED]], [[SOUTH_M2REDUCED]], [[WEST_M2REDUCED]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_M2CLAMPED]], [[EAST_M2FLATHER]], [[EAST_M2GRADIENT]], [[EAST_M2NUDGING]], [[EAST_M2RADIATION]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_M3GRADIENT />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=EAST_M2REDUCED />
-<section begin=EAST_M3NUDGING />;<span id="EAST_M3NUDGING"></span>'''[[EAST_M3NUDGING]]'''
+<section begin=EAST_M3CLAMPED />;<span id="EAST_M3CLAMPED"></span>[[EAST_M3CLAMPED]]
-:Option to
+:Option to use 3D momentum clamped condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_M3CLAMPED]], [[SOUTH_M3CLAMPED]], [[WEST_M3CLAMPED]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_M3GRADIENT]], [[EAST_M3NUDGING]], [[EAST_M3RADIATION]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_M3NUDGING />
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=EAST_M3CLAMPED />
-<section begin=EAST_M3RADIATION />;<span id="EAST_M3RADIATION"></span>'''[[EAST_M3RADIATION]]'''
+<section begin=EAST_M3GRADIENT />;<span id="EAST_M3GRADIENT"></span>[[EAST_M3GRADIENT]]
-:Option to
+:Option to use 3D momentum gradient condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_M3GRADIENT]], [[SOUTH_M3GRADIENT]], [[WEST_M3GRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_M3CLAMPED]], [[EAST_M3NUDGING]], [[EAST_M3RADIATION]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_M3RADIATION />
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=EAST_M3GRADIENT />
-<section begin=EAST_KGRADIENT />;<span id="EAST_KGRADIENT"></span>'''[[EAST_KGRADIENT]]'''
+<section begin=EAST_M3NUDGING />;<span id="EAST_M3NUDGING"></span>[[EAST_M3NUDGING]]
-:Option to
+:Option to use 3D momentum passive/active nudging term for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_M3NUDGING]], [[SOUTH_M3NUDGING]], [[WEST_M3NUDGING]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_M3CLAMPED]], [[EAST_M3GRADIENT]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_KGRADIENT />
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=EAST_M3NUDGING />
-<section begin=EAST_KRADIATION />;<span id="EAST_KRADIATION"></span>'''[[EAST_KRADIATION]]'''
+<section begin=EAST_M3RADIATION />;<span id="EAST_M3RADIATION"></span>[[EAST_M3RADIATION]]
-:Option to
+:Option to use 3D momentum radiation condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_M3RADIATION]], [[SOUTH_M3RADIATION]], [[WEST_M3RADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_M3CLAMPED]], [[EAST_M3GRADIENT]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_KRADIATION />
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=EAST_M3RADIATION />
-<section begin=EAST_TCLAMPED />;<span id="EAST_TCLAMPED"></span>'''[[EAST_TCLAMPED]]'''
+<section begin=EAST_TCLAMPED />;<span id="EAST_TCLAMPED"></span>[[EAST_TCLAMPED]]
-:Option to
+:Option to use tracer clamped condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_TCLAMPED]], [[SOUTH_TCLAMPED]], [[WEST_TCLAMPED]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_TGRADIENT]], [[EAST_TNUDGING]], [[EAST_TRADIATION]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_TCLAMPED />
+:'''routine = ''' [[t3dbc_im.F]]<section end=EAST_TCLAMPED />
-<section begin=EAST_TGRADIENT />;<span id="EAST_TGRADIENT"></span>'''[[EAST_TGRADIENT]]'''
+<section begin=EAST_TGRADIENT />;<span id="EAST_TGRADIENT"></span>[[EAST_TGRADIENT]]
-:Option to
+:Option to use tracer gradient condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_TGRADIENT]], [[SOUTH_TGRADIENT]], [[WEST_TGRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_TCLAMPED]], [[EAST_TNUDGING]], [[EAST_TRADIATION]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_TGRADIENT />
+:'''routine = ''' [[t3dbc_im.F]]<section end=EAST_TGRADIENT />
-<section begin=EAST_TNUDGING />;<span id="EAST_TNUDGING"></span>'''[[EAST_TNUDGING]]'''
+<section begin=EAST_TNUDGING />;<span id="EAST_TNUDGING"></span>[[EAST_TNUDGING]]
-:Option to
+:Option to use tracer passive/active nudging term for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_TNUDGING]], [[SOUTH_TNUDGING]], [[WEST_TNUDGING]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_TCLAMPED]], [[EAST_TGRADIENT]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_TNUDGING />
+:'''routine = ''' [[t3dbc_im.F]]<section end=EAST_TNUDGING />
-<section begin=EAST_TRADIATION />;<span id="EAST_TRADIATION"></span>'''[[EAST_TRADIATION]]'''
+<section begin=EAST_TRADIATION />;<span id="EAST_TRADIATION"></span>[[EAST_TRADIATION]]
-:Option to
+:Option to use tracer radiation condition for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_TRADIATION]], [[SOUTH_TRADIATION]], [[WEST_TRADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_TCLAMPED]], [[EAST_TGRADIENT]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_TRADIATION />
+:'''routine = ''' [[t3dbc_im.F]]<section end=EAST_TRADIATION />
-<section begin=EAST_VOLCONS />;<span id="EAST_VOLCONS"></span>'''[[EAST_VOLCONS]]'''
+<section begin=EAST_VOLCONS />;<span id="EAST_VOLCONS"></span>[[EAST_VOLCONS]]
-:Option to
+:Option to use Southern edge mass conservation enforcement for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_VOLCONS]], [[SOUTH_VOLCONS]], [[WEST_VOLCONS]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EASTERN_WALL]]
-:'''routine = '''  <section end=EAST_VOLCONS />
+:'''routine = ''' [[obc_volcons.F]]<section end=EAST_VOLCONS />
-<section begin=EASTERN_WALL />;<span id="EASTERN_WALL"></span>'''[[EASTERN_WALL]]'''
+<section begin=EASTERN_WALL />;<span id="EASTERN_WALL"></span>[[EASTERN_WALL]]
-:Option to
+:Option to use Southern edge closed wall for the eastern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NORTH_WALL]], [[SOUTH_WALL]], [[WEST_WALL]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[EAST_FSCLAMPED]], [[EAST_FSCHAPMAN]], [[EAST_FSGRADIENT]], [[EAST_FSNUDGING]], [[EAST_FSRADIATION]], [[EAST_KGRADIENT]], [[EAST_KRADIATION]], [[EAST_M2CLAMPED]], [[EAST_M2FLATHER]], [[EAST_M2GRADIENT]], [[EAST_M2NUDGING]], [[EAST_M2RADIATION]], [[EAST_M2REDUCED]], [[EAST_M3CLAMPED]], [[EAST_M3GRADIENT]], [[EAST_M3NUDGING]], [[EAST_M3RADIATION]], [[EAST_TCLAMPED]], [[EAST_TGRADIENT]], [[EAST_TNUDGING]], [[EAST_TRADIATION]], [[EAST_VOLCONS]]
-:'''routine = '''  <section end=EASTERN_WALL />
+:'''routine = ''' [[t3dbc_im.F]], [[tkebc_im.F]], [[u2dbc_im.F]], [[u3dbc_im.F]], [[v2dbc_im.F]], [[v3dbc_im.F]], [[zetabc.F]]<section end=EASTERN_WALL />
-<section begin=ECOSIM />;<span id="ECOSIM"></span>'''[[ECOSIM]]'''
+<section begin=ECOSIM />;<span id="ECOSIM"></span>[[ECOSIM]]
 :Option to activate Bio-optical EcoSim ([[Bibliography#BissettWP_1999a |Bissett et al., 1999a,]] [[Bibliography#BissettWP_1999a |b]]) model.
 :'''related = ''' [[ANA_BIOLOGY]], [[ANA_BPFLUX]], [[ANA_SPFLUX]]
-:'''conflict = ''' [[BIO_FASHAM]], [[NPZD_FRANKS]], [[NPZD_POWELL]]
+:'''conflict = ''' [[BIO_FENNEL]], [[NEMURO]], [[NPZD_FRANKS]], [[NPZD_IRON]], [[NPZD_POWELL]]
-:'''routine = ''' [[ecosim.h]], [[ecosim.in]]<section end=ECOSIM />
+:'''routine = ''' [[ecosim.h]]
+:'''input =''' [[ecosim.in]]<section end=ECOSIM />
-<section begin=EMINUSP />;<span id="EMINUSP"></span>'''[[EMINUSP]]'''
+<section begin=EMINUSP />;<span id="EMINUSP"></span>[[EMINUSP]]
-:Option to
+:Option to compute E-P for surface fluxes formulation using atmospheric boundary layer.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[BULK_FLUXES]]
 :'''conflict = '''
-:'''routine = '''  <section end=EMINUSP />
+:'''routine = ''' [[ad_bulk_fluxes.F]], [[bulk_fluxes.F]], [[rp_bulk_fluxes.F]], [[tl_bulk_fluxes.F]]<section end=EMINUSP />
-<section begin=ENSEMBLE />;<span id="ENSEMBLE"></span>'''[[ENSEMBLE]]'''
+<section begin=ENSEMBLE />;<span id="ENSEMBLE"></span>[[ENSEMBLE]]
-:Option to
+:Option to use ensemble prediction driver.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,059: / Line 1,201: @@
 :'''routine = '''  <section end=ENSEMBLE />
-<section begin=ENERGY1_NORM />;<span id="ENERGY1_NORM"></span>'''[[ENERGY1_NORM]]'''
+<section begin=ESMF_COUPLING />;<span id="ESMF_COUPLING"></span>[[ESMF_COUPLING]]
-:Option to
+:Internal switch to use Earth System Modeling Framework (ESMF) for coupling.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[ESMF_LIB]], [[MCT_LIB]], [[MODEL_COUPLING]]
 :'''conflict = '''
-:'''routine = '''  <section end=ENERGY1_NORM />
+:'''routine = ''' [[mod_coupler.F]]<section end=ESMF_LIB />
-<section begin=ENERGY2_NORM />;<span id="ENERGY2_NORM"></span>'''[[ENERGY2_NORM]]'''
+<section begin=ESMF_LIB />;<span id="ESMF_LIB"></span>[[ESMF_LIB]]
-:Option to
+:Option to use Earth System Modeling Framework (ESMF) library for coupling.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[ESMF_COUPLING]], [[MCT_LIB]], [[MODEL_COUPLING]]
-:'''conflict = '''
+:'''conflict = ''' [[MCT_LIB]]
-:'''routine = '''  <section end=ENERGY2_NORM />
+:'''routine = ''' [[mod_coupler.F]]<section end=ESMF_LIB />
-<section begin=ENERGY3_NORM />;<span id="ENERGY3_NORM"></span>'''[[ENERGY3_NORM]]'''
+<section begin=ESTUARY_TEST />;<span id="ESTUARY_TEST"></span>[[ESTUARY_TEST]]
-:Option to
+:Option to compile and run the test estuary for sediment.
-:'''parameter = '''
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
-:'''required = '''
+:'''required = ''' [[SEDIMENT]]
-:'''related = '''
+:'''related = ''' [[SEDIMENT]]
 :'''conflict = '''
-:'''routine = '''  <section end=ENERGY3_NORM />
+:'''routine = '''
+:'''input = ''' [[roms.in]], [[sediment.in]]<section end=ESTUARY_TEST />
-<section begin=ESTUARY_TEST />;<span id="ESTUARY_TEST"></span>'''[[ESTUARY_TEST]]'''
+<section begin=EW_PERIODIC />;<span id="EW_PERIODIC"></span>[[EW_PERIODIC]]
-:Option to
+:Option to use East-West periodic boundary conditions.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,093: / Line 1,236: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=ESTUARY_TEST />
+:'''routine = ''' <section end=EW_PERIODIC />
-<section begin=EW_PERIODIC />;<span id="EW_PERIODIC"></span>'''[[EW_PERIODIC]]'''
+==<span class="alphabet">F</span>==
-:Option to
+<section begin=FLOAT_OYSTER />;<span id="FLOAT_OYSTER"></span>[[FLOAT_OYSTER]]
+:Option to activate oyster model behavior in Langrangian drifters.
 :'''parameter = '''
-:'''parent = '''
+:'''parent = ''' [[FLOATS]]
-:'''required = '''
+:'''required = ''' [[FLOATS]]
-:'''related = '''
+:'''related = ''' [[FLOATS]]
 :'''conflict = '''
-:'''routine = '''  <section end=EW_PERIODIC />
+:'''routine = '''  <section end=FLOAT_OYSTER />
-==<span class="alphabet">F</span>==
+<section begin=FLOAT_STICKY />;<span id="FLOAT_STICKY"></span>[[FLOAT_STICKY]]
+:Option to reflect or stick floats that hit the surface or bottom in Langrangian drifters.
+:'''parameter = '''
+:'''parent = ''' [[FLOATS]]
+:'''required = ''' [[FLOATS]]
+:'''related = ''' [[FLOATS]]
+:'''conflict = '''
+:'''routine = '''  <section end=FLOAT_STICKY />
-<section begin=FLOATS />;<span id="FLOATS"></span>'''[[FLOATS]]'''
+<section begin=FLOAT_VWALK />;<span id="FLOAT_VWALK"></span>[[FLOAT_VWALK]]
-:Option to
+:Option to use vertical random walk for Langrangian drifters.
 :'''parameter = '''
-:'''parent = '''
+:'''parent = ''' [[FLOATS]]
-:'''required = '''
+:'''required = ''' [[FLOATS]]
-:'''related = '''
+:'''related = ''' [[FLOATS]]
 :'''conflict = '''
-:'''routine = '''  <section end=FLOATS />
+:'''routine = '''  <section end=FLOAT_VWALK />
-<section begin=FLOAT_VWALK />;<span id="FLOAT_VWALK"></span>'''[[FLOAT_VWALK]]'''
+<section begin=FLOATS />;<span id="FLOATS"></span>[[FLOATS]]
-:Option to
+:Option to activate simulated Lagrangian drifters.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[FLOAT_VWALK]], [[VWALK_FORWARD]]
 :'''conflict = '''
-:'''routine = '''  <section end=FLOAT_VWALK />
+:'''routine = ''' <section end=FLOATS />
-<section begin=FLT_TEST />;<span id="FLT_TEST"></span>'''[[FLT_TEST]]'''
+<section begin=FLT_TEST />;<span id="FLT_TEST"></span>[[FLT_TEST]]
-:Option to
+:Option to compile and run float tracking example.
-:'''parameter = '''
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
-:'''required = '''
+:'''required = ''' [[FLOATS]]
-:'''related = '''
+:'''related = ''' [[FLOATS]]
 :'''conflict = '''
-:'''routine = '''  <section end=FLT_TEST />
+:'''routine = '''
+:'''input = ''' [[floats.in]], [[roms.in]] (_flt_test2d and _flt_test3d)<section end=FLT_TEST />
-<section begin=FORCING_SV />;<span id="FORCING_SV"></span>'''[[FORCING_SV]]'''
+<section begin=FORCING_SV />;<span id="FORCING_SV"></span>[[FORCING_SV]]
-:Option to
+:Option to use forcing singular vectors driver.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,140: / Line 1,293: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=FORCING_SV />
+:'''routine = ''' <section end=FORCING_SV />
-<section begin=FORWARD_MIXING />;<span id="FORWARD_MIXING"></span>'''[[FORWARD_MIXING]]'''
+<section begin=FORWARD_MIXING />;<span id="FORWARD_MIXING"></span>[[FORWARD_MIXING]]
-:Option to
+:Option to enable processing forward vertical mixing coefficient for the tangent linear, representer and adjoint models.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,149: / Line 1,302: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=FORWARD_MIXING />
+:'''routine = ''' <section end=FORWARD_MIXING />
-<section begin=FORWARD_READ />;<span id="FORWARD_READ"></span>'''[[FORWARD_READ]]'''
+<section begin=FORWARD_READ />;<span id="FORWARD_READ"></span>[[FORWARD_READ]]
-:Option to
+:Option to enable reading in forward solution, basic state for the tangent linear, representer and adjoint models.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,158: / Line 1,311: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=FORWARD_READ />
+:'''routine = ''' <section end=FORWARD_READ />
-<section begin=FORWARD_RHS />;<span id="FORWARD_RHS"></span>'''[[FORWARD_RHS]]'''
+<section begin=FORWARD_RHS />;<span id="FORWARD_RHS"></span>[[FORWARD_RHS]]
-:Option to
+:Option to enable processing forward right-hand-side terms for the tangent linear, representer and adjoint models.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,167: / Line 1,320: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=FORWARD_RHS />
+:'''routine = ''' <section end=FORWARD_RHS />
-<section begin=FORWARD_WRITE />;<span id="FORWARD_WRITE"></span>'''[[FORWARD_WRITE]]'''
+<section begin=FORWARD_WRITE />;<span id="FORWARD_WRITE"></span>[[FORWARD_WRITE]]
-:Option to
+:Option to enable writing out forward solution, basic state for the tangent linear model.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,176: / Line 1,329: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=FORWARD_WRITE />
+:'''routine = ''' <section end=FORWARD_WRITE />
-<section begin=FSOBC_REDUCED />;<span id="FSOBC_REDUCED"></span>'''[[FSOBC_REDUCED]]'''
+<section begin=FSOBC_REDUCED />;<span id="FSOBC_REDUCED"></span>[[FSOBC_REDUCED]]
-:Option to
+:Option to use SSH data and reduced physics conditions for the computation of the pressure gradient term in Flather or reduced physics boundary conditions (<span class="blue">*_M2FLATHER</span>, <span class="blue">*_M2REDUCED</span>).
 :'''parameter = '''
 :'''parent = '''
-:'''required = '''
+:'''required = ''' [[SSH_TIDES]]
-:'''related = '''
+:'''related = ''' [[SSH_TIDES]], [[ADD_FSOBC]]
 :'''conflict = '''
-:'''routine = '''  <section end=FSOBC_REDUCED />
+:'''routine = ''' [[ad_u2dbc_im.F]], [[ad_v2dbc.im.F]], [[rp_u2dbc_im.F]], [[rp_v2dbc_im.F]], [[tl_u2dbc_im.F]], [[tl_v2dbc_im.F]], [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=FSOBC_REDUCED />
-<section begin=FT_EIGENMODES />;<span id="FT_EIGENMODES"></span>'''[[FT_EIGENMODES]]'''
+<section begin=FT_EIGENMODES />;<span id="FT_EIGENMODES"></span>[[FT_EIGENMODES]]
-:Option to
+:Option to use the finite time eigenmodes driver: normal modes.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,194: / Line 1,347: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=FT_EIGENMODES />
+:'''routine = ''' [[ad_def_his.F]], [[tl_def_his.F]]<section end=FT_EIGENMODES />
-<section begin=FULL_GRID />;<span id="FULL_GRID"></span>'''[[FULL_GRID]]'''
+<section begin=FULL_GRID />;<span id="FULL_GRID"></span>[[FULL_GRID]]
-:Option to
+:Option for processing the full grid range (interior and boundary points) of the state vector in variational data assimilation and generalized stability theory (GST) analysis. Otherwise, only interior points are processed.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,203: / Line 1,356: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=FULL_GRID />
+:'''routine = ''' [[packing.F]]<section end=FULL_GRID />
 ==<span class="alphabet">G</span>==
-<section begin=GLS_MIXING />;<span id="GLS_MIXING"></span>'''[[GLS_MIXING]]'''
+<section begin=GLS_MIXING />;<span id="GLS_MIXING"></span>[[GLS_MIXING]]
-:Option to activate Generic Length Scale vertical mixing parameterization ([[Bibliography#WarnerJC_2005a|Warner et al., 2005]]).
+:Option to activate Generic Length Scale vertical mixing parameterization ([[Bibliography#WarnerJC_2005a|Warner et al., 2005]]) for vertical turbulent mixing of momentum and tracers.
-:'''related = ''' [[CANUTO_A]], [[CANUTO_B]]
+:'''related = ''' [[CANUTO_A]], [[CANUTO_B]], [[CHARNOK]], [[CRAIG_BANNER]], [[KANTHA_CLAYSON]], [[K_C2ADVECTION]], [[K_C4ADVECTION]], [[N2S2_HORAVG]], [[ZOS_HSIG]], [[TKE_WAVEDISS]]
-:'''conflict = ''' [[MY25_MIXING]], [[LMD_MIXING]]
+:'''conflict = ''' [[BVF_MIXING]], [[MY25_MIXING]], [[LMD_MIXING]]
-:'''routine = ''' [[ gls_corstep.F]], [[ gls_prestep.F]], [[ocean.in]]<section end=GLS_MIXING />
+:'''routine = ''' [[ gls_corstep.F]], [[ gls_prestep.F]], [[roms.in]]<section end=GLS_MIXING />
-<section begin=GRADIENT_CHECK />;<span id="GRADIENT_CHECK"></span>'''[[GRADIENT_CHECK]]'''
+<section begin=GRAV_ADJ />;<span id="GRAV_ADJ"></span>[[GRAV_ADJ]]
-:Option to
+:Option to compile and run the gravitational adjustment example.
-:'''parameter = '''
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=GRADIENT_CHECK />
+:'''routine = '''
+:'''input = ''' [[roms.in]]<section end=GRAV_ADJ />
-<section begin=GRAV_ADJ />;<span id="GRAV_ADJ"></span>'''[[GRAV_ADJ]]'''
+==<span class="alphabet">H</span>==
-:Option to
+<section begin=HDF5 />;<span id="HDF5"></span>[[HDF5]] (formerly NETCDF4)
+:Option to create NetCDF-4/HDF5 format files for input/output. This option was named [[Options#NETCDF4|NETCDF4]] prior to '''revision 459'''.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[DEFLATE]]
 :'''conflict = '''
-:'''routine = '''  <section end=GRAV_ADJ />
+:'''routine = ''' [[mod_netcdf.F]]<section end=HDF5 />
-==<span class="alphabet">H</span>==
+<section begin=HOLLING_GRAZING />;<span id="HOLLING_GRAZING"></span>[[HOLLING_GRAZING]]
+:Option to use Holling-type s-shaped curve grazing (implicit) for the Nemuro lower trophic level ecosystem model.
+:'''parameter = '''
+:'''parent = ''' [[NEMURO]]
+:'''required = ''' [[NEMURO]]
+:'''related = ''' [[IVLEV_EXPLICIT]]
+:'''conflict = ''' [[IVLEV_EXPLICIT]]
+:'''routine = ''' [[nemuro.h]]<section end=HOLLING_GRAZING />
 ==<span class="alphabet">I</span>==
+<section begin=I4DVAR />;<span id="I4DVAR"></span>[[I4DVAR]] (Formerly IS4DVAR)
-<section begin=ICESHELF />;<span id="ICESHELF"></span>'''[[ICESHELF]]'''
+:Option to enable the incremental 4D variational (I4DVar), stong contraint, primal formulation data assimilation driver.
-:Option to
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,242: / Line 1,404: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=ICESHELF />
+:'''routine = ''' [[i4dvar_ocean.h]] <section end=I4DVAR />
+<section begin=I4DVAR_ANA_SENSITIVITY />;<span id="I4DVAR_ANA_SENSITIVITY"></span>[[I4DVAR_ANA_SENSITIVITY]] (Formerly IS4DVAR_SENSITIVITY)
+:Option to activate the observation impact and sensitivity driver which quantifies the impact that each observation has on the 4DVAR data assimilation system. By measuring the sensitivity of the data assimilation system to each observation, we can determine the degree to which each observation contributes to the uncertainty in the circulation estimate. This analysis can help us to determine the type of measurements that need to be made, where to observe, and when.
+:'''required = ''' [[ADJOINT]], [[NONLINEAR]], [[TANGENT]]
+:'''related = '''  [[I4DVAR]], [[LANCZOS]]
+:'''routine = ''' [[obs_sen_i4dvar_analysis.h]] <section end=I4DVAR_ANA_SENSITIVITY />
-<section begin=IMPLICIT_VCONV />;<span id="IMPLICIT_VCONV"></span>'''[[IMPLICIT_VCONV]]'''
+<section begin=ICESHELF />;<span id="ICESHELF"></span>[[ICESHELF]]
-:Option to
+:Option to include ice shelf cavities in the model configuration.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,251: / Line 1,419: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=IMPLICIT_VCONV />
+:'''routine = ''' <section end=ICESHELF />
-<section begin=IOM />;<span id="IOM"></span>'''[[IOM]]'''
+<section begin=IMPACT_INNER />;<span id="IMPACT_INNER"></span>[[IMPACT_INNER]]
 :Option to
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,260: / Line 1,428: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=IOM />
+:'''routine = '''  <section end=IMPACT_INNER />
-<section begin=IMPULSE />;<span id="IMPULSE"></span>'''[[IMPULSE]]'''
+<section begin=IMPLICIT_VCONV />;<span id="IMPLICIT_VCONV"></span>[[IMPLICIT_VCONV]]
-:Option to
+:Option to use the implicit vertical convolution algorithm for the tangent linear and adjoint models.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,269: / Line 1,437: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=IMPULSE />
+:'''routine = ''' [[ad_conv_3d.F]], [[ad_conv_bry3d.F]], [[conv_3d.F]], [[conv_bry3d.F]], [[tl_conv_3d.F]], [[tl_conv_bry3d.F]]<section end=IMPLICIT_VCONV />
-<section begin=INLINE_2DIO />;<span id="INLINE_2DIO"></span>'''[[INLINE_2DIO]]'''
+<section begin=IMPULSE />;<span id="IMPULSE"></span>[[IMPULSE]]
-:Option to
+:Option to process adjoint impulse forcing for the adjoint model.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,278: / Line 1,446: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=INLINE_2DIO />
+:'''routine = ''' <section end=IMPULSE />
-<section begin=INNER_PRODUCT />;<span id="INNER_PRODUCT"></span>'''[[INNER_PRODUCT]]'''
+<section begin=INLET_TEST />;<span id="INLET_TEST"></span>[[INLET_TEST]]
-:Option to
+:Option to compile and run the test inlet application.
-:'''parameter = '''
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=INNER_PRODUCT />
+:'''routine = '''
+:'''input = ''' [[roms.in]], [[sediment.in]]<section end=INLET_TEST />
-<section begin=IS4DVAR />;<span id="IS4DVAR"></span>'''[[IS4DVAR]]'''
+<section begin=INLINE_2DIO />;<span id="INLINE_2DIO"></span>[[INLINE_2DIO]]
-:Option to
+:Option 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.
 :'''parameter = '''
 :'''parent = '''
-:'''required = '''
+:'''required = ''' [[SOLVE3D]]
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=IS4DVAR />
+:'''routine = ''' [[nf_fread3d.F]], [[nf_fwrite3d.F]]<section end=INLINE_2DIO />
-==<span class="alphabet">J</span>==
+<section begin=INNER_PRODUCT />;<span id="INNER_PRODUCT"></span>[[INNER_PRODUCT]]
+:Option to enable tangent linear and adjoint inner product check.
-==<span class="alphabet">K</span>==
-<section begin=KANTHA_CLAYSON />;<span id="KANTHA_CLAYSON"></span>'''[[KANTHA_CLAYSON]]'''
-:Option to
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,309: / Line 1,474: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=KANTHA_CLAYSON />
+:'''routine = ''' [[pert_ocean.h]]<section end=INNER_PRODUCT />
-<section begin=KELVIN />;<span id="KELVIN"></span>'''[[KELVIN]]'''
+<section begin=IRON_LIMIT />;<span id="IRON_LIMIT"></span>[[IRON_LIMIT]]
-:Option to
+:Option to impose iron limitation on phytoplankton growth in the NPZD iron ([[Bibliography#FiechterJ_2009a|Fiechter ''et al.'' 2009]]) model.
+:'''parameter = '''
+:'''parent = ''' [[NPZD_IRON]]
+:'''required = ''' [[NPZD_IRON]]
+:'''related = ''' [[IRON_RELAX]], [[NPZD_IRON]]
+:'''conflict = '''
+:'''routine = ''' [[biology.F]], [[npzd_iron.h]]<section end=IRON_LIMIT />
+<section begin=IRON_RELAX />;<span id="IRON_RELAX"></span>[[IRON_RELAX]]
+:Option to allow nudging of iron over the shelf, <math>h <= FeH_{min}</math> in the NPZD iron ([[Bibliography#FiechterJ_2009a|Fiechter ''et al.'' 2009]]) model.
 :'''parameter = '''
-:'''parent = '''
+:'''parent = ''' [[NPZD_IRON]]
-:'''required = '''
+:'''required = ''' [[NPZD_IRON]]
-:'''related = '''
+:'''related = ''' [[IRON_LIMIT]], [[NPZD_IRON]]
 :'''conflict = '''
-:'''routine = '''  <section end=KELVIN />
+:'''routine = ''' [[biology.F]], [[npzd_iron.h]]<section end=IRON_RELAX />
-<section begin=K_C2ADVECTION />;<span id="K_C2ADVECTION"></span>'''[[K_C2ADVECTION]]'''
+<section begin=IS4DVAR />;<span id="IS4DVAR"></span>[[IS4DVAR]] <span class="red">OBSOLETE - Renamed to [[Options#I4DVAR|I4DVAR]] in SVN revision 1022</span>
-:Option to
+:Option to enable the incremental 4d variational (IS4DVar) data assimilation driver.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,327: / Line 1,501: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=K_C2ADVECTION />
+:'''routine = ''' [[is4dvar_ocean.h]]<section end=IS4DVAR />
-<section begin=K_C4ADVECTION />;<span id="K_C4ADVECTION"></span>'''[[K_C4ADVECTION]]'''
+<section begin=IS4DVAR_SENSITIVITY />;<span id="IS4DVAR_SENSITIVITY"></span>[[IS4DVAR_SENSITIVITY]] <span class="red">OBSOLETE - Renamed to [[Options#I4DVAR_ANA_SENSITIVITY|I4DVAR_ANA_SENSITIVITY]] in SVN revision 1022</span>
-:Option to
+:Option to activate the observation sensitivity driver which quantifies the impact that each observation has on the 4DVAR data assimilation system. By measuring the sensitivity of the data assimilation system to each observation, we can determine the degree to which each observation contributes to the uncertainty in the circulation estimate. This analysis can help us to determine the type of measurements that need to be made, where to observe, and when.
+:'''required = ''' [[ADJOINT]], [[NONLINEAR]], [[TANGENT]]
+:'''related = '''  [[IS4DVAR]], [[LANCZOS]]
+:'''routine = ''' [[obs_sen_is4dvar.h]] <section end=IS4DVAR_SENSITIVITY />
+<section begin=IVLEV_EXPLICIT />;<span id="IVLEV_EXPLICIT"></span>[[IVLEV_EXPLICIT]]
+:Option to use Ivlev explicit grazing algorithm for the Nemuro lower trophic level ecosystem model.
+:'''parameter = '''
+:'''parent = ''' [[NEMURO]]
+:'''required = ''' [[NEMURO]]
+:'''related = ''' [[HOLLING_GRAZING]]
+:'''conflict = ''' [[HOLLING_GRAZING]]
+:'''routine = ''' [[nemuro.h]]<section end=IVLEV_EXPLICIT />
+==<span class="alphabet">J</span>==
+==<span class="alphabet">K</span>==
+<section begin=KANTHA_CLAYSON />;<span id="KANTHA_CLAYSON"></span>[[KANTHA_CLAYSON]]
+:Option to use the Kantha and Clayson ([[Bibliography#KanthaLH_1994a|1994]]) stability function for the [[Generic Length Scale]] or Mellor/Yamada level 2.5 closure.
 :'''parameter = '''
+:'''parent = ''' [[GLS_MIXING]] or [[MY25_MIXING]]
+:'''required = ''' [[GLS_MIXING]] or [[MY25_MIXING]]
+:'''related = ''' [[CANUTO_A]], [[CANUTO_B]]
+:'''conflict = ''' [[CANUTO_A]], [[CANUTO_B]]
+:'''routine = ''' [[gls_corstep.F]], [[my25_corstep.F]]<section end=KANTHA_CLAYSON />
+<section begin=KELVIN />;<span id="KELVIN"></span>[[KELVIN]]
+:Option to compile and run the Kelvin wave test.
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=K_C4ADVECTION />
+:'''routine = '''
+:'''input = ''' [[roms.in]]<section end=KELVIN />
+<section begin=K_C2ADVECTION />;<span id="K_C2ADVECTION"></span>[[K_C2ADVECTION]]
+:Option to use 2<sup>nd</sup>-order centered advection for the [[Generic Length Scale]] or Mellor/Yamada level 2.5 closure.
+:'''parameter = '''
+:'''parent = ''' [[GLS_MIXING]] or [[MY25_MIXING]]
+:'''required = ''' [[GLS_MIXING]] or [[MY25_MIXING]]
+:'''related = ''' [K_C4ADVECTION]]
+:'''conflict = ''' [K_C4ADVECTION]]
+:'''routine = ''' [[gls_corstep.F]], [[gls_prestep.F]], [[my25_corstep.F]], [[my25_prestep.F]]<section end=K_C2ADVECTION />
+<section begin=K_C4ADVECTION />;<span id="K_C4ADVECTION"></span>[[K_C4ADVECTION]]
+:Option to use 4<sup>th</sup>-order centered advection for the [[Generic Length Scale]] or Mellor/Yamada level 2.5 closure.
+:'''parameter = '''
+:'''parent = ''' [[GLS_MIXING]] or [[MY25_MIXING]]
+:'''required = ''' [[GLS_MIXING]] or [[MY25_MIXING]]
+:'''related = ''' [[K_C2ADVECTION]]
+:'''conflict = ''' [[K_C2ADVECTION]]
+:'''routine = ''' [[gls_corstep.F]], [[gls_prestep.F]], [[my25_corstep.F]], [[my25_prestep.F]]<section end=K_C4ADVECTION />
 ==<span class="alphabet">L</span>==
-<section begin=LAB_CANYON />;<span id="LAB_CANYON"></span>'''[[LAB_CANYON]]'''
+<section begin=LAB_CANYON />;<span id="LAB_CANYON"></span>[[LAB_CANYON]]
-:Option to
+:Option to compile and run the lab canyon polar coordinates example.
-:'''parameter = '''
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=LAB_CANYON />
+:'''routine = '''
+:'''input = ''' [[roms.in]]<section end=LAB_CANYON />
-<section begin=LAKE_SIGNELL />;<span id="LAKE_SIGNELL"></span>'''[[LAKE_SIGNELL]]'''
+<section begin=LAKE_JERSEY />;<span id="LAKE_JERSEY"></span>[[LAKE_JERSEY]]
-:Option to
+:Option to compile and run the lake Jersey sediment test case. Configurations found on the [[Nesting Examples]] page.
-:'''parameter = '''
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=LAKE_SIGNELL />
+:'''routine = ''' [[roms.in]], [[sediment.in]]<section end=LAKE_JERSEY />
-<section begin=LMD_BKPP />;<span id="LMD_BKPP"></span>'''[[LMD_BKPP]]'''
+<section begin=LAKE_SIGNELL />;<span id="LAKE_SIGNELL"></span>[[LAKE_SIGNELL]]
-:Option to
+:Option to compile and run the lake Signell sediment test case.
-:'''parameter = '''
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=LMD_BKPP />
+:'''routine = ''' [[floats.in]], [[roms.in]], [[sediment.in]]<section end=LAKE_SIGNELL />
-<section begin=LMD_CONVEC />;<span id="LMD_CONVEC"></span>'''[[LMD_CONVEC]]'''
+<section begin=LMD_BKPP />;<span id="LMD_BKPP"></span>[[LMD_BKPP]]
-:Option to
+:Option to use bottom boundary layer KPP mixing for the Large ''et al.'' ([[Bibliography#LargeWG_1994a|1994]]) K-profile parameterization mixing.
 :'''parameter = '''
-:'''parent = '''
+:'''parent = ''' [[LMD_MIXING]]
-:'''required = '''
+:'''required = ''' [[LMD_MIXING]]
-:'''related = '''
+:'''related = ''' [[LMD_CONVEC]], [[LMD_DDMIX]], [[LMD_NONLOCAL]], [[LMD_RIMIX]], [[LMD_SHAPIRO]], [[LMD_SKPP]]
 :'''conflict = '''
-:'''routine = '''  <section end=LMD_CONVEC />
+:'''routine = ''' [[lmd_bkpp.F]], [[lmd_vmix.F]]<section end=LMD_BKPP />
-<section begin=LMD_DDMIX />;<span id="LMD_DDMIX"></span>'''[[LMD_DDMIX]]'''
+<section begin=LMD_CONVEC />;<span id="LMD_CONVEC"></span>[[LMD_CONVEC]]
-:Option to
+:Option to add convective mixing due to shear instability for the Large ''et al.'' ([[Bibliography#LargeWG_1994a|1994]]) K-profile parameterization mixing.
 :'''parameter = '''
-:'''parent = '''
+:'''parent = ''' [[LMD_MIXING]]
-:'''required = '''
+:'''required = ''' [[LMD_MIXING]]
-:'''related = '''
+:'''related = ''' [[LMD_BKPP]], [[LMD_DDMIX]], [[LMD_NONLOCAL]], [[LMD_RIMIX]], [[LMD_SHAPIRO]], [[LMD_SKPP]]
 :'''conflict = '''
-:'''routine = '''  <section end=LMD_DDMIX />
+:'''routine = ''' [[lmd_vmix.F]]<section end=LMD_CONVEC />
-<section begin=LMD_MIXING />;<span id="LMD_MIXING"></span>'''[[LMD_MIXING]]'''
+<section begin=LMD_DDMIX />;<span id="LMD_DDMIX"></span>[[LMD_DDMIX]]
-:Option to
+:Option to add double-diffusive mixing for the Large ''et al.'' ([[Bibliography#LargeWG_1994a|1994]]) K-profile parameterization mixing.
 :'''parameter = '''
-:'''parent = '''
+:'''parent = ''' [[LMD_MIXING]]
-:'''required = '''
+:'''required = ''' [[LMD_MIXING]]
-:'''related = '''
+:'''related = ''' [[LMD_BKPP]], [[LMD_CONVEC]], [[LMD_NONLOCAL]], [[LMD_RIMIX]], [[LMD_SHAPIRO]], [[LMD_SKPP]]
 :'''conflict = '''
-:'''routine = '''  <section end=LMD_MIXING />
+:'''routine = ''' [[lmd_vmix.F]]<section end=LMD_DDMIX />
-<section begin=LMD_NONLOCAL />;<span id="LMD_NONLOCAL"></span>'''[[LMD_NONLOCAL]]'''
+<section begin=LMD_MIXING />;<span id="LMD_MIXING"></span>[[LMD_MIXING]]
-:Option to
+:Option to activate Large ''et al.'' ([[Bibliography#LargeWG_1994a|1994]]) interior closure for vertical turbulent mixing of momentum and tracers.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[LMD_BKPP]], [[LMD_CONVEC]], [[LMD_DDMIX]], [[LMD_NONLOCAL]], [[LMD_RIMIX]], [[LMD_SHAPIRO]], [[LMD_SKPP]]
+:'''conflict = ''' [[BVF_MIXING]], [[GLS_MIXING]], [[MY25_MIXING]]
+:'''routine = ''' [[ad_main3d.F]], [[lmd_vmix.F]], [[main3d.F]], [[rp_main3d.F]], [[tl_main3d.F]]<section end=LMD_MIXING />
+<section begin=LMD_NONLOCAL />;<span id="LMD_NONLOCAL"></span>[[LMD_NONLOCAL]]
+:Option to use nonlocal transport for the Large ''et al.'' ([[Bibliography#LargeWG_1994a|1994]]) K-profile parameterization mixing.
+:'''parameter = '''
+:'''parent = ''' [[LMD_MIXING]]
+:'''required = ''' [[LMD_MIXING]]
+:'''related = ''' [[LMD_BKPP]], [[LMD_CONVEC]], [[LMD_DDMIX]], [[LMD_RIMIX]], [[LMD_SHAPIRO]], [[LMD_SKPP]]
+:'''conflict = '''
+:'''routine = ''' [[ad_pre_step3d.F]], [[lmd_skpp.F]], [[rp_pre_step3d.F]], [[tl_pre_step3d.F]]<section end=LMD_NONLOCAL />
+<section begin=LMD_RIMIX />;<span id="LMD_RIMIX"></span>[[LMD_RIMIX]]
+:Option to add diffusivity due to shear instability for the Large ''et al.'' ([[Bibliography#LargeWG_1994a|1994]]) K-profile parameterization mixing.
+:'''parameter = '''
+:'''parent = ''' [[LMD_MIXING]]
+:'''required = ''' [[LMD_MIXING]]
+:'''related = ''' [[LMD_BKPP]], [[LMD_CONVEC]], [[LMD_DDMIX]], [[LMD_NONLOCAL]], [[LMD_SHAPIRO]], [[LMD_SKPP]]
+:'''conflict = '''
+:'''routine = ''' [[lmd_vmix.F]]<section end=LMD_RIMIX />
+<section begin=LMD_SHAPIRO />;<span id="LMD_SHAPIRO"></span>[[LMD_SHAPIRO]]
+:Option to use Shapiro filtering boundary layer depth for the Large ''et al.'' ([[Bibliography#LargeWG_1994a|1994]]) K-profile parameterization mixing.
+:'''parameter = '''
+:'''parent = ''' [[LMD_MIXING]]
+:'''required = ''' [[LMD_MIXING]]
+:'''related = ''' [[LMD_BKPP]], [[LMD_CONVEC]], [[LMD_DDMIX]], [[LMD_NONLOCAL]], [[LMD_RIMIX]], [[LMD_SKPP]]
 :'''conflict = '''
-:'''routine = '''  <section end=LMD_NONLOCAL />
+:'''routine = ''' [[lmd_bkpp.F]], [[lmd_skpp.F]]<section end=LMD_SHAPIRO />
-<section begin=LMD_RIMIX />;<span id="LMD_RIMIX"></span>'''[[LMD_RIMIX]]'''
+<section begin=LMD_SKPP />;<span id="LMD_SKPP"></span>[[LMD_SKPP]]
-:Option to
+:Option to use surface boundary layer KPP mixing for the Large ''et al.'' ([[Bibliography#LargeWG_1994a|1994]]) K-profile parameterization mixing.
 :'''parameter = '''
+:'''parent = ''' [[LMD_MIXING]]
+:'''required = ''' [[LMD_MIXING]]
+:'''related = ''' [[LMD_BKPP]], [[LMD_CONVEC]], [[LMD_DDMIX]], [[LMD_NONLOCAL]], [[LMD_RIMIX]], [[LMD_SHAPIRO]]
+:'''conflict = '''
+:'''routine = ''' [[ad_lmd_swfrac.F]], [[lmd_skpp.F]], [[lmd_swfrac.F]], [[rp_lmd_swfrac.F]], [[tl_lmd_swfrac.F]]<section end=LMD_SKPP />
+<section begin=LMD_TEST />;<span id="LMD_TEST"></span>[[LMD_TEST]]
+:Option to compile and run the test for LMD and KPP.
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=LMD_RIMIX />
+:'''routine = '''
+:'''input = ''' [[roms.in]], [[stations.in]]<section end=LMD_TEST />
+<section begin=LONGWAVE />;<span id="LONGWAVE"></span>[[LONGWAVE]]
+:Option to compute the net long-wave radiation internally using the Beriland (1952) equation as a function of air temperature, sea surface temperature, relative humidity, and cloud fraction.
+:'''parameter = '''
+:'''parent = ''' [[BULK_FLUXES]]
+:'''required = ''' [[BULK_FLUXES]]
+:'''related = ''' [[LOGWAVE_OUT]]
+:'''conflict = ''' [[LONGWAVE_OUT]]
+:'''routine = ''' [[ad_bulk_flux.F]], [[bulk_flux.F]], [[rp_bulk_flux.F]], [[tl_bulk_flux.F]]<section end=LONGWAVE />
+<section begin=LONGWAVE_OUT />;<span id="LONGWAVE_OUT"></span>[[LONGWAVE_OUT]]
+:Option to provide (read) long-wave downwelling radiation only and then add outgoing long-wave radiation as a function of the model sea surface temperature.
+:'''parameter = '''
+:'''parent = ''' [[BULK_FLUXES]]
+:'''required = ''' [[BULK_FLUXES]]
+:'''related = ''' [[LONGWAVE]]
+:'''conflict = ''' [[LONGWAVE]]
+:'''routine = ''' [[ad_bulk_flux.F]], [[bulk_flux.F]], [[rp_bulk_flux.F]], [[tl_bulk_flux.F]]<section end=LONGWAVE_OUT />
+==<span class="alphabet">M</span>==
-<section begin=LMD_SKPP />;<span id="LMD_SKPP"></span>'''[[LMD_SKPP]]'''
+<section begin=M2CLIMATOLOGY />;<span id="M2CLIMATOLOGY"></span>[[M2CLIMATOLOGY]]
-:Option to
+:'''DEPRICATED''' in favor of [[Variables#Lm2CLM|Lm2CLM]] logical switches to facilitate nesting.<br /><br />Option to read and process 2D momentum climatology fields.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[ANA_M2CLIMA]], [[M2CLM_NUDGING]], [[UV_TIDES]]
 :'''conflict = '''
-:'''routine = '''  <section end=LMD_SKPP />
+:'''routine = ''' [[ad_step2d_LF_AM3.h]], [[set_tides.F]], [[step2d_LF_AM3.h]], [[rp_step2d_LF_AM3.h]], [[tl_step2d_LF_AM3.h]]<section end=M2CLIMATOLOGY />
-<section begin=LMD_TEST />;<span id="LMD_TEST"></span>'''[[LMD_TEST]]'''
+<section begin=M2CLM_NUDGING />;<span id="M2CLM_NUDGING"></span>[[M2CLM_NUDGING]]
-:Option to
+:'''DEPRICATED''' in favor of [[Variables#LnudgeM2CLM|LnudgeM2CLM]] logical switches to facilitate nesting.<br /><br />Option to use nudging of 2D momentum climatology data (primarily in sponge areas).
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[M2CLIMATOLOGY]], [[ANA_M2CLIMA]], [[UV_TIDES]]
 :'''conflict = '''
-:'''routine = '''  <section end=LMD_TEST />
+:'''routine = ''' [[ad_step2d_LF_AM3.h]], [[step2d_LF_AM3.h]], [[rp_step2d_LF_AM3.h]], [[tl_step2d_LF_AM3.h]]<section end=M2CLM_NUDGING />
-<section begin=LONGWAVE />;<span id="LONGWAVE"></span>'''[[LONGWAVE]]'''
+<section begin=M3CLIMATOLOGY />;<span id="M3CLIMATOLOGY"></span>[[M3CLIMATOLOGY]]
-:Option to
+:'''DEPRICATED''' in favor of [[Variables#Lm3CLM|Lm3CLM]] logical switches to facilitate nesting.<br /><br />Option to read and process 3D momentum climatology fields.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[ANA_M3CLIMA]], [[M3CLM_NUDGING]]
 :'''conflict = '''
-:'''routine = '''  <section end=LONGWAVE />
+:'''routine = ''' <section end=M3CLIMATOLOGY />
-<section begin=LONGWAVE_OUT />;<span id="LONGWAVE_OUT"></span>'''[[LONGWAVE_OUT]]'''
+<section begin=M3CLM_NUDGING />;<span id="M3CLM_NUDGING"></span>[[M3CLM_NUDGING]]
-:Option to
+:'''DEPRICATED''' in favor of [[Variables#LnudgeM3CLM|LnudgeM3CLM]] logical switches to facilitate nesting.<br /><br />Option to use nudging of 3D momentum climatology data (primarily in sponge areas).
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[M3CLIMATOLOGY]], [[ANA_M3CLIMA]]
 :'''conflict = '''
-:'''routine = '''  <section end=LONGWAVE_OUT />
+:'''routine = '''  <section end=M3CLM_NUDGING />
-==<span class="alphabet">M</span>==
-<section begin=MAX_SLOPE />;<span id="MAX_SLOPE"></span>'''[[MAX_SLOPE]]'''
+<section begin=MASKING />;<span id="MASKING"></span>[[MASKING]]
-:Option to
+:Option to use land/sea masking.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,457: / Line 1,734: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=MAX_SLOPE />
+:'''routine = '''  <section end=MASKING />
-<section begin=MIN_STRAT />;<span id="MIN_STRAT"></span>'''[[MIN_STRAT]]'''
+<section begin=MAX_SLOPE />;<span id="MAX_SLOPE"></span>[[MAX_SLOPE]]
-:Option to
+:Internal switch to set a maximum density slope in isopycnic diffusion.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,466: / Line 1,743: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=MIN_STRAT />
+:'''routine = '''  <section end=MAX_SLOPE />
-<section begin=M2CLIMATOLOGY />;<span id="M2CLIMATOLOGY"></span>'''[[M2CLIMATOLOGY]]'''
+<section begin=MB_BBL />;<span id="MB_BBL"></span>[[MB_BBL]]
-:Option to
+:Option to use Meinte Blaas bottom boundary layer closure.
 :'''parameter = '''
 :'''parent = '''
-:'''required = '''
+:'''required = ''' [[BBL_MODEL]]
-:'''related = '''
+:'''related = ''' [[MB_CALC_UB]], [[MB_CALC_ZNOT]], [[MB_Z0BIO]], [[MB_Z0BL]], [[MB_Z0RIP]]
+:'''conflict = ''' [[SG_BBL]], [[SSW_BBL]]
+:'''routine = '''  <section end=MB_BBL />
+<section begin=MB_CALC_UB />;<span id="MB_CALC_UB"></span>[[MB_CALC_UB]]
+:Option to use if computing bottom orbital velocity internally for Meinte Blass bottom boundary layer closure
+:'''parameter = '''
+:'''parent = ''' [[MB_BBL]]
+:'''required = ''' [[BBL_MODEL]], [[MB_BBL]]
+:'''related = ''' [[MB_CALC_ZNOT]], [[MB_Z0BIO]], [[MB_Z0BL]], [[MB_Z0RIP]]
 :'''conflict = '''
-:'''routine = '''  <section end=M2CLIMATOLOGY />
+:'''routine = ''' [[mb_bbl.h]]<section end=MB_CALC_UB />
-<section begin=M2CLM_NUDGING />;<span id="M2CLM_NUDGING"></span>'''[[M2CLM_NUDGING]]'''
+<section begin=MB_CALC_ZNOT />;<span id="MB_CALC_ZNOT"></span>[[MB_CALC_ZNOT]]
-:Option to
+:Option to use if computing bottom roughness internally for Meinte Blass bottom boundary layer closure.
 :'''parameter = '''
-:'''parent = '''
+:'''parent = ''' [[MB_BBL]]
-:'''required = '''
+:'''required = ''' [[BBL_MODEL]], [[MB_BBL]]
-:'''related = '''
+:'''related = ''' [[MB_CALC_UB]], [[MB_Z0BIO]], [[MB_Z0BL]], [[MB_Z0RIP]]
 :'''conflict = '''
-:'''routine = '''  <section end=M2CLM_NUDGING />
+:'''routine = ''' [[mb_bbl.h]]<section end=MB_CALC_ZNOT />
-<section begin=M3CLIMATOLOGY />;<span id="M3CLIMATOLOGY"></span>'''[[M3CLIMATOLOGY]]'''
+<section begin=MB_ZOBIO />;<span id="MB_ZOBIO"></span>[[MB_ZOBIO]]
-:Option to
+:Option to use biogenic bedform roughness for ripples for Meinte Blass bottom boundary layer closure.
 :'''parameter = '''
-:'''parent = '''
+:'''parent = ''' [[MB_BBL]]
-:'''required = '''
+:'''required = ''' [[BBL_MODEL]], [[MB_BBL]]
-:'''related = '''
+:'''related = ''' [[MB_CALC_UB]], [[MB_CALC_ZNOT]], [[MB_Z0BL]], [[MB_Z0RIP]]
 :'''conflict = '''
-:'''routine = '''  <section end=M3CLIMATOLOGY />
+:'''routine = ''' [[mb_bbl.h]]<section end=MB_ZOBIO />
-<section begin=M3CLM_NUDGING />;<span id="M3CLM_NUDGING"></span>'''[[M3CLM_NUDGING]]'''
+<section begin=MB_Z0BL />;<span id="MB_Z0BL"></span>[[MB_Z0BL]]
-:Option to
+:Option to use bedload roughness for ripples for Meinte Blass bottom boundary layer closure.
 :'''parameter = '''
-:'''parent = '''
+:'''parent = ''' [[MB_BBL]]
-:'''required = '''
+:'''required = ''' [[BBL_MODEL]], [[MB_BBL]], [[MB_ZORIP]]
-:'''related = '''
+:'''related = ''' [[MB_CALC_UB]], [[MB_CALC_ZNOT]], [[MB_Z0BIO]], [[MB_Z0RIP]]
 :'''conflict = '''
-:'''routine = '''  <section end=M3CLM_NUDGING />
+:'''routine = ''' [[mb_bbl.h]]<section end=MB_Z0BL />
-<section begin=MASKING />;<span id="MASKING"></span>'''[[MASKING]]'''
+<section begin=MB_Z0RIP />;<span id="MB_Z0RIP"></span>[[MB_Z0RIP]]
-:Option to
+:Option to use bedform roughness for ripples for Meinte Blass bottom boundary layer closure.
 :'''parameter = '''
-:'''parent = '''
+:'''parent = ''' [[MB_BBL]]
-:'''required = '''
+:'''required = ''' [[BBL_MODEL]], [[MB_BBL]], [[MB_ZOBL]]
-:'''related = '''
+:'''related = ''' [[MB_CALC_UB]], [[MB_CALC_ZNOT]], [[MB_Z0BIO]], [[MB_Z0BL]]
 :'''conflict = '''
-:'''routine = '''  <section end=MASKING />
+:'''routine = ''' [[mb_bbl.h]]<section end=MB_Z0RIP />
-<section begin=MB_BBL />;<span id="MB_BBL"></span>'''[[MB_BBL]]'''
+<section begin=MCT_LIB />;<span id="MCT_LIB"></span>[[MCT_LIB]]
-:Option to
+:Option to use the Model Coupling Toolkit (MCT) library for coupling.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[ESMF_COUPLING]], [[ESMF_LIB]], [[MODEL_COUPLING]]
-:'''conflict = '''
+:'''conflict = ''' [[ESMF_COUPLING]], [[ESMF_LIB]]
-:'''routine = '''  <section end=MB_BBL />
+:'''routine = ''' [[mod_coupler.F]]<section end=MCT_LIB />
-<section begin=MB_CALC_ZNOT />;<span id="MB_CALC_ZNOT"></span>'''[[MB_CALC_ZNOT]]'''
+<section begin=MIN_STRAT />;<span id="MIN_STRAT"></span>[[MIN_STRAT]]
-:Option to
+:Internal switch to set a minimum density stratification in isopycnic diffusion.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,529: / Line 1,815: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=MB_CALC_ZNOT />
+:'''routine = '''  <section end=MIN_STRAT />
-<section begin=MB_ZOBIO />;<span id="MB_ZOBIO"></span>'''[[MB_ZOBIO]]'''
+<section begin=MIX_GEO_TS />;<span id="MIX_GEO_TS"></span>[[MIX_GEO_TS]]
-:Option to
+:Option to use if mixing on geopotential (constant Z) surfaces for horizontal mixing of tracers.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[MIX_GEO_UV]], [[MIX_ISO_TS]], [[MIX_S_TS]], [[MIX_S_UV]]
-:'''conflict = '''
+:'''conflict = ''' [[MIX_ISO_TS]], [[MIX_S_TS]]
-:'''routine = '''  <section end=MB_ZOBIO />
+:'''routine = ''' [[ad_t3dmix.F]], [[hmixing.F]], [[rp_t3dmix.F]], [[t3dmix.F]], [[tl_t3dmix.F]]<section end=MIX_GEO_TS />
-<section begin=MB_Z0BL />;<span id="MB_Z0BL"></span>'''[[MB_Z0BL]]'''
+<section begin=MIX_GEO_UV />;<span id="MIX_GEO_UV"></span>[[MIX_GEO_UV]]
-:Option to
+:Option to use if mixing on geopotential (constant Z) surfaces for horizontal mixing of momentum.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[MIX_GEO_TS]], [[MIX_ISO_TS]], [[MIX_S_TS]], [[MIX_S_UV]]
-:'''conflict = '''
+:'''conflict = ''' [[MIX_S_UV]]
-:'''routine = '''  <section end=MB_Z0BL />
+:'''routine = ''' [[ad_uv3dmix.F]], [[hmixing.F]], [[rp_uv3dmix.F]], [[tl_uv3dmix.F]], [[uv3dmix.F]]<section end=MIX_GEO_UV />
-<section begin=MB_Z0RIP />;<span id="MB_Z0RIP"></span>'''[[MB_Z0RIP]]'''
+<section begin=MIX_ISO_TS />;<span id="MIX_ISO_TS"></span>[[MIX_ISO_TS]]
-:Option to
+:Option to use if mixing on epineutral (constant RHO) surfaces for horizontal mixing of tracers.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[MIX_GEO_TS]], [[MIX_GEO_UV]], [[MIX_S_TS]], [[MIX_S_UV]]
-:'''conflict = '''
+:'''conflict = ''' [[MIX_GEO_TS]], [[MIX_S_TS]]
-:'''routine = '''  <section end=MB_Z0RIP />
+:'''routine = ''' [[ad_t3dmix.F]], [[rp_t3dmix.F]], [[t3dmix.F]], [[tl_t3dmix.F]]<section end=MIX_ISO_TS />
-<section begin=MIX_ISO_TS />;<span id="MIX_ISO_TS"></span>'''[[MIX_ISO_TS]]'''
+<section begin=MIX_S_TS />;<span id="MIX_S_TS"></span>[[MIX_S_TS]]
-:Option to
+:Option to use if mixing along constant S-surfaces for horizontal mixing of tracers.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[MIX_GEO_TS]], [[MIX_GEO_UV]], [[MIX_ISO_TS]], [[MIX_S_UV]]
-:'''conflict = '''
+:'''conflict = ''' [[MIX_GEO_TS]], [[MIX_ISO_TS]]
-:'''routine = '''  <section end=MIX_ISO_TS />
+:'''routine = ''' [[ad_t3dmix.F]], [[rp_t3dmix.F]], [[t3dmix.F]], [[tl_t3dmix.F]]<section end=MIX_S_TS />
-<section begin=MIX_ISO_TS />;<span id="MIX_ISO_TS"></span>'''[[MIX_ISO_TS]]'''
+<section begin=MIX_S_UV />;<span id="MIX_S_UV"></span>[[MIX_S_UV]]
-:Option to
+:Option to  use if mixing along constant S-surfaces for horizontal mixing of momentum.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[MIX_GEO_TS]], [[MIX_GEO_UV]], [[MIX_ISO_TS]], [[MIX_S_TS]]
-:'''conflict = '''
+:'''conflict = ''' [[MIX_GEO_UV]]
-:'''routine = '''  <section end=MIX_ISO_TS />
+:'''routine = ''' [[ad_uv3dmix.F]], [[rp_uv3dmix.F]], [[tl_uv3dmix.F]], [[uv3dmix.F]]<section end=MIX_S_UV />
-<section begin=MIX_S_TS />;<span id="MIX_S_TS"></span>'''[[MIX_S_TS]]'''
+<section begin=MPI />;<span id="MPI"></span>[[MPI]]
-:Option to
+:Internal switch to configure the model to run in distributed memory (MPI).
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,583: / Line 1,869: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=MIX_S_TS />
+:'''routine = ''' <section end=MPI />
-<section begin=MIX_GEO_UV />;<span id="MIX_GEO_UV"></span>'''[[MIX_GEO_UV]]'''
+<section begin=MULTIPLE_TLM />;<span id="MULTIPLE_TLM"></span>[[MULTIPLE_TLM]]
-:Option to
+:Option to use multiple TLM (Tangent Linear Model) history files in 4DVAR.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,592: / Line 1,878: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=MIX_GEO_UV />
+:'''routine = ''' <section end=MULTIPLE_TLM/>
-<section begin=MIX_S_UV />;<span id="MIX_S_UV"></span>'''[[MIX_S_UV]]'''
+<section begin=MY25_MIXING />;<span id="MY25_MIXING"></span>[[MY25_MIXING]]
-:Option to
+:Option to activate Mellor/Yamada Level-2.5 closure for vertical turbulent mixing of momentum and tracers.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[K_C2ADVECTION]], [[K_C4ADVECTION]], [[KANTHA_CLAYSON]], [[N2S2_HORAVG]]
-:'''conflict = '''
+:'''conflict = ''' [[BVF_MIXING]], [[GLS_MIXING]], [[LMD_MIXING]]
-:'''routine = '''  <section end=MIX_S_UV />
+:'''routine = ''' [[my25_corstep.F]], [[my25_prestep.F]]<section end=MY25_MIXING />
+==<span class="alphabet">N</span>==
-<section begin=MPI />;<span id="MPI"></span>'''[[MPI]]'''
+<section begin=N2S2_HORAVG />;<span id="N2S2_HORAVG"></span>[[N2S2_HORAVG]]
-:Option to
+:Option to use horizontal smoothing of buoyancy/shear for the [[Generic Length Scale]] of Mellor/Yamada level 2.5 closure
 :'''parameter = '''
-:'''parent = '''
+:'''parent = ''' [[GLS_MIXING]] or [[MY25_MIXING]]
-:'''required = '''
+:'''required = ''' [[GLS_MIXING]] or [[MY25_MIXING]]
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=MPI />
+:'''routine = ''' [[gls_corstep.F]], [[my25_corstep.F]]<section end=N2S2_HORAVG />
-<section begin=MY25_MIXING />;<span id="MY25_MIXING"></span>'''[[MY25_MIXING]]'''
+<section begin=NEARSHORE_MELLOR />;<span id="NEARSHORE_MELLOR"></span>[[NEARSHORE_MELLOR]]
-:Option to
+:Option to activate radiation stress terms for near-shore and shallow water models.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,619: / Line 1,907: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=MY25_MIXING />
+:'''routine = ''' <section end=NEARSHORE_MELLOR />
-==<span class="alphabet">N</span>==
+<section begin=NEMURO />;<span id="NEMURO"></span>[[NEMURO]]
+:Option to activate NEMURO model.
+:'''related = ''' [[ANA_BIOLOGY]], [[ANA_BPFLUX]], [[ANA_SPFLUX]]
+:'''conflict = ''' [[BIO_FENNEL]], [[ECOSIM]], [[NPZD_FRANKS]], [[NPZD_IRON]], [[NPZD_POWELL]]
+:'''routine = ''' [[nemuro.h]]
+:'''input =''' [[nemuro.in]]<section end=NEMURO />
-<section begin=NLM_OUTER />;<span id="NLM_OUTER"></span>'''[[NLM_OUTER]]'''
+<section begin=NESTING />;<span id="NESTING"></span>'''NESTING'''
-:Option to
+:Option to enable ROMS grid nesting capabilities.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[ONE_WAY]]
 :'''conflict = '''
-:'''routine = '''  <section end=NLM_OUTER />
+:'''routine = ''' [[nesting.F]]<section end=NESTING />
-<section begin=NONLINEAR />;<span id="NONLINEAR"></span>'''[[NONLINEAR]]'''
+<section begin=NETCDF4 />;<span id="NETCDF4"></span>'''NETCDF4''' (RENAMED)
-:Option to
+:Option to create NetCDF-4/HDF5 format files for input/output. This option was renamed to [[Options#HDF5|HDF5]] in '''revision 459'''.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[DEFLATE]]
 :'''conflict = '''
-:'''routine = '''  <section end=NONLINEAR />
+:'''routine = ''' [[mod_netcdf.F]]<section end=NETCDF4 />
-<section begin=NONLIN_EOS />;<span id="NONLIN_EOS"></span>'''[[NONLIN_EOS]]'''
+<section begin=NJ_BIGHT />;<span id="NJ_BIGHT"></span>[[NJ_BIGHT]]
-:Option to
+:Option to compile and run NJ_BIGHT realistic application.
-:'''parameter = '''
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=NONLIN_EOS />
+:'''routine = '''
+:'''input = ''' [[roms.in]]<section end=NJ_BIGHT />
-<section begin=NORTH_FSCLAMPED />;<span id="NORTH_FSCLAMPED"></span>'''[[NORTH_FSCLAMPED]]'''
+<section begin=NL_BULK_FLUXES />;<span id="NL_BULK_FLUXES"></span>[[NL_BULK_FLUXES]]
-:Option to
+:Option to handle the reading of surface fluxes (E-P) computed by the nonlinear model in the representer model. This option can be also used in the nonlinear model when [[Options#BULK_FLUXES|BULK_FLUXES]] is not defined to read such surface salinity flux if needed.
 :'''parameter = '''
 :'''parent = '''
-:'''required = '''
+:'''required = ''' [[BULK_FLUXES]]
-:'''related = '''
+:'''related = ''' [[COOL_SKIN]], [[EMINUS]], [[LONGWAVE]], [[LONGWAVE_OUT]]
 :'''conflict = '''
-:'''routine = '''  <section end=NORTH_FSCLAMPED />
+:'''routine = ''' <section end=NLM_BULK_FLUXES />
-<section begin=NORTH_FSCHAPMAN />;<span id="NORTH_FSCHAPMAN"></span>'''[[NORTH_FSCHAPMAN]]'''
+<section begin=NLM_OUTER />;<span id="NLM_OUTER"></span>[[NLM_OUTER]]
-:Option to
+:Option to use nonlinear model as basic stat in outer loop with tangent linear, representer and adjoint models.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,666: / Line 1,960: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=NORTH_FSCHAPMAN />
+:'''routine = '''  <section end=NLM_OUTER />
-<section begin=NORTH_FSGRADIENT />;<span id="NORTH_FSGRADIENT"></span>'''[[NORTH_FSGRADIENT]]'''
+<section begin=NO_READ_GHOST />;<span id="NO_READ_GHOST"></span>[[NO_READ_GHOST]]
-:Option to
+:Option to not include ghost points during read/scatter (I/O).
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,675: / Line 1,969: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=NORTH_FSGRADIENT />
+:'''routine = ''' [[nf_fread2d.F]], [[nf_fread3d.F]], [[nf_fread4d.F]]<section end=NO_READ_GHOST />
-<section begin=NORTH_FSNUDGING />;<span id="NORTH_FSNUDGING"></span>'''[[NORTH_FSNUDGING]]'''
+<section begin=NO_WRITE_GRID />;<span id="NO_WRITE_GRID"></span>[[NO_WRITE_GRID]]
-:Option to
+:Option to not write grid arrays.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,684: / Line 1,978: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=NORTH_FSNUDGING />
+:'''routine = ''' [[wrt_info.F]]<section end=NO_WRITE_GRID />
-<section begin=NORTH_FSRADIATION />;<span id="NORTH_FSRADIATION"></span>'''[[NORTH_FSRADIATION]]'''
+<section begin=NONLINEAR />;<span id="NONLINEAR"></span>[[NONLINEAR]]
-:Option to
+:Internal switch to include the nonlinear model in compilation.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[ADJOINT]], [[REPRESENTER]], [[TANGENT]]
 :'''conflict = '''
-:'''routine = '''  <section end=NORTH_FSRADIATION />
+:'''routine = ''' <section end=NONLINEAR />
-<section begin=NORTH_M2CLAMPED />;<span id="NORTH_M2CLAMPED"></span>'''[[NORTH_M2CLAMPED]]'''
+<section begin=NONLIN_EOS />;<span id="NONLIN_EOS"></span>[[NONLIN_EOS]]
-:Option to
+:Option to use the nonlinear equation of state for tracers.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,702: / Line 1,996: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=NORTH_M2CLAMPED />
+:'''routine = ''' [[ad_rho_eos.F]], [[rho_eos.F]], [[rp_rho_eos.F]], [[tl_rho_eos.F]]<section end=NONLIN_EOS />
-<section begin=NORTH_M2FLATHER />;<span id="NORTH_M2FLATHER"></span>'''[[NORTH_M2FLATHER]]'''
+<section begin=NORTH_FSCLAMPED />;<span id="NORTH_FSCLAMPED"></span>[[NORTH_FSCLAMPED]]
-:Option to
+:Option to use free-surface clamped condition for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSCLAMPED]], [[SOUTH_FSCLAMPED]], [[WEST_FSCLAMPED]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_FSCHAPMAN]], [[NORTH_FSGRADIENT]], [[NORTH_FSNUDGING]], [[NORTH_FSRADIATION]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_M2FLATHER />
+:'''routine = ''' [[zetabc.F]]<section end=NORTH_FSCLAMPED />
-<section begin=NORTH_M2GRADIENT />;<span id="NORTH_M2GRADIENT"></span>'''[[NORTH_M2GRADIENT]]'''
+<section begin=NORTH_FSCHAPMAN />;<span id="NORTH_FSCHAPMAN"></span>[[NORTH_FSCHAPMAN]]
-:Option to
+:Option to use free-surface Chapman condition for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSCHAPMAN]], [[SOUTH_FSCHAPMAN]], [[WEST_FSCHAPMAN]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_FSCLAMPED]], [[NORTH_FSGRADIENT]], [[NORTH_FSNUDGING]], [[NORTH_FSRADIATION]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_M2GRADIENT />
+:'''routine = ''' [[zetabc.F]]<section end=NORTH_FSCHAPMAN />
-<section begin=NORTH_M2NUDGING />;<span id="NORTH_M2NUDGING"></span>'''[[NORTH_M2NUDGING]]'''
+<section begin=NORTH_FSGRADIENT />;<span id="NORTH_FSGRADIENT"></span>[[NORTH_FSGRADIENT]]
-:Option to
+:Option to use free-surface gradient condition for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSGRADIENT]], [[SOUTH_FSGRADIENT]], [[WEST_FSGRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_FSCLAMPED]], [[NORTH_FSCHAPMAN]], [[NORTH_FSNUDGING]], [[NORTH_FSRADIATION]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_M2NUDGING />
+:'''routine = ''' [[zetabc.F]]<section end=NORTH_FSGRADIENT />
-<section begin=NORTH_M2RADIATION />;<span id="NORTH_M2RADIATION"></span>'''[[NORTH_M2RADIATION]]'''
+<section begin=NORTH_FSNUDGING />;<span id="NORTH_FSNUDGING"></span>[[NORTH_FSNUDGING]]
-:Option to
+:Option to use free-surface passive/active nudging term for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSNUDGING]], [[SOUTH_FSNUDGING]], [[WEST_FSNUDGING]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_FSCLAMPED]], [[NORTH_FSCHAPMAN]], [[NORTH_FSGRADIENT]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_M2RADIATION />
+:'''routine = ''' [[zetabc.F]]<section end=NORTH_FSNUDGING />
-<section begin=NORTH_M2REDUCED />;<span id="NORTH_M2REDUCED"></span>'''[[NORTH_M2REDUCED]]'''
+<section begin=NORTH_FSRADIATION />;<span id="NORTH_FSRADIATION"></span>[[NORTH_FSRADIATION]]
-:Option to
+:Option to use free-surface radiation condition for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSRADIATION]], [[SOUTH_FSRADIATION]], [[WEST_FSRADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_FSCLAMPED]], [[NORTH_FSCHAPMAN]], [[NORTH_FSGRADIENT]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_M2REDUCED />
+:'''routine = ''' [[zetabc.F]]<section end=NORTH_FSRADIATION />
-<section begin=NORTH_M3CLAMPED />;<span id="NORTH_M3CLAMPED"></span>'''[[NORTH_M3CLAMPED]]'''
+<section begin=NORTH_KGRADIENT />;<span id="NORTH_KGRADIENT"></span>[[NORTH_KGRADIENT]]
-:Option to
+:Option to use TKE fields gradient condition for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_KGRADIENT]], [[SOUTH_KGRADIENT]], [[WEST_KGRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_KRADIATION]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_M3CLAMPED />
+:'''routine = ''' [[tkebc_im.F]]<section end=NORTH_KGRADIENT />
-<section begin=NORTH_M3GRADIENT />;<span id="NORTH_M3GRADIENT"></span>'''[[NORTH_M3GRADIENT]]'''
+<section begin=NORTH_KRADIATION />;<span id="NORTH_KRADIATION"></span>[[NORTH_KRADIATION]]
-:Option to
+:Option to use TKE fields radiation condition for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_KRADIATION]], [[SOUTH_KRADIATION]], [[WEST_KRADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_KGRADIENT]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_M3GRADIENT />
+:'''routine = ''' [[tkebc_im.F]]<section end=NORTH_KRADIATION />
-<section begin=NORTH_M3NUDGING />;<span id="NORTH_M3NUDGING"></span>'''[[NORTH_M3NUDGING]]'''
+<section begin=NORTH_M2CLAMPED />;<span id="NORTH_M2CLAMPED"></span>[[NORTH_M2CLAMPED]]
-:Option to
+:Option to use 2D momentum clamped condition for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M2CLAMPED]], [[SOUTH_M2CLAMPED]], [[WEST_M2CLAMPED]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_M2FLATHER]], [[NORTH_M2GRADIENT]], [[NORTH_M2NUDGING]], [[NORTH_M2RADIATION]], [[NORTH_M2REDUCED]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_M3NUDGING />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=NORTH_M2CLAMPED />
+<section begin=NORTH_M2FLATHER />;<span id="NORTH_M2FLATHER"></span>[[NORTH_M2FLATHER]]
+:Option to use 2D momentum Flather condition for the northern open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_M2FLATHER]], [[SOUTH_M2FLATHER]], [[WEST_M2FLATHER]]
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_M2CLAMPED]], [[NORTH_M2GRADIENT]], [[NORTH_M2NUDGING]], [[NORTH_M2RADIATION]], [[NORTH_M2REDUCED]], [[NORTHERN_WALL]]
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=NORTH_M2FLATHER />
-<section begin=NORTH_M3RADIATION />;<span id="NORTH_M3RADIATION"></span>'''[[NORTH_M3RADIATION]]'''
+<section begin=NORTH_M2GRADIENT />;<span id="NORTH_M2GRADIENT"></span>[[NORTH_M2GRADIENT]]
-:Option to
+:Option to use 2D momentum gradient condition for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M2GRADIENT]], [[SOUTH_M2GRADIENT]], [[WEST_M2GRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_M2CLAMPED]], [[NORTH_M2FLATHER]], [[NORTH_M2NUDGING]], [[NORTH_M2RADIATION]], [[NORTH_M2REDUCED]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_M3RADIATION />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=NORTH_M2GRADIENT />
-<section begin=NORTH_KGRADIENT />;<span id="NORTH_KGRADIENT"></span>'''[[NORTH_KGRADIENT]]'''
+<section begin=NORTH_M2NUDGING />;<span id="NORTH_M2NUDGING"></span>[[NORTH_M2NUDGING]]
-:Option to
+:Option to use 2D momentum passive/active nudging term for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M2NUDGING]], [[SOUTH_M2NUDGING]], [[WEST_M2NUDGING]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_M2CLAMPED]], [[NORTH_M2FLATHER]], [[NORTH_M2GRADIENT]], [[NORTH_M2REDUCED]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_KGRADIENT />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=NORTH_M2NUDGING />
-<section begin=NORTH_KRADIATION />;<span id="NORTH_KRADIATION"></span>'''[[NORTH_KRADIATION]]'''
+<section begin=NORTH_M2RADIATION />;<span id="NORTH_M2RADIATION"></span>[[NORTH_M2RADIATION]]
-:Option to
+:Option to use 2D momentum radiation condition for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M2RADIATION]], [[SOUTH_M2RADIATION]], [[WEST_M2RADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_M2CLAMPED]], [[NORTH_M2FLATHER]], [[NORTH_M2GRADIENT]], [[NORTH_M2REDUCED]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_KRADIATION />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=NORTH_M2RADIATION />
-<section begin=NORTH_TCLAMPED />;<span id="NORTH_TCLAMPED"></span>'''[[NORTH_TCLAMPED]]'''
+<section begin=NORTH_M2REDUCED />;<span id="NORTH_M2REDUCED"></span>[[NORTH_M2REDUCED]]
-:Option to
+:Option to use 2D momentum reduced-physics for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M2REDUCED]], [[SOUTH_M2REDUCED]], [[WEST_M2REDUCED]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_M2CLAMPED]], [[NORTH_M2FLATHER]], [[NORTH_M2GRADIENT]], [[NORTH_M2NUDGING]], [[NORTH_M2RADIATION]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_TCLAMPED />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=NORTH_M2REDUCED />
-<section begin=NORTH_TGRADIENT />;<span id="NORTH_TGRADIENT"></span>'''[[NORTH_TGRADIENT]]'''
+<section begin=NORTH_M3CLAMPED />;<span id="NORTH_M3CLAMPED"></span>[[NORTH_M3CLAMPED]]
-:Option to
+:Option to use 3D momentum clamped condition for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M3CLAMPED]], [[SOUTH_M3CLAMPED]], [[WEST_M3CLAMPED]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_M3GRADIENT]], [[NORTH_M3NUDGING]], [[NORTH_M3RADIATION]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_TGRADIENT />
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=NORTH_M3CLAMPED />
-<section begin=NORTH_TNUDGING />;<span id="NORTH_TNUDGING"></span>'''[[NORTH_TNUDGING]]'''
+<section begin=NORTH_M3GRADIENT />;<span id="NORTH_M3GRADIENT"></span>[[NORTH_M3GRADIENT]]
-:Option to
+:Option to use 3D momentum gradient condition for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M3GRADIENT]], [[SOUTH_M3GRADIENT]], [[WEST_M3GRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_M3CLAMPED]], [[NORTH_M3NUDGING]], [[NORTH_M3RADIATION]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_TNUDGING />
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=NORTH_M3GRADIENT />
-<section begin=NORTH_TRADIATION />;<span id="NORTH_TRADIATION"></span>'''[[NORTH_TRADIATION]]'''
+<section begin=NORTH_M3NUDGING />;<span id="NORTH_M3NUDGING"></span>[[NORTH_M3NUDGING]]
-:Option to
+:Option to use 3D momentum passive/active nudging term for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M3NUDGING]], [[SOUTH_M3NUDGING]], [[WEST_M3NUDGING]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_M3CLAMPED]], [[NORTH_M3GRADIENT]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_TRADIATION />
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=NORTH_M3NUDGING />
-<section begin=NORTH_VOLCONS />;<span id="NORTH_VOLCONS"></span>'''[[NORTH_VOLCONS]]'''
+<section begin=NORTH_M3RADIATION />;<span id="NORTH_M3RADIATION"></span>[[NORTH_M3RADIATION]]
-:Option to
+:Option to use 3D momentum radiation condition for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M3RADIATION]], [[SOUTH_M3RADIATION]], [[WEST_M3RADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_M3CLAMPED]], [[NORTH_M3GRADIENT]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTH_VOLCONS />
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=NORTH_M3RADIATION />
-<section begin=NORTHERN_WALL />;<span id="NORTHERN_WALL"></span>'''[[NORTHERN_WALL]]'''
+<section begin=NORTH_TCLAMPED />;<span id="NORTH_TCLAMPED"></span>[[NORTH_TCLAMPED]]
-:Option to
+:Option to use tracer clamped condition for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_TCLAMPED]], [[SOUTH_TCLAMPED]], [[WEST_TCLAMPED]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_TGRADIENT]], [[NORTH_TNUDGING]], [[NORTH_TRADIATION]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NORTHERN_WALL />
+:'''routine = ''' [[t3dbc_im.F]]<section end=NORTH_TCLAMPED />
-<section begin=NO_WRITE_GRID />;<span id="NO_WRITE_GRID"></span>'''[[NO_WRITE_GRID]]'''
+<section begin=NORTH_TGRADIENT />;<span id="NORTH_TGRADIENT"></span>[[NORTH_TGRADIENT]]
-:Option to
+:Option to use tracer gradient condition for the northern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_TGRADIENT]], [[SOUTH_TGRADIENT]], [[WEST_TGRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_TCLAMPED]], [[NORTH_TNUDGING]], [[NORTH_TRADIATION]], [[NORTHERN_WALL]]
-:'''routine = '''  <section end=NO_WRITE_GRID />
+:'''routine = ''' [[t3dbc_im.F]]<section end=NORTH_TGRADIENT />
+<section begin=NORTH_TNUDGING />;<span id="NORTH_TNUDGING"></span>[[NORTH_TNUDGING]]
+:Option to use tracer passive/active nudging term for the northern open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_TNUDGING]], [[SOUTH_TNUDGING]], [[WEST_TNUDGING]]
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_TCLAMPED]], [[NORTH_TGRADIENT]], [[NORTHERN_WALL]]
+:'''routine = ''' [[t3dbc_im.F]]<section end=NORTH_TNUDGING />
+<section begin=NORTH_TRADIATION />;<span id="NORTH_TRADIATION"></span>[[NORTH_TRADIATION]]
+:Option to use tracer radiation condition for the northern open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_TRADIATION]], [[SOUTH_TRADIATION]], [[WEST_TRADIATION]]
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_TCLAMPED]], [[NORTH_TGRADIENT]], [[NORTHERN_WALL]]
+:'''routine = ''' [[t3dbc_im.F]]<section end=NORTH_TRADIATION />
+<section begin=NORTH_VOLCONS />;<span id="NORTH_VOLCONS"></span>[[NORTH_VOLCONS]]
+:Option to use Southern edge mass conservation enforcement for the northern open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_VOLCONS]], [[SOUTH_VOLCONS]], [[WEST_VOLCONS]]
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTHERN_WALL]]
+:'''routine = ''' [[obc_volcons.F]]<section end=NORTH_VOLCONS />
+<section begin=NORTHERN_WALL />;<span id="NORTHERN_WALL"></span>[[NORTHERN_WALL]]
+:Option to use Southern edge closed wall for the northern open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_WALL]], [[SOUTH_WALL]], [[WEST_WALL]]
+:'''conflict = ''' [[NS_PERIODIC]], [[NORTH_FSCLAMPED]], [[NORTH_FSCHAPMAN]], [[NORTH_FSGRADIENT]], [[NORTH_FSNUDGING]], [[NORTH_FSRADIATION]], [[NORTH_KGRADIENT]], [[NORTH_KRADIATION]], [[NORTH_M2CLAMPED]], [[NORTH_M2FLATHER]], [[NORTH_M2GRADIENT]], [[NORTH_M2NUDGING]], [[NORTH_M2RADIATION]], [[NORTH_M2REDUCED]], [[NORTH_M3CLAMPED]], [[NORTH_M3GRADIENT]], [[NORTH_M3NUDGING]], [[NORTH_M3RADIATION]], [[NORTH_TCLAMPED]], [[NORTH_TGRADIENT]], [[NORTH_TNUDGING]], [[NORTH_TRADIATION]], [[NORTH_VOLCONS]]
+:'''routine = ''' [[t3dbc_im.F]], [[tkebc_im.F]], [[u2dbc_im.F]], [[u3dbc_im.F]], [[v2dbc_im.F]], [[v3dbc_im.F]], [[zetabc.F]]<section end=NORTHERN_WALL />
-<section begin=NPZD_FRANKS />;<span id="NPZD_FRANKS"></span>'''[[NPZD_FRANKS]]'''
+<section begin=NPZD_FRANKS />;<span id="NPZD_FRANKS"></span>[[NPZD_FRANKS]]
 :Option to activate [[Bibliography#FranksPJS_1986a | Franks et al. (1986)]] NPZD biological model.
 :'''related = ''' [[ANA_BIOLOGY]], [[ANA_BPFLUX]], [[ANA_SPFLUX]]
-:'''conflict = ''' [[BIO_FASHAM]], [[ECOSIM]], [[NPZD_POWELL]]
+:'''conflict = ''' [[BIO_FENNEL]], [[ECOSIM]], [[NEMURO]], [[NPZD_IRON]], [[NPZD_POWELL]]
-:'''routine = ''' [[npzd_Franks.h]], [[npzd_Franks.in]]<section end=NPZD_FRANKS />
+:'''routine = ''' [[npzd_Franks.h]]
+:'''input = ''' [[npzd_Franks.in]]<section end=NPZD_FRANKS />
+<section begin=NPZD_IRON />;<span id="NPZD_IRON"></span>[[NPZD_IRON]]
+:Option to activate [[Bibliography#FeichterJ_2009 | Fiechter et al. (2009)]] iron NPZD biological model.
+:'''related = ''' [[ANA_BIOLOGY]], [[ANA_BPFLUX]], [[ANA_SPFLUX]]
+:'''conflict = ''' [[BIO_FENNEL]], [[ECOSIM]], [[NEMURO]], [[NPZD_FRANKS]], [[NPZD_POWELL]]
+:'''routine = ''' [[npzd_iron.h]]
+:'''input = ''' [[npzd_iron.in]]<section end=NPZD_IRON />
-<section begin=NPZD_POWELL />;<span id="NPZD_POWELL"></span>'''[[NPZD_POWELL]]'''
+<section begin=NPZD_POWELL />;<span id="NPZD_POWELL"></span>[[NPZD_POWELL]]
 :Option to activate [[Bibliography#PowellTO_2006a | Powell et al. (2006)]] NPZD biological model.
 :'''related = ''' [[ANA_BIOLOGY]], [[ANA_BPFLUX]], [[ANA_SPFLUX]]
-:'''conflict = ''' [[BIO_FASHAM]], [[ECOSIM]], [[NPZD_FRANKS]]
+:'''conflict = ''' [[BIO_FENNEL]], [[ECOSIM]], [[NEMURO]], [[NPZD_FRANKS]], [[NPZD_IRON]]
-:'''routine = ''' [[npzd_Powell.h]], [[npzd_Powell.in]]<section end=NPZD_POWELL />
+:'''routine = ''' [[npzd_Powell.h]]
+:'''input = ''' [[npzd_Powell.in]]<section end=NPZD_POWELL />
-<section begin=NS_PERIODIC />;<span id="NS_PERIODIC"></span>'''[[NS_PERIODIC]]'''
+<section begin=NS_PERIODIC />;<span id="NS_PERIODIC"></span>[[NS_PERIODIC]]
-:Option to
+:Option to use North_South periodic boundary conditions.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,887: / Line 2,235: @@
 :'''routine = '''  <section end=NS_PERIODIC />
-<section begin=NUDGING_SSH />;<span id="NUDGING_SSH"></span>'''[[NUDGING_SSH]]'''
+<section begin=NUDGING_SSH />;<span id="NUDGING_SSH"></span>[[NUDGING_SSH]]
-:Option to
+:Option to nudge sea surface height observations (altimetry).
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NUDGING_SSH]], [[NUDGING_SST]], [[NUDGING_T]], [[NUDGING_UV]], [[NUDGING_UVsur]]
-:'''conflict = '''
+:'''conflict = ''' [[ASSIMILATION_SSH]]
 :'''routine = '''  <section end=NUDGING_SSH />
-<section begin=NUDGING_SST />;<span id="NUDGING_SST"></span>'''[[NUDGING_SST]]'''
+<section begin=NUDGING_SST />;<span id="NUDGING_SST"></span>[[NUDGING_SST]]
-:Option to
+:Option to nudge sea surface temperature observations.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NUDGING_SSH]], [[NUDGING_T]], [[NUDGING_UV]], [[NUDGING_UVsur]]
-:'''conflict = '''
+:'''conflict = ''' [[ASSIMILATION_SST]]
 :'''routine = '''  <section end=NUDGING_SST />
-<section begin=NUDGING_T />;<span id="NUDGING_T"></span>'''[[NUDGING_T]]'''
+<section begin=NUDGING_T />;<span id="NUDGING_T"></span>[[NUDGING_T]]
-:Option to
+:Option to nudge tracer-type observations (temperature and salinity).
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NUDGING_SSH]], [[NUDGING_SST]], [[NUDGING_UV]], [[NUDGING_UVsur]]
-:'''conflict = '''
+:'''conflict = ''' [[ASSIMILATION_T]]
 :'''routine = '''  <section end=NUDGING_T />
-<section begin=NUDGING_UV />;<span id="NUDGING_UV"></span>'''[[NUDGING_UV]]'''
+<section begin=NUDGING_UV />;<span id="NUDGING_UV"></span>[[NUDGING_UV]]
-:Option to
+:Option to nudge horizontal current observations.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NUDGING_SSH]], [[NUDGING_SST]], [[NUDGING_T]], [[NUDGING_UVsur]]
-:'''conflict = '''
+:'''conflict = ''' [[ASSIMILATION_UV]]
 :'''routine = '''  <section end=NUDGING_UV />
-<section begin=NUDGING_UVsur />;<span id="NUDGING_UVsur"></span>'''[[NUDGING_UVsur]]'''
+<section begin=NUDGING_UVsur />;<span id="NUDGING_UVsur"></span>[[NUDGING_UVsur]]
-:Option to
+:Option to nudge surface current observations.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[NUDGING_SSH]], [[NUDGING_SST]], [[NUDGING_T]], [[NUDGING_UV]]
+:'''conflict = ''' [[ASSIMILATION_UVsur]]
+:'''routine = '''  <section end=NUDGING_UVsur />
+==<span class="alphabet">O</span>==
+<section begin=OBC />;<span id="OBC"></span>[[OBC]]
+:Internal option indicating open boundary conditions.
+:'''related = ''' [[EAST_FSOBC]], [[EAST_M2OBC]], [[EAST_M3OBC]], [[EAST_TOBC]]
+:'''related = ''' [[WEST_FSOBC]], [[WEST_M2OBC]], [[WEST_M3OBC]], [[WEST_TOBC]]
+:'''related = ''' [[NORTH_FSOBC]], [[NORTH_M2OBC]], [[NORTH_M3OBC]], [[NORTH_TOBC]]
+:'''related = ''' [[SOUTH_FSOBC]], [[SOUTH_M2OBC]], [[SOUTH_M3OBC]], [[SOUTH_TOBC]]
+:'''routine = ''' [[globaldefs.h]]<section end=OBC />
+<section begin=OBS_IMPACT />;<span id="OBS_IMPACT"></span>[[OBS_IMPACT]]
+:Option to to compute the observation impact to [[Options#RBL4DVAR_ANA_SENSITIVITY|RBL4DVAR_ANA_SENSITIVITY]], [[Options#R4DVAR_ANA_SENSITIVITY|R4DVAR_ANA_SENSITIVITY]], and [[Options#I4DVAR_ANA_SENSITIVITY|I4DVAR_ANA_SENSITIVITY]] algorithms.
+:'''parameter = '''
+:'''parent = '''
+:'''required = ''' [[Options#RBL4DVAR_ANA_SENSITIVITY|RBL4DVAR_ANA_SENSITIVITY]], [[Options#R4DVAR_ANA_SENSITIVITY|R4DVAR_ANA_SENSITIVITY]], or [[Options#I4DVAR_ANA_SENSITIVITY|I4DVAR_ANA_SENSITIVITY]]
+:'''related = ''' [[Options#OBS_IMPACT_SPLIT|OBS_IMPACT_SPLIT]]
 :'''conflict = '''
-:'''routine = '''  <section end=NUDGING_UVsur />
+:'''routine = '''  <section end=OBS_IMPACT />
-<section begin=N2NORM_PROFILE />;<span id="N2NORM_PROFILE"></span>'''[[N2NORM_PROFILE]]'''
+<section begin=OBS_IMPACT_SPLIT />;<span id="OBS_IMPACT_SPLIT"></span>[[OBS_IMPACT_SPLIT]]
-:Option to
+:Option to compute the contributions due to initial conditions, surface forcing, and boundary conditions. This option needs to be used with [[Options#OBS_IMPACT|OBS_IMPACT]] and [[Options#RBL4DVAR_ANA_SENSITIVITY|RBL4DVAR_ANA_SENSITIVITY]] or [[Options#R4DVAR_ANA_SENSITIVITY|R4DVAR_ANA_SENSITIVITY]].
 :'''parameter = '''
 :'''parent = '''
-:'''required = '''
+:'''required = ''' [[Options#OBS_IMPACT|OBS_IMPACT]] and [[Options#RBL4DVAR_ANA_SENSITIVITY|RBL4DVAR_ANA_SENSITIVITY]] or [[Options#R4DVAR_ANA_SENSITIVITY|R4DVAR_ANA_SENSITIVITY]]
-:'''related = '''
+:'''related = ''' [[Options#OBS_IMPACT|OBS_IMPACT]]
 :'''conflict = '''
-:'''routine = '''  <section end=N2NORM_PROFILE />
+:'''routine = '''  <section end=OBS_IMPACT_SPLIT />
-<section begin=N2S2_HORAVG />;<span id="N2S2_HORAVG"></span>'''[[N2S2_HORAVG]]'''
+<section begin=OBS_SPACE />;<span id="OBS_SPACE"></span>[[OBS_SPACE]]
-:Option to
+:Option to compute the forecast error metrics in observation space.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,948: / Line 2,315: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=N2S2_HORAVG />
+:'''routine = ''' [[ad_htobs.F]], [[def_info.F]], [[globaldefs.h]], [[mod_fourdvar.F]], [[mod_iounits.F]], [[obs_sen_rbl4dvar_forecast.h]], [[read_asspar.F]], [[read_phypar.F]] <section end=OBS_IMPACT_SPLIT />
-==<span class="alphabet">O</span>==
+<section begin=OBSERVATIONS />;<span id="OBSERVATIONS"></span>[[OBSERVATIONS]]
+:Internal switch to process observations in tangent linear, representer and adjoint models.
-<section begin=OBC />;<span id="OBC"></span>'''[[OBC]]'''
-:Internal option indicating open boundary conditions.
-:'''related = ''' [[EAST_FSOBC]], [[EAST_M2OBC]], [[EAST_M3OBC]], [[EAST_TOBC]]
-:'''related = ''' [[WEST_FSOBC]], [[WEST_M2OBC]], [[WEST_M3OBC]], [[WEST_TOBC]]
-:'''related = ''' [[NORTH_FSOBC]], [[NORTH_M2OBC]], [[NORTH_M3OBC]], [[NORTH_TOBC]]
-:'''related = ''' [[SOUTH_FSOBC]], [[SOUTH_M2OBC]], [[SOUTH_M3OBC]], [[SOUTH_TOBC]]
-:'''routine = ''' [[globaldefs.h]]<section end=OBC />
-<section begin=OBSERVATIONS />;<span id="OBSERVATIONS"></span>'''[[OBSERVATIONS]]'''
-:Option to
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,969: / Line 2,326: @@
 :'''routine = '''  <section end=OBSERVATIONS />
-<section begin=OCMIP_OXYGEN_SC />;<span id="OCMIP_OXYGEN_SC"></span>'''[[OCMIP_OXYGEN_SC]]'''
+<section begin=OCMIP_OXYGEN_SC />;<span id="OCMIP_OXYGEN_SC"></span>[[OCMIP_OXYGEN_SC]]
 :Option to use the [[Biblography#KeelingRF_1998a | Keeling et al. (1998)]] formulae for the Schmit number to model O<sub>2</sub> gas exchange. If deactivated, the formulation of [[Biblography#WanninkhofR_1992a | Wanninkhof (1992)]] is used instead.
-:'''parent = ''' [[BIO_FASHAM]]
+:'''parent = ''' [[BIO_FENNEL]]
 :'''required = ''' [[OXYGEN]]
-:'''routine = ''' [[fasham.h]]<section end=OCMIP_OXYGEN_SC />
+:'''routine = ''' [[fennel.h]]<section end=OCMIP_OXYGEN_SC />
+<section begin=ONE_WAY />;<span id="ONE_WAY"></span>[[ONE_WAY]]
+:Option to activate One-way grid nesting in refinement grids instead of the default two way nesting.
+:'''parent = ''' [[NESTING]]
+:'''required = ''' [[NESTING]]
+:'''routine = ''' [[nesting.F]]<section end=ONE_WAY />
-<section begin=OPT_OBSERVATIONS />;<span id="OPT_OBSERVATIONS"></span>'''[[OPT_OBSERVATIONS]]'''
+<section begin=OPT_OBSERVATIONS />;<span id="OPT_OBSERVATIONS"></span>[[OPT_OBSERVATIONS]]
-:Option to
+:Option to use the optimal observations driver.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,982: / Line 2,345: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=OPT_OBSERVATIONS />
+:'''routine = ''' <section end=OPT_OBSERVATIONS />
-<section begin=OPT_PERTURBATION />;<span id="OPT_PERTURBATION"></span>'''[[OPT_PERTURBATION]]'''
+<section begin=OPT_PERTURBATION />;<span id="OPT_PERTURBATION"></span>[[OPT_PERTURBATION]]
-:Option to
+:Option to use the optimal perturbations driver, singular vectors.
 :'''parameter = '''
 :'''parent = '''
@@ Line 1,991: / Line 2,354: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=OPT_PERTURBATION />
+:'''routine = ''' <section end=OPT_PERTURBATION />
-<section begin=OUT_DOUBLE />;<span id="OUT_DOUBLE"></span>'''[[OUT_DOUBLE]]'''
+<section begin=OUT_DOUBLE />;<span id="OUT_DOUBLE"></span>[[OUT_DOUBLE]]
-:Option to
+:Option to write double precision output fields to output NetCDF files.
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,000: / Line 2,363: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=OUT_DOUBLE />
+:'''routine = ''' [[mod_netcdf.F]]<section end=OUT_DOUBLE />
-<section begin=OVERFLOW />;<span id="OVERFLOW"></span>'''[[OVERFLOW]]'''
+<section begin=OVERFLOW />;<span id="OVERFLOW"></span>[[OVERFLOW]]
-:Option to
+:Option to compile and run the gravitational/overflow example.
-:'''parameter = '''
+:'''parameter = ''' [[Variables#MyAppCPP|MyAppCPP]]
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=OVERFLOW />
+:'''routine = ''' [[roms.in]]<section end=OVERFLOW />
-<section begin=OXYGEN />;<span id="OXYGEN"></span>'''[[OXYGEN]]'''
+<section begin=OXYGEN />;<span id="OXYGEN"></span>[[OXYGEN]]
-:Option to include oxygen dynamics in Fasham-type biological model. Currently, an additional tracer is added for dissolved oxygen concentration ([[Variables#iOxyg|iOxyg]]).
+:Option to include oxygen dynamics in the Fennel biological model. Currently, an additional tracer is added for dissolved oxygen concentration ([[Variables#iOxyg|iOxyg]]).
-:'''parent = ''' [[BIO_FASHAM]]
+:'''parent = ''' [[BIO_FENNEL]]
-:'''routine = ''' [[fasham.h]]<section end=OXYGEN />
+:'''routine = ''' [[fennel.h]]<section end=OXYGEN />
-<section begin=_OPENMP />;<span id="_OPENMP"></span>'''[[_OPENMP]]'''
+<section begin=_OPENMP />;<span id="_OPENMP"></span>[[_OPENMP]]
-:Option to
+:Internal switch to activate OpenMP (shared memory) for parallel runs.
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,023: / Line 2,386: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=_OPENMP />
+:'''routine = ''' <section end=_OPENMP />
 ==<span class="alphabet">P</span>==
-<section begin=PICARD_TEST />;<span id="PICARD_TEST"></span>'''[[PICARD_TEST]]'''
+<section begin=PERFECT_RESTART />;<span id="PERFECT_RESTART"></span>[[PERFECT_RESTART]]
-:Option to
+:Option to include perfect restart variables in the restart output NetCDF file.
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,034: / Line 2,397: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=PICARD_TEST />
+:'''routine = '''  <section end=PERFECT_RESTART />
-<section begin=PJ_GRADP />;<span id="PJ_GRADP"></span>'''[[PJ_GRADP]]'''
+<section begin=PARALLEL_IO />;<span id="PARALLEL_IO"></span>[[PARALLEL_IO]]
-:Option to
+:Option to use parallel I/O via HDF5 or pnetcdf libraries.
 :'''parameter = '''
 :'''parent = '''
-:'''required = '''
+:'''required = ''' [[HDF5]] or [[PNETCDF]]
-:'''related = '''
+:'''related = ''' [[HDF5]], [[PNETCDF]]
 :'''conflict = '''
-:'''routine = '''  <section end=PJ_GRADP />
+:'''routine = ''' [[mod_netcdf.F]]<section end=PERFECT_RESTART />
-<section begin=PJ_GRADPQ2 />;<span id="PJ_GRADPQ2"></span>'''[[PJ_GRADPQ2]]'''
+<section begin=PICARD_TEST />;<span id="PICARD_TEST"></span>[[PICARD_TEST]]
-:Option to
+:Option to use representer tangent linear model test driver.
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,052: / Line 2,415: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=PJ_GRADPQ2 />
+:'''routine = ''' <section end=PICARD_TEST />
+<section begin=PJ_GRADP />;<span id="PJ_GRADP"></span>[[PJ_GRADP]]
+:Option to use finite volume pressure Jacobian (Lin, 1997) for pressure gradient algorithm.
+:'''parameter = '''
+:'''parent = '''
+:'''required = ''' [[SOLVE3D]]
+:'''related = ''' [[ATM_PRESS]], [[DJ_GRADPS]], [[PJ_GRADPQ2]], [[PJ_GRADPQ4]], [[WJ_GRADP]]
+:'''conflict = ''' [[DJ_GRADPS]], [[PJ_GRADPQ2]], [[PJ_GRADPQ4]], [[WJ_GRADP]]
+:'''routine = ''' [[ad_prsgrd.F]], [[prsgrd.F]], [[rp_prsgrd.F]], [[tl_prsgrd.F]]<section end=PJ_GRADP />
+<section begin=PJ_GRADPQ2 />;<span id="PJ_GRADPQ2"></span>[[PJ_GRADPQ2]]
+:Option to use quadratic 2 pressure Jacobian (Shchepetkin, 2000) for pressure gradient algorithm.
+:'''parameter = '''
+:'''parent = '''
+:'''required = ''' [[SOLVE3D]]
+:'''related = ''' [[ATM_PRESS]], [[DJ_GRADPS]], [[PJ_GRADP]], [[PJ_GRADPQ4]], [[WJ_GRADP]]
+:'''conflict = ''' [[DJ_GRADPS]], [[PJ_GRADP]], [[PJ_GRADPQ4]], [[WJ_GRADP]]
+:'''routine = ''' [[ad_prsgrd.F]], [[prsgrd.F]], [[rp_prsgrd.F]], [[tl_prsgrd.F]]<section end=PJ_GRADPQ2 />
+<section begin=PJ_GRADPQ4 />;<span id="PJ_GRADPQ4"></span>[[PJ_GRADPQ4]]
+:Option to use quadratic 4 pressure Jacobian (Shchepetkin, 2000) for pressure gradient algorithm.
+:'''parameter = '''
+:'''parent = '''
+:'''required = ''' [[SOLVE3D]]
+:'''related = ''' [[ATM_PRESS]], [[DJ_GRADPS]], [[PJ_GRADP]], [[PJ_GRADPQ2]], [[WJ_GRADP]]
+:'''conflict = ''' [[DJ_GRADPS]], [[PJ_GRADP]], [[PJ_GRADPQ2]], [[WJ_GRADP]]
+:'''routine = ''' [[ad_prsgrd.F]], [[prsgrd.F]], [[rp_prsgrd.F]], [[tl_prsgrd.F]]<section end=PJ_GRADPQ4 />
-<section begin=PJ_GRADPQ4 />;<span id="PJ_GRADPQ4"></span>'''[[PJ_GRADPQ4]]'''
+<section begin=PNETCDF />;<span id="PNETCDF"></span>[[PNETCDF]]
-:Option to
+:Option to use parallel I/O with pnetcdf (classic format).
 :'''parameter = '''
 :'''parent = '''
-:'''required = '''
+:'''required = ''' [[PARALLEL_IO]]
 :'''related = '''
-:'''conflict = '''
+:'''conflict = ''' [[HDF5]]
-:'''routine = '''  <section end=PJ_GRADPQ4 />
+:'''routine = '''  [[mod_netcdf.F]]<section end=PERFECT_RESTART />
-<section begin=POWER_LAW />;<span id="POWER_LAW"></span>'''[[POWER_LAW]]'''
+<section begin=POSTERIOR_EOFS />;<span id="POSTERIOR_EOFS"></span>[[POSTERIOR_EOFS]]
-:Option to
+:Option to include the dominant EOFs of the posterior (''analysis'') error covariance matrix, [[Variables#Ea|Ea]], for the estimated initial conditions. These EOFs contain information about the patterns of largest uncertainty in the 4DVAR estimate.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[POSTERIOR_ERROR_F]] [[POSTERIOR_ERROR_I]]
 :'''conflict = '''
-:'''routine = '''  <section end=POWER_LAW />
+:'''routine = ''' <section end=POSTERIOR_EOFS />
-<section begin=PROFILE />;<span id="PROFILE"></span>'''[[PROFILE]]'''
+<section begin=POSTERIOR_ERROR_F />;<span id="POSTERIOR_ERROR_F"></span>[[POSTERIOR_ERROR_F]]
-:Option to
+:Option to compute the final assimilation time-window posterior error covariance matrix for the [[Options#RBL4DVAR|RBL4DVAR]] and [[Options#R4DVAR|R4DVAR]] algorithms. This represents the diagonal elements of the full error analysis covariance matrix. These should be compared to the background error variances (squared standard deviations) for each variable which are specified in the [[Variables#STDnameI|STDnameI]], [[Variables#STDnameI|STDnameI]], [[Variables#STDnameB|STDnameB]], [[Variables#STDnameF|STDnameF]] input NetCDF files. The analysis error covariance are written to a new NetCDF file ([[Variables#ERRname|ERRname]]) which is specified in [[s4dvar.in]]. Currently, the analysis error is only possible for a single outer loop, [[Variables#Nouter|Nouter]]=1.<br><br>This option must never be run at the same time as [[Options#POSTERIOR_ERROR_I|POSTERIOR_ERROR_I]]. If the [[Options#POSTERIOR_EOFS|POSTERIOR_EOFS]] option is defined, the EOFS of the analysis error covariance matrix are also computed along with the trace estimate. They are saved in the [[Variables#HSSname|HSSname]] output NetCDF file.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[POSTERIOR_EOFS]]
-:'''conflict = '''
+:'''conflict = ''' [[POSTERIOR_ERROR_I]]
-:'''routine = '''  <section end=PROFILE />
+:'''routine = '''  <section end=POSTERIOR_ERROR_F />
-<section begin=PSEUDOSPECTRA />;<span id="PSEUDOSPECTRA"></span>'''[[PSEUDOSPECTRA]]'''
+<section begin=POSTERIOR_ERROR_I />;<span id="POSTERIOR_ERROR_I"></span>[[POSTERIOR_ERROR_I]]
-:Option to
+:Option to compute the initial assimilation time-window posterior error covariance matrix for the [[Options#RBL4DVAR|RBL4DVAR]] and [[Options#R4DVAR|R4DVAR]] algorithms. This represents the diagonal elements of the full error analysis covariance matrix. These should be compared to the background error variances (squared standard deviations) for each variable which are specified in the [[Variables#STDnameI|STDnameI]], [[Variables#STDnameI|STDnameI]], [[Variables#STDnameB|STDnameB]], [[Variables#STDnameF|STDnameF]] input NetCDF files. The analysis error covariance are written to a new NetCDF file ([[Variables#ERRname|ERRname]]) which is specified in [[s4dvar.in]]. Currently, the analysis error is only possible for a single outer loop, [[Variables#Nouter|Nouter]]=1.<br><br>This option must never be run at the same time as [[Options#POSTERIOR_ERROR_F|POSTERIOR_ERROR_F]]. If the [[Options#POSTERIOR_EOFS|POSTERIOR_EOFS]] option is defined, the EOFS of the analysis error covariance matrix are also computed along with the trace estimate. They are saved in the [[Variables#HSSname|HSSname]] output NetCDF file.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
+:'''related = ''' [[POSTERIOR_EOFS]]
+:'''conflict = ''' [[POSTERIOR_ERROR_F]]
+:'''routine = '''  <section end=POSTERIOR_ERROR_I />
+<section begin=POWER_LAW />;<span id="POWER_LAW"></span>[[POWER_LAW]]
+:Internal switch to use power law time-averaging filter for barotropic fields.
+:'''parameter = '''
+:'''parent = '''
+:'''required = ''' [[SOLVE3D]]
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=PSEUDOSPECTRA />
+:'''routine = ''' <section end=POWER_LAW />
-==<span class="alphabet">Q</span>==
-<section begin=QCORRECTION />;<span id="QCORRECTION"></span>'''[[QCORRECTION]]'''
+<section begin=PROFILE />;<span id="PROFILE"></span>[[PROFILE]]
-:Option to
+:Option to use time profiling.
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,099: / Line 2,496: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=QCORRECTION />
+:'''routine = ''' <section end=PROFILE />
-<section begin=Q_PSOURCE />;<span id="Q_PSOURCE"></span>'''[[Q_PSOURCE]]'''
+<section begin=PSEUDOSPECTRA />;<span id="PSEUDOSPECTRA"></span>[[PSEUDOSPECTRA]]
+:Option to use pseudospectra of tangent linear resolvant driver.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = '''
+:'''conflict = '''
+:'''routine = ''' <section end=PSEUDOSPECTRA />
+==<span class="alphabet">Q</span>==
+<section begin=QCORRECTION />;<span id="QCORRECTION"></span>[[QCORRECTION]]
+:Option to use net heat flux correction for tracers.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = '''
+:'''conflict = '''
+:'''routine = ''' [[ad_set_vbc.F]], [[rp_set_vbc.F]], [[set_vbc.F]], [[tl_set_vbc.F]]<section end=QCORRECTION />
+<section begin=Q_PSOURCE />;<span id="Q_PSOURCE"></span>[[Q_PSOURCE]] ('''OBSOLETE as of revision 701''')
 :Option to activate/deactivate point sources/sinks of momentum. This option is used to specify the mass transport in the vertical, such as precipitation or groundwater discharge.
 :'''variable = ''' [[Variables#Dsrc | Dsrc(1:Nsrc)]], [[Variables#Qsrc | Qsrc(1:Nsrc,k)]]
 :'''related = ''' [[ANA_PSOURCE]], [[TS_PSOURCE]]
-:'''confict = ''' [[BBL_MODEL]], [[UV_LOGDRAG]], [[UV_QDRAG]]
+:'''confict = '''
 :'''routine = ''' [[step2d.F]], [[step3d_uv.F]]<section end=Q_PSOURCE />
 ==<span class="alphabet">R</span>==
-<section begin=RADIATION_2D />;<span id="RADIATION_2D"></span>'''[[RADIATION_2D]]'''
+<section begin=R_SYMMETRY />;<span id="R_SYMMETRY"></span>[[R_SYMMETRY]]
 :Option to
 :'''parameter = '''
@@ Line 2,117: / Line 2,534: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=RADIATION_2D />
+:'''routine = '''  <section end=R_SYMMETRY />
-<section begin=RAMP_TIDES />;<span id="RAMP_TIDES"></span>'''[[RAMP_TIDES]]'''
+<section begin=R4DVAR />;<span id="R4DVAR"></span>[[R4DVAR]] (Formerly W4DVAR)
-:Option to
+:Option to activate indirect Representers 4D-Var; strong/weak constraint, dual formulation. This algorithm is no longer developed due to its instability in multiple outer loops in applications with high Rossby number. It is keep for instructional usage. We do not recommend to be used in realistic applications. Use instead the [[Options#RBL4DVAR|RBL4D-Var]] algorithm, which has a more efficient minimization RBLanczos solver.
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,126: / Line 2,543: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=RAMP_TIDES />
+:'''routine = ''' [[r4dvar_ocean.h]] <section end=R4DVAR />
-<section begin=READ_WATER />;<span id="READ_WATER"></span>'''[[READ_WATER]]'''
+<section begin=R4DVAR_ANA_SENSITIVITY />;<span id="R4DVAR_ANA_SENSITIVITY"></span>[[R4DVAR_ANA_SENSITIVITY]] (Formerly W4DVAR_SENSITIVITY)
-:Option to
+:Option to activate R4D-Var Analysis Observation Impact and Observations Sensitivity.
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,135: / Line 2,552: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=READ_WATER />
+:'''routine = ''' [[obs_sen_r4dvar_analysis.h]] <section end=R4DVAR_ANA_SENSITIVITY />
-<section begin=RIVERPLUME1 />;<span id="RIVERPLUME1"></span>'''[[RIVERPLUME1]]'''
+<section begin=RADIATION_2D />;<span id="RADIATION_2D"></span>[[RADIATION_2D]]
-:Option to
+:Option to use tangential phase speed in radiation open boundary conditions.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSRADIATION]], [[EAST_KRADIATION]], [[EAST_M2RADIATION]], [[EAST_M3RADIATION]], [[EAST_TRADIATION]], [[NORTH_FSRADIATION]], [[NORTH_KRADIATION]], [[NORTH_M2RADIATION]], [[NORTH_M3RADIATION]], [[NORTH_TRADIATION]][[SOUTH_FSRADIATION]], [[SOUTH_KRADIATION]], [[SOUTH_M2RADIATION]], [[SOUTH_M3RADIATION]], [[SOUTH_TRADIATION]][[WEST_FSRADIATION]], [[WEST_KRADIATION]], [[WEST_M2RADIATION]], [[WEST_M3RADIATION]], [[WEST_TRADIATION]]
 :'''conflict = '''
-:'''routine = '''  <section end=RIVERPLUME1 />
+:'''routine = '''  <section end=RADIATION_2D />
-<section begin=RIVERPLUME2 />;<span id="RIVERPLUME2"></span>'''[[RIVERPLUME2]]'''
+<section begin=RAMP_TIDES />;<span id="RAMP_TIDES"></span>[[RAMP_TIDES]]
-:Option to
+:Option to ramp (over one day) tidal forcing at open boundaries.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[SSH_TIDES]], [[UV_TIDES]]
 :'''conflict = '''
-:'''routine = '''  <section end=RIVERPLUME2 />
+:'''routine = '''  <section end=RAMP_TIDES />
-<section begin=RIVER_BIOLOGY />;<span id="RIVER_BIOLOGY"></span>'''[[RIVER_BIOLOGY]]'''
+<section begin=RBL4DVAR />;<span id="RBL4DVAR"></span>[[RBL4DVAR]] (Formerly W4DPSAS)
-:Option to
+:Option to activate Restricted B-preconditioned Lanczos 4D-Var; strong/weak constraint, dual formulation. This driver has evolved throught the years and it is no longer a PSAS algorithm. See Gürol et al. (2014) for full description of the RBLanczos methodology.
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,162: / Line 2,579: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=RIVER_BIOLOGY />
+:'''routine = ''' [[rbl4dvar_ocean.h]] <section end=RBL4DVAR />
-<section begin=RIVER_SEDIMENT />;<span id="RIVER_SEDIMENT"></span>'''[[RIVER_SEDIMENT]]'''
+<section begin=RBL4DVAR_FCT_SENSITIVITY />;<span id="RBL4DVAR_FCT_SENSITIVITY"></span>[[RBL4DVAR_FCT_SENSITIVITY]] (Formerly W4DPSAS_FCT_SENSITIVITY)
-:Option to
+:Option to activate RBL4D-Var Forecast Observation Impact and Observations Sensitivity.
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,171: / Line 2,588: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=RIVER_SEDIMENT />
+:'''routine = ''' [[ad_htobs.F]], [[ad_rpcg_lanczos.F]], [[ceckdefs.F]], [[def_info.F]], [[def_ini.F]], [[def_mod.F]], [[get_state.F]], [[globaldefs.h]], [[mod_iounits.F]], [[mod_fourdvar.F]], [[obs_sen_rbl4dvar_forecast.h]], [[read_asspar.F]], [[read_phypar.F]], [[rpcg_lanczos.F]], [[tl_rpcg_lanczos.F]], [[wrt_info.F]] <section end=RBL4DVAR_FCT_SENSITIVITY />
-<section begin=RI_HORAVG />;<span id="RI_HORAVG"></span>'''[[RI_HORAVG]]'''
+<section begin=RBL4DVAR_ANA_SENSITIVITY />;<span id="RBL4DVAR_ANA_SENSITIVITY"></span>[[RBL4DVAR_ANA_SENSITIVITY]] (Formerly W4DPSAS_SENSITIVITY)
-:Option to
+:Option to activate RBL4D-Var analysis observation impact and observations sensitivity.
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,180: / Line 2,597: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=RI_HORAVG />
+:'''routine = ''' [[obs_sen_rbl4dvar_analysis.h]] <section end=RBL4DVAR_ANA_SENSITIVITY />
-<section begin=RI_VERAVG />;<span id="RI_VERAVG"></span>'''[[RI_VERAVG]]'''
+<section begin=READ_WATER />;<span id="READ_WATER"></span>[[READ_WATER]]
 :Option to
 :'''parameter = '''
@@ Line 2,189: / Line 2,606: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=RI_VERAVG />
+:'''routine = '''  <section end=READ_WATER />
-<section begin=RHO_SURF />;<span id="RHO_SURF"></span>'''[[RHO_SURF]]'''
+<section begin=REFDIF_COUPLING />;<span id="REFDIF_COUPLING"></span>[[REFDIF_COUPLING]]
 :Option to
 :'''parameter = '''
@@ Line 2,198: / Line 2,615: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=RHO_SURF />
+:'''routine = '''  <section end=REFDIF_COUPLING />
-<section begin=RPM_DRIVER />;<span id="RPM_DRIVER"></span>'''[[RPM_DRIVER]]'''
+<section begin=RI_HORAVG />;<span id="RI_HORAVG"></span>[[RI_HORAVG]]
 :Option to
 :'''parameter = '''
@@ Line 2,207: / Line 2,624: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=RPM_DRIVER />
+:'''routine = '''  <section end=RI_HORAVG />
-<section begin=RST_SINGLE />;<span id="RST_SINGLE"></span>'''[[RST_SINGLE]]'''
+<section begin=RI_VERAVG />;<span id="RI_VERAVG"></span>[[RI_VERAVG]]
 :Option to
 :'''parameter = '''
@@ Line 2,216: / Line 2,633: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=RST_SINGLE />
+:'''routine = '''  <section end=RI_VERAVG />
-<section begin=R_SYMMETRY />;<span id="R_SYMMETRY"></span>'''[[R_SYMMETRY]]'''
+<section begin=RIVERPLUME1 />;<span id="RIVERPLUME1"></span>[[RIVERPLUME1]]
 :Option to
 :'''parameter = '''
@@ Line 2,225: / Line 2,642: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=R_SYMMETRY />
+:'''routine = '''  <section end=RIVERPLUME1 />
-==<span class="alphabet">S</span>==
+<section begin=RIVERPLUME2 />;<span id="RIVERPLUME2"></span>[[RIVERPLUME2]]
-<section begin=SALINITY />;<span id="SALINITY"></span>'''[[SALINITY]]'''
 :Option to
 :'''parameter = '''
@@ Line 2,236: / Line 2,651: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SALINITY />
+:'''routine = '''  <section end=RIVERPLUME2 />
-<section begin=SANITY_CHECK />;<span id="SANITY_CHECK"></span>'''[[SANITY_CHECK]]'''
+<section begin=RHO_SURF />;<span id="RHO_SURF"></span>[[RHO_SURF]]
 :Option to
 :'''parameter = '''
@@ Line 2,245: / Line 2,660: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SANITY_CHECK />
+:'''routine = '''  <section end=RHO_SURF />
-<section begin=SCORRECTION />;<span id="SCORRECTION"></span>'''[[SCORRECTION]]'''
+<section begin=RPM_DRIVER />;<span id="RPM_DRIVER"></span>[[RPM_DRIVER]]
 :Option to
 :'''parameter = '''
@@ Line 2,254: / Line 2,669: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SCORRECTION />
+:'''routine = '''  <section end=RPM_DRIVER />
-<section begin=SEAMOUNT />;<span id="SEAMOUNT"></span>'''[[SEAMOUNT]]'''
+<section begin=RPM_RELAXATION />;<span id="RPM_RELAXATION"></span>[[RPM_RELAXATION]]
 :Option to
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,263: / Line 2,678: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SEAMOUNT />
+:'''routine = '''  <section end=RPM_RELAXATION/>
-<section begin=SEDIMENT />;<span id="SEDIMENT"></span>'''[[SEDIMENT]]'''
+<section begin=RST_SINGLE />;<span id="RST_SINGLE"></span>[[RST_SINGLE]]
-:Option to activate cohesive and non-cohesive sediment model ([[Bibliography#WarnerJC_2006a |Warner et al., 2006]]).
-:'''related = ''' [[ANA_BPFLUX]], [[ANA_SEDIMENT]], [[ANA_SPFLUX]]
-:'''related = ''' [[BEDLOAD]], [[RIVER_SEDIMENT]], [[SED_DENS]], [[SED_MORPH]], [[SUSPLOAD]]
-:'''routine = ''' [[sediment.F]], [[sediment.in]]<section end=SEDIMENT />
-<section begin=SED_DENS />;<span id="SED_DENS"></span>'''[[SED_DENS]]'''
 :Option to
 :'''parameter = '''
@@ Line 2,278: / Line 2,687: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SED_DENS />
+:'''routine = '''  <section end=RST_SINGLE />
+==<span class="alphabet">S</span>==
-<section begin=SED_MORPH />;<span id="SED_MORPH"></span>'''[[SED_MORPH]]'''
+<section begin=SALINITY />;<span id="SALINITY"></span>[[SALINITY]]
 :Option to
 :'''parameter = '''
@@ Line 2,287: / Line 2,698: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SED_MORPH />
+:'''routine = '''  <section end=SALINITY />
-<section begin=SED_TEST1 />;<span id="SED_TEST1"></span>'''[[SED_TEST1]]'''
+<section begin=SANITY_CHECK />;<span id="SANITY_CHECK"></span>[[SANITY_CHECK]]
 :Option to
 :'''parameter = '''
@@ Line 2,296: / Line 2,707: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SED_TEST1 />
+:'''routine = '''  <section end=SANITY_CHECK />
-<section begin=SED_TOY />;<span id="SED_TOY"></span>'''[[SED_TOY]]'''
+<section begin=SCORRECTION />;<span id="SCORRECTION"></span>[[SCORRECTION]]
 :Option to
 :'''parameter = '''
@@ Line 2,305: / Line 2,716: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SED_TOY />
+:'''routine = '''  <section end=SCORRECTION />
-<section begin=SG_BBL />;<span id="SG_BBL"></span>'''[[SG_BBL]]'''
+<section begin=SEAMOUNT />;<span id="SEAMOUNT"></span>[[SEAMOUNT]]
 :Option to
 :'''parameter = '''
@@ Line 2,314: / Line 2,725: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SG_BBL />
+:'''routine = '''  <section end=SEAMOUNT />
-<section begin=SG_CALC_SNOT />;<span id="SG_CALC_SNOT"></span>'''[[SG_CALC_SNOT]]'''
+<section begin=SEDIMENT />;<span id="SEDIMENT"></span>[[SEDIMENT]]
+:Option to activate cohesive and non-cohesive sediment model ([[Bibliography#WarnerJC_2006a |Warner et al., 2006]]).
+:'''related = ''' [[ANA_BPFLUX]], [[ANA_SEDIMENT]], [[ANA_SPFLUX]]
+:'''related = ''' [[BEDLOAD]], [[RIVER_SEDIMENT]], [[SED_DENS]], [[SED_MORPH]], [[SUSPLOAD]]
+:'''routine = ''' [[sediment.F]], [[sediment.in]]<section end=SEDIMENT />
+<section begin=SED_DENS />;<span id="SED_DENS"></span>[[SED_DENS]]
 :Option to
 :'''parameter = '''
@@ Line 2,323: / Line 2,740: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SG_CALC_SNOT />
+:'''routine = '''  <section end=SED_DENS />
-<section begin=SG_LOGINT />;<span id="SG_LOGINT"></span>'''[[SG_LOGINT]]'''
+<section begin=SED_MORPH />;<span id="SED_MORPH"></span>[[SED_MORPH]]
 :Option to
 :'''parameter = '''
@@ Line 2,332: / Line 2,749: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SG_LOGINT />
+:'''routine = '''  <section end=SED_MORPH />
-<section begin=SOLAR_SOURCE />;<span id="SOLAR_SOURCE"></span>'''[[SOLAR_SOURCE]]'''
+<section begin=SED_TEST1 />;<span id="SED_TEST1"></span>[[SED_TEST1]]
 :Option to
 :'''parameter = '''
@@ Line 2,341: / Line 2,758: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SOLAR_SOURCE />
+:'''routine = '''  <section end=SED_TEST1 />
-<section begin=SOLITON />;<span id="SOLITON"></span>'''[[SOLITON]]'''
+<section begin=SED_TOY />;<span id="SED_TOY"></span>[[SED_TOY]]
 :Option to
 :'''parameter = '''
@@ Line 2,350: / Line 2,767: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SOLITON />
+:'''routine = '''  <section end=SED_TOY />
-<section begin=SOLVE3D />;<span id="SOLVE3D"></span>'''[[SOLVE3D]]'''
-:Option to activate/deactivate 3D model configuration. If activated, ROMS solves 3D (baroclinic) primitive equations. If deactivated, ROMS solves vertically-integrated, shallow water (barotropic) equations.
-:'''routine = ''' [[main2d.F]], [[main3d.F]]<section end=SOLVE3D />
-<section begin=SOUTH_FSCLAMPED />;<span id="SOUTH_FSCLAMPED"></span>'''[[SOUTH_FSCLAMPED]]'''
+<section begin=SG_BBL />;<span id="SG_BBL"></span>[[SG_BBL]]
-:Option to
+:Option to use Styles and Glenn ([[Bibliography#StylesR_2000a|2000]]) bottom boundary layer closure.
 :'''parameter = '''
 :'''parent = '''
-:'''required = '''
+:'''required = ''' [[BBL_MODEL]]
-:'''related = '''
+:'''related = ''' [[SG_CALC_UB]], [[SG_CALC_ZNOT]], [[SG_LOGINT]]
 :'''conflict = '''
-:'''routine = '''  <section end=SOUTH_FSCLAMPED />
+:'''routine = ''' [[sg_bbl.h]]<section end=SG_BBL />
-<section begin=SOUTH_FSCHAPMAN />;<span id="SOUTH_FSCHAPMAN"></span>'''[[SOUTH_FSCHAPMAN]]'''
+<section begin=SG_CALC_UB />;<span id="SG_CALC_UB"></span>[[SG_CALC_UB]]
-:Option to
+:Option to use if computing bottom orbital velocity internally for Styles and Glenn ([[Bibliography#StylesR_2000a|2000]]) bottom boundary layer closure.
 :'''parameter = '''
-:'''parent = '''
+:'''parent = ''' [[SG_BBL]]
-:'''required = '''
+:'''required = ''' [[BBL_MODEL]], [[SG_BBL]]
-:'''related = '''
+:'''related = ''' [[SG_CALC_ZNOT]], [[SG_LOGINT]]
 :'''conflict = '''
-:'''routine = '''  <section end=SOUTH_FSCHAPMAN />
+:'''routine = ''' [[sg_bbl.h]]<section end=SG_CALC_UB />
-<section begin=SOUTH_FSGRADIENT />;<span id="SOUTH_FSGRADIENT"></span>'''[[SOUTH_FSGRADIENT]]'''
+<section begin=SG_CALC_ZNOT />;<span id="SG_CALC_ZNOT"></span>[[SG_CALC_ZNOT]]
-:Option to
+:Option to use if computing bottom roughness internally for Styles and Glenn ([[Bibliography#StylesR_2000a|2000]]) bottom boundary layer closure.
 :'''parameter = '''
-:'''parent = '''
+:'''parent = ''' [[SG_BBL]]
-:'''required = '''
+:'''required = ''' [[BBL_MODEL]], [[SG_BBL]]
-:'''related = '''
+:'''related = ''' [[SG_CALC_UB]], [[SG_LOGINT]]
 :'''conflict = '''
-:'''routine = '''  <section end=SOUTH_FSGRADIENT />
+:'''routine = ''' [[sg_bbl.h]]<section end=SG_CALC_ZNOT />
-<section begin=SOUTH_FSNUDGING />;<span id="SOUTH_FSNUDGING"></span>'''[[SOUTH_FSNUDGING]]'''
+<section begin=SG_LOGINT />;<span id="SG_LOGINT"></span>[[SG_LOGINT]]
-:Option to
+:Option to use logarithmic interpolation of ([[Variables#Ur|Ur]],[[Variables#Vr|Vr]]) for Styles and Glenn ([[Bibliography#StylesR_2000a|2000]]) bottom boundary layer closure.
 :'''parameter = '''
-:'''parent = '''
+:'''parent = ''' [[SG_BBL]]
-:'''required = '''
+:'''required = ''' [[BBL_MODEL]], [[SG_BBL]]
-:'''related = '''
+:'''related = ''' [[SG_CALC_UB]], [[SG_CALC_ZNOT]]
 :'''conflict = '''
-:'''routine = '''  <section end=SOUTH_FSNUDGING />
+:'''routine = ''' [[sg_bbl.h]]<section end=SG_LOGINT />
-<section begin=SOUTH_FSRADIATION />;<span id="SOUTH_FSRADIATION"></span>'''[[SOUTH_FSRADIATION]]'''
+<section begin=SHOREFACE />;<span id="SHOREFACE"></span>[[SHOREFACE]]
 :Option to
 :'''parameter = '''
@@ Line 2,399: / Line 2,812: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SOUTH_FSRADIATION />
+:'''routine = '''  <section end=SHOREFACE />
-<section begin=SOUTH_M2CLAMPED />;<span id="SOUTH_M2CLAMPED"></span>'''[[SOUTH_M2CLAMPED]]'''
+<section begin=SO_SEMI />;<span id="SO_SEMI"></span>[[SO_SEMI]]
 :Option to
 :'''parameter = '''
@@ Line 2,408: / Line 2,821: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SOUTH_M2CLAMPED />
+:'''routine = '''  <section end=SO_SEMI />
-<section begin=SOUTH_M2FLATHER />;<span id="SOUTH_M2FLATHER"></span>'''[[SOUTH_M2FLATHER]]'''
+<section begin=SO_SEMI_WHITE />;<span id="SO_SEMI_WHITE"></span>[[SO_SEMI_WHITE]]
 :Option to
 :'''parameter = '''
@@ Line 2,417: / Line 2,830: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SOUTH_M2FLATHER />
+:'''routine = '''  <section end=SO_SEMI_WHITE />
-<section begin=SOUTH_M2GRADIENT />;<span id="SOUTH_M2GRADIENT"></span>'''[[SOUTH_M2GRADIENT]]'''
+<section begin=SO_TRACE />;<span id="SO_TRACE"></span>[[SO_TRACE]]
 :Option to
 :'''parameter = '''
@@ Line 2,426: / Line 2,839: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SOUTH_M2GRADIENT />
+:'''routine = '''  <section end=SO_TRACE />
-<section begin=SOUTH_M2NUDGING />;<span id="SOUTH_M2NUDGING"></span>'''[[SOUTH_M2NUDGING]]'''
+<section begin=SOLAR_SOURCE />;<span id="SOLAR_SOURCE"></span>[[SOLAR_SOURCE]]
 :Option to
 :'''parameter = '''
@@ Line 2,435: / Line 2,848: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SOUTH_M2NUDGING />
+:'''routine = '''  <section end=SOLAR_SOURCE />
-<section begin=SOUTH_M2RADIATION />;<span id="SOUTH_M2RADIATION"></span>'''[[SOUTH_M2RADIATION]]'''
+<section begin=SOLITON />;<span id="SOLITON"></span>[[SOLITON]]
 :Option to
 :'''parameter = '''
@@ Line 2,444: / Line 2,857: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SOUTH_M2RADIATION />
+:'''routine = '''  <section end=SOLITON />
-<section begin=SOUTH_M2REDUCED />;<span id="SOUTH_M2REDUCED"></span>'''[[SOUTH_M2REDUCED]]'''
+<section begin=SOLVE3D />;<span id="SOLVE3D"></span>[[SOLVE3D]]
-:Option to
+:Option to activate/deactivate 3D model configuration. If activated, ROMS solves 3D (baroclinic) primitive equations. If deactivated, ROMS solves vertically-integrated, shallow water (barotropic) equations.
+:'''routine = ''' [[main2d.F]], [[main3d.F]]<section end=SOLVE3D />
+<section begin=SOUTH_FSCLAMPED />;<span id="SOUTH_FSCLAMPED"></span>[[SOUTH_FSCLAMPED]]
+:Option to use free-surface clamped condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSCLAMPED]], [[NORTH_FSCLAMPED]], [[WEST_FSCLAMPED]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_FSCHAPMAN]], [[SOUTH_FSGRADIENT]], [[SOUTH_FSNUDGING]], [[SOUTH_FSRADIATION]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SOUTH_M2REDUCED />
+:'''routine = ''' [[zetabc.F]]<section end=SOUTH_FSCLAMPED />
-<section begin=SOUTH_M3CLAMPED />;<span id="SOUTH_M3CLAMPED"></span>'''[[SOUTH_M3CLAMPED]]'''
+<section begin=SOUTH_FSCHAPMAN />;<span id="SOUTH_FSCHAPMAN"></span>[[SOUTH_FSCHAPMAN]]
-:Option to
+:Option to use free-surface Chapman condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSCHAPMAN]], [[NORTH_FSCHAPMAN]], [[WEST_FSCHAPMAN]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_FSCLAMPED]], [[SOUTH_FSGRADIENT]], [[SOUTH_FSNUDGING]], [[SOUTH_FSRADIATION]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SOUTH_M3CLAMPED />
+:'''routine = ''' [[zetabc.F]]<section end=SOUTH_FSCHAPMAN />
-<section begin=SOUTH_M3GRADIENT />;<span id="SOUTH_M3GRADIENT"></span>'''[[SOUTH_M3GRADIENT]]'''
+<section begin=SOUTH_FSGRADIENT />;<span id="SOUTH_FSGRADIENT"></span>[[SOUTH_FSGRADIENT]]
-:Option to
+:Option to use free-surface gradient condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSGRADIENT]], [[NORTH_FSGRADIENT]], [[WEST_FSGRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_FSCLAMPED]], [[SOUTH_FSCHAPMAN]], [[SOUTH_FSNUDGING]], [[SOUTH_FSRADIATION]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SOUTH_M3GRADIENT />
+:'''routine = ''' [[zetabc.F]]<section end=SOUTH_FSGRADIENT />
-<section begin=SOUTH_M3NUDGING />;<span id="SOUTH_M3NUDGING"></span>'''[[SOUTH_M3NUDGING]]'''
+<section begin=SOUTH_FSNUDGING />;<span id="SOUTH_FSNUDGING"></span>[[SOUTH_FSNUDGING]]
-:Option to
+:Option to use free-surface passive/active nudging term for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSNUDGING]], [[NORTH_FSNUDGING]], [[WEST_FSNUDGING]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_FSCLAMPED]], [[SOUTH_FSCHAPMAN]], [[SOUTH_FSGRADIENT]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SOUTH_M3NUDGING />
+:'''routine = ''' [[zetabc.F]]<section end=SOUTH_FSNUDGING />
-<section begin=SOUTH_M3RADIATION />;<span id="SOUTH_M3RADIATION"></span>'''[[SOUTH_M3RADIATION]]'''
+<section begin=SOUTH_FSRADIATION />;<span id="SOUTH_FSRADIATION"></span>[[SOUTH_FSRADIATION]]
-:Option to
+:Option to use free-surface radiation condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSRADIATION]], [[NORTH_FSRADIATION]], [[WEST_FSRADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_FSCLAMPED]], [[SOUTH_FSCHAPMAN]], [[SOUTH_FSGRADIENT]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SOUTH_M3RADIATION />
+:'''routine = ''' [[zetabc.F]]<section end=SOUTH_FSRADIATION />
-<section begin=SOUTH_KGRADIENT />;<span id="SOUTH_KGRADIENT"></span>'''[[SOUTH_KGRADIENT]]'''
+<section begin=SOUTH_KGRADIENT />;<span id="SOUTH_KGRADIENT"></span>[[SOUTH_KGRADIENT]]
-:Option to
+:Option to use TKE fields gradient condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_KGRADIENT]], [[NORTH_KGRADIENT]], [[WEST_KGRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_KRADIATION]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SOUTH_KGRADIENT />
+:'''routine = ''' [[tkebc_im.F]]<section end=SOUTH_KGRADIENT />
-<section begin=SOUTH_KRADIATION />;<span id="SOUTH_KRADIATION"></span>'''[[SOUTH_KRADIATION]]'''
+<section begin=SOUTH_KRADIATION />;<span id="SOUTH_KRADIATION"></span>[[SOUTH_KRADIATION]]
-:Option to
+:Option to use TKE fields radiation condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_KRADIATION]], [[NORTH_KRADIATION]], [[WEST_KRADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_KGRADIENT]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SOUTH_KRADIATION />
+:'''routine = ''' [[tkebc_im.F]]<section end=SOUTH_KRADIATION />
-<section begin=SOUTH_TCLAMPED />;<span id="SOUTH_TCLAMPED"></span>'''[[SOUTH_TCLAMPED]]'''
+<section begin=SOUTH_M2CLAMPED />;<span id="SOUTH_M2CLAMPED"></span>[[SOUTH_M2CLAMPED]]
-:Option to
+:Option to use 2D momentum clamped condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M2CLAMPED]], [[NORTH_M2CLAMPED]], [[WEST_M2CLAMPED]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_M2FLATHER]], [[SOUTH_M2GRADIENT]], [[SOUTH_M2NUDGING]], [[SOUTH_M2RADIATION]], [[SOUTH_M2REDUCED]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SOUTH_TCLAMPED />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=SOUTH_M2CLAMPED />
-<section begin=SOUTH_TGRADIENT />;<span id="SOUTH_TGRADIENT"></span>'''[[SOUTH_TGRADIENT]]'''
+<section begin=SOUTH_M2FLATHER />;<span id="SOUTH_M2FLATHER"></span>[[SOUTH_M2FLATHER]]
-:Option to
+:Option to use 2D momentum Flather condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M2FLATHER]], [[NORTH_M2FLATHER]], [[WEST_M2FLATHER]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_M2CLAMPED]], [[SOUTH_M2GRADIENT]], [[SOUTH_M2NUDGING]], [[SOUTH_M2RADIATION]], [[SOUTH_M2REDUCED]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SOUTH_TGRADIENT />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=SOUTH_M2FLATHER />
-<section begin=SOUTH_TNUDGING />;<span id="SOUTH_TNUDGING"></span>'''[[SOUTH_TNUDGING]]'''
+<section begin=SOUTH_M2GRADIENT />;<span id="SOUTH_M2GRADIENT"></span>[[SOUTH_M2GRADIENT]]
-:Option to
+:Option to use 2D momentum gradient condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M2GRADIENT]], [[NORTH_M2GRADIENT]], [[WEST_M2GRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_M2CLAMPED]], [[SOUTH_M2FLATHER]], [[SOUTH_M2NUDGING]], [[SOUTH_M2RADIATION]], [[SOUTH_M2REDUCED]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SOUTH_TNUDGING />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=SOUTH_M2GRADIENT />
-<section begin=SOUTH_TRADIATION />;<span id="SOUTH_TRADIATION"></span>'''[[SOUTH_TRADIATION]]'''
+<section begin=SOUTH_M2NUDGING />;<span id="SOUTH_M2NUDGING"></span>[[SOUTH_M2NUDGING]]
-:Option to
+:Option to use 2D momentum passive/active nudging term for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M2NUDGING]], [[NORTH_M2NUDGING]], [[WEST_M2NUDGING]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_M2CLAMPED]], [[SOUTH_M2FLATHER]], [[SOUTH_M2GRADIENT]], [[SOUTH_M2REDUCED]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SOUTH_TRADIATION />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=SOUTH_M2NUDGING />
-<section begin=SOUTH_VOLCONS />;<span id="SOUTH_VOLCONS"></span>'''[[SOUTH_VOLCONS]]'''
+<section begin=SOUTH_M2RADIATION />;<span id="SOUTH_M2RADIATION"></span>[[SOUTH_M2RADIATION]]
-:Option to
+:Option to use 2D momentum radiation condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M2RADIATION]], [[NORTH_M2RADIATION]], [[WEST_M2RADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_M2CLAMPED]], [[SOUTH_M2FLATHER]], [[SOUTH_M2GRADIENT]], [[SOUTH_M2REDUCED]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SOUTH_VOLCONS />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=SOUTH_M2RADIATION />
-<section begin=SOUTHERN_WALL />;<span id="SOUTHERN_WALL"></span>'''[[SOUTHERN_WALL]]'''
+<section begin=SOUTH_M2REDUCED />;<span id="SOUTH_M2REDUCED"></span>[[SOUTH_M2REDUCED]]
-:Option to
+:Option to use 2D momentum reduced-physics for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M2REDUCED]], [[NORTH_M2REDUCED]], [[WEST_M2REDUCED]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_M2CLAMPED]], [[SOUTH_M2FLATHER]], [[SOUTH_M2GRADIENT]], [[SOUTH_M2NUDGING]], [[SOUTH_M2RADIATION]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SOUTHERN_WALL />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=SOUTH_M2REDUCED />
-<section begin=SO_SEMI />;<span id="SO_SEMI"></span>'''[[SO_SEMI]]'''
+<section begin=SOUTH_M3CLAMPED />;<span id="SOUTH_M3CLAMPED"></span>[[SOUTH_M3CLAMPED]]
-:Option to
+:Option to use 3D momentum clamped condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M3CLAMPED]], [[NORTH_M3CLAMPED]], [[WEST_M3CLAMPED]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_M3GRADIENT]], [[SOUTH_M3NUDGING]], [[SOUTH_M3RADIATION]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SO_SEMI />
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=SOUTH_M3CLAMPED />
-<section begin=SO_SEMI_WHITE />;<span id="SO_SEMI_WHITE"></span>'''[[SO_SEMI_WHITE]]'''
+<section begin=SOUTH_M3GRADIENT />;<span id="SOUTH_M3GRADIENT"></span>[[SOUTH_M3GRADIENT]]
-:Option to
+:Option to use 3D momentum gradient condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M3GRADIENT]], [[NORTH_M3GRADIENT]], [[WEST_M3GRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_M3CLAMPED]], [[SOUTH_M3NUDGING]], [[SOUTH_M3RADIATION]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SO_SEMI_WHITE />
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=SOUTH_M3GRADIENT />
-<section begin=SO_TRACE />;<span id="SO_TRACE"></span>'''[[SO_TRACE]]'''
+<section begin=SOUTH_M3NUDGING />;<span id="SOUTH_M3NUDGING"></span>[[SOUTH_M3NUDGING]]
-:Option to
+:Option to use 3D momentum passive/active nudging term for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M3NUDGING]], [[NORTH_M3NUDGING]], [[WEST_M3NUDGING]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_M3CLAMPED]], [[SOUTH_M3GRADIENT]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SO_TRACE />
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=SOUTH_M3NUDGING />
-<section begin=SPLINES />;<span id="SPLINES"></span>'''[[SPLINES]]'''
+<section begin=SOUTH_M3RADIATION />;<span id="SOUTH_M3RADIATION"></span>[[SOUTH_M3RADIATION]]
-:Option to
+:Option to use 3D momentum radiation condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M3RADIATION]], [[NORTH_M3RADIATION]], [[WEST_M3RADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_M3CLAMPED]], [[SOUTH_M3GRADIENT]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SPLINES />
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=SOUTH_M3RADIATION />
-<section begin=SPHERICAL />;<span id="SPHERICAL"></span>'''[[SPHERICAL]]'''
+<section begin=SOUTH_TCLAMPED />;<span id="SOUTH_TCLAMPED"></span>[[SOUTH_TCLAMPED]]
-:Option to
+:Option to use tracer clamped condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_TCLAMPED]], [[NORTH_TCLAMPED]], [[WEST_TCLAMPED]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_TGRADIENT]], [[SOUTH_TNUDGING]], [[SOUTH_TRADIATION]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SPHERICAL />
+:'''routine = ''' [[t3dbc_im.F]]<section end=SOUTH_TCLAMPED />
-<section begin=SPONGE />;<span id="SPONGE"></span>'''[[SPONGE]]'''
+<section begin=SOUTH_TGRADIENT />;<span id="SOUTH_TGRADIENT"></span>[[SOUTH_TGRADIENT]]
-:Option to
+:Option to use tracer gradient condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_TGRADIENT]], [[NORTH_TGRADIENT]], [[WEST_TGRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_TCLAMPED]], [[SOUTH_TNUDGING]], [[SOUTH_TRADIATION]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SPONGE />
+:'''routine = ''' [[t3dbc_im.F]]<section end=SOUTH_TGRADIENT />
-<section begin=SRELAXATION />;<span id="SRELAXATION"></span>'''[[SRELAXATION]]'''
+<section begin=SOUTH_TNUDGING />;<span id="SOUTH_TNUDGING"></span>[[SOUTH_TNUDGING]]
-:Option to
+:Option to use tracer passive/active nudging term for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_TNUDGING]], [[NORTH_TNUDGING]], [[WEST_TNUDGING]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_TCLAMPED]], [[SOUTH_TGRADIENT]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SRELAXATION />
+:'''routine = ''' [[t3dbc_im.F]]<section end=SOUTH_TNUDGING />
-<section begin=SSH_TIDES />;<span id="SSH_TIDES"></span>'''[[SSH_TIDES]]'''
+<section begin=SOUTH_TRADIATION />;<span id="SOUTH_TRADIATION"></span>[[SOUTH_TRADIATION]]
-:Option to
+:Option to use tracer radiation condition for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_TRADIATION]], [[NORTH_TRADIATION]], [[WEST_TRADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_TCLAMPED]], [[SOUTH_TGRADIENT]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SSH_TIDES />
+:'''routine = ''' [[t3dbc_im.F]]<section end=SOUTH_TRADIATION />
-<section begin=SSW_BBL />;<span id="SSW_BBL"></span>'''[[SSW_BBL]]'''
+<section begin=SOUTH_VOLCONS />;<span id="SOUTH_VOLCONS"></span>[[SOUTH_VOLCONS]]
-:Option to
+:Option to use Southern edge mass conservation enforcement for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_VOLCONS]], [[NORTH_VOLCONS]], [[WEST_VOLCONS]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTHERN_WALL]]
-:'''routine = '''  <section end=SSW_BBL />
+:'''routine = ''' [[obc_volcons.F]]<section end=SOUTH_VOLCONS />
-<section begin=SSW_CALC_ZNOT />;<span id="SSW_CALC_ZNOT"></span>'''[[SSW_CALC_ZNOT]]'''
+<section begin=SOUTHERN_WALL />;<span id="SOUTHERN_WALL"></span>[[SOUTHERN_WALL]]
-:Option to
+:Option to use Southern edge closed wall for the southern open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_WALL]], [[NORTH_WALL]], [[WEST_WALL]]
-:'''conflict = '''
+:'''conflict = ''' [[NS_PERIODIC]], [[SOUTH_FSCLAMPED]], [[SOUTH_FSCHAPMAN]], [[SOUTH_FSGRADIENT]], [[SOUTH_FSNUDGING]], [[SOUTH_FSRADIATION]], [[SOUTH_KGRADIENT]], [[SOUTH_KRADIATION]], [[SOUTH_M2CLAMPED]], [[SOUTH_M2FLATHER]], [[SOUTH_M2GRADIENT]], [[SOUTH_M2NUDGING]], [[SOUTH_M2RADIATION]], [[SOUTH_M2REDUCED]], [[SOUTH_M3CLAMPED]], [[SOUTH_M3GRADIENT]], [[SOUTH_M3NUDGING]], [[SOUTH_M3RADIATION]], [[SOUTH_TCLAMPED]], [[SOUTH_TGRADIENT]], [[SOUTH_TNUDGING]], [[SOUTH_TRADIATION]], [[SOUTH_VOLCONS]]
-:'''routine = '''  <section end=SSW_CALC_ZNOT />
+:'''routine = ''' [[t3dbc_im.F]], [[tkebc_im.F]], [[u2dbc_im.F]], [[u3dbc_im.F]], [[v2dbc_im.F]], [[v3dbc_im.F]], [[zetabc.F]]<section end=SOUTHERN_WALL />
-<section begin=SSW_LOGINT />;<span id="SSW_LOGINT"></span>'''[[SSW_LOGINT]]'''
+<section begin=SPLINES />;<span id="SPLINES"></span>[[SPLINES]]
 :Option to
 :'''parameter = '''
@@ Line 2,660: / Line 3,077: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SSW_LOGINT />
+:'''routine = '''  <section end=SPLINES />
-<section begin=STATIONS />;<span id="STATIONS"></span>'''[[STATIONS]]'''
+<section begin=SPLINES_VCONV />;<span id="SPLINES_VCONV"></span>[[SPLINES_VCONV]]
 :Option to
 :'''parameter = '''
@@ Line 2,669: / Line 3,086: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=STATIONS />
+:'''routine = '''  <section end=SPLINES_VCONV />
-<section begin=STATIONS_CGRID />;<span id="STATIONS_CGRID"></span>'''[[STATIONS_CGRID]]'''
+<section begin=SPHERICAL />;<span id="SPHERICAL"></span>[[SPHERICAL]]
 :Option to
 :'''parameter = '''
@@ Line 2,678: / Line 3,095: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=STATIONS_CGRID />
+:'''routine = '''  <section end=SPHERICAL />
-<section begin=STOCHASTIC_OPT />;<span id="STOCHASTIC_OPT"></span>'''[[STOCHASTIC_OPT]]'''
+<section begin=SPONGE />;<span id="SPONGE"></span>[[SPONGE]]
-:Option to
+:'''DEPRICATED''' in favor of [[Variables#LuvSponge|LuvSponge]] and [[Variables#LtracerSponge|LtracerSponge]] logical switches to facilitate nesting.<br /><br />Option to impose a sponge layer near the lateral boundary. Used in areas of enhanced viscosity/diffusion.
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,687: / Line 3,104: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=STOCHASTIC_OPT />
+:'''routine = '''  <section end=SPONGE />
-<section begin=SUSPLOAD />;<span id="SUSPLOAD"></span>'''[[SUSPLOAD]]'''
+<section begin=SRELAXATION />;<span id="SRELAXATION"></span>[[SRELAXATION]]
 :Option to
 :'''parameter = '''
@@ Line 2,696: / Line 3,113: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=SUSPLOAD />
+:'''routine = '''  <section end=SRELAXATION />
-<section begin=S4DVAR />;<span id="S4DVAR"></span>'''[[S4DVAR]]'''
+<section begin=SSH_TIDES />;<span id="SSH_TIDES"></span>[[SSH_TIDES]]
-:Option to
+:Option to impose tidal elevation for tidal forcing at the open boundaries.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[ADD_FSOBC]], [[FSOBC_REDUCED]], [[RAMP_TIDES]]
 :'''conflict = '''
-:'''routine = '''  <section end=S4DVAR />
+:'''routine = '''  <section end=SSH_TIDES />
-==<span class="alphabet">T</span>==
+<section begin=SSW_BBL />;<span id="SSW_BBL"></span>[[SSW_BBL]]
+:Option to use the Sherwood/Signell/Warner bottom boundary layer closure.
+:'''parameter = '''
+:'''parent = '''
+:'''required = ''' [[BBL_MODEL]]
+:'''related = ''' [[SSW_CALC_UB]], [[SSW_CALC_ZNOT]], [[SSW_FORM_DRAG_COR]], [[SSW_LOGINT]], [[SSW_ZOBIO]], [[SSW_ZOBL]], [[SSW_ZORIP]]
+:'''conflict = ''' [[SG_BBL]], [[MB_BBL]]
+:'''routine = ''' [[bbl.F]], [[ssw_bbl.h]]<section end=SSW_BBL />
-<section begin=TALK_PROGNOSTIC />;<span id="TALK_PROGNOSTIC"></span>'''[[TALK_PROGNOSTIC]]'''
+<section begin=SSW_CALC_UB />;<span id="SSW_CALC_UB"></span>[[SSW_CALC_UB]]
-:Option to activate prognostic computation of alkalinity.
+:Option to compute bottom orbital velocity internally for the Sherwood/Signell/Warner bottom boundary layer closure.
-:'''parent = ''' [[BIO_FASHAM]]
+:'''parameter = '''
-:'''required = ''' [[CARBON]]
+:'''parent = ''' [[SSW_BBL]]
-:'''routine = ''' [[fasham.h]]<section end=TALK_PROGNOSTIC />
+:'''required = ''' [[BBL_MODEL]], [[SSW_BBL]]
+:'''related = ''' [[SSW_CALC_ZNOT]], [[SSW_FORM_DRAG_COR]], [[SSW_LOGINT]], [[SSW_ZOBIO]], [[SSW_ZOBL]], [[SSW_ZORIP]]
+:'''conflict = '''
+:'''routine = ''' [[ssw_bbl.h]]<section end=SSW_CALC_UB />
-<section begin=TANGENT />;<span id="TANGENT"></span>'''[[TANGENT]]'''
+<section begin=SSW_CALC_ZNOT />;<span id="SSW_CALC_ZNOT"></span>[[SSW_CALC_ZNOT]]
-:Option to
+:Option to compute bottom roughness internally for the Sherwood/Signell/Warner bottom boundary layer closure.
+:'''parameter = '''
+:'''parent = ''' [[SSW_BBL]]
+:'''required = ''' [[BBL_MODEL]], [[SSW_BBL]]
+:'''related = ''' [[SSW_CALC_UB]], [[SSW_FORM_DRAG_COR]], [[SSW_LOGINT]], [[SSW_ZOBIO]], [[SSW_ZOBL]], [[SSW_ZORIP]]
+:'''conflict = '''
+:'''routine = ''' [[ssw_bbl.h]]<section end=SSW_CALC_ZNOT />
+<section begin=SSW_FORM_DRAG_COR />;<span id="SSW_FORM_DRAG_COR"></span>[[SSW_FORM_DRAG_COR]]
+:Option to activate form drag coefficient for the Sherwood/Signell/Warner bottom boundary layer closure.
+:'''parameter = '''
+:'''parent = ''' [[SSW_BBL]]
+:'''required = ''' [[BBL_MODEL]], [[SSW_BBL]]
+:'''related = ''' [[SSW_CALC_UB]], [[SSW_CALC_ZNOT]], [[SSW_LOGINT]], [[SSW_ZOBIO]], [[SSW_ZOBL]], [[SSW_ZORIP]]
+:'''conflict = '''
+:'''routine = ''' [[ssw_bbl.h]]<section end=SSW_FORM_DRAG_COR />
+<section begin=SSW_LOGINT />;<span id="SSW_LOGINT"></span>[[SSW_LOGINT]]
+:Option to use logarithmic interpolation of ([[Variables#Ur|Ur]],[[Variables#Vr|Vr]]) for the Sherwood/Signell/Warner bottom boundary layer closure.
+:'''parameter = '''
+:'''parent = ''' [[SSW_BBL]]
+:'''required = ''' [[BBL_MODEL]], [[SSW_BBL]]
+:'''related = ''' [[SSW_CALC_UB]], [[SSW_CALC_ZNOT]], [[SSW_FORM_DRAG_COR]], [[SSW_ZOBIO]], [[SSW_ZOBL]], [[SSW_ZORIP]]
+:'''conflict = '''
+:'''routine = ''' [[ssw_bbl.h]]<section end=SSW_LOGINT />
+<section begin=SSW_ZOBIO />;<span id="SSW_ZOBIO"></span>[[SSW_ZOBIO]]
+:Option to use biogenic bedform roughness from ripples for the Sherwood/Signell/Warner bottom boundary layer closure.
+:'''parameter = '''
+:'''parent = ''' [[SSW_BBL]]
+:'''required = ''' [[BBL_MODEL]], [[SSW_BBL]]
+:'''related = ''' [[SSW_CALC_UB]], [[SSW_CALC_ZNOT]], [[SSW_FORM_DRAG_COR]], [[SSW_LOGINT]], [[SSW_ZOBL]], [[SSW_ZORIP]]
+:'''conflict = '''
+:'''routine = ''' [[ssw_bbl.h]]<section end=SSW_ZOBIO />
+<section begin=SSW_ZOBL />;<span id="SSW_ZOBL"></span>[[SSW_ZOBL]]
+:Option to use bedload roughness for ripples for the Sherwood/Signell/Warner bottom boundary layer closure.
+:'''parameter = '''
+:'''parent = ''' [[SSW_BBL]]
+:'''required = ''' [[BBL_MODEL]], [[SSW_BBL]]
+:'''related = ''' [[SSW_CALC_UB]], [[SSW_CALC_ZNOT]], [[SSW_FORM_DRAG_COR]], [[SSW_LOGINT]], [[SSW_ZOBIO]], [[SSW_ZORIP]]
+:'''conflict = '''
+:'''routine = ''' [[ssw_bbl.h]]<section end=SSW_ZOBL />
+<section begin=SSW_ZORIP />;<span id="SSW_ZORIP"></span>[[SSW_ZORIP]]
+:Option to use bedform roughness from ripples for the Sherwood/Signell/Warner bottom boundary layer closure.
+:'''parameter = '''
+:'''parent = ''' [[SSW_BBL]]
+:'''required = ''' [[BBL_MODEL]], [[SSW_BBL]]
+:'''related = ''' [[SSW_CALC_UB]], [[SSW_CALC_ZNOT]], [[SSW_FORM_DRAG_COR]], [[SSW_LOGINT]], [[SSW_ZOBIO]], [[SSW_ZOBL]]
+:'''conflict = '''
+:'''routine = ''' [[ssw_bbl.h]]<section end=SSW_ZORIP />
+<section begin=STATIONS />;<span id="STATIONS"></span>[[STATIONS]]
+:Option to activate writing out station data
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,722: / Line 3,203: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TANGENT />
+:'''routine = ''' [[stations.in]]<section end=STATIONS />
-<section begin=TCLIMATOLOGY />;<span id="TCLIMATOLOGY"></span>'''[[TCLIMATOLOGY]]'''
+<section begin=STATIONS_CGRID />;<span id="STATIONS_CGRID"></span>[[STATIONS_CGRID]]
 :Option to
 :'''parameter = '''
@@ Line 2,731: / Line 3,212: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TCLIMATOLOGY />
+:'''routine = '''  <section end=STATIONS_CGRID />
-<section begin=TCLM_NUDGING />;<span id="TCLM_NUDGING"></span>'''[[TCLM_NUDGING]]'''
+<section begin=STOCHASTIC_OPT />;<span id="STOCHASTIC_OPT"></span>[[STOCHASTIC_OPT]]
 :Option to
 :'''parameter = '''
@@ Line 2,740: / Line 3,221: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TCLM_NUDGING />
+:'''routine = '''  <section end=STOCHASTIC_OPT />
+<section begin=SUBOBJECT_DEALLOCATION />;<span id="SUBOBJECT_DEALLOCATION"></span>[[SUBOBJECT_DEALLOCATION]]
+:Option to de-allocate each pointer variable within a structure object individually. This option is mostly to maintain backwards compatibility with older versions of Fortran compilers that don't contain the '''Fortran 2003''' standards. If your compiler is '''Fortran 2003''' capable, we do not recommend activating this option. See Trac ticket [https://www.myroms.org/projects/src/ticket/897 #897] for more details.
+:'''routines = ''' [[mod_average.F]], [[mod_bbl.F]], [[mod_boundary.F]], [[mod_clima.F]], [[mod_coupling.F]], [[mod_diags.F]], [[mod_floats.F]], [[mod_forces.F]], [[mod_grid.F]], [[mod_mixing.F]], [[mod_nesting.F]], [[mod_ocean.F]], [[mod_param.F]], [[mod_scalars.F]], [[mod_sedbed_mod.h]], [[mod_sources.F]], [[mod_storage.F]], and [[mod_tides.F]] <section end=SUBOBJECT_DEALLOCATION />
-<section begin=TKE_DIF2 />;<span id="TKE_DIF2"></span>'''[[TKE_DIF2]]'''
+<section begin=SUSPLOAD />;<span id="SUSPLOAD"></span>[[SUSPLOAD]]
 :Option to
 :'''parameter = '''
@@ Line 2,749: / Line 3,234: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TKE_DIF2 />
+:'''routine = '''  <section end=SUSPLOAD />
-<section begin=TKE_DIF4 />;<span id="TKE_DIF4"></span>'''[[TKE_DIF4]]'''
+<section begin=SWAN_COUPLING />;<span id="SWAN_COUPLING"></span>[[SWAN_COUPLING]]
 :Option to
 :'''parameter = '''
@@ Line 2,758: / Line 3,243: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TKE_DIF4 />
+:'''routine = '''  <section end=SWAN_COUPLING />
+==<span class="alphabet">T</span>==
-<section begin=TLM_CHECK />;<span id="TLM_CHECK"></span>'''[[TLM_CHECK]]'''
+<section begin=T_PASSIVE />;<span id="T_PASSIVE"></span>[[T_PASSIVE]]
 :Option to
 :'''parameter = '''
@@ Line 2,767: / Line 3,254: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TLM_CHECK />
+:'''routine = '''  <section end=T_PASSIVE />
-<section begin=TLM_DRIVER />;<span id="TLM_DRIVER"></span>'''[[TLM_DRIVER]]'''
+<section begin=TALK_NONCONSERV />;<span id="TALK_NONCONSERV"></span>[[TALK_NONCONSERV]]
 :Option to
 :'''parameter = '''
@@ Line 2,776: / Line 3,263: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TLM_DRIVER />
+:'''routine = '''  <section end=TALK_NONCONSERV />
+<section begin=TALK_PROGNOSTIC />;<span id="TALK_PROGNOSTIC"></span>[[TALK_PROGNOSTIC]]
+:Option to activate prognostic computation of alkalinity.
+:'''parent = ''' [[BIO_FENNEL]]
+:'''required = ''' [[CARBON]]
+:'''routine = ''' [[fennel.h]]<section end=TALK_PROGNOSTIC />
-<section begin=THREE_GHOST />;<span id="THREE_GHOST"></span>'''[[THREE_GHOST]]'''
+<section begin=TANGENT />;<span id="TANGENT"></span>[[TANGENT]]
 :Option to
 :'''parameter = '''
@@ Line 2,785: / Line 3,278: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=THREE_GHOST />
+:'''routine = '''  <section end=TANGENT />
-<section begin=TL_IOMS />;<span id="TL_IOMS"></span>'''[[TL_IOMS]]'''
+<section begin=TCLIMATOLOGY />;<span id="TCLIMATOLOGY"></span>[[TCLIMATOLOGY]]
-:Option to
+:'''DEPRICATED''' in favor of [[Variables#LtracerCLM|LtracerCLM]] logical switches to facilitate nesting.<br /><br />Option to read and process tracers in climatology fields.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[ANA_TCLIMA]], [[TCLM_NUDGING]]
 :'''conflict = '''
-:'''routine = '''  <section end=TL_IOMS />
+:'''routine = '''  <section end=TCLIMATOLOGY />
-<section begin=TS_MPDATA />;<span id="TS_MPDATA"></span>'''[[TS_MPDATA]]'''
+<section begin=TCLM_NUDGING />;<span id="TCLM_NUDGING"></span>[[TCLM_NUDGING]]
-:Option to
+:Option to use nudging for tracer climatology data (primarily in sponge areas).
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[ANA_TCLIMA]], [[TCLIMATOLOGY]]
 :'''conflict = '''
-:'''routine = '''  <section end=TS_MPDATA />
+:'''routine = '''  <section end=TCLM_NUDGING />
-<section begin=TS_A4HADVECTION />;<span id="TS_A4HADVECTION"></span>'''[[TS_A4HADVECTION]]'''
+<section begin=TEST_CHAN />;<span id="TEST_CHAN"></span>[[TEST_CHAN]]
 :Option to
 :'''parameter = '''
@@ Line 2,812: / Line 3,305: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TS_A4HADVECTION />
+:'''routine = '''  <section end=TEST_CHAN />
-<section begin=TS_A4VADVECTION />;<span id="TS_A4VADVECTION"></span>'''[[TS_A4VADVECTION]]'''
+<section begin=TEST_HEAD />;<span id="TEST_HEAD"></span>[[TEST_HEAD]]
 :Option to
 :'''parameter = '''
@@ Line 2,821: / Line 3,314: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TS_A4VADVECTION />
+:'''routine = '''  <section end=TEST_HEAD />
-<section begin=TS_C2HADVECTION />;<span id="TS_C2HADVECTION"></span>'''[[TS_C2HADVECTION]]'''
+<section begin=THREE_GHOST />;<span id="THREE_GHOST"></span>[[THREE_GHOST]]
 :Option to
 :'''parameter = '''
@@ Line 2,830: / Line 3,323: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TS_C2HADVECTION />
+:'''routine = '''  <section end=THREE_GHOST />
-<section begin=TS_C2VADVECTION />;<span id="TS_C2VADVECTION"></span>'''[[TS_C2VADVECTION]]'''
+<section begin=TKE_DIF2 />;<span id="TKE_DIF2"></span>[[TKE_DIF2]]
 :Option to
 :'''parameter = '''
@@ Line 2,839: / Line 3,332: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TS_C2VADVECTION />
+:'''routine = '''  <section end=TKE_DIF2 />
-<section begin=TS_C4HADVECTION />;<span id="TS_C4HADVECTION"></span>'''[[TS_C4HADVECTION]]'''
+<section begin=TKE_DIF4 />;<span id="TKE_DIF4"></span>[[TKE_DIF4]]
 :Option to
 :'''parameter = '''
@@ Line 2,848: / Line 3,341: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TS_C4HADVECTION />
+:'''routine = '''  <section end=TKE_DIF4 />
-<section begin=TS_C4VADVECTION />;<span id="TS_C4VADVECTION"></span>'''[[TS_C4VADVECTION]]'''
+<section begin=TKE_WAVEDISS />;<span id="TKE_WAVEDISS"></span>[[TKE_WAVEDISS]]
-:Option to
+:Option to use wave breaking surface flux from wave amplitude for the Generic Length-Scale closure ([[Bibliography#WarnerJC_2005a|Warner ''et al.'', 2005]]).
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,857: / Line 3,350: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TS_C4VADVECTION />
+:'''routine = '''  <section end=TKE_WAVEDISS />
-<section begin=TS_DIF2 />;<span id="TS_DIF2"></span>'''[[TS_DIF2]]'''
+<section begin=TL_R4DVAR />;<span id="TL_R4DVAR"></span>[[TL_R4DVAR]] (Formerly TL_W4DVAR)
-:Option to
+:Option to activate tangent linearization of the R4D-Var data assimilation system.
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,866: / Line 3,359: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TS_DIF2 />
+:'''routine = ''' [[tl_r4dvar_ocean.h]] <section end=TL_R4DVAR />
-<section begin=TS_DIF4 />;<span id="TS_DIF4"></span>'''[[TS_DIF4]]'''
+<section begin=TL_RBL4DVAR />;<span id="TL_RBL4DVAR"></span>[[TL_RBL4DVAR]] (Formerly TL_W4DPSAS)
-:Option to
+:Option to activate tangent linearization of the RBL4D-Var data assimilation system.
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,875: / Line 3,368: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TS_DIF4 />
+:'''routine = ''' [[tl_rbl4dvar_ocean.h]] <section end=TL_RBL4DVAR />
-<section begin=TS_FIXED />;<span id="TS_FIXED"></span>'''[[TS_FIXED]]'''
+<section begin=TL_W4DPSAS />;<span id="TL_W4DPSAS"></span>[[TL_W4DPSAS]] <span class="red">OBSOLETE - Renamed to [[Options#TL_RBL4DVAR|TL_RBL4DVAR]] in SVN revision 1022</span>
-:Option to
+:Option to activate tangent linearization of the W4DPSAS data assimilation system.
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,884: / Line 3,377: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TS_FIXED />
+:'''routine = ''' [[tl_w4dpsas_ocean.h]] <section end=TL_W4DPSAS />
-<section begin=TS_PSOURCE />;<span id="TS_PSOURCE"></span>'''[[TS_PSOURCE]]'''
+<section begin=TL_W4DVAR />;<span id="TL_W4DVAR"></span>[[TL_W4DVAR]] <span class="red">OBSOLETE - Renamed to [[Options#TL_R4DVAR|TL_R4DVAR]] in SVN revision 1022</span>
-:Option to
+:Option to activate tangent linearization of the W4DVAR data assimilation system.
 :'''parameter = '''
 :'''parent = '''
@@ Line 2,893: / Line 3,386: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TS_PSOURCE />
+:'''routine = ''' [[tl_w4dvar_ocean.h]] <section end=TL_W4DPSAS />
-<section begin=TS_SVADVECTION />;<span id="TS_SVADVECTION"></span>'''[[TS_SVADVECTION]]'''
+<section begin=TLM_CHECK />;<span id="TLM_CHECK"></span>[[TLM_CHECK]]
 :Option to
 :'''parameter = '''
@@ Line 2,902: / Line 3,395: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TS_SVADVECTION />
+:'''routine = '''  <section end=TLM_CHECK />
-<section begin=TS_U3HADVECTION />;<span id="TS_U3HADVECTION"></span>'''[[TS_U3HADVECTION]]'''
+<section begin=TLM_DRIVER />;<span id="TLM_DRIVER"></span>[[TLM_DRIVER]]
 :Option to
 :'''parameter = '''
@@ Line 2,911: / Line 3,404: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=TS_U3HADVECTION />
+:'''routine = '''  <section end=TLM_DRIVER />
-<section begin=T_PASSIVE />;<span id="T_PASSIVE"></span>'''[[T_PASSIVE]]'''
+<section begin=TS_A4HADVECTION />;<span id="TS_A4HADVECTION"></span>[[TS_A4HADVECTION]]
 :Option to
 :'''parameter = '''
@@ Line 2,920: / Line 3,413: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=T_PASSIVE />
+:'''routine = '''  <section end=TS_A4HADVECTION />
-==<span class="alphabet">U</span>==
+<section begin=TS_A4VADVECTION />;<span id="TS_A4VADVECTION"></span>[[TS_A4VADVECTION]]
+:Option to
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = '''
+:'''conflict = '''
+:'''routine = '''  <section end=TS_A4VADVECTION />
-<section begin=UPWELLING />;<span id="UPWELLING"></span>'''[[UPWELLING]]'''
+<section begin=TS_C2HADVECTION />;<span id="TS_C2HADVECTION"></span>[[TS_C2HADVECTION]]
 :Option to
 :'''parameter = '''
@@ Line 2,931: / Line 3,431: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=UPWELLING />
+:'''routine = '''  <section end=TS_C2HADVECTION />
-<section begin=UV_ADV />;<span id="UV_ADV"></span>'''[[UV_ADV]]'''
+<section begin=TS_C2VADVECTION />;<span id="TS_C2VADVECTION"></span>[[TS_C2VADVECTION]]
-:Option to activate/deactivate horizontal and vertical advection of momentum.  If no additional options are specified, the default is to discretize the horizontal momentum with a third-order upstream bias advection scheme with velocity dependent hyper-viscosity and the vertical momentum with a fourth-order, centered differences scheme. Since there is some implicit viscosity associated with the default discretization, the user may avoid adding an explicity vicosity to the solution to suppress excisive smoothing.
+:Option to
-:'''routine = ''' [[step2d.F]], [[rhs3d.F]]<section end=UV_ADV />
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = '''
+:'''conflict = '''
+:'''routine = '''  <section end=TS_C2VADVECTION />
-<section begin=UV_BAROCLINIC />;<span id="UV_BAROCLINIC"></span>'''[[UV_BAROCLINIC]]'''
+<section begin=TS_C4HADVECTION />;<span id="TS_C4HADVECTION"></span>[[TS_C4HADVECTION]]
 :Option to
 :'''parameter = '''
@@ Line 2,944: / Line 3,449: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=UV_BAROCLINIC />
+:'''routine = '''  <section end=TS_C4HADVECTION />
-<section begin=UV_COR />;<span id="UV_COR"></span>'''[[UV_COR]]'''
+<section begin=TS_C4VADVECTION />;<span id="TS_C4VADVECTION"></span>[[TS_C4VADVECTION]]
-:Option to activate/deactivate Coriolis acceleration term in momentum equations.
+:Option to
-:'''routine = ''' [[step2d.F]], [[rhs3d.F]]<section end=UV_COR />
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = '''
+:'''conflict = '''
+:'''routine = '''  <section end=TS_C4VADVECTION />
-<section begin=UV_C2ADVECTION />;<span id="UV_C2ADVECTION"></span>'''[[UV_C2ADVECTION]]'''
+<section begin=TS_DIF2 />;<span id="TS_DIF2"></span>[[TS_DIF2]]
-:Option to use second-order, centered, finite differences in advection of momentum.
+:Option to
-:'''parent = ''' [[UV_ADV]]
+:'''parameter = '''
-:'''conflit = ''' [[UV_C4ADVECTION]]<section end=UV_C2ADVECTION />
+:'''parent = '''
+:'''required = '''
+:'''related = '''
+:'''conflict = '''
+:'''routine = '''  <section end=TS_DIF2 />
-<section begin=UV_C4ADVECTION />;<span id="UV_C4ADVECTION"></span>'''[[UV_C4ADVECTION]]'''
+<section begin=TS_DIF4 />;<span id="TS_DIF4"></span>[[TS_DIF4]]
-:Option to use fourth-order, centered, finite differences in advection of momentum.
+:Option to
-:'''parent = ''' [[UV_ADV]]
+:'''parameter = '''
-:'''conflit = ''' [[UV_C2ADVECTION]]<section end=UV_C4ADVECTION />
+:'''parent = '''
+:'''required = '''
+:'''related = '''
+:'''conflict = '''
+:'''routine = '''  <section end=TS_DIF4 />
-<section begin=UV_LDRAG />;<span id="UV_LDRAG"></span>'''[[UV_LDRAG]]'''
+<section begin=TS_FIXED />;<span id="TS_FIXED"></span>[[TS_FIXED]]
-:Option to activate/deactivate linear bottom friction of momentum.
+:Option to
-:'''parameter = ''' [[Variables#rdrg | rdrg(ng)]]
+:'''parameter = '''
-:'''confict = ''' [[BBL_MODEL]], [[UV_LOGDRAG]], [[UV_QDRAG]]
+:'''parent = '''
-:'''routine = ''' [[set_vbc.F]]<section end=UV_LDRAG />
+:'''required = '''
+:'''related = '''
+:'''conflict = '''
+:'''routine = '''  <section end=TS_FIXED />
-<section begin=UV_LOGDRAG />;<span id="UV_LOGDRAG"></span>'''[[UV_LOGDRAG]]'''
+<section begin=TS_MPDATA />;<span id="TS_MPDATA"></span>[[TS_MPDATA]]
-:Option to activate/deactivate logarithmic bottom friction of momentum.
+:Option to
-:'''parameter = ''' [[Variables#Zob | Zob(ng)]]
+:'''parameter = '''
-:'''required = ''' [[SOLVE3D]]
+:'''parent = '''
-:'''confict = ''' [[BBL_MODEL]], [[UV_LDRAG]], [[UV_QDRAG]]
+:'''required = '''
-:'''routine = ''' [[set_vbc.F]]<section end=UV_LOGDRAG />
+:'''related = '''
+:'''conflict = '''
+:'''routine = '''  <section end=TS_MPDATA />
-<section begin=UV_PSOURCE />;<span id="UV_PSOURCE"></span>'''[[UV_PSOURCE]]'''
+<section begin=TS_PSOURCE />;<span id="TS_PSOURCE"></span>[[TS_PSOURCE]] ('''OBSOLETE as of revision 701''')
-:Option to activate/deactivate point sources/sinks of momentum. This option is used to specify the mass transport in river runoff.
+:Option to
-:'''variable = ''' [[Variables#Dsrc | Dsrc(1:Nsrc)]], [[Variables#Qsrc | Qsrc(1:Nsrc,k)]]
+:'''parameter = '''
-:'''related = ''' [[ANA_PSOURCE]], [[TS_PSOURCE]]
+:'''parent = '''
-:'''confict = ''' [[BBL_MODEL]], [[UV_LOGDRAG]], [[UV_QDRAG]]
+:'''required = '''
-:'''routine = ''' [[step2d.F]], [[step3d_uv.F]]<section end=UV_PSOURCE />
+:'''related = '''
+:'''conflict = '''
+:'''routine = '''  <section end=TS_PSOURCE />
-<section begin=UV_QDRAG />;<span id="UV_QDRAG"></span>'''[[UV_QDRAG]]'''
+<section begin=TS_SMAGORINSKY />;<span id="TS_SMAGORINSKY"></span>[[TS_SMAGORINSKY]]
-:Option to activate/deactivate quadratic bottom friction of momentum.
+:Option to
-:'''parameter = ''' [[Variables#rdrg2 | rdrg2(ng)]]
+:'''parameter = '''
-:'''confict = ''' [[BBL_MODEL]], [[UV_LDRAG]], [[UV_LOGDRAG]]
+:'''parent = '''
-:'''routine = ''' [[set_vbc.F]]<section end=UV_QDRAG />
+:'''required = '''
+:'''related = ''' [[UV_SMAGORINSKY]]
+:'''conflict = '''
+:'''routine = '''  <section end=TS_SMAGORINSKY />
-<section begin=UV_SADVECTION />;<span id="UV_SADVECTION"></span>'''[[UV_SADVECTION]]'''
+<section begin=TS_SVADVECTION />;<span id="TS_SVADVECTION"></span>[[TS_SVADVECTION]]
-:Option to use conservative, parabolic splines discretization of momentum vertical advection. This scheme requires high vertical resolution so it is recommended to use this option in shallow, coastal applications.
-:'''parent = ''' [[UV_ADV]]
-:'''conflit = ''' [[UV_C2ADVECTION]], [[UV_C4ADVECTION]]<section end=UV_SADVECTION />
-<section begin=UV_TIDES />;<span id="UV_TIDES"></span>'''[[UV_TIDES]]'''
 :Option to
 :'''parameter = '''
@@ Line 2,998: / Line 3,521: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=UV_TIDES />
+:'''routine = '''  <section end=TS_SVADVECTION />
-<section begin=UV_U3HADVECTION />;<span id="UV_U3HADVECTION"></span>'''[[UV_U3HADVECTION]]'''
+<section begin=TS_U3ADV_SPLIT />;<span id="TS_U3ADV_SPLIT"></span>[[TS_U3ADV_SPLIT]]
 :Option to
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[UV_U3ADV_SPLIT]]
 :'''conflict = '''
-:'''routine = '''  <section end=UV_U3HADVECTION />
+:'''routine = '''  <section end=TS_U3ADV_SPLIT />
-<section begin=UV_VIS2 />;<span id="UV_VIS2"></span>'''[[UV_VIS2]]'''
+<section begin=TS_U3HADVECTION />;<span id="TS_U3HADVECTION"></span>[[TS_U3HADVECTION]]
-:Option to activate/deactivate horizontal, harmonic viscosity of momentum. The hamonic mixing of momentum can be applied along terrain-following or geopotential levels. In ROMS, the viscosity is derived from the horizontal divergence of the deviatory stress tensor ([[Bibliography#WajsowiczRC_1993a |Wajsowicz, 1993]]).
+:Option to
-:'''parameter = ''' [[Variables#visc2 | visc2(ng)]]
-:'''variable = ''' [[Variables#visc2_p | visc2_p(:,:)]], [[Variables#visc2_r | visc2_r(:,:)]]
-:'''required = ''' [[MIX_S_UV]], [[MIX_GEO_UV]]
-:'''related = ''' [[VISC_GRID]]
-:'''routine = ''' [[uv3dmix2_s.h]], [[uv3dmix2_geo.h]], [[uv3dmix.F]]<section end=UV_VIS2 />
-<section begin=UV_VIS4 />;<span id="UV_VIS4"></span>'''[[UV_VIS4]]'''
-:Option to activate/deactivate horizontal, biharmonic viscosity of momentum. The bihamonic mixing of momentum can be applied along terrain-following or geopotential levels. In ROMS, the viscosity is derived from the horizontal divergence of the deviatory stress tensor ([[Bibliography#WajsowiczRC_1993a |Wajsowicz, 1993]]).
-:'''parameter = ''' [[Variables#visc4 | visc4(ng)]]
-:'''variable = ''' [[Variables#visc4_p | visc4_p(:,:)]], [[Variables#visc4_r | visc4_r(:,:)]]
-:'''required = ''' [[MIX_S_UV]], [[MIX_GEO_UV]]
-:'''related = ''' [[VISC_GRID]]
-:'''routine = ''' [[uv3dmix4_s.h]], [[uv3dmix4_geo.h]], [[uv3dmix.F]]<section end=UV_VIS4 />
-==<span class="alphabet">V</span>==
-<section begin=VAR_RHO_2D />;<span id="VAR_RHO_2D"></span>'''[[VAR_RHO_2D]]'''
-:Option to
 :'''parameter = '''
 :'''parent = '''
@@ Line 3,034: / Line 3,539: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=VAR_RHO_2D />
+:'''routine = '''  <section end=TS_U3HADVECTION />
+==<span class="alphabet">U</span>==
-<section begin=VCONVOLUTION />;<span id="VCONVOLUTION"></span>'''[[VCONVOLUTION]]'''
+<section begin=UPWELLING />;<span id="UPWELLING"></span>[[UPWELLING]]
 :Option to
 :'''parameter = '''
@@ Line 3,043: / Line 3,550: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=VCONVOLUTION />
+:'''routine = '''  <section end=UPWELLING />
-<section begin=VERIFICATION />;<span id="VERIFICATION"></span>'''[[VERIFICATION]]'''
+<section begin=UV_ADV />;<span id="UV_ADV"></span>[[UV_ADV]]
-:Option to
+:Option to activate/deactivate horizontal and vertical advection of momentum.  If no additional options are specified, the default is to discretize the horizontal momentum with a third-order upstream bias advection scheme with velocity dependent hyper-viscosity and the vertical momentum with a fourth-order, centered differences scheme. Since there is some implicit viscosity associated with the default discretization, the user may avoid adding an explicity vicosity to the solution to suppress excisive smoothing.
-:'''parameter = '''
+:'''routine = ''' [[step2d.F]], [[rhs3d.F]]<section end=UV_ADV />
-:'''parent = '''
-:'''required = '''
-:'''related = '''
-:'''conflict = '''
-:'''routine = '''  <section end=VERIFICATION />
-<section begin=VISC_GRID />;<span id="VISC_GRID"></span>'''[[VISC_GRID]]'''
+<section begin=UV_BAROCLINIC />;<span id="UV_BAROCLINIC"></span>[[UV_BAROCLINIC]]
 :Option to
 :'''parameter = '''
@@ Line 3,061: / Line 3,563: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=VISC_GRID />
+:'''routine = '''  <section end=UV_BAROCLINIC />
-==<span class="alphabet">W</span>==
+<section begin=UV_COR />;<span id="UV_COR"></span>[[UV_COR]]
+:Option to activate/deactivate Coriolis acceleration term in momentum equations.
+:'''routine = ''' [[step2d.F]], [[rhs3d.F]]<section end=UV_COR />
-<section begin=WEAK_CONSTRAINT />;<span id="WEAK_CONSTRAINT"></span>'''[[WEAK_CONSTRAINT]]'''
+<section begin=UV_C2ADVECTION />;<span id="UV_C2ADVECTION"></span>[[UV_C2ADVECTION]]
-:Option to
+:Option to use second-order, centered, finite differences in advection of momentum.
-:'''parameter = '''
+:'''parent = ''' [[UV_ADV]]
-:'''parent = '''
+:'''conflit = ''' [[UV_C4ADVECTION]]<section end=UV_C2ADVECTION />
-:'''required = '''
-:'''related = '''
-:'''conflict = '''
-:'''routine = '''  <section end=WEAK_CONSTRAINT />
-<section begin=WEDDELL />;<span id="WEDDELL"></span>'''[[WEDDELL]]'''
+<section begin=UV_C4ADVECTION />;<span id="UV_C4ADVECTION"></span>[[UV_C4ADVECTION]]
-:Option to
+:Option to use fourth-order, centered, finite differences in advection of momentum.
-:'''parameter = '''
+:'''parent = ''' [[UV_ADV]]
-:'''parent = '''
+:'''conflit = ''' [[UV_C2ADVECTION]]<section end=UV_C4ADVECTION />
-:'''required = '''
-:'''related = '''
-:'''conflict = '''
-:'''routine = '''  <section end=WEDDELL />
-<section begin=WEST_FSCLAMPED />;<span id="WEST_FSCLAMPED"></span>'''[[WEST_FSCLAMPED]]'''
+<section begin=UV_LDRAG />;<span id="UV_LDRAG"></span>[[UV_LDRAG]]
-:Option to
+:Option to activate/deactivate linear bottom friction of momentum.
-:'''parameter = '''
+:'''parameter = ''' [[Variables#rdrg | rdrg(ng)]]
-:'''parent = '''
+:'''confict = ''' [[BBL_MODEL]], [[UV_LOGDRAG]], [[UV_QDRAG]]
-:'''required = '''
+:'''routine = ''' [[set_vbc.F]]<section end=UV_LDRAG />
-:'''related = '''
-:'''conflict = '''
-:'''routine = '''  <section end=WEST_FSCLAMPED />
-<section begin=WEST_FSCHAPMAN />;<span id="WEST_FSCHAPMAN"></span>'''[[WEST_FSCHAPMAN]]'''
+<section begin=UV_LOGDRAG />;<span id="UV_LOGDRAG"></span>[[UV_LOGDRAG]]
-:Option to
+:Option to activate/deactivate logarithmic bottom friction of momentum.
+:'''parameter = ''' [[Variables#Zob | Zob(ng)]]
+:'''required = ''' [[SOLVE3D]]
+:'''confict = ''' [[BBL_MODEL]], [[UV_LDRAG]], [[UV_QDRAG]]
+:'''routine = ''' [[set_vbc.F]]<section end=UV_LOGDRAG />
+<section begin=UV_PSOURCE />;<span id="UV_PSOURCE"></span>[[UV_PSOURCE]] ('''OBSOLETE as of revision 701''')
+:Option to activate/deactivate point sources/sinks of momentum. This option is used to specify the mass transport in river runoff.
+:'''variable = ''' [[Variables#Dsrc | Dsrc(1:Nsrc)]], [[Variables#Qsrc | Qsrc(1:Nsrc,k)]]
+:'''related = ''' [[ANA_PSOURCE]], [[TS_PSOURCE]]
+:'''confict = ''' [[BBL_MODEL]], [[UV_LOGDRAG]], [[UV_QDRAG]]
+:'''routine = ''' [[step2d.F]], [[step3d_uv.F]]<section end=UV_PSOURCE />
+<section begin=UV_QDRAG />;<span id="UV_QDRAG"></span>[[UV_QDRAG]]
+:Option to activate/deactivate quadratic bottom friction of momentum.
+:'''parameter = ''' [[Variables#rdrg2 | rdrg2(ng)]]
+:'''confict = ''' [[BBL_MODEL]], [[UV_LDRAG]], [[UV_LOGDRAG]]
+:'''routine = ''' [[set_vbc.F]]<section end=UV_QDRAG />
+<section begin=UV_SADVECTION />;<span id="UV_SADVECTION"></span>[[UV_SADVECTION]]
+:Option to use conservative, parabolic splines discretization of momentum vertical advection. This scheme requires high vertical resolution so it is recommended to use this option in shallow, coastal applications.
+:'''parent = ''' [[UV_ADV]]
+:'''conflit = ''' [[UV_C2ADVECTION]], [[UV_C4ADVECTION]]<section end=UV_SADVECTION />
+<section begin=UV_SMAGORINSKY />;<span id="UV_SMAGORINSKY"></span>[[UV_SMAGORINSKY]]
+:Option to use Smagorinsky-like viscosity.
+:'''related = ''' [[TS_SMAGORINSKY]]
+:'''routine = ''' [[hmixing.F]] <section end=UV_SMAGORINSKY />
+<section begin=UV_TIDES />;<span id="UV_TIDES"></span>[[UV_TIDES]]
+:Option to impose tidal currents for tidal forcing at open boundaries.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[ADD_M2OBC]], [[RAMP_TIDES]]
 :'''conflict = '''
-:'''routine = '''  <section end=WEST_FSCHAPMAN />
+:'''routine = '''  <section end=UV_TIDES />
-<section begin=WEST_FSGRADIENT />;<span id="WEST_FSGRADIENT"></span>'''[[WEST_FSGRADIENT]]'''
+<section begin=UV_U3ADV_SPLIT />;<span id="UV_U3ADV_SPLIT"></span>[[UV_U3ADV_SPLIT]]
-:Option to
+:Option to use 3rd-order upstream split momentum advection. This 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]].
-:'''parameter = '''
+:'''related = ''' [[TS_U3ADV_SPLIT]]
-:'''parent = '''
+:'''routine = ''' [[hmixing.F]] <section end=UV_U3ADV_SPLIT />
-:'''required = '''
-:'''related = '''
-:'''conflict = '''
-:'''routine = '''  <section end=WEST_FSGRADIENT />
-<section begin=WEST_FSNUDGING />;<span id="WEST_FSNUDGING"></span>'''[[WEST_FSNUDGING]]'''
+<section begin=UV_U3HADVECTION />;<span id="UV_U3HADVECTION"></span>[[UV_U3HADVECTION]]
 :Option to
 :'''parameter = '''
@@ Line 3,117: / Line 3,636: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=WEST_FSNUDGING />
+:'''routine = '''  <section end=UV_U3HADVECTION />
-<section begin=WEST_FSRADIATION />;<span id="WEST_FSRADIATION"></span>'''[[WEST_FSRADIATION]]'''
+<section begin=UV_VIS2 />;<span id="UV_VIS2"></span>[[UV_VIS2]]
-:Option to
+:Option to activate/deactivate horizontal, harmonic viscosity of momentum. The hamonic mixing of momentum can be applied along terrain-following or geopotential levels. In ROMS, the viscosity is derived from the horizontal divergence of the deviatory stress tensor ([[Bibliography#WajsowiczRC_1993a |Wajsowicz, 1993]]).
+:'''parameter = ''' [[Variables#visc2 | visc2(ng)]]
+:'''variable = ''' [[Variables#visc2_p | visc2_p(:,:)]], [[Variables#visc2_r | visc2_r(:,:)]]
+:'''required = ''' [[MIX_S_UV]], [[MIX_GEO_UV]]
+:'''related = ''' [[VISC_GRID]]
+:'''routine = ''' [[uv3dmix2_s.h]], [[uv3dmix2_geo.h]], [[uv3dmix.F]]<section end=UV_VIS2 />
+<section begin=UV_VIS4 />;<span id="UV_VIS4"></span>[[UV_VIS4]]
+:Option to activate/deactivate horizontal, biharmonic viscosity of momentum. The bihamonic mixing of momentum can be applied along terrain-following or geopotential levels. In ROMS, the viscosity is derived from the horizontal divergence of the deviatory stress tensor ([[Bibliography#WajsowiczRC_1993a |Wajsowicz, 1993]]).
+:'''parameter = ''' [[Variables#visc4 | visc4(ng)]]
+:'''variable = ''' [[Variables#visc4_p | visc4_p(:,:)]], [[Variables#visc4_r | visc4_r(:,:)]]
+:'''required = ''' [[MIX_S_UV]], [[MIX_GEO_UV]]
+:'''related = ''' [[VISC_GRID]]
+:'''routine = ''' [[uv3dmix4_s.h]], [[uv3dmix4_geo.h]], [[uv3dmix.F]]<section end=UV_VIS4 />
+==<span class="alphabet">V</span>==
+<section begin=VAR_RHO_2D />;<span id="VAR_RHO_2D"></span>[[VAR_RHO_2D]]
+:Option to
 :'''parameter = '''
 :'''parent = '''
@@ Line 3,126: / Line 3,663: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=WEST_FSRADIATION />
+:'''routine = '''  <section end=VAR_RHO_2D />
-<section begin=WEST_M2CLAMPED />;<span id="WEST_M2CLAMPED"></span>'''[[WEST_M2CLAMPED]]'''
+<section begin=VCONVOLUTION />;<span id="VCONVOLUTION"></span>[[VCONVOLUTION]]
 :Option to
 :'''parameter = '''
@@ Line 3,135: / Line 3,672: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=WEST_M2CLAMPED />
+:'''routine = '''  <section end=VCONVOLUTION />
-<section begin=WEST_M2FLATHER />;<span id="WEST_M2FLATHER"></span>'''[[WEST_M2FLATHER]]'''
+<section begin=VERIFICATION />;<span id="VERIFICATION"></span>[[VERIFICATION]]
 :Option to
 :'''parameter = '''
@@ Line 3,144: / Line 3,681: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=WEST_M2FLATHER />
+:'''routine = '''  <section end=VERIFICATION />
-<section begin=WEST_M2GRADIENT />;<span id="WEST_M2GRADIENT"></span>'''[[WEST_M2GRADIENT]]'''
+<section begin=VISC_GRID />;<span id="VISC_GRID"></span>[[VISC_GRID]]
 :Option to
 :'''parameter = '''
@@ Line 3,153: / Line 3,690: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=WEST_M2GRADIENT />
+:'''routine = '''  <section end=VISC_GRID />
-<section begin=WEST_M2NUDGING />;<span id="WEST_M2NUDGING"></span>'''[[WEST_M2NUDGING]]'''
+<section begin=VWALK_FORWARD />;<span id="VWALK_FORWARD"></span>[[VWALK_FORWARD]]
-:Option to
+:Option to activate the old forward step vertical random walk computation.
 :'''parameter = '''
 :'''parent = '''
@@ Line 3,162: / Line 3,699: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=WEST_M2NUDGING />
+:'''routine = '''  <section end=VISC_GRID />
-<section begin=WEST_M2RADIATION />;<span id="WEST_M2RADIATION"></span>'''[[WEST_M2RADIATION]]'''
+==<span class="alphabet">W</span>==
-:Option to
+<section begin=W4DPSAS />;<span id="W4DPSAS"></span>[[W4DPSAS]] <span class="red">OBSOLETE - Renamed to [[Options#RBL4DVAR|RBL4DVAR]] in SVN revision 1022</span>
+:Option to Option to activate Lanczos 4D-Var, strong/weak constraint, dual formulation.
 :'''parameter = '''
 :'''parent = '''
@@ Line 3,171: / Line 3,710: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=WEST_M2RADIATION />
+:'''routine = ''' [[w4dpsas_ocean.h]] <section end=W4DPSAS />
-<section begin=WEST_M2REDUCED />;<span id="WEST_M2REDUCED"></span>'''[[WEST_M2REDUCED]]'''
+<section begin=W4DPSAS_FCT_SENSITIVITY />;<span id="W4DPSAS_FCT_SENSITIVITY"></span>[[W4DPSAS_FCT_SENSITIVITY]] <span class="red">OBSOLETE - Renamed to [[Options#RBL4DVAR_FCT_SENSITIVITY|RBL4DVAR_FCT_SENSITIVITY]] in SVN revision 1022</span>
-:Option to
+:Option to activate the observation impact driver for the forecast cycles.
 :'''parameter = '''
 :'''parent = '''
@@ Line 3,180: / Line 3,719: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=WEST_M2REDUCED />
+:'''routine = ''' [[ad_htobs.F]], [[ad_rpcg_lanczos.F]], [[ceckdefs.F]], [[def_info.F]], [[def_ini.F]], [[def_mod.F]], [[get_state.F]], [[globaldefs.h]], [[mod_iounits.F]], [[mod_fourdvar.F]], [[obs_sen_w4dpsas_forecast.h]], [[read_asspar.F]], [[read_phypar.F]], [[rpcg_lanczos.F]], [[tl_rpcg_lanczos.F]], [[wrt_info.F]] <section end=W4DPSAS_FCT_SENSITIVITY />
-<section begin=WEST_M3CLAMPED />;<span id="WEST_M3CLAMPED"></span>'''[[WEST_M3CLAMPED]]'''
+<section begin=W4DPSAS_SENSITIVITY />;<span id="W4DPSAS_SENSITIVITY"></span>[[W4DPSAS_SENSITIVITY]] <span class="red">OBSOLETE - Renamed to [[Options#RBL4DVAR_ANA_SENSITIVITY|RBL4DVAR_ANA_SENSITIVITY]] in SVN revision 1022</span>
-:Option to
+:Option to activate Lanczos 4D-Var, strong/weak constraint, dual formulation analysis of observation impact and observations sensitivity.
 :'''parameter = '''
 :'''parent = '''
@@ Line 3,189: / Line 3,728: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=WEST_M3CLAMPED />
+:'''routine = ''' [[obs_sen_w4dpsas.h]] <section end=W4DPSAS_SENSITIVITY />
-<section begin=WEST_M3GRADIENT />;<span id="WEST_M3GRADIENT"></span>'''[[WEST_M3GRADIENT]]'''
+<section begin=W4DVAR />;<span id="W4DVAR"></span>[[W4DVAR]] <span class="red">OBSOLETE - Renamed to [[Options#R4DVAR|R4DVAR]] in SVN revision 1022</span>
-:Option to
+:Option to activate indirect Representers 4D-Var, strong/weak constraint, dual formulation. This algorithm is no longer developed due to its instability in multiple outer loops in applications with high Rossby number. It is keep for instructional usage. We do not recommend to be used in realistic applications. Use instead the RBL4D-Var algorithm, which has a more efficient minimization RBLanczos solver.
 :'''parameter = '''
 :'''parent = '''
@@ Line 3,198: / Line 3,737: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=WEST_M3GRADIENT />
+:'''routine = ''' [[w4dvar_ocean.h]] <section end=W4DVAR />
-<section begin=WEST_M3NUDGING />;<span id="WEST_M3NUDGING"></span>'''[[WEST_M3NUDGING]]'''
+<section begin=W4DVAR_SENSITIVITY />;<span id="W4DVAR_SENSITIVITY"></span>[[W4DVAR_SENSITIVITY]] <span class="red">OBSOLETE - Renamed to [[Options#R4DVAR_ANA_SENSITIVITY|R4DVAR_ANA_SENSITIVITY]] in SVN revision 1022</span>
-:Option to
+:Option to activate R4D-Var Analysis Observation Impact and Observations Sensitivity
 :'''parameter = '''
 :'''parent = '''
@@ Line 3,207: / Line 3,746: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=WEST_M3NUDGING />
+:'''routine = ''' [[obs_sen_w4dvar.h]] <section end=W4DVAR_SENSITIVITY />
-<section begin=WEST_M3RADIATION />;<span id="WEST_M3RADIATION"></span>'''[[WEST_M3RADIATION]]'''
+<section begin=WEAK_CONSTRAINT />;<span id="WEAK_CONSTRAINT"></span>[[WEAK_CONSTRAINT]]
 :Option to
 :'''parameter = '''
@@ Line 3,216: / Line 3,755: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=WEST_M3RADIATION />
+:'''routine = '''  <section end=WEAK_CONSTRAINT />
-<section begin=WEST_KGRADIENT />;<span id="WEST_KGRADIENT"></span>'''[[WEST_KGRADIENT]]'''
+<section begin=WEDDELL />;<span id="WEDDELL"></span>[[WEDDELL]]
 :Option to
 :'''parameter = '''
@@ Line 3,225: / Line 3,764: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=WEST_KGRADIENT />
+:'''routine = '''  <section end=WEDDELL />
-<section begin=WEST_KRADIATION />;<span id="WEST_KRADIATION"></span>'''[[WEST_KRADIATION]]'''
+<section begin=WEST_FSCLAMPED />;<span id="WEST_FSCLAMPED"></span>[[WEST_FSCLAMPED]]
-:Option to
+:Option to use free-surface clamped condition for the western open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSCLAMPED]], [[NORTH_FSCLAMPED]], [[SOUTH_FSCLAMPED]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_FSCHAPMAN]], [[WEST_FSGRADIENT]], [[WEST_FSNUDGING]], [[WEST_FSRADIATION]], [[WESTERN_WALL]]
-:'''routine = '''  <section end=WEST_KRADIATION />
+:'''routine = ''' [[zetabc.F]]<section end=WEST_FSCLAMPED />
-<section begin=WEST_TCLAMPED />;<span id="WEST_TCLAMPED"></span>'''[[WEST_TCLAMPED]]'''
+<section begin=WEST_FSCHAPMAN />;<span id="WEST_FSCHAPMAN"></span>[[WEST_FSCHAPMAN]]
-:Option to
+:Option to use free-surface Chapman condition for the western open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSCHAPMAN]], [[NORTH_FSCHAPMAN]], [[SOUTH_FSCHAPMAN]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_FSCLAMPED]], [[WEST_FSGRADIENT]], [[WEST_FSNUDGING]], [[WEST_FSRADIATION]], [[WESTERN_WALL]]
-:'''routine = '''  <section end=WEST_TCLAMPED />
+:'''routine = ''' [[zetabc.F]]<section end=WEST_FSCHAPMAN />
-<section begin=WEST_TGRADIENT />;<span id="WEST_TGRADIENT"></span>'''[[WEST_TGRADIENT]]'''
+<section begin=WEST_FSGRADIENT />;<span id="WEST_FSGRADIENT"></span>[[WEST_FSGRADIENT]]
-:Option to
+:Option to use free-surface gradient condition for the western open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSGRADIENT]], [[NORTH_FSGRADIENT]], [[SOUTH_FSGRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_FSCLAMPED]], [[WEST_FSCHAPMAN]], [[WEST_FSNUDGING]], [[WEST_FSRADIATION]], [[WESTERN_WALL]]
-:'''routine = '''  <section end=WEST_TGRADIENT />
+:'''routine = ''' [[zetabc.F]]<section end=WEST_FSGRADIENT />
-<section begin=WEST_TNUDGING />;<span id="WEST_TNUDGING"></span>'''[[WEST_TNUDGING]]'''
+<section begin=WEST_FSNUDGING />;<span id="WEST_FSNUDGING"></span>[[WEST_FSNUDGING]]
-:Option to
+:Option to use free-surface passive/active nudging term for the western open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSNUDGING]], [[NORTH_FSNUDGING]], [[SOUTH_FSNUDGING]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_FSCLAMPED]], [[WEST_FSCHAPMAN]], [[WEST_FSGRADIENT]], [[WESTERN_WALL]]
-:'''routine = '''  <section end=WEST_TNUDGING />
+:'''routine = ''' [[zetabc.F]]<section end=WEST_FSNUDGING />
-<section begin=WEST_TRADIATION />;<span id="WEST_TRADIATION"></span>'''[[WEST_TRADIATION]]'''
+<section begin=WEST_FSRADIATION />;<span id="WEST_FSRADIATION"></span>[[WEST_FSRADIATION]]
-:Option to
+:Option to use free-surface radiation condition for the western open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_FSRADIATION]], [[NORTH_FSRADIATION]], [[SOUTH_FSRADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_FSCLAMPED]], [[WEST_FSCHAPMAN]], [[WEST_FSGRADIENT]], [[WESTERN_WALL]]
-:'''routine = '''  <section end=WEST_TRADIATION />
+:'''routine = ''' [[zetabc.F]]<section end=WEST_FSRADIATION />
-<section begin=WEST_VOLCONS />;<span id="WEST_VOLCONS"></span>'''[[WEST_VOLCONS]]'''
+<section begin=WEST_KGRADIENT />;<span id="WEST_KGRADIENT"></span>[[WEST_KGRADIENT]]
-:Option to
+:Option to use TKE fields gradient condition for the western open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_KGRADIENT]], [[NORTH_KGRADIENT]], [[SOUTH_KGRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_KRADIATION]], [[WESTERN_WALL]]
-:'''routine = '''  <section end=WEST_VOLCONS />
+:'''routine = ''' [[tkebc_im.F]]<section end=WEST_KGRADIENT />
-<section begin=WESTERN_WALL />;<span id="WESTERN_WALL"></span>'''[[WESTERN_WALL]]'''
+<section begin=WEST_KRADIATION />;<span id="WEST_KRADIATION"></span>[[WEST_KRADIATION]]
-:Option to
+:Option to use TKE fields radiation condition for the western open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_KRADIATION]], [[NORTH_KRADIATION]], [[SOUTH_KRADIATION]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_KGRADIENT]], [[WESTERN_WALL]]
-:'''routine = '''  <section end=WESTERN_WALL />
+:'''routine = ''' [[tkebc_im.F]]<section end=WEST_KRADIATION />
-<section begin=WET_DRY />;<span id="WET_DRY"></span>'''[[WET_DRY]]'''
+<section begin=WEST_M2CLAMPED />;<span id="WEST_M2CLAMPED"></span>[[WEST_M2CLAMPED]]
-:Option to activate wetting and drying.
+:Option to use 2D momentum clamped condition for the western open boundary condition.
-:'''parameter = ''' [[Variables#Dcrit|Dcrit]]
+:'''parameter = '''
-:'''variable = ''' [[Variables#rmask_wet|rmask_wet]], [[Variables#umask_wet|umask_wet]], [[Variables#vmask_wet|vmask_wet]]
+:'''parent = '''
-:'''routine = '''  [[step2d.F]] <section end=WET_DRY />
+:'''required = '''
+:'''related = ''' [[EAST_M2CLAMPED]], [[NORTH_M2CLAMPED]], [[SOUTH_M2CLAMPED]]
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_M2FLATHER]], [[WEST_M2GRADIENT]], [[WEST_M2NUDGING]], [[WEST_M2RADIATION]], [[WEST_M2REDUCED]], [[WESTERN_WALL]]
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=WEST_M2CLAMPED />
-<section begin=WINDBASIN />;<span id="WINDBASIN"></span>'''[[WINDBASIN]]'''
+<section begin=WEST_M2FLATHER />;<span id="WEST_M2FLATHER"></span>[[WEST_M2FLATHER]]
-:Option to
+:Option to use 2D momentum Flather condition for the western open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M2FLATHER]], [[NORTH_M2FLATHER]], [[SOUTH_M2FLATHER]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_M2CLAMPED]], [[WEST_M2GRADIENT]], [[WEST_M2NUDGING]], [[WEST_M2RADIATION]], [[WEST_M2REDUCED]], [[WESTERN_WALL]]
-:'''routine = '''  <section end=WINDBASIN />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=WEST_M2FLATHER />
-<section begin=WIND_WAVES />;<span id="WIND_WAVES"></span>'''[[WIND_WAVES]]'''
+<section begin=WEST_M2GRADIENT />;<span id="WEST_M2GRADIENT"></span>[[WEST_M2GRADIENT]]
-:Option to
+:Option to use 2D momentum gradient condition for the western open boundary condition.
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
-:'''related = '''
+:'''related = ''' [[EAST_M2GRADIENT]], [[NORTH_M2GRADIENT]], [[SOUTH_M2GRADIENT]]
-:'''conflict = '''
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_M2CLAMPED]], [[WEST_M2FLATHER]], [[WEST_M2NUDGING]], [[WEST_M2RADIATION]], [[WEST_M2REDUCED]], [[WESTERN_WALL]]
-:'''routine = '''  <section end=WIND_WAVES />
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=WEST_M2GRADIENT />
-<section begin=WJ_GRADP />;<span id="WJ_GRADP"></span>'''[[WJ_GRADP]]'''
+<section begin=WEST_M2NUDGING />;<span id="WEST_M2NUDGING"></span>[[WEST_M2NUDGING]]
-:Option to
+:Option to use 2D momentum passive/active nudging term for the western open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_M2NUDGING]], [[NORTH_M2NUDGING]], [[SOUTH_M2NUDGING]]
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_M2CLAMPED]], [[WEST_M2FLATHER]], [[WEST_M2GRADIENT]], [[WEST_M2REDUCED]], [[WESTERN_WALL]]
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=WEST_M2NUDGING />
+<section begin=WEST_M2RADIATION />;<span id="WEST_M2RADIATION"></span>[[WEST_M2RADIATION]]
+:Option to use 2D momentum radiation condition for the western open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_M2RADIATION]], [[NORTH_M2RADIATION]], [[SOUTH_M2RADIATION]]
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_M2CLAMPED]], [[WEST_M2FLATHER]], [[WEST_M2GRADIENT]], [[WEST_M2REDUCED]], [[WESTERN_WALL]]
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=WEST_M2RADIATION />
+<section begin=WEST_M2REDUCED />;<span id="WEST_M2REDUCED"></span>[[WEST_M2REDUCED]]
+:Option to use 2D momentum reduced-physics for the western open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_M2REDUCED]], [[NORTH_M2REDUCED]], [[SOUTH_M2REDUCED]]
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_M2CLAMPED]], [[WEST_M2FLATHER]], [[WEST_M2GRADIENT]], [[WEST_M2NUDGING]], [[WEST_M2RADIATION]], [[WESTERN_WALL]]
+:'''routine = ''' [[u2dbc_im.F]], [[v2dbc_im.F]]<section end=WEST_M2REDUCED />
+<section begin=WEST_M3CLAMPED />;<span id="WEST_M3CLAMPED"></span>[[WEST_M3CLAMPED]]
+:Option to use 3D momentum clamped condition for the western open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_M3CLAMPED]], [[NORTH_M3CLAMPED]], [[SOUTH_M3CLAMPED]]
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_M3GRADIENT]], [[WEST_M3NUDGING]], [[WEST_M3RADIATION]], [[WESTERN_WALL]]
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=WEST_M3CLAMPED />
+<section begin=WEST_M3GRADIENT />;<span id="WEST_M3GRADIENT"></span>[[WEST_M3GRADIENT]]
+:Option to use 3D momentum gradient condition for the western open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_M3GRADIENT]], [[NORTH_M3GRADIENT]], [[SOUTH_M3GRADIENT]]
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_M3CLAMPED]], [[WEST_M3NUDGING]], [[WEST_M3RADIATION]], [[WESTERN_WALL]]
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=WEST_M3GRADIENT />
+<section begin=WEST_M3NUDGING />;<span id="WEST_M3NUDGING"></span>[[WEST_M3NUDGING]]
+:Option to use 3D momentum passive/active nudging term for the western open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_M3NUDGING]], [[NORTH_M3NUDGING]], [[SOUTH_M3NUDGING]]
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_M3CLAMPED]], [[WEST_M3GRADIENT]], [[WESTERN_WALL]]
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=WEST_M3NUDGING />
+<section begin=WEST_M3RADIATION />;<span id="WEST_M3RADIATION"></span>[[WEST_M3RADIATION]]
+:Option to use 3D momentum radiation condition for the western open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_M3RADIATION]], [[NORTH_M3RADIATION]], [[SOUTH_M3RADIATION]]
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_M3CLAMPED]], [[WEST_M3GRADIENT]], [[WESTERN_WALL]]
+:'''routine = ''' [[u3dbc_im.F]], [[v3dbc_im.F]]<section end=WEST_M3RADIATION />
+<section begin=WEST_TCLAMPED />;<span id="WEST_TCLAMPED"></span>[[WEST_TCLAMPED]]
+:Option to use tracer clamped condition for the western open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_TCLAMPED]], [[NORTH_TCLAMPED]], [[SOUTH_TCLAMPED]]
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_TGRADIENT]], [[WEST_TNUDGING]], [[WEST_TRADIATION]], [[WESTERN_WALL]]
+:'''routine = ''' [[t3dbc_im.F]]<section end=WEST_TCLAMPED />
+<section begin=WEST_TGRADIENT />;<span id="WEST_TGRADIENT"></span>[[WEST_TGRADIENT]]
+:Option to use tracer gradient condition for the western open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_TGRADIENT]], [[NORTH_TGRADIENT]], [[SOUTH_TGRADIENT]]
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_TCLAMPED]], [[WEST_TNUDGING]], [[WEST_TRADIATION]], [[WESTERN_WALL]]
+:'''routine = ''' [[t3dbc_im.F]]<section end=WEST_TGRADIENT />
+<section begin=WEST_TNUDGING />;<span id="WEST_TNUDGING"></span>[[WEST_TNUDGING]]
+:Option to use tracer passive/active nudging term for the western open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_TNUDGING]], [[NORTH_TNUDGING]], [[SOUTH_TNUDGING]]
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_TCLAMPED]], [[WEST_TGRADIENT]], [[WESTERN_WALL]]
+:'''routine = ''' [[t3dbc_im.F]]<section end=WEST_TNUDGING />
+<section begin=WEST_TRADIATION />;<span id="WEST_TRADIATION"></span>[[WEST_TRADIATION]]
+:Option to use tracer radiation condition for the western open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_TRADIATION]], [[NORTH_TRADIATION]], [[SOUTH_TRADIATION]]
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_TCLAMPED]], [[WEST_TGRADIENT]], [[WESTERN_WALL]]
+:'''routine = ''' [[t3dbc_im.F]]<section end=WEST_TRADIATION />
+<section begin=WEST_VOLCONS />;<span id="WEST_VOLCONS"></span>[[WEST_VOLCONS]]
+:Option to use Southern edge mass conservation enforcement for the western open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_VOLCONS]], [[NORTH_VOLCONS]], [[SOUTH_VOLCONS]]
+:'''conflict = ''' [[EW_PERIODIC]], [[WESTERN_WALL]]
+:'''routine = ''' [[obc_volcons.F]]<section end=WEST_VOLCONS />
+<section begin=WESTERN_WALL />;<span id="WESTERN_WALL"></span>[[WESTERN_WALL]]
+:Option to use Southern edge closed wall for the western open boundary condition.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[EAST_WALL]], [[NORTH_WALL]], [[SOUTH_WALL]]
+:'''conflict = ''' [[EW_PERIODIC]], [[WEST_FSCLAMPED]], [[WEST_FSCHAPMAN]], [[WEST_FSGRADIENT]], [[WEST_FSNUDGING]], [[WEST_FSRADIATION]], [[WEST_KGRADIENT]], [[WEST_KRADIATION]], [[WEST_M2CLAMPED]], [[WEST_M2FLATHER]], [[WEST_M2GRADIENT]], [[WEST_M2NUDGING]], [[WEST_M2RADIATION]], [[WEST_M2REDUCED]], [[WEST_M3CLAMPED]], [[WEST_M3GRADIENT]], [[WEST_M3NUDGING]], [[WEST_M3RADIATION]], [[WEST_TCLAMPED]], [[WEST_TGRADIENT]], [[WEST_TNUDGING]], [[WEST_TRADIATION]], [[WEST_VOLCONS]]
+:'''routine = ''' [[t3dbc_im.F]], [[tkebc_im.F]], [[u2dbc_im.F]], [[u3dbc_im.F]], [[v2dbc_im.F]], [[v3dbc_im.F]], [[zetabc.F]]<section end=WESTERN_WALL />
+<section begin=WET_DRY />;<span id="WET_DRY"></span>[[WET_DRY]]
+:Option to activate wetting and drying.
+:'''parameter = ''' [[Variables#Dcrit|Dcrit]]
+:'''variable = ''' [[Variables#rmask_wet|rmask_wet]], [[Variables#umask_wet|umask_wet]], [[Variables#vmask_wet|vmask_wet]]
+:'''routine = '''  [[step2d.F]] <section end=WET_DRY />
+<section begin=WINDBASIN />;<span id="WINDBASIN"></span>[[WINDBASIN]]
+:Option to
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=WJ_GRADP />
+:'''routine = '''  <section end=WINDBASIN />
-<section begin=WRITE_WATER />;<span id="WRITE_WATER"></span>'''[[WRITE_WATER]]'''
+<section begin=WIND_WAVES />;<span id="WIND_WAVES"></span>[[WIND_WAVES]]
 :Option to
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=WRITE_WATER />
+:'''routine = '''  <section end=WIND_WAVES />
-<section begin=W4DPSAS />;<span id="W4DPSAS"></span>'''[[W4DPSAS]]'''
+<section begin=WJ_GRADP />;<span id="WJ_GRADP"></span>[[WJ_GRADP]]
 :Option to
 :'''parameter = '''
 :'''parent = '''
 :'''required = '''
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=W4DPSAS />
+:'''routine = '''  <section end=WJ_GRADP />
+<section begin=WRITE_WATER />;<span id="WRITE_WATER"></span>[[WRITE_WATER]]
+:Option to
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = '''
+:'''conflict = '''
+:'''routine = '''  <section end=WRITE_WATER />
+<section begin=WRF_COUPLING />;<span id="WRF_COUPLING"></span>[[WRF_COUPLING]]
+:Option to
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = '''
+:'''conflict = '''
+:'''routine = '''  <section end=WRF_COUPLING />
+==<span class="alphabet">X</span>==
+==<span class="alphabet">Y</span>==
+==<span class="alphabet">Z</span>==
+<section begin=ZCLIMATOLOGY />;<span id="ZCLIMATOLOGY"></span>[[ZCLIMATOLOGY]]
+:'''DEPRICATED''' in favor of [[Variables#LsshCLM|LsshCLM]] logical switches to facilitate nesting.<br /><br />Option to read and process SSH climatology fields.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[ANA_SSH]], [[SSH_TIDES]], [[ZCLM_NUDGING]]
+:'''conflict = '''
+:'''routine = '''  <section end=ZCLIMATOLOGY />
+<section begin=ZCLM_NUDGING />;<span id="ZCLM_NUDGING"></span>[[ZCLM_NUDGING]]
+:Option to nudge SSH climatology data (primarily in sponge areas.
+:'''parameter = '''
+:'''parent = '''
+:'''required = '''
+:'''related = ''' [[ANA_SSH]], [[SSH_TIDES]], [[ZCLIMATOLOGY]]
+:'''conflict = '''
+:'''routine = '''  <section end=ZCLM_NUDGING />
-<section begin=W4DVAR />;<span id="W4DVAR"></span>'''[[W4DVAR]]'''
+<section begin=ZETA_ELLIPTIC />;<span id="ZETA_ELLIPTIC"></span>[[ZETA_ELLIPTIC]]
-:Option to
+:Option to compute the balanced free-surface increment by solving an elliptical equation as in [[Bibliography#Fukomuri...1998a|Fukomuri ''et al.'' (1998)]].
 :'''parameter = '''
 :'''parent = '''
@@ Line 3,348: / Line 4,055: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=W4DVAR />
+:'''routine = '''  <section end=ZETA_ELLIPTIC />
-==<span class="alphabet">X</span>==
+<section begin=ZOS_HSIG />;<span id="ZOS_HSIG"></span>[[ZOS_HSIG]]
+:Option to use horizontal smoothing of buoyancy/shear for the Generic Length-Scale closure ([[Bibliography#WarnerJC_2005a|Warner ''et al.'', 2005]]).
-==<span class="alphabet">Y</span>==
-==<span class="alphabet">Z</span>==
-<section begin=ZCLIMATOLOGY />;<span id="ZCLIMATOLOGY"></span>'''[[ZCLIMATOLOGY]]'''
-:Option to
 :'''parameter = '''
 :'''parent = '''
@@ Line 3,363: / Line 4,064: @@
 :'''related = '''
 :'''conflict = '''
-:'''routine = '''  <section end=ZCLIMATOLOGY />
+:'''routine = '''  <section end=ZOS_HSIG />
-<section begin=ZCLM_NUDGING />;<span id="ZCLM_NUDGING"></span>'''[[ZCLM_NUDGING]]'''
-:Option to
-:'''parameter = '''
-:'''parent = '''
-:'''required = '''
-:'''related = '''
-:'''conflict = '''
-:'''routine = '''  <section end=ZCLM_NUDGING />