Variables: Difference between revisions

Latest revision as of 20:09, 19 August 2020

Variables

This wikipage includes all ROMS global variables in alphabetic order. A single long page is built to facilitate printing. Each variable has a unique anchor tag to facilitate linking from any wikipage.

A

ad_Akt_fac: Adjoint-based algorithms vertical mixing, basic state, scale factor (nondimensional) for active (NAT) and inert (NPT) tracer variables. In some applications, smaller/larger values of vertical mixing are necessary for stability. It is only used when the CPP option FORWARD_MIXING is activated.; dimension = ad_Akt_fac(MT,Ngrids); option = FORWARD_MIXING; routine = mod_scalars.F; keyword = ad_AKT_fac; input = bio_Fennel.in, ecosim.in, nemuro.in, npzd_Franks.in, npzd_iron.in, npzd_Powell.in, roms.in

ad_Akv_fac: Adjoint-based algorithms vertical mixing, basic state, scale factor (nondimensional) for momentum. In some applications, smaller/larger values of vertical mixing are necessary for stability. It is only used when the CPP option FORWARD_MIXING is activated.; dimension = ad_Akv_fac(Ngrids); option = FORWARD_MIXING; routine = mod_scalars.F; keyword = ad_AKV_fac; input = roms.in

ad_LBC: Adjoint-based algorithms lateral boundary conditions.; dimension = ad_LBC(4,nLBCvar,Ngrids); option =; routine = mod_param.F; keyword = ad_LBC; input = bio_Fennel.in, ecosim.in, nemuro.in, npzd_Franks.in, npzd_iron.in, npzd_Powell.in, roms.in

ad_tnu2: Adjoint-based algorithms lateral, harmonic, constant, mixing coefficient (m²/s) for active (NAT) and inert (NPT) tracer variables. If variable horizontal diffusion is activated, ad_tnu2 is the mixing coefficient for the largest grid-cell in the domain. In some applications, a larger value than what is used in the nonlinear model (basic state) is necessary for stability.; dimension = ad_tnu2(MT,Ngrids); option =; routine = mod_scalars.F; keyword = ad_TNU2; input = bio_Fennel.in, ecosim.in, nemuro.in, npzd_Franks.in, npzd_iron.in, npzd_Powell.in, roms.in

ad_tnu4: Adjoint-based algorithms lateral, harmonic, constant, mixing coefficient (m⁴/s) for active (NAT) and inert (NPT) tracer variables. If variable horizontal diffusion is activated, ad_tnu4 is the mixing coefficient for the largest grid-cell in the domain. In some applications, a larger value than what is used in the nonlinear model (basic state) is necessary for stability.; dimension = ad_tnu4(MT,Ngrids); option =; routine = mod_scalars.F; keyword = ad_TNU4; input = bio_Fennel.in, ecosim.in, nemuro.in, npzd_Franks.in, npzd_iron.in, npzd_Powell.in, roms.in

ad_visc2: Adjoint-based algorithms lateral, harmonic, constant, mixing coefficient (m²/s) momentum. If variable horizontal viscosity is activated, ad_visc2 is the mixing coefficient for the largest grid-cell in the domain. In some applications, a larger value than what is used in the nonlinear model (basic state) is necessary for stability.; dimension = ad_visc2(Ngrids); option =; routine = mod_scalars.F; keyword = ad_VISC2; input = roms.in

ad_visc4: Adjoint-based algorithms lateral, harmonic, constant, mixing coefficient (m⁴/s) for momentum. If variable horizontal viscosity is activated, ad_visc4 is the mixing coefficient for the largest grid-cell in the domain. In some applications, a larger value than what is used in the nonlinear model (basic state) is necessary for stability.; dimension = ad_visc4(Ngrids); option =; routine = mod_scalars.F; keyword = ad_VISC4; input = roms.in

ad_VolCons: Lateral open boundary edge volume conservation switch for adjoint-based algorithms. This is usually activated with radiation boundary conditions to enforce global mass conservation. Notice that these switches should not be activated if tidal forcing enabled.; dimension = ad_VolCons(4,Ngrids); option =; routine = mod_scalars.F; keyword = ad_VolCons; input = roms.in

ADM: Adjoint output NetCDF file name. Ngrids values are expected.; dimension = ADM(Ngrids); option =; routine = mod_iounits.F; keyword = ADJNAME; input = roms.in

ADS: Adjoint sensitivity functionals input NetCDF file name. Ngrids values are expected.; dimension = ADS(Ngrids); option =; routine = mod_iounits.F; keyword = ADSNAME; input = roms.in

Akk_bak: Background vertical mixing coefficient for turbulent kinetic energy. Ngrids values are expected.; dimension = Akk_bak(Ngrids); units = meters² second^-1; option =; routine = mod_mixing.F, mod_scalars.F; keyword = AKK_BAK; input = roms.in

Akp_bak: Background vertical mixing coefficient for turbulent kinetic generic statistical field, psi. Ngrids values are expected.; dimension = Akp_bak(Ngrids); units = meters² second^-1; option =; routine = mod_mixing.F, mod_scalars.F; keyword = AKP_BAK; input = roms.in

Akt_bak: Background vertical mixing coefficient for tracer type variables.; dimension = Akt_bak(MT,Ngrids); units = meters² second^-1; option =; routine = mod_mixing.F, mod_scalars.F; keywords = AKT_BAK, MUD_AKT_BAK, SAND_AKT_BAK; input = biology.in, roms.in, sediment.in

Akt_limit: Upper threshold values to limit vertical mixing coefficients computed from vertical mixing parameterizations for tracer type variables. Although this is an engineering fix, the vertical mixing values inferred from ocean observations are rarely higher than this upper limit value.; dimension =; units = meters² second^-1; option =; routine = gls_corstep.F, lmd_vmix.F, mod_scalars.F, my25_corstep.F; keywords = AKT_LIMIT; input = roms.in

Akv_bak: Background vertical mixing coefficient for momentum. Ngrids values are expected.; dimension = Akv_bak(Ngrids); units = meters² second^-1; option =; routine = mod_mixing.F, mod_scalars.F; keyword = AKV_BAK; input = roms.in

Akv_limit: Upper threshold values to limit vertical mixing coefficients computed from vertical mixing parameterizations for momentum. Although this is an engineering fix, the vertical mixing values inferred from ocean observations are rarely higher than this upper limit value.; dimension =; units = meters² second^-1; option =; routine = gls_corstep.F, lmd_vmix.F, mod_scalars.F, my25_corstep.F; keywords = AKV_LIMIT; input = roms.in

Aout: Set of switches that determine what fields are written to the averages output file (AVGname).; dimension = Aout(NV,Ngrids); option =; routine = mod_ncparam.F; keyword = Aout; input = roms.in

aparnam: Assimilation parameters input file name.; option =; routine = mod_iounits.F; keyword = APARNAM; input = roms.in

AVG: Averages output NetCDF file name. Ngrids values are expected.; dimension = AVG(Ngrids); option =; routine = mod_iounits.F; keyword = AVGNAME; input = roms.in

B

balance

Balance operator logical switches for state variables to consider in the error covariance off-diagonal multivariate constraints:

balance(isSalt) = T, salinity
balance(isFsur) = T, free-surface
balance(isVbar) = F, 2D momentum (ubar, vbar)
balance(isVvel) = T, 3D momentum (u, v)

Guidlines:

The salinity contribution, balance(isSalt), depends only on temperature. Notice that temperature is used establish the balanced part of the other state variables.
The free-surface contribution, balance(isFsur), depends on salinity since we need to compute balanced density and integrate properly using LNM_flag and LNM_depth. This implies that balance(isSalt) needs to be TRUE too. It is independent of the 2D or 3D balance velocity terms.
The 3D momentum, balance(isVvel), depends on salinity since we need to compute balanced density. This implies that balance(isSalt) needs to be TRUE too.

dimension = balance(NV)

routine = ad_balance.F, mod_scalars.F, read_asspar.F, tl_balance.F, zeta_balance.F

keyword = balance

input = s4dvar.in

blk_ZQ: Height of surface air humidity measurement. Usually recorded at 10 meters. Ngrids values are expected.; dimension = blk_ZQ(Ngrids); units = meters; option =; routine = mod_scalars.F; keyword = BLK_ZQ; input = roms.in

blk_ZT: Height of surface air temperature measurement. Usually recorded at 2 or 10 meters. Ngrids values are expected.; dimension = blk_ZT(Ngrids); units = meters; option =; routine = mod_scalars.F; keyword = BLK_ZT; input = roms.in

blk_ZW: Height of surface winds measurement. Usually recorded at 10 meters. Ngrids values are expected.; dimension = blk_ZW(Ngrids); units = meters; option =; routine = mod_scalars.F; keyword = BLK_ZW; input = roms.in

bparnam: Biology parameters input file name.; option =; routine = mod_iounits.F; keyword = BPARNAM; input = roms.in

BRY: Open boundary conditions input NetCDF file name. Ngrids values are expected.; dimension = BRY(Ngrids); option =; routine = mod_iounits.F; keyword = BRYNAME; input = roms.in

bvf_bak: Background Brunt-Vaisala frequency squared. Typical values for the ocean range (as a function of depth) from 1.0E-4 to 1.0E-6.; units = seconds^-2; routine = mod_scalars.F; keyword = BVF_BAK; input = roms.in

C

charnok_alpha: Charnok surface roughness used in the various formulations of surface turbulent kinetic energy flux in the GLS. Ngrids values are expected.; dimension = charnok_alpha(Ngrids); option = GLS_MIXING; routine = mod_scalars.F; keyword = CHARNOK_ALPHA; input = roms.in

CLM: Climatology input NetCDF file name. Ngrids values are expected.; dimension = CLM(Ngrids); option =; routine = mod_iounits.F; keyword = CLMNAME; input = roms.in

CnormB

Compute (T/F) open boundary conditions error covariance normalization factors:

CnormB(isFsur) free-surface
CnormB(isUbar) 2D U-momentum
CnormB(isVbar) 2D V-momentum
CnormB(isUvel) 3D U-momentum
CnormB(isVvel) 3D V-momentum
CnormB(isTvar) tracers (NT values exppected)

dimension = CnormB(MstateVar, 4)

routine = mod_scalars.F, normalization.F, read_asspar.F

keyword = CnormB

input = s4dvar.in

CnormF

Compute (T/F) surface forcing error covariance normalization factors:

CnormF(isTsur) tracer flux (NT values exppected)
CnormF(isUstr) wind U-stress
CnormF(isVstr) wind V-stress

dimension = CnormF(2 + NT)

routine = read_asspar.F

keyword = CnormF

input = s4dvar.in

CnormI

Compute (T/F) initial conditions error covariance normalization factors:

CnormI(isFsur) free-surface
CnormI(isUbar) 2D U-momentum
CnormI(isVbar) 2D V-momentum
CnormI(isUvel) 3D U-momentum
CnormI(isVvel) 3D V-momentum
CnormI(isTvar) tracers (NT values exppected)

dimension = CnormI(MstateVar)

routine = read_asspar.F

keyword = CnormI

input = s4dvar.in

CnormM

Compute (T/F) model error covariance normalization factors:

CnormM(isFsur) free-surface
CnormM(isUbar) 2D U-momentum
CnormM(isVbar) 2D V-momentum
CnormM(isUvel) 3D U-momentum
CnormM(isVvel) 3D V-momentum
CnormM(isTvar) tracers (NT values exppected)

dimension = CnormM(MstateVar)

routine = read_asspar.F

keyword = CnormM

input = s4dvar.in

crgban_cw: Surface flux due to Craig and Banner wave breaking used in the various formulations of surface turbulent kinetic energy flux in the GLS. Ngrids values are expected.; dimension = crgban_cw(Ngrids); option = GLS_MIXING; routine = mod_scalars.F; keyword = CRGBAN_CW; input = roms.in

Csed: Sediment concentration used in analytical initial conditions. It is used to initialize full 3D cohesive and non-cohesive constant (homogeneous) concentrations of sediment.; dimension = Csed(NST,Ngrids); units = kilograms meter^-3; option = SEDIMENT; routine = mod_sediment.F; keywords = MUD_CSED, SAND_CSED; input = sediment.in

D

Dcrit: Minimum depth for wetting and drying. Ngrids values are expected.; dimension = Dcrit(Ngrids); units = meters; option =; routine = mod_scalars.F; keyword = DCRIT; input = roms.in

DendS: Ending day for adjoint sensitivity forcing. Ngrids values are expected.; Note: The adjoint forcing is applied at every time step according to desired state functional stored in the adjoint sensitivity NetCDF file. DstrS must be less than or equal to DendS. If both values are zero, their values are reset internally to the full range of the adjoint integration.; dimension = DendS(Ngrids); option =; routine = mod_scalars.F; keyword = DendS; input = roms.in

DIA: Diagnostics output NetCDF file name. Ngrids values are expected.; dimension = DIA(Ngrids); option =; routine = mod_iounits.F; keyword = DIANAME; input = roms.in

Dout: Set of switches that determine what fields are written to the diagnostics output file (DIAname).; dimension = Dout(NV,Ngrids); option =; routine = mod_ncparam.F; keyword = Dout; input = roms.in

dstart: Time stamp assigned to model initialization. Usually a Calendar linear coordinate, like modified Julian Day.; option =; units = days; routine = mod_scalars.F; keyword = DSTART; input = roms.in

DstrS: Starting day for adjoint sensitivity forcing. Ngrids values are expected.; Note: The adjoint forcing is applied at every time step according to desired state functional stored in the adjoint sensitivity NetCDF file. DstrS must be less than or equal to DendS. If both values are zero, their values are reset internally to the full range of the adjoint integration.; dimension = DstrS(Ngrids); option =; routine = mod_scalars.F; keyword = DstrS; input = roms.in

dt: Time-Step size in seconds. If 3D configuration, dt is the size of the baroclinic time-step. If only 2D configuration, dt is the size of the barotropic time-step. Ngrids values are expected.; dimension = dt(Ngrids); option =; routine = mod_scalars.F; keyword = DT; input = roms.in

dTdz_min: Minimum d(T)/d(z) above which the balanced salinity (deltaS_b) is computed. Ngrids values are expected.; dimension = dTdz_min(Ngrids); option =; routine = ad_balance.F, mod_scalars.F, read_asspar.F, tl_balance.F; keyword = dTdz_min; input = s4dvar.in

Dwave: wind-induced wave direction. Direction the waves are coming from; measured clockwise from geographic North. (nautical convention).; dimension = Dwave(LBi:UBi,LBj:UBj); pointer = FORCES(ng)%Dwave; units = degrees; grid = rho-points; option =; routine = ssw_bbl.h, mb_bbl.h, sg_bbl.h, ana_wwave.h, radiation_stress.F

E

Erate: Surface erosion rate for cohesive and non-cohesive sediment.; dimension = Erate(NST,Ngrids); units = kilograms meter^-2 second^-1; option = SEDIMENT; routine = mod_sediment.F; keywords = MUD_ERATE, SAND_ERATE; input = sediment.in

ERstr: Starting ensemble run (perturbation or iteration) number.; option =; routine = mod_scalars.F; keyword = ERstr; input = roms.in

ERend: Ending ensemble run (perturbation or iteration) number.; option =; routine = mod_scalars.F; keyword = ERend; input = roms.in

EWperiodic: East-West periodic boundary condition.; dimension = EWperiodic(Ngrids); option =

F

fbionam: Input script file name containing biological floats behavior model parameters.; option = FLOATS; routine = inp_par.F, mod_iounits.F, read_fltpar.F; keyword = FBIONAM; input = floats.in

Fcoor: Initial horizontal location (Fx0 and Fy0) coordinate type. If Fcoor = 0 then rho grid points are used. If Fcoor = 1 then location is given in latitude and longitude. Fcoor is column C in the POS specification at the end of the floats.in file.; option = FLOATS; routine = inp_par.F; input = floats.in

Fcount: Number of floats to be released at the specified (Fx0,Fy0,Fz0) location. It must be equal or greater than one. If Fcount is greater than one, a cluster distribution of floats centered at (Fx0,Fy0,Fz0) is activated. The total number of floats trajectories to compute must add up to NFLOATS. Fcount is column N in the POS specification at the end of the floats.in file.; option = FLOATS; routine = inp_par.F; input = floats.in

FCTA: Input NetCDF filename for the forecasts initialized from the analysis of the current 4D-Var cycle.; option =; routine =; keyword = FCTnameA; input = roms.in

FCTB: Input NetCDF filename for the forecasts initialized from the analysis of the previous 4D-Var cycle.; option =; routine =; keyword = FCTnameB; input = roms.in

Fdt: Float cluster release time interval in days. This is only used if Fcount is greater than 1. If Fdt gt; 0 a cluster of floats will be deployed from (Fx0,Fy0,Fz0) at Fdt intervals until Fcount floats are released. If Fdt = 0 Fcount floats will be deployed simultaneously with a distribution centered at (Fx0,Fy0,Fz0) and defined by (Fdx,Fdy,Fdz). This value must be of type real (i.e. 5.d0).; option = FLOATS; routine = inp_par.F; input = floats.in

Fdx: Cluster x-distribution parameter. This is only used if Fcount is greater than 1 and Fdt = 0. This value must be of type real (i.e. 5.d0).; option = FLOATS; routine = inp_par.F; input = floats.in

Fdy: Cluster y-distribution parameter. This is only used if Fcount is greater than 1 and Fdt = 0. This value must be of type real (i.e. 5.d0).; option = FLOATS; routine = inp_par.F; input = floats.in

Fdz: Cluster z-distribution parameter. This is only used if Fcount is greater than 1 and Fdt = 0. This value must be of type real (i.e. 5.d0).; option = FLOATS; routine = inp_par.F; input = floats.in

FLT: floats output NetCDF file name. Ngrids values are expected.; dimension = FLT(Ngrids); option =; routine = mod_iounits.F; keyword = FLTNAME; input = roms.in

FOIA: Input adjoint forcing NetCDF filename for computing observations impacts during the analysis-forecast cycle. If the forecast error metric is defined in state-space, then FOInameA should be regular adjoint forcing files just like ADSname. If the forecast error metric is defined in observation space (OBS_SPACE is activated) then the forecast is initialized OIFnameA (specified in s4dvar4.in input script) will have the structure of a 4D-Var observation file.; option =; routine =; keyword = FOInameA; input = roms.in

FOIB: Input adjoint forcing NetCDF filename for computing observations impacts during the analysis-forecast cycle. If the forecast error metric is defined in state-space, then FOInameB should be regular adjoint forcing files just like ADSname. If the forecast error metric is defined in observation space (OBS_SPACE is activated) then the forecast is initialized OIFnameB (specified in s4dvar4.in input script) will have the structure of a 4D-Var observation file.; option =; routine =; keyword = FOInameB; input = roms.in

food_supply: Initial food supply (constant source) concentration (mg Carbon/l). Ngrids values are expected.; dimension = food_supply(Ngrids); option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = food_supply; input = behavior_oyster.in

fposnam: Input initial floats positions file name (floats.in).; option = FLOATS; routine = mod_iounits.F; keyword = FPOSNAM; input = roms.in

Fprint: Switch to control the printing of floats positions to standard output file. This switch can be used to turn off the printing of information when thousands of floats are released. This information is still in the output floats NetCDF file. Ngrids values are expected.; dimension = Fprint(Ngrids); option = FLOATS; routine = mod_floats.F, read_fltpar.F; keyword = Fprint; input = floats.in

FRC: Input forcing fields file name(s). Ngrids values are expected.; dimension = FRC(Ngrids); option =; routine = mod_iounits.F; keyword = FRCNAME; input = roms.in

frrec: Flag to indicate re-start from a previous solution. Ngrids values are expected. For new solutions (not a model restart) use frrec = 0. In a re-start solution, frrec is the time index in the floats NetCDF file assigned for initialization. If frrec is negative (say frrec = -1), the floats will re-start from the most recent time record. That is, the initialization record is assigned internally.; dimension = frrec(Ngrids); option = FLOATS; routine = mod_scalars.F; keyword = FRREC; input = floats.in

Ft0: Time, in days, of float release after model initialization. This value must be of type real (i.e. 0.d0).; option = FLOATS; routine = inp_par.F; input = floats.in

Ftype: Float trajectory type. If Ftype = 1, float(s) will be 3D Lagrangrian particles. If Ftype = 2, float(s) will be isobaric particles ( $p=g*(z+zeta)={\text{constant}}$ ). If Ftype = 3, float(s) will be geopotential (constant depth) particles.; option = FLOATS; routine = inp_par.F; input = floats.in

FWD: Forward trajectory input NetCDF file name. Ngrids values are expected.; dimension = FWD(Ngrids); option =; routine = read_phypar.F; keyword = FWDNAME; input = roms.in

Fx0: Initial float(s) x-location in grid units or longitude depending on the value of Fcoor. This value must be of type real (i.e. 5.d0).; option = FLOATS; routine = inp_par.F; input = floats.in

Fy0: Initial float(s) y-location in grid units or longitude depending on the value of Fcoor. This value must be of type real (i.e. 5.d0).; option = FLOATS; routine = inp_par.F; input = floats.in

Fz0: Initial float(s) z-location in vertical levels or depth. If Fz0 is less than or equal to zero then Fz0 is the initial depth in meters. If Fz0 is greater than 0 and less than N(ng) the initial position is relative to the W grid (0 is the bottom and N is the surface). This value must be of type real (i.e. -45.d0).; option = FLOATS; routine = inp_par.F; input = floats.in

G

gamma2: Slipperiness variable, either 1.0 (free slip) or -1.0 (no slip). Ngrids values are expected.; dimension = gamma2(Ngrids); routine = mod_grid.F, mod_scalars.F; keyword = GAMMA2; input = roms.in

Gfactor_DS: Salinity I-axis increment for planktonic larvae growth rate factor (nondimensional) as a function salinity and temperature.; option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Gfactor_DS; input = behavior_oyster.in

Gfactor_DT: Temperature J-axis increment for planktonic larvae growth rate factor (nondimensional) as a function salinity and temperature.; option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Gfactor_DT; input = behavior_oyster.in

Gfactor_Im: Number of values in salinity I-axis for planktonic larvae growth rate factor (nondimensional) as a function salinity and temperature.; option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Gfactor_Im; input = behavior_oyster.in

Gfactor_Jm: Number of values in temperature J-axis for planktonic larvae growth rate factor (nondimensional) as a function salinity and temperature.; option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Gfactor_Jm; input = behavior_oyster.in

Gfactor_S0: Starting value for salinity I-axis for planktonic larvae growth rate factor (nondimensional) as a function salinity and temperature.; option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Gfactor_S0; input = behavior_oyster.in

Gfactor_T0: Starting value for temperature J-axis for planktonic larvae growth rate factor (nondimensional) as a function salinity and temperature.; option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Gfactor_T0; input = behavior_oyster.in

Gfactor_table: Look-up table, Gfactor(15,24), for planktonic larvae growth rate factor (nondimensional) as a function salinity and temperature.; option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Gfactor_table; input = behavior_oyster.in

gls_c1: Generic length-scale closure independent shear production coefficient. Ngrids values are expected.; dimension = gls_c1(Ngrids); option = GLS_MIXING; routine = mod_scalars.F; keyword = GLS_C1; input = roms.in

gls_c2: Generic length-scale closure independent dissipation coefficient. Ngrids values are expected.; dimension = gls_c2(Ngrids); option = GLS_MIXING; routine = mod_scalars.F; keyword = GLS_C2; input = roms.in

gls_c3m: Generic length-scale closure independent buoyancy production coefficient (minus). Ngrids values are expected.; dimension = gls_c3m(Ngrids); option = GLS_MIXING; routine = mod_scalars.F; keyword = GLS_C3M; input = roms.in

gls_c3p: Generic length-scale closure independent buoyancy production coefficient (plus). Ngrids values are expected.; dimension = gls_c3p(Ngrids); option = GLS_MIXING; routine = mod_scalars.F; keyword = GLS_C3P; input = roms.in

gls_cmu0: Generic length-scale closure independent stability coefficient. Ngrids values are expected.; dimension = gls_cmu0(Ngrids); option = GLS_MIXING; routine = mod_scalars.F; keyword = GLS_CMU0; input = roms.in

gls_Kmin: Generic length-scale minimum value of specific turbulent kinetic energy. Ngrids values are expected.; dimension = gls_Kmin(Ngrids); option = GLS_MIXING; routine = mod_mixing.F, mod_scalars.F; keyword = GLS_KMIN; input = roms.in

gls_m: Generic length-scale turbulent kinetic energy exponent. Ngrids values are expected.; dimension = gls_m(Ngrids); option = GLS_MIXING; routine = mod_mixing.F, mod_scalars.F; keyword = GLS_M; input = roms.in

gls_n: Generic length-scale turbulent length scale exponent. Ngrids values are expected.; dimension = gls_n(Ngrids); option = GLS_MIXING; routine = mod_mixing.F, mod_scalars.F; keyword = GLS_N; input = roms.in

gls_p: Generic length-scale stability exponent. Ngrids values are expected.; dimension = gls_p(Ngrids); option = GLS_MIXING; routine = mod_mixing.F, mod_scalars.F; keyword = GLS_P; input = roms.in

gls_Pmin: Generic length-scale minimum value of dissipation. Ngrids values are expected.; dimension = gls_Pmin(Ngrids); option = GLS_MIXING; routine = mod_mixing.F, mod_scalars.F; keyword = GLS_PMIN; input = roms.in

gls_sigk: Generic length-scale closure independent constant Schmidt number for turbulent kinetic energy diffusivity. Ngrids values are expected.; dimension = gls_sigk(Ngrids); option = GLS_MIXING; routine = mod_scalars.F; keyword = GLS_SIGK; input = roms.in

gls_sigp: Generic length-scale closure independent constant Schmidt number for turbulent generic statistical field, psi. Ngrids values are expected.; dimension = gls_sigp(Ngrids); option = GLS_MIXING; routine = mod_scalars.F; keyword = GLS_SIGP; input = roms.in

GradErr: Upper bound on the relative error of the gradient for the Lanczos conjugate gradient algorithm.; routine = mod_fourdvar.F, read_asspar.F; keyword = GradErr; input = s4dvar.in

Grate_DF: Food supply I-axis increment for planktonic larvae growth rate (um/day) as a function of food supply (mg Carbon /l) and larval size (um).; option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Grate_DF; input = behavior_oyster.in

Grate_DL: Larval size J-axis increment for planktonic larvae growth rate (um/day) as a function of food supply (mg Carbon /l) and larval size (um).; option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Grate_DL; input = behavior_oyster.in

Grate_F0: Starting value for food supply I-axis for planktonic larvae growth rate (um/day) as a function of food supply (mg Carbon /l) and larval size (um).; option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Grate_F0; input = behavior_oyster.in

Grate_Im: Number of values in food supply I-axis for planktonic larvae growth rate (um/day) as a function of food supply (mg Carbon /l) and larval size (um).; option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Grate_Im; input = behavior_oyster.in

Grate_Jm: Number of values in larval size J-axis for planktonic larvae growth rate (um/day) as a function of food supply (mg Carbon /l) and larval size (um).; option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Grate_Jm; input = behavior_oyster.in

Grate_L0: Starting value for larval size J-axis for planktonic larvae growth rate (um/day) as a function of food supply (mg Carbon /l) and larval size (um).; option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Grate_L0; input = behavior_oyster.in

Grate_table: Look-up table, Grate(31,52), for planktonic larvae growth rate (um/day) as a function of food supply (mg Carbon /l) and larval size (um).; option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Grate_table; input = behavior_oyster.in

GRD: Grid Input NetCDF file name. Ngrids values are expected.; dimension = GRD(Ngrids); routine = mod_iounits.F; keyword = GRDNAME; input = roms.in

GridsInLayer: Number of grids in each nested layer. NestLayers values are expected.; dimension = GridsInLayer(NestLayers); option =; routine = mod_scalars.F; keyword = GridsInLayer; input = roms.in

GST: GST analysis input/output check pointing NetCDF file name. Ngrids values are expected.; dimension = GST(Ngrids); option =; routine = mod_iounits.F; keyword = GSTNAME; input = roms.in

H

HAR: Least-squares detiding harmonics output NetCDF file name. Ngrids values are expected.; dimension = HAR(Ngrids); option =; routine = mod_iounits.F; keyword = HARNAME; input = roms.in

HdecayB

Boundary conditions error covariance horizontal, isotropic decorrelation scales (m). A value is expected for each boundary edge in the following order:

1: west 2: south 3:east 4: north

HdecayB(isFsur) free-surface
HdecayB(isUbar) 2D U-momentum
HdecayB(isVbar) 2D V-momentum
HdecayB(isUvel) 3D U-momentum
HdecayB(isVvel) 3D V-momentum
HdecayB(isTvar) tracers (NT, Ngrids values expected)

dimension = HdecayB(4,MstateVar, Ngrids)

units = meters

routine = metrics.F, mod_netcdf.F, mod_scalars.F, normalization.F, read_asspar.F

keyword = HdecayB

input = s4dvar.in

HdecayF

Surface forcing error covariance horizontal, isotropic decorrelation scales (m):

HdecayF(isTsur) tracers flux (NT, Ngrids values expected)
HdecayF(isUstr) wind U-stress
HdecayF(isVstr) wind V-stress

dimension = HdecayF(2 + NT, Ngrids)

units = meters

routine = metrics.F, mod_netcdf.F, mod_scalars.F, normalization.F, read_asspar.F

keyword = HdecayF

input = s4dvar.in

HdecayI

Initial conditions error covariance horizontal, isotropic decorrelation scales (m):

HdecayI(isFsur) free-surface
HdecayI(isUbar) 2D U-momentum
HdecayI(isVbar) 2D V-momentum
HdecayI(isUvel) 3D U-momentum
HdecayI(isVvel) 3D V-momentum
HdecayI(isTvar) tracers (NT, Ngrids values expected)

dimension = HdecayI(MstateVar, Ngrids)

units = meters

routine = metrics.F, mod_netcdf.F, mod_scalars.F, normalization.F, read_asspar.F

keyword = HdecayI

input = s4dvar.in

HdecayM

Model error covariance horizontal, isotropic decorrelation scales (m):

HdecayM(isFsur) free-surface
HdecayM(isUbar) 2D U-momentum
HdecayM(isVbar) 2D V-momentum
HdecayM(isUvel) 3D U-momentum
HdecayM(isVvel) 3D V-momentum
HdecayM(isTvar) tracers (NT, Ngrids values expected)

dimension = HdecayM(MstateVar, Ngrids)

units = meters

routine = metrics.F, mod_netcdf.F, mod_scalars.F, normalization.F, read_asspar.F

keyword = HdecayM

input = s4dvar.in

HevecErr: Maximum error bound on Hessian eigenvectors in the Lanczos conjugate gradient algorithm. Note that even quite inaccurate eigenvectors are useful for pre-conditioning purposes.; routine = cgradient.F, congrad.F, mod_fourdvar.F, posterior.F, read_asspar.F, rpcg_lanczos.F; keyword = HevecErr; input = s4dvar.in

Hgamma

Horizontal stability and accuracy factor (< 1) used to scale the time-step of the convolution operator below its theoretical limit. Notice that four values are needed for Hgamma to facilitate the error covariance modeling for:

[1] initial conditions

[2] model

[3] boundary conditions

[4] surface forcing

dimension = Hgamma(4)

routine = metrics.F, mod_netcdf.F, mod_scalars.F, read_asspar.F

keyword = Hgamma

input = s4dvar.in

HIS: Output history data file name. Ngrids values are expected.; dimension = HIS(Ngrids); option =; routine = mod_iounits.F; keyword = HISNAME; input = roms.in

HISname: History output NetCDF file name. Ngrids values are expected.; dimension = HISname(Ngrids); option =; routine = mod_iounits.F; keyword = HISNAME; input = roms.in

Hout: Set of switches that determine what fields are written to the history output file (HISname).; dimension = Hout(NV,Ngrids); option =; routine = mod_ncparam.F; keyword = Hout; input = roms.in

Hz: Vertical level thicknesses, $\,H_{z}\,(\xi ,\eta ,s)$ .; dimension = Hz(LBi:UBi,LBj:UBj,N(ng)); pointer = GRID(ng)%Hz; tangent = tl_Hz; adjoint = ad_Hz; units = meter; grid = ρ-points; option = SOLVE3D; routine = set_depths.F

I

IAD: Adjoint initial conditions input NetCDF file name. Ngrids values are expected.; dimension = IAD(Ngrids); option =; routine = mod_iounits.F; keyword = IADNAME; input = roms.in

idbio: Identification indexes for biological tracer variables, t(:,:,:,:,idbio(:)).; dimension = idbio(NBT); option = BIOLOGY; routine = mod_scalars.F

idsed: Identification indexes for biological tracer variables, t(:,:,:,:,idsed(:)).; dimension = idsed(NST); option = SEDIMENT; routine = mod_scalars.F

ieast: Index of eastern boundary.; option =; routine = mod_scalars.F

Iend: Non-overlapping upper bound tile index in the i-direction. Its value depends on the tile rank (sub-domain partition).; routine = tile.h, get_tile.F

inert: Identification indexes for inert tracer variables, t(:,:,:,:,inert(:)).; dimension = inert(NPT); option = T_PASSIVE; routine = mod_scalars.F

INI: Nonlinear initial conditions input NetCDF file name. Ngrids values are expected.; dimension = INI(Ngrids); option =; routine = mod_iounits.F; keyword = ININAME; input = roms.in

inorth: Index of northern boundary.; option =; routine = mod_scalars.F

IRP: Representer initial conditions input NetCDF file name. Ngrids values are expected.; dimension = IRP(Ngrids); option =; routine = mod_iounits.F; keyword = IRPNAME; input = roms.in

isFsur: Assimilation state variable index for free-surface.; value = 1; routine = mod_ncparam.F

isalt: Tracer identification index for salinity, t(:,:,:,:,isalt).; routine = mod_scalars.F

isouth: Index of southern boundary.; option =; routine = mod_scalars.F

Istr: Non-overlapping lower bound tile index in the i-direction. Its value depends on the tile rank (sub-domain partition).; routine = tile.h, get_tile.F

isTvar: Assimilation state variable indices for tracers.; dimension = isTvar(MT); routine = mod_ncparam.F

isUbar: Assimilation state variable index for 2D U-momentum.; value = 2; routine = mod_ncparam.F

isVbar: Assimilation state variable index for 2D V-momentum.; value = 3; routine = mod_ncparam.F

isUvel: Assimilation state variable index for 3D U-momentum.; value = 4; routine = mod_ncparam.F

isVvel: Assimilation state variable index for 3D V-momentum.; value = 5; routine = mod_ncparam.F

itemp: Tracer identification index for potential temperature, t(:,:,:,:,itemp).; routine = mod_scalars.F

ITL: Tangent linear initial conditions input NetCDF file name. Ngrids values are expected.; dimension = ITL(Ngrids); option =; routine = mod_iounits.F; keyword = ITLNAME; input = roms.in

iwest: Index of western boundary.; option =; routine = mod_scalars.F

J

Jend: Non-overlapping upper bound tile index in the j-direction. Its value depends on the tile rank (sub-domain partition).; routine = tile.h, get_tile.F

Jstr: Non-overlapping lower bound tile index in the j-direction. Its value depends on the tile rank (sub-domain partition).; routine = tile.h, get_tile.F

Jwtype: Jerlov water type: an integer value from 1 to 5.; option =; routine = mod_mixing.F; keyword = WTYPE; input = roms.in

K

KendS: Ending vertical level of the 3D adjoint state variables whose sensitivity is required. Ngrids values are expected.; dimension = KendS(Ngrids); option =; routine = mod_scalars.F; keyword = KendS; input = roms.in

KstrS: Starting vertical level of the 3D adjoint state variables whose sensitivity is required. Ngrids values are expected.; dimension = KstrS(Ngrids); option =; routine = mod_scalars.F; keyword = KstrS; input = roms.in

L

Larvae_size0: Initial planktonic larvae size in terms of length (um). Ngrids values are expected.; dimension = Larvae_size0(Ngrids); option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Larvae_size0; input = behavior_oyster.in

Larvae_GR0: Initial planktonic larvae growth rate (um/day). Ngrids values are expected.; dimension = Larvae_GR0(Ngrids); option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = Larvae_GR0; input = behavior_oyster.in

LBC: Lateral boundary conditions.; dimension = LBC(4,nLBCvar,Ngrids); option =; routine = mod_param.F; keyword = LBC; input = bio_Fennel.in, ecosim.in, nemuro.in, npzd_Franks.in, npzd_iron.in, npzd_Powell.in, roms.in

LBi: Array lower bound dimension in the i-direction. In serial and shared-memory applications its value is LBi = -2 for East-West periodic grids or LBi = 0 for non-periodic grids . In distributed-memory its value is a function of the tile partition, LBi = Istr - NghostPoints.; option = LOWER_BOUND_I; routine = get_bounds.F, get_tile.F

LBj: Array lower bound dimension in the j-direction. In serial and shared-memory applications its value is LBj = -2 for North-South periodic grids or LBj = 0 for non-periodic grids . In distributed-memory its value is a function of the tile partition, LBj = Jstr - NghostPoints.; option = LOWER_BOUND_J; routine = get_bounds.F, get_tile.F

LcycleADJ: Logical switch(s) (T/F) used to recycle time records in output adjoint file. Ngrids values are expected. If TRUE, only the latest two re-start time records are maintained. If FALSE, all adjoint fields are saved every nADJ time-steps without recycling.; dimension = LcycleADJ(Ngrids); option =; routine = mod_scalars.F; keyword = LcycleADJ; input = roms.in

LcycleRST: Logical switch(s) (T/F) used to recycle time records in output re-start file. Ngrids values are expected. If TRUE, only the latest two re-start time records are maintained. If FALSE, all re-start fields are saved every nRST time-steps without recycling. The re-start fields are written at all levels in double precision unless the RST_SINGLE CPP option is activated.; dimension = LcycleRST(Ngrids); option = PERFECT_RESTART, RST_SINGLE; routine = mod_scalars.F; keyword = LcycleRST; input = roms.in

LcycleTLM: Logical switch(s) (T/F) used to recycle time records in output tangent linear file. Ngrids values are expected. If TRUE, only the latest two re-start time records are maintained. If FALSE, all tangent linear fields are saved every nTLM time-steps without recycling.; dimension = LcycleTLM(Ngrids); option =; routine = mod_scalars.F; keyword = LcycleTLM; input = roms.in

LdefNRM

Logical switch(s) (T/F) used to create new normalization NetCDF file for:

LdefNRM(1,:) initial conditions error covariance
LdefNRM(2,:) model error covariance
LdefNRM(3,:) boundary conditions error covariance
LdefNRM(4,:) surface forcing error covariance

The computation of the correlation normalization coefficients is very expensive and needs to be computed only once for a particular application provided that grid, land/sea masking (if any), and decorrelation scales (see HdecayM, VdecayM, TdecayM, HdecayI, VdecayI, HdecayB, VdecayB, HdecayF) remain the same. The user can use this switch in conjunction with the CnormM, CnormI, CnormB, CnormF switches to compute each coefficient separately. The normalization NetCDF file only needs to be created once and simultaneous runs can write to the same file. If using this approach, compute the normalization factors with the CORRELATION CPP-option and not I4DVAR, RBL4DVAR or R4DVAR.

dimension = LdefNRM(4, Ngrids)

option = I4DVAR, RBL4DVAR, R4DVAR, CORRELATION

routine = correlation.h, mod_scalars.F, read_asspar.F

keyword = LdefNRM

input = s4dvar.in

ldefout: Logical switch(s) (T/F) used to create new output files when initializing from a re-start file, |nrrec| > 0. Ngrids values are expected. If TRUE and applicable, a new history, average, diagnostic and station files are created during the initialization stage. If FALSE and applicable, data is appended to existing history, average, diagnostic and station files. See also parameters ndefHIS, ndefAVG and ndefDIA.; dimension = ldefout(Ngrids); option = PERFECT_RESTART; routine = mod_scalars.F; keyword = LDEFOUT; input = roms.in

levbfrc: Shallowest level to apply bottom momentum stress as a body-force. Ngrids values are expected.; dimension = levbfrc(Ngrids); option = BODYFORCE; routine = mod_scalars.F; keyword = LEVBFRC; input = roms.in

levsfrc: Deepest level to apply surface momentum stress as a body-force. Ngrids values are expected.; dimension = levsfrc(Ngrids); option = BODYFORCE; routine = mod_scalars.F; keyword = LEVSFRC; input = roms.in

Lfloats: Logical switch(s) (T/F) used to control the computation of floats trajectories within nested and/or multiple connected grids. Ngrids values are expected. By default this switch is set to TRUE in mod_scalars.F for all grids when the CPP option FLOATS is activated. The user can control which grids to process by turning on/off this switch.; dimension = Lfloats(Ngrids); option = FLOATS; routine = mod_scalars.F; keyword = Lfloats; input = floats.in

LhessianEV: Switch (T/F) to compute approximated Hessian eigenpairs in the Lanzos conjugate gradient algorithm.; routine = cgradient.F, congrad.F, mod_fourdvar.F, read_asspar.F, rpcg_lanczos.F; keyword = LhessianEV; input = s4dvar.in

LhotStart: Switch (T/F) to activate hot start in weak-constraint (R4DVAR and RBL4DVAR) algorithms of subsequent outer loops.; routine = ad_congrad.F, congrad.F, mod_fourdvar.F, read_asspar.F, tl_congrad.F; keyword = LhotStart; input = s4dvar.in

Lm: Number of interior grid points in the ξ-direction. Ngrids values are expected.; dimension = Lm(Ngrids); routine = mod_param.F; keyword = Lm; input = roms.in

Lm2CLM: Logical switch(s) (T/F) used to process 2D momentum (ubar, vbar) climatology. The CPP option M2CLIMATOLOGY is now obsolete and replaced with these switches to facilitate nesting applications. Currently, CLIMA(ng)%ubarclm and CLIMA(ng)%vbarclm are used for sponges and nudging. If using tidal forcing, the climatological values are adjusted to include tides.; dimension = Lm2CLM(Ngrids); routine = mod_scalars.F; keyword = Lm2CLM; input = roms.in

Lm3CLM: Logical switch(s) (T/F) used to process 3D momentum (u, v) climatology. The CPP option M3CLIMATOLOGY is now obsolete and replaced with these switches to facilitate nesting applications. Currently, CLIMA(ng)%uclm and CLIMA(ng)%vclm are used for sponges and nudging.; dimension = Lm3CLM(Ngrids); routine = mod_scalars.F; keyword = Lm3CLM; input = roms.in

LNM_depth: Level of no motion depth (m; positive) used to compute the balanced free-surface contribution in the error covariance balance operator. It is only relevant when LNM_flag=1, balance(isFsur)=T, and ZETA_ELLIPTIC is NOT activated. It is used to integrate the non-hydrostatic equation. Ngrids values are expected.; dimension = LNM_depth(Ngrids); units = meters; routine = ad_balance.F, mod_scalars.F, read_asspar.F, tl_balance.F; keyword = LNM_depth; input = s4dvar.in

LNM_flag

Level of no motion integration flag used to used to compute the balanced free-surface contribution:

LNM_flag = 0, integrate from local bottom to the surface

LNM_flag = 1, integrate from LNM_depth to surface or integrate from local bottom if shallower than LNM_depth

routine = ad_balance.F, mod_scalars.F, read_asspar.F, tl_balance.F

keyword = LNM_flag

input = s4dvar.in

LnudgeM2CLM: Logical switch(s) (T/F) used to activate the nudging of 2D momentum climatology. The CPP option M2CLM_NUDGING is now obsolete and replaced with these switches to facilitate nesting applications.

Users also need turn on (set to T) the logical switch Lm2CLM to process the required 2D momentum climatology data. This data can be set with analytical functions (ANA_M2CLIMA) or read from input climatology NetCDF files(s).

The nudging coefficients (CLIMA(ng)%M2nudgcof) can be set with analytical functions in ana_nudgcoef.h using CPP option ANA_NUDGCOEF. Otherwise it will be read from NetCDF file NUDNAME.; dimension = LnudgeM2CLM(Ngrids); routine = mod_scalars.F; keyword = LnudgeM2CLM; input = roms.in

LnudgeM3CLM: Logical switch(s) (T/F) used to activate the nudging of 3D momentum climatology. The CPP option M3CLM_NUDGING is now obsolete and replaced with these switches to facilitate nesting applications.

Users also need turn on (set to T) the logical switch Lm3CLM to process the required 3D momentum climatology data. This data can be set with analytical functions (ANA_M3CLIMA) or read from input climatology NetCDF files(s).

The nudging coefficients (CLIMA(ng)%M3nudgcof) can be set with analytical functions in ana_nudgcoef.h using CPP option ANA_NUDGCOEF. Otherwise it will be read from NetCDF file NUDNAME.; dimension = LnudgeM3CLM(Ngrids); routine = mod_scalars.F; keyword = LnudgeM3CLM; input = roms.in

LnudgeTCLM: Logical switch(s) (T/F) used to activate the nudging of active and inert tracer climatology variables. These switches also control which tracer variables to nudge. The CPP option TCLM_NUDGING is now obsolete and replaced with these switches to facilitate nesting applications.

Only NAT active tracers (temperature, salinity) and NPT inert tracers need to be specified here.
LnudgeTCLM(itemp,ng) for temperature (itemp=1)
LnudgeTCLM(isalt,ng) for salinity (isalt=2)
LnudgeTCLM(NAT+1,ng) for inert tracer 1
... ...
LnudgeTCLM(NAT+NPT,ng) for inert tracer NPT
Other biological and sediment tracers switches are specified in their respective input scripts.

Users also need turn on (set to T) the logical switch LtracerCLM to process the required 3D tracer climatology data. This data can be set with analytical functions (ANA_TCLIMA) or read from input climatology NetCDF files(s).

The nudging coefficients (CLIMA(ng)%Tnudgcof) can be set with analytical functions in ana_nudgcoef.h using CPP option ANA_NUDGCOEF. Otherwise it will be read from NetCDF file NUDNAME.; dimension = LnudgeTCLM(Ngrids); routine = mod_scalars.F; keyword = LnudgeTCLM; input = bio_Fennel.in, ecosim.in, nemuro.in, npzd_Franks.in, npzd_iron.in, npzd_Powell.in, roms.in

Lprecond

Switch (T/F) to activate preconditioning in the I4DVAR algorithm. Two types of Limited-Memory preconditioners (LMP) are available Tshimanga et al., (2008): Spectral and Ritz.

If Lprecond=T and Lritz=F, Spectral LMP

If Lprecond=T and Lritz=T, Ritz LMP

routine = ad_congrad.F, cgradient.F, congrad.F, mod_fourdvar.F, read_asspar.F, rpcg_lanczos.F, tl_congrad.F

keyword = Lprecond

input = s4dvar.in

Lritz: Switch to activate either Ritz Limited-Memory Preconditioner (T) or spectral Limited-Memory Preconditioner (F) in the I4DVAR algorithm using eigenpairs approximation for the Hessian matrix. The accuracy of the Hessian eigenvectors (HevecErr) can be used to fine tune the minimization. That is, HevecErr can be used to control the number of eigenvalues of the preconditioning Hessian matrix. See Tshimanga et al., (2008) for details.; routine = cgradient.F, congrad.F, mod_fourdvar.F, read_asspar.F, rpcg_lanczos.F; keyword = Lritz; input = s4dvar.in

LrstGST: Logical switch(s) (T/F) used to restart GST analysis. If TRUE, the check pointing data is read in from the GST restart NetCDF file. If FALSE and applicable, the check pointing GST data is saved and overwritten every nGST iterations of the algorithm.; dimension =; option =; routine = mod_scalars.F; keyword = LcycleTLM; input = roms.in

Lsediment: Logical switch(s) (T/F) used to control sediment model computation within nested and/or multiple connected grids. Ngrids values are expected. By default this switch is set to TRUE in mod_scalars.F for all grids when the CPP option SEDIMENT is activated. The user can control which grids to process by turning on/off this switch.; dimension = Lsediment(Ngrids); option = SEDIMENT; routine = mod_scalars.F; keyword = Lsediment; input = sediment.in

LsshCLM: Logical switch(s) (T/F) used to process sea-surface height climatology. The CPP option ZCLIMATOLOGY is now obsolete and replaced with these switches to facilitate nesting applications. Currently, the sea-surface height climatology, CLIMA(ng)%ssh, is not used but is kept for future use.

The nudging of SSH on the free-surface governing equation (vertically integrated continuity equation) is not allowed because it violates mass/volume conservation. Recall that the time rate of change of free-surface is computed from the divergence of ubar and vbar. If such a nudging term is required, it needs to be specified on the momentum equations for (u,v) and/or (ubar,vbar). If done on (u,v) only, its effects enter the 2D momentum equations via the residual vertically integrated forcing term.; dimension = LsshCLM(Ngrids); routine = mod_scalars.F; keyword = LsshCLM; input = roms.in

Lstate: Logical switches (T/F) to specify the adjoint state variables whose sensitivity is required. Ngrids values are expected for each state variable.; routine = mod_scalars.F; keyword = Lstate; input = roms.in

Lstations: Logical switch(s) (T/F) used to control the writing of station data within nested and/or multiple connected grids. Ngrids values are expected. By default this switch is set to TRUE in mod_scalars.F for all grids when the CPP option STATIONS is activated. The user can control which grids to process by turning on/off this switch.; dimension = Lstations(Ngrids); option = STATIONS; routine = mod_scalars.F; keyword = Lstations; input = stations.in

LtracerCLM: Logical switch(s) (T/F) used to process active and inert climatology tracer variables. The CPP option TCLIMATOLOGY is now obsolete and replaced with these switches to facilitate nesting applications. Currently, CLIMA(ng)%tclm is used for horizontal mixing, sponges, and nudging.

Only NAT active tracers (temperature, salinity) and NPT inert tracers need to be specified here.
LtracerCLM(itemp,ng) for temperature (itemp=1)
LtracerCLM(isalt,ng) for salinity (isalt=2)
LtracerCLM(NAT+1,ng) for inert tracer 1
... ...
LtracerCLM(NAT+NPT,ng) for inert tracer NPT
Other biological and sediment tracers switches are specified in their respective input scripts.

These switches also control which climatology tracer fields (especially passive tracers) need to be processed so we may reduce the memory allocation for the CLIMA(ng)%tclm array.; dimension = LtracerCLM(MT,Ngrids); routine = mod_scalars.F; keyword = LtracerCLM; input = bio_Fennel.in, ecosim.in, nemuro.in, npzd_Franks.in, npzd_iron.in, npzd_Powell.in, roms.in

LtracerSponge: Logical switch(s) (T/F) to increase/decrease horizontal diffusivity in specific areas of the domain. It can be used to specify sponge areas with larger horizontal mixing coefficients for damping of high frequency noise due to open boundary conditions or nesting. The CPP option SPONGE is now obsolete and replaced with these switches to facilitate or not sponge areas over a particular nested grid.

The horizontal mixing distribution is specified in ini_hmixcoef.F as:
diff2(i,j,itrc) = diff_factor(i,j) * diff2(i,j,itrc)
diff4(i,j,itrc) = diff_factor(i,j) * diff4(i,j,itrc)
The variable diff_factor can be read from the grid NetCDF file. Alternately, the horizontal viscosity in the sponge area can be set-up with analytical functions in ana_sponge.h using CPP ANA_SPONGE when the LuvSponge is turned ON for a particular grid.; dimension = LtracerSponge(MT,Ngrids); routine = mod_scalars.F; keyword = LtracerSponge; input = roms.in

LtracerSrc: Logical switch(s) (T/F) used to activate tracers point Sources/Sinks (like river runoff) and to specify which tracer variables to consider. Only NAT active tracers (temperature, salinity) and NPT inert tracers need to be specified here.; dimension = LtracerSrc(MT,Ngrids); routine = mod_scalars.F; keyword = LtracerSrc; input = bio_Fennel.in, ecosim.in, nemuro.in, npzd_Franks.in, npzd_iron.in, npzd_Powell.in, roms.in

Other biological and sediment tracers switches are activated in their respective input scripts.

In nesting applications, turn on only the grids that require activation and processing of tracers point Sources/Sinks.

LuvSponge: Logical switch(s) (T/F) to increase/decrease horizontal viscosity in specific areas of the domain. It can be used to specify sponge areas with larger horizontal mixing coefficients for damping of high frequency noise due to open boundary conditions or nesting. The CPP option SPONGE is now obsolete and replaced with these switches to facilitate or not sponge areas over a particular nested grid.

The horizontal mixing distribution is specified in ini_hmixcoef.F as:
visc2_r(i,j) = visc_factor(i,j) * visc2_r(i,j)
visc4_r(i,j) = visc_factor(i,j) * visc4_r(i,j)
The variable visc_factor can be read from the grid NetCDF file. Alternately, the horizontal viscosity in the sponge area can be set-up with analytical functions in ana_sponge.h using CPP ANA_SPONGE when the switch LuvSponge is turned ON for a particular grid.; dimension = LuvSponge(Ngrids); routine = mod_scalars.F; keyword = LuvSponge; input = roms.in

LuvSrc: Logical switch(s) (T/F) used to activate momentum horizontal transport points Sources/Sinks. Usually it is used to turn on/off river runoff transport (u or v variables) in an application. In nesting applications, turn on only the grids that require activation and processing of momentum point Sources/Sinks.; dimension = LuvSrc(Ngrids); routine = mod_scalars.F; keyword = LuvSrc; input = roms.in

LwSrc: Logical switch(s) (T/F) used to activate mass points Sources/Sinks. Usually it is used to turn on/off volume vertical influx (w) in an application. In nesting applications, turn on only the grids that require activation and processing of mass influx point Sources/Sinks.; dimension = LwSrc(Ngrids); routine = mod_scalars.F; keyword = LwSrc; input = roms.in

LwrtNRM

Logical switch(s) (T/F) to write out correlation normalization factors for:

LwrtNRM(1,:) initial conditions error covariance
LwrtNRM(2,:) model error covariance
LwrtNRM(3,:) boundary conditions error covariance
LwrtNRM(4,:) surface forcing error covariance

If TRUE, these factors computed and written to NRMnameI, NRMnameM, NRMnameB, and NRMnameF NetCDF files, respectively. If FALSE, they are read from NRMname NetCDF file.

dimension = LwrtNRM(4, Ngrids)

option = I4DVAR, RBL4DVAR, R4DVAR, CORRELATION

routine = correlation.h, mod_scalars.F, normalization.F, read_asspar.F

keyword = LwrtNRM

input = s4dvar.in

M

M2nudg: Nudging time scale for 2D momentum. Ngrids values are expected.; dimension = M2nudg(Ngrids); units = days; option =; routine = mod_scalars.F; keyword = M2NUDG; input = roms.in

M3nudg: Nudging time scale for 3D momentum. Ngrids values are expected.; dimension = M3nudg(Ngrids); units = days; option =; routine = mod_scalars.F; keyword = M3NUDG; input = roms.in

MaxIterGST: Maximum number of GST algorithm iterations.; dimension =; option =; routine = mod_scalars.F; keyword = MaxIterGST; input = roms.in

ml_depth: Mixed-layer depth (m; positive) in deltaS_b smoothing coefficient. Ngrids values are expected.; dimension = ml_depth(Ngrids); units = meters; routine = ad_balance.F, mod_scalars.F, read_asspar.F, tl_balance.F; keyword = ml_depth; input = s4dvar.in

Mm: Number of interior grid points in the η-direction. Ngrids values are expected.; dimension = Mm(Ngrids); routine = mod_param.F; keyword = Mm; input = roms.in

morph_fac: Morphological scale factor for cohesive and non-cohesive sediment.; dimension = morph_fac(NST,Ngrids); option = SEDIMENT; routine = mod_sediment.F; keywords = MUD_MORPH_FAC, SAND_MORPH_FAC; input = sediment.in

MyAppCPP: C-preprocessing flag to define the specific configuration. In versions up to 2.3 this flag was one of the predefined model applications that headed the cppdefs.h file. You must make the value of MyAppCPP consistent with variable ROMS_APPLICATION in the build script or makefile if you are not using build.sh or build.bash. ROMS converts the ROMS_APPLICATION variable to lowercase to determine the name of the file to include.; keyword = MyAppCPP; input = roms.in

MT: The maximum number of tracers between all nested grids. Basically the sum of all NT.

N

N: Number of vertical levels for each nested grid. Ngrids values are expected.; dimension = N(Ngrids); routine = mod_param.F; keyword = N; input = roms.in

NAT: Number of active tracer-type variables. Usually, it has a value of two for potential temperature and salinty.; option = SOLVE3D; routine = mod_param.F; keyword = NAT; input = roms.in

nADJ: Number of time-steps between writing fields into adjoint model file. Ngrids values are expected.; dimension = nADJ(Ngrids); routine = mod_scalars.F; keyword = NADJ; input = roms.in

nAVG: Number of time-steps between writing time-averaged data into averages file. Averaged date is written for all fields. Ngrids values are expected.; dimension = nAVG(Ngrids); routine = mod_scalars.F; keyword = NAVG; input = roms.in

Nbed: Number of sediment bed layers.; routine = mod_param.F; keyword = Nbed; input = roms.in

Nbico: Number of iterations in the biconjugate gradient algorithm used to solve the elliptic equation for sea surface height in the error covariance balance operator. We need as many iterations are required to decrease the error value of the reference free-surface to 1E-8 or smaller. In some applications Nbico=200 will do the job. Ngrids values are expected.; Warning: Be aware that there are 4 arrays that are allocated with this parameter and its value may be constrained by available memory:
FOURDVAR(ng) % p_r2d (LBi:UBi,LBj:UBj,Nbico(ng))
FOURDVAR(ng) % r_r2d (LBi:UBi,LBj:UBj,Nbico(ng))
FOURDVAR(ng) % bp_r2d (LBi:UBi,LBj:UBj,Nbico(ng))
FOURDVAR(ng) % br_r2d (LBi:UBi,LBj:UBj,Nbico(ng))
All the iteration values are needed in the backward stepping of the adjoint.; dimension = Nbico(Ngrids); routine = ad_balance.F, mod_fourdvar.F, mod_param.F, read_asspar.F, tl_balance, zeta_balance.F; keyword = Nbico; input = s4dvar.in

NBT: Number of biological tracer-type variables.; option = BIOLOGY; routine = mod_param.F; keyword = NBT; input = biology.in

NCS: Number of cohesive (mud) sediment tracer-type variables.; option = SEDIMENT; routine = mod_param.F; keyword = NCS; input = roms.in

NCV: Number of eigenvectors to compute for the Lanczos/Arnoldi problem. NCV must be greater than NEV.; option =; routine = mod_storage.F; keyword = NCV; input = roms.in

ndefADJ: Number of time-steps between the creation of new adjoint file. If ndefADJ = 0, the model will only process one adjoint file. This feature is useful for long simulations when output NetCDF files get too large; it creates a new file every ndefADJ time-steps. Ngrids values are expected.; dimension = ndefADJ(Ngrids); routine = mod_scalars.F; keyword = NDEFADJ; input = roms.in

ndefAVG: Number of time-steps between the creation of new average file. If ndefAVG = 0, the model will only process one average file. This feature is useful for long simulations when average files get too large; it creates a new file every ndefAVG time-steps. Ngrids values are expected.; dimension = ndefAVG(Ngrids); routine = mod_scalars.F; keyword = NDEFAVG; input = roms.in

ndefDIA: Number of time-steps between the creation of new time-averaged diagnostics file. If ndefDIA = 0, the model will only process one diagnostics file. This feature is useful for long simulations when diagnostics files get too large; it creates a new file every ndefDIA time-steps. Ngrids values are expected.; dimension = ndefDIA(Ngrids); routine = mod_scalars.F; keyword = NDEFDIA; input = roms.in

ndefHIS: Number of time-steps between the creation of new history file. If ndefHIS = 0, the model will only process one history file. This feature is useful for long simulations when history files get too large; it creates a new file every ndefHIS time-steps. Ngrids values are expected.; dimension = ndefHIS(Ngrids); routine = mod_scalars.F; keyword = NDEFHIS; input = roms.in

ndefTLM: Number of time-steps between the creation of new tangent linear file. If ndefTLM = 0, the model will only process one tangent linear file. This feature is useful for long simulations when output NetCDF files get too large; it creates a new file every ndefTLM time-steps. Ngrids values are expected.; dimension = ndefTLM(Ngrids); routine = mod_scalars.F; keyword = NDEFTLM; input = roms.in

nDIA: Number of time-steps between writing time-averaged diagnostics data into diagnostics file. Averaged date is written for all fields. Ngrids values are expected.; dimension = nDIA(Ngrids); routine = mod_scalars.F; keyword = NDIA; input = roms.in

ndtfast: Number of barotropic time-steps between each baroclinic time step. If only 2D configuration, ndtfast should be unity since there is no need to split time-stepping.; option =; routine = mod_scalars.F; keyword = NDTFAST; input = roms.in

NestLayers: Number of grid nesting layers. This parameter is used to allow refinement and composite grid combinations as shown for the Refinement and Partial Boundary Composite Sub-Classes. In non-nesting applications, set NestLayers = 1.; option =; routine = mod_param.F; keyword = NestLayers; input = roms.in

NEV: Number of eigenvalues to compute for the Lanczos/Arnoldi problem. Notice that the model memory requirement increases substantially as NEV increases. The GST requires NEV+1 copies of the model state vector. The memory requirements are decreased in distributed-memory applications.; option =; routine = mod_storage.F; keyword = NEV; input = roms.in

nFfiles: Number of forcing NetCDF files. Ngrids values are expected.; dimension = nFfiles(Ngrids); option =; routine = mod_iounits.F; keyword = NFFILES; input = roms.in

nFLT: Number of time-steps between writing data into floats file (FLTname). Ngrids values are expected.; dimension = nFLT(Ngrids); option = FLOATS; routine = mod_scalars.F; keyword = NFLT; input = roms.in

Nfloats: Number of floats to release in each nested grid. Value(s) are used to dynamically allocate the arrays in the FLOATS array structure. Ngrids values are expected.; dimension = Nfloats(Ngrids); option = FLOATS; routine = mod_floats.F init_param.F; keyword = NFLOATS; input = floats.in

NGCname: Input nested grids contact points information file name. This NetCDF file is currently generated using script matlab/grid/contact.m from the ROMS Matlab repository. The nesting information is not trivial and this Matlab scripts is quite complex. See Nested_Grids and Grid_Processing_Scripts for more information.; option = NESTING; routine = mod_iounits.F; keyword = NGCNAME; input = roms.in

NghostPoints: Number of ghost points in the halo region used in distributed-memory configurations.; option = GHOST_POINTS; routine = mod_param.F

Ngrids: Number of nested and/or multiple connected grids to solve.; routine = mod_param.F

nGST: Number of GST iterations between storing of check pointing data into NetCDF file. The restart data is always saved if MaxIterGST is reached without convergence. It is also saved when convergence is achieved. It is always a good idea to save the check pointing data at regular intervals so there is a mechanism to recover from an unexpected interruption in this very expensive computation. The check pointing data can be also be used to recompute the Ritz vectors by changing some of the parameters, like convergence criteria (Ritz_tol) and number of Arnoldi iterations (iparam(3)).; routine = mod_scalars.F; keyword = NGST; input = roms.in

nHIS: Number of time-steps between writing fields into history file. Ngrids values are expected.; dimension = nHIS(Ngrids); routine = mod_scalars.F; keyword = NHIS; input = roms.in

Nimpact: If observations impact or observations sensitivity, set the 4D-Var outer loop to consider in the computation of the observations impact or observation sensitivity. It must be less than or equal to Nouter. This facilitates the computations with multiple outer loop 4D-Var applications. The observation analysis needs to be computed separately for each outer loop. The full analysis for all outer loops is combined offline.; routine = mod_fourdvar.F, obs_sen_i4dvar_analysis.h, obs_sen_rbl4dvar_analysis.h, read_asspar.F; keyword = Nimpact; input = s4dvar.in

ninfo: Number of time-steps between printing of single line information to standard output. It also determines the interval between the computation of global energy diagnostics. Ngrids values are expected.; dimension = ninfo(Ngrids); option =; routine = mod_scalars.F; keyword = NINFO; input = roms.in

Ninner: Maximum number of 4DVAR inner loop iterations.; option =; routine = mod_scalars.F; keyword = Ninner; input = roms.in

Nintervals: Number of time interval divisions for stochastic optimals computations. It must be a multiple of ntimes.; option =; routine = mod_scalars.F; keyword = Nintervals; input = roms.in

nLBCvar: Number of lateral boundary condition variables.; option =; routine = mod_scalars.F

Nmethod

Correlation normalization method:

[0] Exact, very expensive

[1] Approximated, randomization

Ngrids values are expected.

dimension = Nmethod(Ngrids)

routine = mod_fourdvar.F, nomalization.F, read_asspar.F

keyword = Nmethod

input = s4dvar.in

NNS: Number of non-cohesive (sand) sediment tracer-type variables.; option = SEDIMENT; routine = mod_param.F; keyword = NNS; input = roms.in

nOBC: Number of time-steps between 4DVAR adjustment of open boundary fields. Ngrids values are expected. In strong constraint 4DVAR, it is possible to adjust open boundaries at other time intervals in addition to initial time. This parameter is used to store the appropriate number of open boundary records in the output history NetCDF files: 1 + ntimes / nOBC records. nOBC must be a factor of ntimes or greater than ntimes. If nOBC > ntimes, only one record is stored in the NetCDF files and the adjustment is for constant forcing with constant correction. This parameter is only relevant in 4DVAR when activating ADJUST_BOUNDARY.; dimension = nOBC(Ngrids); routine = mod_scalars.F; keyword = NOBC; input = roms.in

Nouter: Maximum number of 4DVAR outer loop iterations.; option =; routine = mod_scalars.F; keyword = Nouter; input = roms.in

NpostI: If weak constraint 4DVar (RBL4DVAR or R4DVAR), set number of iterations in the Lanczos algorithm used to estimate the posterior analysis error covariance matrix.; routine = mod_fourdvar.F, posterior.F, read_asspar.F; keyword = NpostI; input = s4dvar.in

NPT: Number of inert tracer-type variables. Currently, an inert passive tracer is one that it is only advected and diffused. Other processes are ignored. These tracers include, for example, dyes, pollutants, oil spills, etc.; option = T_PASSIVE; routine = mod_param.F; keyword = NPT; input = roms.in

Nrandom: Number of iterations to compute correlation normalization factors using the randomization approach of Fisher and Courtier (1995). A large number is required to be statistically meaningful and achieve zero expectation mean and unit variance, approximately. These factors ensure that the error covariance diagonal elements are equal to unity.; routine = nomalization.F, read_asspar.F; keyword = Nrandom; input = s4dvar.in

NritzEV: If preconditioning, specify number of eigenpairs to use. If zero, use HevecErr parameter to determine the number of converged eigenpairs.; routine = cgradient.F, congrad.F, mod_fourdvar.F, read_asspar.F, rpcg_lanczos.F; keyword = NritzEV; input = s4dvar.in

nrrec: Switch(s) to indicate re-start from a previous solution. Ngrids values are expected. Use nrrec = 0 for new solutions. In a re-start solution, nrrec is the time index of the re-start NetCDF file assigned for initialization. If nrrec is negative (say nrrec = -1), the model will re-start from the most recent time record. That is, the initialization record is assigned internally. Notice that it is also possible to re-start from a history or time-averaged NetCDF file. If a history or time-averaged NetCDF file is used for re-start, it must contain all the necessary primitive variables at all levels.; dimension = nrrec(Ngrids); option = PERFECT_RESTART; routine = mod_scalars.F; keyword = NRREC; input = roms.in

nRST: Number of time-steps between writing of re-start fields. Ngrids values are expected.; dimension = nRST(Ngrids); option = PERFECT_RESTART; routine = mod_scalars.F; keyword = NRST; input = roms.in

nSFF: Number of time-steps between 4DVAR adjustment of surface forcing fluxes. Ngrids values are expected. In strong constraint 4DVAR, it is possible to adjust surface forcing at other time intervals in addition to initial time. This parameter is used to store the appropriate number of surface forcing records in the output history NetCDF files: 1 + ntimes / nSFF records. nSFF must be a factor of ntimes or greater than ntimes. If nSFF > ntimes, only one record is stored in the NetCDF files and the adjustment is for constant forcing with constant correction. This parameter is only relevant in 4DVAR when activating either ADJUST_STFLUX or ADJUST_WSTRESS.; dimension = nSFF(Ngrids); routine = mod_scalars.F; keyword = NSFF; input = roms.in

NSperiodic: North-South periodic boundary condition.; dimension = NSperiodic(Ngrids); option =

NST: Number of sediment tracer-type variables, NST=NCS+NNS.; option = SEDIMENT; routine = mod_param.F

nSTA: Number of time-steps between writing data into stations file. Station data is written at all levels. Ngrids values are expected.; dimension = nSTA(Ngrids); option = STATIONS; routine = mod_scalars.F; keyword = NSTA; input = roms.in

Nstation: Number of stations to process in each nested grid. Value(s) are used to dynamically allocate the station arrays. Ngrids values are expected.; dimension = Nstation(Ngrids); option = STATIONS; routine = mod_param.F; keyword = NSTATION; input = stations.in

NT: Total number of tracer-type variables for each nested grid. Currently, NT=NAT+NPT+NST+NBT.; dimension = NT(Ngrids); option = SOLVE3D; routine = mod_param.F; input = roms.in (derived from NAT+NPT+NST+NBT)

NtileI: Number of domain partitions in the I-direction (ξ-coordinate). It must be equal to or greater than one. Ngrids values are expected.; dimension = NtileI(Ngrids); option =; routine = mod_param.F; keyword = NtileI; input = roms.in

NtileJ: Number of domain partitions in the J-direction (η-coordinate). It must be equal to or greater than one. Ngrids values are expected.; dimension = NtileJ(Ngrids); option =; routine = mod_param.F; keyword = NtileJ; input = roms.in

ntimes: Total number time-steps in current run. If 3D configuration, ntimes is the total of baroclinic time-steps. If only 2D configuration, ntimes is the total of barotropic time-steps.; option =; routine = mod_scalars.F; keyword = NTIMES; input = roms.in

ntimes_ana: Total number time-steps for computing observations impacts interval during the analysis cycle. It is only used when RBL4DVAR_FCT_SENSITIVITY is activated.; option = RBL4DVAR_FCT_SENSITIVITY; routine = mod_fourdvar.F, obs_sen_rbl4dvar_forecast.h; keyword = NTIMES_ANA; input = roms.in

ntimes_fct: Total number of timesteps for computing observations impacts interval during the forecast cycle. It is only used when RBL4DVAR_FCT_SENSITIVITY is activated.; option = RBL4DVAR_FCT_SENSITIVITY; routine = mod_fourdvar.F, obs_sen_rbl4dvar_forecast.h; keyword = NTIMES_FCT; input = roms.in

nTLM: Number of time-steps between writing fields into tangent linear model file. Ngrids values are expected.; dimension = nTLM(Ngrids); routine = mod_scalars.F; keyword = NTLM; input = roms.in

ntsAVG: Starting time-step for the accumulation of output time-averaged data. Ngrids values are expected.; dimension = ntsAVG(Ngrids); routine = mod_scalars.F; keyword = NTSAVG; input = roms.in

ntsDIA: Starting time-step for the accumulation of output time-averaged diagnostics data. Ngrids values are expected.; dimension = ntsDIA(Ngrids); routine = mod_scalars.F; keyword = NTSDIA; input = roms.in

NUD: Input nudging coefficients file(s).; dimension = NUD(Ngrids); option = NESTING; routine = read_phypar.F, get_nudgcoef.F; keyword = NUDNAME; input = roms.in

Nuser: Number of generic user parameters to consider (integer). This integer and the number of values in USER must be the same.; routine = mod_scalars.F; keyword = NUSER; input = roms.in

NV: Maximum number of variables in information arrays. Currently, 500.; option =; routine = mod_ncparam.F; input = roms.in

Nvct: Parameter to process the Nvct eigenvector of the stabilized representer matrix when computing array modes (here, Nvct=Ninner is the most important while Nvct=1 is the least important) OR cut-off parameter for the clipped analysis to disregard potentially unphysical array modes (that is, all the eigenvectors < Nvct are disregarded).; option =; routine = mod_fourdvar.F, inp_par.F; keyword = Nvct; input = s4dvar.in

O

obcfac: Factor between passive (outflow) and active (inflow) open boundary conditions. The nudging time scales for the active (inflow) conditions are obtained by multiplying the passive values by obcfac. If obcfac > 1, nudging on inflow is stronger than on outflow (recommended). Ngrids values are expected.; dimension = obcfac(Ngrids); option =; routine = mod_scalars.F; keyword = OBCFAC; input = roms.in

OIFA: Input forcing filename at observation locations for computing observations impacts during the analysis-forecast cycle when the forecast is initialized with the 4D-Var analysis.; dimension =; option =; routine = mod_iounits.F; keyword = OIFnameA; input = s4dvar.in

OIFB: Input forcing filename at observation locations for computing observations impacts during the analysis-forecast cycle when the forecast is initialized with the 4D-Var background.; dimension =; option =; routine = mod_iounits.F; keyword = OIFnameB; input = s4dvar.in

P

poros: Porosity for cohesive and non-cohesive sediment.; dimension = poros(NST,Ngrids); option = SEDIMENT; routine = mod_ocean.F, mod_sediment.F; keywords = MUD_POROS, SAND_POROS; input = sediment.in

Q

R

R0: Background density value used in Linear Equation of State. Ngrids values are expected.; dimension = R0(Ngrids); units = kilograms meters^-3; option =; routine = mod_scalars.F; keyword = R0; input = roms.in

rdrg: Linear bottom drag coefficient used in the computation of momentum stress. Ngrids values are expected.; dimension = rdrg(Ngrids); units = meters seconds^-1; option =; routine = mod_scalars.F; keyword = RDRG; input = roms.in

rdrg2: Quadratic bottom drag coefficient used in the computation of momentum stress. Ngrids values are expected.; dimension = rdrg2(Ngrids); option =; routine = mod_scalars.F; keyword = RDRG2; input = roms.in

rho

In situ density anomaly computed as a function of potential temperature, salinity, and depth.

\sigma (\xi ,\eta ,s)=\rho (\xi ,\eta ,s)-1000

.

dimension = rho(LBi:UBi,LBj:UBj,N(ng))

pointer = OCEAN(ng)%rho

tangent = tl_rho

adjoint = ad_rho

units = kilogram meter^-3

grid = ρ-points

option = SOLVE3D, NONLIN_EOS

routine = rho_eos.F

It can computed using a linear or nonlinear equation of state. The nonlinear equation of state is based on Jackett and McDougall (1992) polynomial expressions.

rho0

Mean density used when the Boussinesq approximation is inferred.

units = kilograms meters^-3

routine = mod_scalars.F

keyword = RHO0

input = roms.in

Ritz_tol: Relative accuracy of the Ritz values computed in the GST analysis.; routine = mod_scalars.F; keyword = Ritz_tol; input = roms.in

Rscheme

Random number generation scheme if randomization:

[1] Gaussian distributed deviates, numerical recipes

Ngrids values are expected.

dimension = Rscheme(Ngrids)

routine = nomalization.F, read_asspar.F, white_noise.F

keyword = Rscheme

input = s4dvar.in

RST: Restart NetCDF file name. Ngrids values are expected.; dimension = RST(Ngrids); option =; routine = mod_iounits.F; keyword = RSTNAME; input = roms.in

S

S0: Background salinity (nondimensional) constant used in Linear Equation of State. Ngrids values are expected.; dimension = S0(Ngrids); option =; routine = mod_scalars.F; keyword = S0; input = roms.in

Scoef: Saline contraction coefficient in Linear Equation of State. Ngrids values are expected.; dimension = Scoef(Ngrids); option =; routine = mod_scalars.F; keyword = SCOEF; input = roms.in

Sd50: Median grain diameter for cohesive and non-cohesive sediment.; dimension = Sd50(NST,Ngrids); units = millimeters; option = SEDIMENT; routine = mod_ncparam.F, mod_ocean.F, mod_sediment.F; keywords = MUD_SD50, SAND_SD50; input = sediment.in

settle_size: Planktonic larvae settlement size (um). Ngrids values are expected.; dimension = settle_size(Ngrids); option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = settle_size; input = behavior_oyster.in

sink_base: Larval sinking exponential factor (mm/s) for larval sinking rate (mm/s), as a function of larval size (um). Ngrids values are expected.; dimension = sink_base(Ngrids); option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = sink_base; input = behavior_oyster.in

sink_rate: Sinking exponential rate factor (1/um) for larval sinking rate (mm/s), as a function of larval size (um). Ngrids values are expected.; dimension = sink_rate(Ngrids); option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = sink_rate; input = behavior_oyster.in

sink_size: Larval size (um) for mean exponential sinking for larval sinking rate (mm/s), as a function of larval size (um). Ngrids values are expected.; dimension = sink_size(Ngrids); option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = sink_size; input = behavior_oyster.in

slope_Sdec: Coefficient {d} due to decreasing salinity. Ngrids values are expected.; dimension = slope_Sdec(Ngrids); option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = slope_Sdec; input = behavior_oyster.in

slope_Sinc: Coefficient {c} due to increasing salinity. Ngrids values are expected.; dimension = slope_Sinc(Ngrids); option = FLOATS, Options#FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = slope_Sinc; input = behavior_oyster.in

SO_decay: Stochastic optimals time decorrelation scale assumed for red noise processes. Ngrids values are expected.; dimension = SO_decay(Ngrids); units = days; option =; routine = mod_scalars.F; keyword = SO_decay; input = roms.in

SO_sdev: Stochastic optimals surface forcing standard deviation for dimensionalization.; routine = mod_scalars.F; keyword = SO_sdev; input = roms.in

SOstate: Logical switches (T/F) to specify the state surface forcing variables whose stochastic optimals are required.; routine = mod_scalars.F; keyword = SOstate; input = roms.in

Sout: Set of switches that determine what fields are written to the stations output file (STAname).; dimension = Sout(NV,Ngrids); option = STATIONS; routine = mod_ncparam.F; keyword = Sout; input = stations.in

sparnam: Input sediment transport parameters (sediment.in) file name.; option = SEDIMENT; routine = mod_iounits.F; keyword = SPARNAM; input = roms.in

sposnam: Input initial stations positions (stations.in) file name.; option = STATIONS; routine = mod_iounits.F; keyword = SPOSNAM; input = roms.in

Srho: Sediment grain density for cohesive and non-cohesive sediment.; dimension = Srho(NST,Ngrids); units = kilograms meter^-3; option = SEDIMENT; routine = mod_sediment.F; keywords = MUD_SRHO, SAND_SRHO; input = sediment.in

SSF: River runoff data. This file is separated from the regular forcing files to allow manipulations over nested grids. A particular nesting grid may or may not have Sources/Sinks forcing. Ngrids values are expected.; dimension = SSF(Ngrids); option = TS_SOURCE; routine = read_phypar.F; keyword = SSFNAME; input = roms.in

For example, in an application with 3 nested grids but with river forcing in grids 1 and 3 we would have:

LuvSrc == T F T
LtracerSrc == 2*T 2*F 2*T

SSFNAME == my_rivers_grid1.nc \
my_rivers_grid2.nc \
my_rivers_grid3.nc

Here, my_rivers_grid2.nc is a dummy name that will never be processed in ROMS because the logical switches are FALSE in the second grid.

STA: Stations output NetCDF file name. Ngrids values are expected.; dimension = STA(Ngrids); option =; routine = mod_iounits.F; keyword = STANAME; input = roms.in

swim_DL: Larval size J-axis increment for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius).; option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = swim_DL; input = behavior_oyster.in

swim_DT: Temperature I-axis increment for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius).; option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = swim_DT; input = behavior_oyster.in

swim_Im: Number of values in larval size I-axix for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius).; option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = swim_Im; input = behavior_oyster.in

swim_Jm: Number of values in temperature J-axis for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius).; option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = swim_Jm; input = behavior_oyster.in

swim_L0: Starting value for temperature I-axis for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius).; option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = swim_; input = behavior_oyster.in

swim_Sdec: Fraction active {f} due to decreasing salinity for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius). Ngrids values are expected.; dimension = swim_Sdec(Ngrids); option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = swim_Sdec; input = behavior_oyster.in

swim_Sinc: Fraction active {d} due to increasing salinity for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius). Ngrids values are expected.; dimension = swim_Sinc(Ngrids); option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = swim_Sinc; input = behavior_oyster.in

swim_T0: Starting value for larval size J-axis for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius).; option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = swim_T0; input = behavior_oyster.in

swim_table: Look-up table, swim_table(58,24) for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius).; option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = swim_table; input = behavior_oyster.in

swim_Tmax: Maximum swimming time fraction for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius). Ngrids values are expected.; dimension = swim_Tmax(Ngrids); option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = swim_Tmax; input = behavior_oyster.in

swim_Tmin: Minimum swimming time fraction for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius). Ngrids values are expected.; dimension = swim_Tmin(Ngrids); option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = swim_Tmin; input = behavior_oyster.in

sz_alpha: Surface flux from wave dissipation used in the various formulations of surface turbulent kinetic energy flux in the GLS. Ngrids values are expected.; dimension = sz_alpha(Ngrids); option = GLS_MIXING; routine = mod_scalars.F; keyword = SZ_ALPHA; input = roms.in

T

t: Tracer-type variables, $T(\xi ,\eta ,s,t,itrc)$ .; dimension = t(LBi:UBi,LBj:UBj,N(ng),3,NT(ng)); pointer = OCEAN(ng)%t; tangent = tl_t; adjoint = ad_t; grid = ρ-points; option = SOLVE3D; routine = step3d_t.F

This array contains all the tracer fields. They are classified as active (potential temperature, salinity), inert (dyes, pollutants, oil spills, etc), passive (sediment, biology). There is a index identifier for each tracer field (see table below). Notice that salinity does not have physical units. Usually PSU is used to indicate that the practical salinity scale was used to determine conductivity.

Index	Field	Units	CPP
itemp	Potential temperature	Celsius	SOLVE3D
isalt	Salinity	None	SALINITY
inert(1:NPT)	NPT inert tracers	kilogram meter^-3	T_PASSIVE
idsed(1:NST)	NST sediment tracers	kilogram meter^-3	SEDIMENT
idbio(1:NBT)	NBT biology tracers	millimole meter^-3	BIOLOGY

T0: Background potential temperature constant used in Linear Equation of State. Ngrids values are expected.; dimension = T0(Ngrids); units = Celsius; option =; routine = mod_scalars.F; keyword = T0; input = roms.in

tau_cd: Kinematic critical shear for deposition of cohesive and non-cohesive sediment. This is ignored for cohesive sediment.; dimension = tau_cd(NST,Ngrids); units = Newton meter^-2; option = SEDIMENT; routine = mod_sediment.F; keywords = MUD_TAU_CD, SAND_TAU_CD; input = sediment.in

tau_ce: Kinematic critical shear for erosion of cohesive and non-cohesive sediment.; dimension = tau_ce(NST,Ngrids); units = Newton meter^-2; option = SEDIMENT; routine = mod_sediment.F; keywords = MUD_TAU_CE, SAND_TAU_CE; input = sediment.in

Tcoef: Thermal expansion coefficient in Linear Equation of State. Ngrids values are expected.; dimension = Tcoef(Ngrids); option =; routine = mod_scalars.F; keyword = TCOEF; input = roms.in

Tcline: Width of surface or bottom boundary layer in which higher vertical resolution is required during stretching. Ngrids values are expected. WARNING: Users need to experiment with theta_b, theta_s and Tcline. We have found out that the model goes unstable with high values of theta_s. In steep and very tall topography, it is recommended to use theta_s < 3.0.; dimension = Tcline(Ngrids); units = meters; routine = mod_scalars.F; keyword = TCLINE; input = roms.in

theta_b: S-coordinate bottom control parameter, (0 < theta_b < 1). Ngrids values are expected. WARNING: Users need to experiment with theta_b, theta_s and Tcline. We have found out that the model goes unstable with high values of theta_s. In steep and very tall topography, it is recommended to use theta_s < 3.0.; dimension = theta_b(Ngrids); routine = mod_scalars.F; keyword = THETA_B; input = roms.in

theta_s: S-coordinate surface control parameter, (0 < theta_s < 20). Ngrids values are expected. WARNING: Users need to experiment with theta_b, theta_s and Tcline. We have found out that the model goes unstable with high values of theta_s. In steep and very tall topography, it is recommended to use theta_s < 3.0.; dimension = theta_s(Ngrids); routine = mod_scalars.F; keyword = THETA_S; input = roms.in

TIDE: Input tidal forcing file name. Ngrids values are expected.; dimension = TIDE(Ngrids); option =; routine = read_phypar.F; keyword = TIDENAME; input = roms.in

tide_start: Reference time origin for tidal forcing. This is the time used when processing input tidal model data. It is needed in routine set_tides.F to compute the correct phase lag with respect ROMS/TOMS initialization time.; option =; units = days; routine = mod_scalars.F; keyword = TIDE_START; input = roms.in

time_ref: Reference time (yyyymmdd.f) used to compute relative time: elapsed time interval since reference-time.; option =; routine = mod_scalars.F; keyword = TIME_REF; input = roms.in

title: Title of model run.; keyword = TITLE; input = roms.in

tkenu2: Lateral harmonic constant mixing coefficient for turbulent closure variables. Ngrids values are expected.; dimension = tkenu2(Ngrids); units = meters² second^-1; option =; routine = mod_scalars.F; keyword = TKENU2; input = roms.in

tkenu4: Lateral biharmonic constant mixing coefficient for turbulent closure variables. Ngrids values are expected.; dimension = tkenu4(Ngrids); units = meters⁴ second^-1; option =; routine = mod_scalars.F; keyword = TKENU4; input = roms.in

tl_LBC: Lateral boundary conditions for tangent linear model.; dimension = tl_LBC(4,nLBCvar,Ngrids); option =; routine = mod_param.F

tl_M2diff: If weak constraint 4DVar and the RPM_RELAXATION flag is activated, this coefficient is used to relax 2D momentum in the representer tangent linear solution to the previous outer loop linearized trajectory during the Picard iterations. The user may turn off relaxation by setting this to zero. Ngrids values are expected.; dimension = tl_M2diff(Ngrids); units = meters² second^-1; routine = mod_scalars.F, read_asspar.F, rp_step2d_LF_AM3.h; keyword = tl_M2diff; input = s4dvar.in

tl_M3diff: If weak constraint 4DVar and the RPM_RELAXATION flag is activated, this coefficient is used to relax 3D momentum in the representer tangent linear solution to the previous outer loop linearized trajectory during the Picard iterations. The user may turn off relaxation by setting this to zero. Ngrids values are expected.; dimension = tl_M3diff(Ngrids); units = meters² second^-1; routine = ad_uv3drelax.F, mod_scalars.F, read_asspar.F, rp_uv3drelax.F, tl_uv3drelax.F; keyword = tl_M3diff; input = s4dvar.in

tl_Tdiff: If weak constraint 4DVar and the RPM_RELAXATION flag is activated, this coefficient is used to relax tracer type variables diffusion in the representer tangent linear solution to the previous outer loop linearized trajectory during the Picard iterations. The user may turn off relaxation by setting this to zero. MT values are expected.; dimension = tl_Tdiff(NT,Ngrids); units = meters² second^-1; routine = ad_t3drelax.F, mod_scalars.F, read_asspar.F, rp_t3drelax.F, tl_t3drelax.F; keyword = tl_Tdiff; input = s4dvar.in

TLF: Impulse tangent linear forcing output NetCDF file name. Ngrids values are expected.; dimension = TLF(Ngrids); option =; routine = mod_iounits.F; keyword = TLFNAME; input = roms.in

TLM: Tangent linear history output NetCDF file name. Ngrids values are expected.; dimension = TLM(Ngrids); option =; routine = mod_iounits.F; keyword = TLMNAME; input = roms.in

tnu2: Lateral harmonic constant mixing coefficient for tracer type variables. If variable horizontal diffusion is activated, tnu2 is the mixing coefficient for the largest grid-cell in the domain.; dimension = tnu2(MT,Ngrids); units = meter² second^-1; option = SEDIMENT, BIOLOGY; routine = mod_mixing.F, mod_scalars.F; keywords = MUD_TNU2, SAND_TNU2, TNU2; input = biology.in, sediment.in

tnu4: Square root lateral biharmonic constant mixing coefficient for tracer type variables. If variable horizontal diffusion is activated, tnu4 is the mixing coefficient for the largest grid-cell in the domain.; dimension = tnu4(MT,Ngrids); units = meter⁴ second^-1; option = SEDIMENT, BIOLOGY; routine = mod_mixing.F, mod_scalars.F; keywords = MUD_TNU4, SAND_TNU4, TNU4; input = biology.in, sediment.in

Tnudg: Inverse time-scale for nudging tracers at open boundaries and sponge areas.; dimension = Tnudg(MT,Ngrids); option = SEDIMENT, BIOLOGY; routine = mod_scalars.F; keywords = MUD_TNUDG, SAND_TNUDG, TNUDG; input = biology.in, sediment.in

turb_ambi: Ambient turbidity level, {turb}, (g/l) for turbidity effects on planktonic larvae growth. Ngrids values are expected.; dimension = turb_ambi(Ngrids); option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = turb_ambi; input = behavior_oyster.in

turb_axis: Turbidity linear axis crossing {c} for turbidity effects on planktonic larvae growth. Ngrids values are expected.; dimension = turb_axis(Ngrids); option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = turb_axis; input = behavior_oyster.in

turb_base: Turbidity base factor, {b}, (g/l) for turbidity effects on planktonic larvae growth. Ngrids values are expected.; dimension = turb_base(Ngrids); option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = turb_base; input = behavior_oyster.in

turb_crit: Critical turbidity value (g/l) for turbidity effects on planktonic larvae growth. Ngrids values are expected.; dimension = turb_crit(Ngrids); option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = turb_crit; input = behavior_oyster.in

turb_mean: Turbidity mean, {turb0}, (g/l) for turbidity effects on planktonic larvae growth. Ngrids values are expected.; dimension = turb_mean(Ngrids); option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = turb_mean; input = behavior_oyster.in

turb_rate: Turbidity rate, {beta}, (1/(g/l)) for turbidity effects on planktonic larvae growth. Ngrids values are expected.; dimension = turb_rate(Ngrids); option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = turb_rate; input = behavior_oyster.in

turb_size: Minimum larvae size (um) affected by tubidity for turbidity effects on planktonic larvae growth. Ngrids values are expected.; dimension = turb_size(Ngrids); option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = turb_size; input = behavior_oyster.in

turb_slop: Turbidity linear slope, {m}, (1/(g/l)) for turbidity effects on planktonic larvae growth. Ngrids values are expected.; dimension = turb_slop(Ngrids); option = FLOATS, FLOAT_OYSTER; routine = oyster_floats.h, oyster_floats_def.h, oyster_floats_inp.h, oyster_floats_mod.h, oyster_floats_wrt.h; keyword = turb_slop; input = behavior_oyster.in

U

u: Total momentum component in the $\xi$ -direction, $u(\xi ,\eta ,s,t)$ .; dimension = u(LBi:UBi,LBj:UBj,N(ng),2); pointer = OCEAN(ng)%u; tangent = tl_u; adjoint = ad_u; units = meter second^-1; grid = u-points; option = SOLVE3D; routine = step3d_uv.F

ubar

Vertically-integrated momentum component in the

\xi

-direction,

{\bar {u}}(\xi ,\eta ,t)

.

{\bar {u}}={\frac {1}{D}}\int _{-h}^{\zeta }u\,H_{z}\,dz

dimension = ubar(LBi:UBi,LBj:UBj,3)

pointer = OCEAN(ng)%ubar

tangent = tl_ubar

adjoint = ad_ubar

units = meter second^-1

grid = u-points

routine = step2d.F

UBi: Array upper bound dimension in the i-direction. In serial and shared-memory applications its value is govern by the value of UPPER_BOUND_I. In distributed-memory its value is a function of the tile partition, UBi=Iend+NghostPoints.; option = UPPER_BOUND_I; routine = get_bounds.F, get_tile.F

UBj: Array upper bound dimension in the j-direction. In serial and shared-memory applications its value is govern by the value of UPPER_BOUND_J. In distributed-memory its value is a function of the tile partition, UBj=Jend+NghostPoints.; option = UPPER_BOUND_J; routine = get_bounds.F, get_tile.F

user: Generic User parameters, NUSER values are expected.; routine = mod_scalars.F; keyword = USER; input = roms.in

USRname: USER's input generic file name.; routine = mod_iounits.F; keyword = USRNAME; input = roms.in

V

v: 3D momentum component in the η-direction, $v(\xi ,\eta ,s,t)$ .; dimension = v(LBi:UBi,LBj:UBj,N(ng),2); pointer = OCEAN(ng)%v; tangent = tl_u; adjoint = ad_u; units = meter second^-1; grid = v-points; option = SOLVE3D; routine = step3d_uv.F

varname: Input variable information file name. This file needs to be processed first so all information arrays can be initialized properly. The default file is at ROMS/External/varinfo.dat.; keyword = VARNAME; input = roms.in

vbar

Vertically-integrated momentum component in the η-direction,

{\bar {v}}(\xi ,\eta ,t)

.

{\bar {v}}={\frac {1}{D}}\int _{-h}^{\zeta }v\,H_{z}\,dz

dimension = vbar(LBi:UBi,LBj:UBj,3)

pointer = OCEAN(ng)%vbar

tangent = tl_vbar

adjoint = ad_vbar

units = meter second^-1

grid = v-points

routine = step2d.F

Vgamma

Vertical stability and accuracy factor (< 1) used to scale the time-step of the convolution operator below its theoretical limit. Notice that four values are needed for Vgamma to facilitate the error covariance modeling for:

[1] initial conditions

[2] model

[3] boundary conditions

[4] surface forcing

dimension = Vgamma(4)

routine = metrics.F, mod_netcdf.F, mod_scalars.F, read_asspar.F

keyword = Vgamma

input = s4dvar.in

visc2: Lateral harmonic constant mixing coefficient for momentum. Ngrids values are expected. If variable horizontal viscosity is activated, visc2 is the mixing coefficient for the largest grid-cell in the domain.; dimension = visc2(Ngrids); units = meters² second^-1; option =; routine = mod_mixing.F, mod_scalars.F; keyword = VISC2; input = roms.in

visc4: Lateral biharmonic constant mixing coefficient for momentum. Ngrids values are expected. If variable horizontal viscosity is activated, visc4 is the mixing coefficient for the largest grid-cell in the domain.; dimension = visc4(Ngrids); units = meters⁴ second^-1; option =; routine = mod_mixing.F, mod_scalars.F; keyword = VISC4; input = roms.in

VolCons: Lateral open boundary edge volume conservation switch for the nonlinear model. This is usually activated with radiation boundary conditions to enforce global mass conservation. Notice that these switches should not be activated if tidal forcing enabled.; dimension = VolCons(4,Ngrids); option =; routine = mod_scalars.F; keyword = VolCons; input = roms.in

Vstretching

Selects the vertical stretching function, C(s). Ngrids values are expected. Possible values are:

1 - Original function in ROMS from the very beginning from Song and Haidvogel (1994)

2 - A. Shchepetkin function from UCLA-ROMS

3 - R. Geyer function for shallow sediment applications

4 - A. Shchepetkin improved double stretching

5 - Souza et al. quadratic Legendre polynomial function that allows higher resolution near the surface

See Vertical S-coordinate for more information.

dimension = Vstretching(Ngrids)

routine = mod_scalars.F

keyword = Vstretching

input = roms.in

Vtransform

Selects the vertical transform equation. Ngrids values are expected. Possible values are:

1 - Original formulation that has been in ROMS since 1999 described in Shchepetkin and McWilliams (2005)

2 - New formulation developed by A. Shchepetkin

See Vertical S-coordinate for more information.

dimension = Vtransform(Ngrids)

routine = mod_scalars.F

keyword = Vtransform

input = roms.in

W

W: Terrain-following, vertical velocity component, $\Omega (\xi ,\eta ,s)\,H_{z}/mn$ .; dimension = W(LBi:UBi,LBj:UBj,0:N(ng)); pointer = OCEAN(ng)%W; tangent = tl_W; adjoint = ad_W; units = meter³ second^-1; sign = positive downwards (downwelling), negative upwards (upwelling); grid = w-points; option = SOLVE3D; routine = omega.F

Wsed: Particle settling velocity for cohesive and non-cohesive sediment.; dimension = Wsed(NST,Ngrids); option = SEDIMENT; routine = mod_ncparam.F, mod_ocean.F, mod_sediment.F; keywords = MUD_WSED, SAND_WSED; input = sediment.in

wvel: True vertical velocity component, $w(\xi ,\eta ,s)$ . It is computed only for output purposes.; dimension = wvel(LBi:UBi,LBj:UBj,0:N(ng)); pointer = OCEAN(ng)%wvel; units = meter second^-1; sign = positive downwards (downwelling), negative upwards (upwelling; grid = w-points; option = SOLVE3D; routine = wvelocity.F

X

Y

Z

zeta: Free-surface, $\zeta (\xi ,\eta ,t)$ .; dimension = zeta(LBi:UBi,LBj:UBj,3); pointer = OCEAN(ng)%zeta; tangent = tl_zeta; adjoint = ad_zeta; units = meter; grid = ρ-points; routine = step2d.F

z_r: Actual depths of variables at ρ-points, $Z_{r}(\xi ,\eta ,s)$ .; dimension = z_r(LBi:UBi,LBj:UBj,N(ng)); pointer = GRID(ng)%z_r; units = meter; sign = negative downwards; grid = ρ-points; option = SOLVE3D; routine = set_depths.F

z_w: Actual depths of variables at w-points, $Z_{w}(\xi ,\eta ,s)$ .; dimension = z_w(LBi:UBi,LBj:UBj,0:N(ng)); pointer = GRID(ng)%z_w; units = meter; sign = negative downwards; grid = w-points; option = SOLVE3D; routine = set_depths.F

Znudg: Nudging time scale for free-surface. Ngrids values are expected.; dimension = Znudg(Ngrids); units = days; option =; routine = mod_scalars.F; keyword = ZNUDG; input = roms.in

Zob: Bottom roughness used in the computation of momentum stress. Ngrids values are expected.; dimension = Zob(Ngrids); units = meters; option =; routine = mod_scalars.F; keyword = Zob; input = roms.in

Zos: Surface roughness used in the computation of momentum stress. Ngrids values are expected.; dimension = Zos(Ngrids); units = meters; option =; routine = mod_scalars.F; keyword = Zos; input = roms.in

zos_hsig_alpha: Roughness from wave amplitude used in the various formulations of surface turbulent kinetic energy flux in the GLS. Ngrids values are expected.; dimension = zos_hsig_alpha(Ngrids); option = GLS_MIXING; routine = mod_scalars.F; keyword = ZOS_HSIG_ALPHA; input = roms.in

Variables: Difference between revisions

Latest revision as of 20:09, 19 August 2020

Contents

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@@ Line 1: / Line 1: @@
+<div class="title">Variables</div>
+This wikipage includes all ROMS global variables in alphabetic order. A single long page
+is built to facilitate printing. Each variable has a unique anchor tag to facilitate
+linking from any wikipage.
+<!-- The automatic table of contents is disabled here to allow a simplified table -->
+__NOTOC__
+<table id="toc" class="toc" summary="Contents">
+<tr><td colspan="26"><h2>Contents</h2></tr>
+<tr>
+<td class="alphabetlist">[[#A|A]]</td>
+<td class="alphabetlist">[[#B|B]]</td>
+<td class="alphabetlist">[[#C|C]]</td>
+<td class="alphabetlist">[[#D|D]]</td>
+<td class="alphabetlist">[[#E|E]]</td>
+<td class="alphabetlist">[[#F|F]]</td>
+<td class="alphabetlist">[[#G|G]]</td>
+<td class="alphabetlist">[[#H|H]]</td>
+<td class="alphabetlist">[[#I|I]]</td>
+<td class="alphabetlist">[[#J|J]]</td>
+<td class="alphabetlist">[[#K|K]]</td>
+<td class="alphabetlist">[[#L|L]]</td>
+<td class="alphabetlist">[[#M|M]]</td>
+<td class="alphabetlist">[[#N|N]]</td>
+<td class="alphabetlist">[[#O|O]]</td>
+<td class="alphabetlist">[[#P|P]]</td>
+<td class="alphabetlist">[[#Q|Q]]</td>
+<td class="alphabetlist">[[#R|R]]</td>
+<td class="alphabetlist">[[#S|S]]</td>
+<td class="alphabetlist">[[#T|T]]</td>
+<td class="alphabetlist">[[#U|U]]</td>
+<td class="alphabetlist">[[#V|V]]</td>
+<td class="alphabetlist">[[#W|W]]</td>
+<td class="alphabetlist">[[#X|X]]</td>
+<td class="alphabetlist">[[#Y|Y]]</td>
+<td class="alphabetlist">[[#Z|Z]]</td>
+</tr></table>
 ==<span class="alphabet">A</span>==
+;<span id="ad_Akt_fac"></span>ad_Akt_fac
+:Adjoint-based algorithms vertical mixing, basic state, scale factor (nondimensional) for active ([[#NAT|NAT]]) and inert ([[#NPT|NPT]]) tracer variables. In some applications, smaller/larger values of vertical mixing are necessary for stability. It is only used when the [[C Preprocessor|CPP option]] [[Options#FORWARD_MIXING|FORWARD_MIXING]] is activated.
+:'''dimension =''' '''ad_Akt_fac'''([[#MT|MT]],[[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FORWARD_MIXING|FORWARD_MIXING]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' ad_AKT_fac
+:'''input =''' [[bio_Fennel.in]], [[ecosim.in]], [[nemuro.in]], [[npzd_Franks.in]], [[npzd_iron.in]], [[npzd_Powell.in]], [[roms.in]]
+;<span id="ad_Akv_fac"></span>ad_Akv_fac
+:Adjoint-based algorithms vertical mixing, basic state, scale factor (nondimensional) for momentum. In some applications, smaller/larger values of vertical mixing are necessary for stability. It is only used when the [[C Preprocessor|CPP option]] [[Options#FORWARD_MIXING|FORWARD_MIXING]] is activated.
+:'''dimension =''' '''ad_Akv_fac'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FORWARD_MIXING|FORWARD_MIXING]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' ad_AKV_fac
+:'''input =''' [[roms.in]]
+;<span id="ad_LBC"></span>ad_LBC
+:Adjoint-based algorithms lateral boundary conditions.
+:'''dimension =''' '''ad_LBC'''(4,[[#nLBCvar|nLBCvar]],[[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_param.F]]
+:'''keyword =''' ad_LBC
+:'''input =''' [[bio_Fennel.in]], [[ecosim.in]], [[nemuro.in]], [[npzd_Franks.in]], [[npzd_iron.in]], [[npzd_Powell.in]], [[roms.in]]
+;<span id="ad_tnu2"></span>ad_tnu2
+:Adjoint-based algorithms lateral, harmonic, constant, mixing coefficient (m<sup>2</sup>/s) for active ([[#NAT|NAT]]) and inert ([[#NPT|NPT]]) tracer variables. If variable horizontal diffusion is activated, ad_tnu2 is the mixing coefficient for the largest grid-cell in the domain. In some applications, a larger value than what is used in the nonlinear model (basic state) is necessary for stability.
+:'''dimension =''' '''ad_tnu2'''([[#MT|MT]],[[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' ad_TNU2
+:'''input =''' [[bio_Fennel.in]], [[ecosim.in]], [[nemuro.in]], [[npzd_Franks.in]], [[npzd_iron.in]], [[npzd_Powell.in]], [[roms.in]]
+;<span id="ad_tnu4"></span>ad_tnu4
+:Adjoint-based algorithms lateral, harmonic, constant, mixing coefficient (m<sup>4</sup>/s) for active ([[#NAT|NAT]]) and inert ([[#NPT|NPT]]) tracer variables. If variable horizontal diffusion is activated, ad_tnu4 is the mixing coefficient for the largest grid-cell in the domain. In some applications, a larger value than what is used in the nonlinear model (basic state) is necessary for stability.
+:'''dimension =''' '''ad_tnu4'''([[#MT|MT]],[[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' ad_TNU4
+:'''input =''' [[bio_Fennel.in]], [[ecosim.in]], [[nemuro.in]], [[npzd_Franks.in]], [[npzd_iron.in]], [[npzd_Powell.in]], [[roms.in]]
+;<span id="ad_visc2"></span>ad_visc2
+:Adjoint-based algorithms lateral, harmonic, constant, mixing coefficient (m<sup>2</sup>/s) momentum. If variable horizontal viscosity is activated, ad_visc2 is the mixing coefficient for the largest grid-cell in the domain. In some applications, a larger value than what is used in the nonlinear model (basic state) is necessary for stability.
+:'''dimension =''' '''ad_visc2'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' ad_VISC2
+:'''input =''' [[roms.in]]
+;<span id="ad_visc4"></span>ad_visc4
+:Adjoint-based algorithms lateral, harmonic, constant, mixing coefficient (m<sup>4</sup>/s) for momentum. If variable horizontal viscosity is activated, ad_visc4 is the mixing coefficient for the largest grid-cell in the domain. In some applications, a larger value than what is used in the nonlinear model (basic state) is necessary for stability.
+:'''dimension =''' '''ad_visc4'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' ad_VISC4
+:'''input =''' [[roms.in]]
+;<span id="ad_VolCons"></span>ad_VolCons
+:Lateral open boundary edge volume conservation switch for adjoint-based algorithms. This is usually activated with radiation boundary conditions to enforce global mass conservation. Notice that these switches should not be activated if tidal forcing enabled.
+:'''dimension =''' '''ad_VolCons'''(4,[[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' ad_VolCons
+:'''input =''' [[roms.in]]
+;<span id="ADM"></span>ADM
+:Adjoint output NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''ADM'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' ADJNAME
+:'''input =''' [[roms.in]]
+;<span id="ADS"></span>ADS
+:Adjoint sensitivity functionals input NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''ADS'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' ADSNAME
+:'''input =''' [[roms.in]]
+;<span id="Akk_bak"></span>Akk_bak
+:Background vertical mixing coefficient for turbulent kinetic energy. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Akk_bak'''([[#Ngrids|Ngrids]])
+:'''units =''' meters<sup>2</sup> second<sup>-1</sup>
+:'''option = '''
+:'''routine =''' [[mod_mixing.F]], [[mod_scalars.F]]
+:'''keyword =''' AKK_BAK
+:'''input =''' [[roms.in]]
+;<span id="Akp_bak"></span>Akp_bak
+:Background vertical mixing coefficient for turbulent kinetic generic statistical field, '''psi'''. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Akp_bak'''([[#Ngrids|Ngrids]])
+:'''units =''' meters<sup>2</sup> second<sup>-1</sup>
+:'''option = '''
+:'''routine =''' [[mod_mixing.F]], [[mod_scalars.F]]
+:'''keyword =''' AKP_BAK
+:'''input =''' [[roms.in]]
+;<span id="Akt_bak"></span>Akt_bak
+:Background vertical mixing coefficient for tracer type variables.
+:'''dimension =''' '''Akt_bak'''([[#MT|MT]],[[#Ngrids|Ngrids]])
+:'''units =''' meters<sup>2</sup> second<sup>-1</sup>
+:'''option = '''
+:'''routine =''' [[mod_mixing.F]], [[mod_scalars.F]]
+:'''keywords =''' AKT_BAK, MUD_AKT_BAK, SAND_AKT_BAK
+:'''input =''' [[biology.in]], [[roms.in]], [[sediment.in]]
+;<span id="Akt_limit"></span>Akt_limit
+:Upper threshold values to limit vertical mixing coefficients computed from vertical mixing parameterizations for tracer type variables. Although this is an engineering fix, the vertical mixing values inferred from ocean observations are rarely higher than this upper limit value.
+:'''dimension ='''
+:'''units =''' meters<sup>2</sup> second<sup>-1</sup>
+:'''option = '''
+:'''routine =''' [[gls_corstep.F]], [[lmd_vmix.F]], [[mod_scalars.F]], [[my25_corstep.F]]
+:'''keywords =''' AKT_LIMIT
+:'''input =''' [[roms.in]]
+;<span id="Akv_bak"></span>Akv_bak
+:Background vertical mixing coefficient for momentum. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Akv_bak'''([[#Ngrids|Ngrids]])
+:'''units =''' meters<sup>2</sup> second<sup>-1</sup>
+:'''option = '''
+:'''routine =''' [[mod_mixing.F]], [[mod_scalars.F]]
+:'''keyword =''' AKV_BAK
+:'''input =''' [[roms.in]]
+;<span id="Akv_limit"></span>Akv_limit
+:Upper threshold values to limit vertical mixing coefficients computed from vertical mixing parameterizations for momentum. Although this is an engineering fix, the vertical mixing values inferred from ocean observations are rarely higher than this upper limit value.
+:'''dimension ='''
+:'''units =''' meters<sup>2</sup> second<sup>-1</sup>
+:'''option = '''
+:'''routine =''' [[gls_corstep.F]], [[lmd_vmix.F]], [[mod_scalars.F]], [[my25_corstep.F]]
+:'''keywords =''' AKV_LIMIT
+:'''input =''' [[roms.in]]
+<section begin=Aout />;<span id="Aout"></span>[[Aout]]
+:Set of switches that determine what fields are written to the averages output file ([[Variables#AVGname|AVGname]]).
+:'''dimension =''' '''Aout'''([[Variables#NV|NV]],[[Variables#Ngrids|Ngrids]])
+:'''option = '''
+:'''routine =''' [[mod_ncparam.F]]
+:'''keyword =''' Aout
+:'''input =''' [[roms.in]]<section end=Aout />
+;<span id="aparnam"></span>aparnam
+:Assimilation parameters input file name.
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' APARNAM
+:'''input =''' [[roms.in]]
+;<span id="AVG"></span>AVG
+:Averages output NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''AVG'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' AVGNAME
+:'''input =''' [[roms.in]]
 ==<span class="alphabet">B</span>==
+;<span id="balance"></span>balance
+:Balance operator logical switches for state variables to consider in the error covariance off-diagonal multivariate constraints:
+::<div class="box"><span class="blue">balance</span>([[#isSalt|isSalt]]) = T,         salinity<br /><span class="blue">balance</span>([[#isFsur|isFsur]]) = T,         free-surface<br /><span class="blue">balance</span>([[#isVbar|isVbar]]) = F,         2D momentum (ubar, vbar)<br /><span class="blue">balance</span>([[#isVvel|isVvel]]) = T,         3D momentum (u, v)</div>
+:Guidlines:
+:#The salinity contribution, <span class="blue">balance</span>([[#isSalt|isSalt]]), depends only on temperature. Notice that temperature is used establish the balanced part of the other state variables.
+:#The free-surface contribution, <span class="blue">balance</span>([[#isFsur|isFsur]]), depends on salinity since we need to compute balanced density and integrate properly using [[#LNM_flag|LNM_flag]] and [[#LNM_depth|LNM_depth]]. This implies that <span class="blue">balance</span>([[#isSalt|isSalt]]) needs to be '''TRUE''' too. It is independent of the 2D or 3D balance velocity terms.
+:#The 3D momentum, <span class="blue">balance</span>([[#isVvel|isVvel]]), depends on salinity since we need to compute balanced density.  This implies that <span class="blue">balance</span>([[#isSalt|isSalt]]) needs to be '''TRUE''' too.
+:'''dimension =''' '''balance'''([[#NV|NV]])
+:'''routine =''' [[ad_balance.F]], [[mod_scalars.F]], [[read_asspar.F]], [[tl_balance.F]], [[zeta_balance.F]]
+:'''keyword =''' balance
+:'''input =''' [[s4dvar.in]]
+;<span id="blk_ZQ"></span>blk_ZQ
+:Height of surface air humidity measurement. Usually recorded at 10 meters. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''blk_ZQ'''([[#Ngrids|Ngrids]])
+:'''units =''' meters
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' BLK_ZQ
+:'''input =''' [[roms.in]]
+;<span id="blk_ZT"></span>blk_ZT
+:Height of surface air temperature measurement. Usually recorded at 2 or 10 meters. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''blk_ZT'''([[#Ngrids|Ngrids]])
+:'''units =''' meters
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' BLK_ZT
+:'''input =''' [[roms.in]]
+;<span id="blk_ZW"></span>blk_ZW
+:Height of surface winds measurement. Usually recorded at 10 meters. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''blk_ZW'''([[#Ngrids|Ngrids]])
+:'''units =''' meters
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' BLK_ZW
+:'''input =''' [[roms.in]]
+;<span id="bparnam"></span>bparnam
+:Biology parameters input file name.
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' BPARNAM
+:'''input =''' [[roms.in]]
+;<span id="BRY"></span>BRY
+:Open boundary conditions input NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''BRY'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' BRYNAME
+:'''input =''' [[roms.in]]
+;<span id="bvf_bak"></span>bvf_bak
+:Background Brunt-Vaisala frequency squared. Typical values for the ocean range (as a function of depth) from 1.0E-4 to 1.0E-6.
+:'''units =''' seconds<sup>-2</sup>
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' BVF_BAK
+:'''input =''' [[roms.in]]
 ==<span class="alphabet">C</span>==
+;<span id="charnok_alpha"></span>charnok_alpha
+:Charnok surface roughness used in the various formulations of surface turbulent kinetic energy flux in the GLS. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''charnok_alpha'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' CHARNOK_ALPHA
+:'''input =''' [[roms.in]]
+;<span id="CLM"></span>CLM
+:Climatology input NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''CLM'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' CLMNAME
+:'''input =''' [[roms.in]]
+;<span id="CnormB"></span>CnormB
+:Compute (T/F) open boundary conditions error covariance normalization factors:
+::<div class="box">CnormB([[#isFsur|isFsur]])   free-surface<br />CnormB([[#isUbar|isUbar]])   2D U-momentum<br />CnormB([[#isVbar|isVbar]])   2D V-momentum<br />CnormB([[#isUvel|isUvel]])   3D U-momentum<br />CnormB([[#isVvel|isVvel]])   3D V-momentum<br />CnormB([[#isTvar|isTvar]])   tracers ([[#NT|NT]] values exppected)</div>
+:'''dimension =''' '''CnormB'''([[#MstateVar|MstateVar]], 4)
+:'''routine =''' [[mod_scalars.F]], [[normalization.F]], [[read_asspar.F]]
+:'''keyword =''' CnormB
+:'''input =''' [[s4dvar.in]]
+;<span id="CnormF"></span>CnormF
+:Compute (T/F) surface forcing error covariance normalization factors:
+::<div class="box">CnormF([[#isTsur|isTsur]])   tracer flux ([[#NT|NT]] values exppected)<br />CnormF([[#isUstr|isUstr]])   wind U-stress<br />CnormF([[#isVstr|isVstr]])   wind V-stress</div>
+:'''dimension =''' '''CnormF'''(2 + [[#NT|NT]])
+:'''routine =''' [[read_asspar.F]]
+:'''keyword =''' CnormF
+:'''input =''' [[s4dvar.in]]
+;<span id="CnormI"></span>CnormI
+:Compute (T/F) initial conditions error covariance normalization factors:
+::<div class="box">CnormI([[#isFsur|isFsur]])   free-surface<br />CnormI([[#isUbar|isUbar]])   2D U-momentum<br />CnormI([[#isVbar|isVbar]])   2D V-momentum<br />CnormI([[#isUvel|isUvel]])   3D U-momentum<br />CnormI([[#isVvel|isVvel]])   3D V-momentum<br />CnormI([[#isTvar|isTvar]])   tracers ([[#NT|NT]] values exppected)</div>
+:'''dimension =''' '''CnormI'''([[#MstateVar|MstateVar]])
+:'''routine =''' [[read_asspar.F]]
+:'''keyword =''' CnormI
+:'''input =''' [[s4dvar.in]]
+;<span id="CnormM"></span>CnormM
+:Compute (T/F) model error covariance normalization factors:
+::<div class="box">CnormM([[#isFsur|isFsur]])   free-surface<br />CnormM([[#isUbar|isUbar]])   2D U-momentum<br />CnormM([[#isVbar|isVbar]])   2D V-momentum<br />CnormM([[#isUvel|isUvel]])   3D U-momentum<br />CnormM([[#isVvel|isVvel]])   3D V-momentum<br />CnormM([[#isTvar|isTvar]])   tracers ([[#NT|NT]] values exppected)</div>
+:'''dimension =''' '''CnormM'''([[#MstateVar|MstateVar]])
+:'''routine =''' [[read_asspar.F]]
+:'''keyword =''' CnormM
+:'''input =''' [[s4dvar.in]]
+;<span id="crgban_cw"></span>crgban_cw
+:Surface flux due to Craig and Banner wave breaking used in the various formulations of surface turbulent kinetic energy flux in the GLS. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''crgban_cw'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' CRGBAN_CW
+:'''input =''' [[roms.in]]
+;<span id="Csed"></span>Csed
+:Sediment concentration used in analytical initial conditions. It is used to initialize full 3D cohesive and non-cohesive constant (homogeneous) concentrations of sediment.
+:'''dimension =''' '''Csed'''([[#NST|NST]],[[#Ngrids|Ngrids]])
+:'''units =''' kilograms meter<sup>-3</sup>
+:'''option = ''' [[Options#SEDIMENT|SEDIMENT]]
+:'''routine =''' [[mod_sediment.F]]
+:'''keywords =''' MUD_CSED, SAND_CSED
+:'''input =''' [[sediment.in]]
 ==<span class="alphabet">D</span>==
+;<span id="Dcrit"></span>Dcrit
+: Minimum depth for wetting and drying. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Dcrit'''([[#Ngrids|Ngrids]])
+:'''units =''' meters
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' DCRIT
+:'''input =''' [[roms.in]]
+;<span id="DendS"></span>DendS
+:Ending day for adjoint sensitivity forcing. [[#Ngrids|Ngrids]] values are expected.
+:<span class="red">Note:</span> The adjoint forcing is applied at every time step according to desired state functional stored in the adjoint sensitivity NetCDF file. [[#DstrS|DstrS]] must be less than or equal to <span class="blue">DendS</span>. If both values are zero, their values are reset internally to the full range of the adjoint integration.
+:'''dimension =''' '''DendS'''([[#Ngrids|Ngrids]])
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' DendS
+:'''input =''' [[roms.in]]
+;<span id="DIA"></span>DIA
+:Diagnostics output NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''DIA'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' DIANAME
+:'''input =''' [[roms.in]]
+<section begin=Dout />;<span id="Dout"></span>[[Dout]]
+:Set of switches that determine what fields are written to the diagnostics output file ([[Variables#DIAname|DIAname]]).
+:'''dimension =''' '''Dout'''([[Variables#NV|NV]],[[Variables#Ngrids|Ngrids]])
+:'''option = '''
+:'''routine =''' [[mod_ncparam.F]]
+:'''keyword =''' Dout
+:'''input =''' [[roms.in]]<section end=Dout />
+<section begin=dstart />;<span id="dstart"></span>[[dstart]]
+:Time stamp assigned to model initialization.  Usually a Calendar linear coordinate, like modified Julian Day.
+:'''option ='''
+:'''units =''' days
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' DSTART
+:'''input =''' [[roms.in]]<section end=dstart />
+;<span id="DstrS"></span>DstrS
+:Starting day for adjoint sensitivity forcing. [[#Ngrids|Ngrids]] values are expected.
+:<span class="red">Note:</span> The adjoint forcing is applied at every time step according to desired state functional stored in the adjoint sensitivity NetCDF file. <span class="blue">DstrS</span> must be less than or equal to [[#DendS|DendS]]. If both values are zero, their values are reset internally to the full range of the adjoint integration.
+:'''dimension =''' '''DstrS'''([[#Ngrids|Ngrids]])
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' DstrS
+:'''input =''' [[roms.in]]
+;<span id="dt"></span>dt
+:Time-Step size in seconds.  If 3D configuration, dt is the size of the baroclinic time-step.  If only 2D configuration, dt is the size of the barotropic time-step. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''dt'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' DT
+:'''input =''' [[roms.in]]
+;<span id="dTdz_min"></span>dTdz_min
+:Minimum d(T)/d(z) above which the balanced salinity ([[#deltaS_b|deltaS_b]]) is computed. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''dTdz_min'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[ad_balance.F]], [[mod_scalars.F]], [[read_asspar.F]], [[tl_balance.F]]
+:'''keyword =''' dTdz_min
+:'''input =''' [[s4dvar.in]]
+;<span id="Dwave"></span>Dwave
+:wind-induced wave direction. Direction the waves are coming from; measured clockwise from geographic North. (nautical convention).
+:'''dimension =''' '''Dwave'''([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]])
+:'''pointer =''' [[mod_forces.F|FORCES(ng)%]]'''Dwave'''
+:'''units =''' degrees
+:'''grid =''' rho-points
+:'''option ='''
+:'''routine =''' [[ssw_bbl.h]], [[mb_bbl.h]], [[sg_bbl.h]], [[ana_wwave.h]], [[radiation_stress.F]]
 ==<span class="alphabet">E</span>==
+;<span id="Erate"></span>Erate
+:Surface erosion rate for cohesive and non-cohesive sediment.
+:'''dimension =''' '''Erate'''([[#NST|NST]],[[#Ngrids|Ngrids]])
+:'''units =''' kilograms meter<sup>-2</sup> second<sup>-1</sup>
+:'''option = ''' [[Options#SEDIMENT|SEDIMENT]]
+:'''routine =''' [[mod_sediment.F]]
+:'''keywords =''' MUD_ERATE, SAND_ERATE
+:'''input =''' [[sediment.in]]
+;<span id="ERstr"></span>ERstr
+:Starting ensemble run (perturbation or iteration) number.
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' ERstr
+:'''input =''' [[roms.in]]
+;<span id="ERend"></span>ERend
+:Ending ensemble run (perturbation or iteration) number.
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' ERend
+:'''input =''' [[roms.in]]
+;<span id="EWperiodic"></span>EWperiodic
+:East-West periodic boundary condition.
+:'''dimension =''' '''EWperiodic'''([[#Ngrids|Ngrids]])
+:'''option = '''
+<!--
+;<span id="ExtraIndex"></span>ExtraIndex
+:Extra-observation class identification indices, as specified in input observation NetCDF file variable "obs_type".  The index has to be a number greater than 7 + 2 * [[#NT|NT]], where NT is the total of active plus passive tracers. [[#NextraObs|NextraObs]] values are expected for this Keyword. This parameter is only processed when [[#NextraObs|NextraObs]] > 0.
+:'''dimension =''' '''ExtraIndex'''([[#NextraObs|NextraObs]])
+:'''routine =''' [[mod_fourdvar.F]], [[read_asspar.F]]
+:'''keyword =''' ExtraIndex
+:'''input =''' [[s4dvar.in]]
+;<span id="ExtraName"></span>ExtraName
+:Extra-observation class names. [[#NextraObs|NextraObs]] values are expected. This parameter is only processed when [[#NextraObs|NextraObs]] > 0.  Enter one class type name per line and use a backslash for continuation. For example:
+::<div class="box">ExtraName = radials  \<br>            pressure<br></div>
+:Currently, however, only the radials operator is coded.
+:'''dimension =''' '''ExtraName'''([[#NextraObs|NextraObs]])
+:'''routine =''' [[mod_fourdvar.F]], [[read_asspar.F]]
+:'''keyword =''' ExtraName
+:'''input =''' [[s4dvar.in]]
+-->
 ==<span class="alphabet">F</span>==
+;<span id="fbionam"></span>fbionam
+:Input script file name containing biological floats behavior model parameters.
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[inp_par.F]], [[mod_iounits.F]], [[read_fltpar.F]]
+:'''keyword =''' FBIONAM
+:'''input =''' [[floats.in]]
+;<span id="Fcoor"></span>Fcoor
+:Initial horizontal location ([[#Fx0|Fx0]] and [[#Fy0|Fy0]]) coordinate type. If <span class="blue">Fcoor</span>&nbsp;=&nbsp;0 then rho grid points are used. If <span class="blue">Fcoor</span>&nbsp;=&nbsp;1 then location is given in latitude and longitude. <span class="blue">Fcoor</span> is column '''C''' in the [[POS]] specification at the end of the [[floats.in]] file.
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[inp_par.F]]
+:'''input =''' [[floats.in]]
+;<span id="Fcount"></span>Fcount
+:Number of floats to be released at the specified ([[#Fx0|Fx0]],[[#Fy0|Fy0]],[[#Fz0|Fz0]]) location. It must be equal or greater than one. If <span class="blue">Fcount</span> is greater than one, a cluster distribution of floats centered at ([[#Fx0|Fx0]],[[#Fy0|Fy0]],[[#Fz0|Fz0]]) is activated. The total number of floats trajectories to compute must add up to [[#Nfloats|NFLOATS]]. <span class="blue">Fcount</span> is column '''N''' in the [[POS]] specification at the end of the [[floats.in]] file.
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[inp_par.F]]
+:'''input =''' [[floats.in]]
+;<span id="FCTA"></span>FCTA
+:Input NetCDF filename for the forecasts initialized from the analysis of the current 4D-Var cycle.
+:'''option ='''
+:'''routine ='''
+:'''keyword = ''' FCTnameA
+:'''input =''' [[roms.in]]
+;<span id="FCTB"></span>FCTB
+:Input NetCDF filename for the forecasts initialized from the analysis of the previous 4D-Var cycle.
+:'''option ='''
+:'''routine ='''
+:'''keyword = ''' FCTnameB
+:'''input =''' [[roms.in]]
+;<span id="Fdt"></span>Fdt
+:Float cluster release time interval in days. This is only used if [[#Fcount|Fcount]] is greater than 1. If <span class="blue">Fdt</span> gt; 0 a cluster of floats will be deployed from ([[#Fx0|Fx0]],[[#Fy0|Fy0]],[[#Fz0|Fz0]]) at <span class="blue">Fdt</span> intervals until [[#Fcount|Fcount]] floats are released. If <span class="blue">Fdt</span> = 0 [[#Fcount|Fcount]] floats will be deployed simultaneously with a distribution centered at ([[#Fx0|Fx0]],[[#Fy0|Fy0]],[[#Fz0|Fz0]]) and defined by ([[#Fdx|Fdx]],[[#Fdy|Fdy]],[[#Fdz|Fdz]]). This value must be of type real (i.e. 5.d0).
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[inp_par.F]]
+:'''input =''' [[floats.in]]
+;<span id="Fdx"></span>Fdx
+:Cluster x-distribution parameter. This is only used if [[#Fcount|Fcount]] is greater than '''1''' and [[#Fdt|Fdt]]&nbsp;=&nbsp;0. This value must be of type real (''i.e.'' 5.d0).
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[inp_par.F]]
+:'''input =''' [[floats.in]]
+;<span id="Fdy"></span>Fdy
+:Cluster y-distribution parameter. This is only used if [[#Fcount|Fcount]] is greater than '''1''' and [[#Fdt|Fdt]]&nbsp;=&nbsp;0. This value must be of type real (''i.e.'' 5.d0).
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[inp_par.F]]
+:'''input =''' [[floats.in]]
+;<span id="Fdz"></span>Fdz
+:Cluster z-distribution parameter. This is only used if [[#Fcount|Fcount]] is greater than '''1''' and [[#Fdt|Fdt]]&nbsp;=&nbsp;0. This value must be of type real (''i.e.'' 5.d0).
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[inp_par.F]]
+:'''input =''' [[floats.in]]
+;<span id="FLT"></span>FLT
+:floats output NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''FLT'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' FLTNAME
+:'''input =''' [[roms.in]]
+;<span id="FOIA"></span>FOIA
+:Input adjoint forcing NetCDF filename for computing observations impacts during the analysis-forecast cycle. If the forecast error metric is defined in state-space, then FOInameA should be regular adjoint forcing files just like [[ADSname]]. If the forecast error metric is defined in observation space ([[Options#OBS_SPACE|OBS_SPACE]] is activated) then the forecast is initialized OIFnameA (specified in [[s4dvar4.in]] input script) will have the structure of a 4D-Var observation file.
+:'''option ='''
+:'''routine ='''
+:'''keyword = ''' FOInameA
+:'''input =''' [[roms.in]]
+;<span id="FOIB"></span>FOIB
+:Input adjoint forcing NetCDF filename for computing observations impacts during the analysis-forecast cycle. If the forecast error metric is defined in state-space, then FOInameB should be regular adjoint forcing files just like [[ADSname]]. If the forecast error metric is defined in observation space ([[Options#OBS_SPACE|OBS_SPACE]] is activated) then the forecast is initialized OIFnameB (specified in [[s4dvar4.in]] input script) will have the structure of a 4D-Var observation file.
+:'''option ='''
+:'''routine ='''
+:'''keyword = ''' FOInameB
+:'''input =''' [[roms.in]]
+;<span id="food_supply"></span>food_supply
+:Initial food supply (constant source) concentration (mg Carbon/l). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''food_supply'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' food_supply
+:'''input =''' [[behavior_oyster.in]]
+;<span id="fposnam"></span>fposnam
+:Input initial floats positions file name ([[floats.in]]).
+:'''option = ''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword = ''' FPOSNAM
+:'''input =''' [[roms.in]]
+;<span id="Fprint"></span>Fprint
+:Switch to control the printing of floats positions to standard output file. This switch can be used to turn off the printing of information when thousands of floats are released. This information is still in the output floats NetCDF file. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Fprint'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[mod_floats.F]], [[read_fltpar.F]]
+:'''keyword =''' Fprint
+:'''input =''' [[floats.in]]
+;<span id="FRC"></span>FRC
+:Input forcing fields file name(s). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''FRC'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' FRCNAME
+:'''input =''' [[roms.in]]
+;<span id="frrec"></span>frrec
+:Flag to indicate re-start from a previous solution. [[#Ngrids|Ngrids]] values are expected. For new solutions (not a model restart) use <span class="blue">frrec</span>&nbsp;=&nbsp;0. In a re-start solution, <span class="blue">frrec</span> is the time index in the floats NetCDF file assigned for initialization.  If <span class="blue">frrec</span> is negative (say <span class="blue">frrec</span>&nbsp;=&nbsp;-1), the floats will re-start from the most recent time record. That is, the initialization record is assigned internally.
+:'''dimension =''' '''frrec'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' FRREC
+:'''input =''' [[floats.in]]
+;<span id="Ft0"></span>Ft0
+:Time, in days, of float release after model initialization. This value must be of type real (i.e. 0.d0).
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[inp_par.F]]
+:'''input =''' [[floats.in]]
+;<span id="Ftype"></span>Ftype
+:Float trajectory type. If [[Variables#Ftype|Ftype]]&nbsp;=&nbsp;1, float(s) will be 3D Lagrangrian particles.  If [[Variables#Ftype|Ftype]]&nbsp;=&nbsp;2, float(s) will be isobaric particles (<math>p=g*(z+zeta)=\text{constant}</math>). If [[Variables#Ftype|Ftype]]&nbsp;=&nbsp;3, float(s) will be geopotential (constant depth) particles.
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[inp_par.F]]
+:'''input =''' [[floats.in]]
+;<span id="FWD"></span>FWD
+:Forward trajectory input NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''FWD'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[read_phypar.F]]
+:'''keyword =''' FWDNAME
+:'''input =''' [[roms.in]]
+;<span id="Fx0"></span>Fx0
+:Initial float(s) x-location in grid units or longitude depending on the value of [[#Fcoor|Fcoor]]. This value must be of type real (''i.e.'' 5.d0).
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[inp_par.F]]
+:'''input =''' [[floats.in]]
+;<span id="Fy0"></span>Fy0
+:Initial float(s) y-location in grid units or longitude depending on the value of [[#Fcoor|Fcoor]]. This value must be of type real (''i.e.'' 5.d0).
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[inp_par.F]]
+:'''input =''' [[floats.in]]
+;<span id="Fz0"></span>Fz0
+:Initial float(s) z-location in vertical levels or depth. If <span class="blue">Fz0</span> is less than or equal to zero then <span class="blue">Fz0</span> is the initial depth in meters. If <span class="blue">Fz0</span> is greater than 0 and less than [[#N|N(ng)]] the initial position is relative to the W grid (0 is the bottom and N is the surface).  This value must be of type real (''i.e.'' -45.d0).
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[inp_par.F]]
+:'''input =''' [[floats.in]]
 ==<span class="alphabet">G</span>==
+;<span id="gamma2"></span>gamma2
+:Slipperiness variable, either 1.0 (free slip) or -1.0 (no slip). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''gamma2'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_grid.F]], [[mod_scalars.F]]
+:'''keyword =''' GAMMA2
+:'''input =''' [[roms.in]]
+;<span id="Gfactor_DS"></span>Gfactor_DS
+:Salinity I-axis increment for planktonic larvae growth rate factor (nondimensional) as a function salinity and temperature.
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Gfactor_DS
+:'''input =''' [[behavior_oyster.in]]
+;<span id="Gfactor_DT"></span>Gfactor_DT
+:Temperature J-axis increment for planktonic larvae growth rate factor (nondimensional) as a function salinity and temperature.
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Gfactor_DT
+:'''input =''' [[behavior_oyster.in]]
+;<span id="Gfactor_Im"></span>Gfactor_Im
+:Number of values in salinity I-axis for planktonic larvae growth rate factor (nondimensional) as a function salinity and temperature.
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Gfactor_Im
+:'''input =''' [[behavior_oyster.in]]
+;<span id="Gfactor_Jm"></span>Gfactor_Jm
+:Number of values in temperature J-axis for planktonic larvae growth rate factor (nondimensional) as a function salinity and temperature.
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Gfactor_Jm
+:'''input =''' [[behavior_oyster.in]]
+;<span id="Gfactor_S0"></span>Gfactor_S0
+:Starting value for salinity I-axis for planktonic larvae growth rate factor (nondimensional) as a function salinity and temperature.
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Gfactor_S0
+:'''input =''' [[behavior_oyster.in]]
+;<span id="Gfactor_T0"></span>Gfactor_T0
+:Starting value for temperature J-axis for planktonic larvae growth rate factor (nondimensional) as a function salinity and temperature.
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Gfactor_T0
+:'''input =''' [[behavior_oyster.in]]
+;<span id="Gfactor_table"></span>Gfactor_table
+:Look-up table, '''Gfactor'''(15,24), for planktonic larvae growth rate factor (nondimensional) as a function salinity and temperature.
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Gfactor_table
+:'''input =''' [[behavior_oyster.in]]
+;<span id="gls_c1"></span>gls_c1
+:Generic length-scale closure independent shear production coefficient. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''gls_c1'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' GLS_C1
+:'''input =''' [[roms.in]]
+;<span id="gls_c2"></span>gls_c2
+:Generic length-scale closure independent dissipation coefficient. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''gls_c2'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' GLS_C2
+:'''input =''' [[roms.in]]
+;<span id="gls_c3m"></span>gls_c3m
+:Generic length-scale closure independent buoyancy production coefficient (minus). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''gls_c3m'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' GLS_C3M
+:'''input =''' [[roms.in]]
+;<span id="gls_c3p"></span>gls_c3p
+:Generic length-scale closure independent buoyancy production coefficient (plus). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''gls_c3p'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' GLS_C3P
+:'''input =''' [[roms.in]]
+;<span id="gls_cmu0"></span>gls_cmu0
+:Generic length-scale closure independent stability coefficient. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''gls_cmu0'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' GLS_CMU0
+:'''input =''' [[roms.in]]
+;<span id="gls_Kmin"></span>gls_Kmin
+:Generic length-scale minimum value of specific turbulent kinetic energy. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''gls_Kmin'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_mixing.F]], [[mod_scalars.F]]
+:'''keyword =''' GLS_KMIN
+:'''input =''' [[roms.in]]
+;<span id="gls_m"></span>gls_m
+:Generic length-scale turbulent kinetic energy exponent. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''gls_m'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_mixing.F]], [[mod_scalars.F]]
+:'''keyword =''' GLS_M
+:'''input =''' [[roms.in]]
+;<span id="gls_n"></span>gls_n
+:Generic length-scale turbulent length scale exponent. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''gls_n'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_mixing.F]], [[mod_scalars.F]]
+:'''keyword =''' GLS_N
+:'''input =''' [[roms.in]]
+;<span id="gls_p"></span>gls_p
+:Generic length-scale stability exponent. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''gls_p'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_mixing.F]], [[mod_scalars.F]]
+:'''keyword =''' GLS_P
+:'''input =''' [[roms.in]]
+;<span id="gls_Pmin"></span>gls_Pmin
+:Generic length-scale minimum value of dissipation. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''gls_Pmin'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_mixing.F]], [[mod_scalars.F]]
+:'''keyword =''' GLS_PMIN
+:'''input =''' [[roms.in]]
+;<span id="gls_sigk"></span>gls_sigk
+:Generic length-scale closure independent constant Schmidt number for turbulent kinetic energy diffusivity. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''gls_sigk'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' GLS_SIGK
+:'''input =''' [[roms.in]]
+;<span id="gls_sigp"></span>gls_sigp
+:Generic length-scale closure independent constant Schmidt number for turbulent generic statistical field, '''psi'''. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''gls_sigp'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' GLS_SIGP
+:'''input =''' [[roms.in]]
+;<span id="GradErr"></span>GradErr
+:Upper bound on the relative error of the gradient for the Lanczos conjugate gradient algorithm.
+:'''routine =''' [[mod_fourdvar.F]], [[read_asspar.F]]
+:'''keyword =''' GradErr
+:'''input =''' [[s4dvar.in]]
+;<span id="Grate_DF"></span>Grate_DF
+:Food supply I-axis increment for planktonic larvae growth rate (um/day) as a function of food supply (mg Carbon /l) and larval size (um).
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Grate_DF
+:'''input =''' [[behavior_oyster.in]]
+;<span id="Grate_DL"></span>Grate_DL
+:Larval size J-axis increment for planktonic larvae growth rate (um/day) as a function of food supply (mg Carbon /l) and larval size (um).
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Grate_DL
+:'''input =''' [[behavior_oyster.in]]
+;<span id="Grate_F0"></span>Grate_F0
+:Starting value for food supply I-axis for planktonic larvae growth rate (um/day) as a function of food supply (mg Carbon /l) and larval size (um).
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Grate_F0
+:'''input =''' [[behavior_oyster.in]]
+;<span id="Grate_Im"></span>Grate_Im
+:Number of values in food supply I-axis for planktonic larvae growth rate (um/day) as a function of food supply (mg Carbon /l) and larval size (um).
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Grate_Im
+:'''input =''' [[behavior_oyster.in]]
+;<span id="Grate_Jm"></span>Grate_Jm
+:Number of values in larval size J-axis for planktonic larvae growth rate (um/day) as a function of food supply (mg Carbon /l) and larval size (um).
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Grate_Jm
+:'''input =''' [[behavior_oyster.in]]
+;<span id="Grate_L0"></span>Grate_L0
+:Starting value for larval size J-axis for planktonic larvae growth rate (um/day) as a function of food supply (mg Carbon /l) and larval size (um).
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Grate_L0
+:'''input =''' [[behavior_oyster.in]]
+;<span id="Grate_table"></span>Grate_table
+:Look-up table, '''Grate'''(31,52), for planktonic larvae growth rate (um/day) as a function of food supply (mg Carbon /l) and larval size (um).
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Grate_table
+:'''input =''' [[behavior_oyster.in]]
+;<span id="GRD"></span>GRD
+:Grid Input NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''GRD'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' GRDNAME
+:'''input =''' [[roms.in]]
+<section begin=GridsInLayer />;<span id="GridsInLayer"></span>[[GridsInLayer]]
+:Number of grids in each nested layer. [[Variables#NestLayers|NestLayers]] values are expected.
+:'''dimension =''' '''GridsInLayer'''([[Variables#NestLayers|NestLayers]])
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' GridsInLayer
+:'''input =''' [[roms.in]]<section end=GridsInLayer />
+;<span id="GST"></span>GST
+:GST analysis input/output check pointing NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''GST'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' GSTNAME
+:'''input =''' [[roms.in]]
 ==<span class="alphabet">H</span>==
-;<span id="Hz"></span>'''Hz'''
+;<span id="HAR"></span>HAR
+:Least-squares detiding harmonics output NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''HAR'''([[#Ngrids|Ngrids]])
+:'''option = '''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' HARNAME
+:'''input =''' [[roms.in]]
+;<span id="HdecayB"></span>HdecayB
+:Boundary conditions error covariance horizontal, isotropic decorrelation scales (m). A value is expected for each boundary edge in the following order:
+:::1: west&emsp;&emsp;&emsp;2: south&emsp;&emsp;&emsp;3:east&emsp;&emsp;&emsp;4: north
+::<div class="box">HdecayB([[#isFsur|isFsur]])   free-surface<br />HdecayB([[#isUbar|isUbar]])   2D U-momentum<br />HdecayB([[#isVbar|isVbar]])   2D V-momentum<br />HdecayB([[#isUvel|isUvel]])   3D U-momentum<br />HdecayB([[#isVvel|isVvel]])   3D V-momentum<br />HdecayB([[#isTvar|isTvar]])   tracers ([[#NT|NT]], [[#Ngrids|Ngrids]] values expected)</div>
+:'''dimension =''' '''HdecayB'''(4,[[#MstateVar|MstateVar]], [[#Ngrids|Ngrids]])
+:'''units =''' meters
+:'''routine =''' [[metrics.F]], [[mod_netcdf.F]], [[mod_scalars.F]], [[normalization.F]], [[read_asspar.F]]
+:'''keyword =''' HdecayB
+:'''input =''' [[s4dvar.in]]
+;<span id="HdecayF"></span>HdecayF
+:Surface forcing error covariance horizontal, isotropic decorrelation scales (m):
+::<div class="box">HdecayF([[#isTsur|isTsur]])   tracers flux ([[#NT|NT]], [[#Ngrids|Ngrids]] values expected)<br />HdecayF([[#isUstr|isUstr]])   wind U-stress<br />HdecayF([[#isVstr|isVstr]])   wind V-stress</div>
+:'''dimension =''' '''HdecayF'''(2 + [[#NT|NT]], [[#Ngrids|Ngrids]])
+:'''units =''' meters
+:'''routine =''' [[metrics.F]], [[mod_netcdf.F]], [[mod_scalars.F]], [[normalization.F]], [[read_asspar.F]]
+:'''keyword =''' HdecayF
+:'''input =''' [[s4dvar.in]]
+;<span id="HdecayI"></span>HdecayI
+:Initial conditions error covariance horizontal, isotropic decorrelation scales (m):
+::<div class="box">HdecayI([[#isFsur|isFsur]])   free-surface<br />HdecayI([[#isUbar|isUbar]])   2D U-momentum<br />HdecayI([[#isVbar|isVbar]])   2D V-momentum<br />HdecayI([[#isUvel|isUvel]])   3D U-momentum<br />HdecayI([[#isVvel|isVvel]])   3D V-momentum<br />HdecayI([[#isTvar|isTvar]])   tracers ([[#NT|NT]], [[#Ngrids|Ngrids]] values expected)</div>
+:'''dimension =''' '''HdecayI'''([[#MstateVar|MstateVar]], [[#Ngrids|Ngrids]])
+:'''units =''' meters
+:'''routine =''' [[metrics.F]], [[mod_netcdf.F]], [[mod_scalars.F]], [[normalization.F]], [[read_asspar.F]]
+:'''keyword =''' HdecayI
+:'''input =''' [[s4dvar.in]]
+;<span id="HdecayM"></span>HdecayM
+:Model error covariance horizontal, isotropic decorrelation scales (m):
+::<div class="box">HdecayM([[#isFsur|isFsur]])   free-surface<br />HdecayM([[#isUbar|isUbar]])   2D U-momentum<br />HdecayM([[#isVbar|isVbar]])   2D V-momentum<br />HdecayM([[#isUvel|isUvel]])   3D U-momentum<br />HdecayM([[#isVvel|isVvel]])   3D V-momentum<br />HdecayM([[#isTvar|isTvar]])   tracers ([[#NT|NT]], [[#Ngrids|Ngrids]] values expected)</div>
+:'''dimension =''' '''HdecayM'''([[#MstateVar|MstateVar]], [[#Ngrids|Ngrids]])
+:'''units =''' meters
+:'''routine =''' [[metrics.F]], [[mod_netcdf.F]], [[mod_scalars.F]], [[normalization.F]], [[read_asspar.F]]
+:'''keyword =''' HdecayM
+:'''input =''' [[s4dvar.in]]
+;<span id="HevecErr"></span>HevecErr
+:Maximum error bound on Hessian eigenvectors in the Lanczos conjugate gradient algorithm.  Note that even quite inaccurate eigenvectors are useful for pre-conditioning purposes.
+:'''routine =''' [[cgradient.F]], [[congrad.F]], [[mod_fourdvar.F]], [[posterior.F]], [[read_asspar.F]], [[rpcg_lanczos.F]]
+:'''keyword =''' HevecErr
+:'''input =''' [[s4dvar.in]]
+;<span id="Hgamma"></span>Hgamma
+:Horizontal stability and accuracy factor (< 1) used to scale the time-step of the convolution operator below its theoretical limit. Notice that four values are needed for <span class="blue">Hgamma</span> to facilitate the error covariance modeling for:
+::[1] initial conditions
+::[2] model
+::[3] boundary conditions
+::[4] surface forcing
+:'''dimension =''' '''Hgamma'''(4)
+:'''routine =''' [[metrics.F]], [[mod_netcdf.F]], [[mod_scalars.F]], [[read_asspar.F]]
+:'''keyword =''' Hgamma
+:'''input =''' [[s4dvar.in]]
+;<span id="HIS"></span>HIS
+:Output history data file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''HIS'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' HISNAME
+:'''input =''' [[roms.in]]
+;<span id="HISname"></span>HISname
+:History output NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''HISname'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' HISNAME
+:'''input =''' [[roms.in]]
+<section begin=Hout />;<span id="Hout"></span>[[Hout]]
+:Set of switches that determine what fields are written to the history output file ([[Variables#HISname|HISname]]).
+:'''dimension =''' '''Hout'''([[Variables#NV|NV]],[[Variables#Ngrids|Ngrids]])
+:'''option = '''
+:'''routine =''' [[mod_ncparam.F]]
+:'''keyword =''' Hout
+:'''input =''' [[roms.in]]<section end=Hout />
+;<span id="Hz"></span>Hz
 :Vertical level thicknesses, <math>\,H_z\,(\xi,\eta,s)</math>.
 :'''dimension =''' '''Hz'''([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],[[#N|N(ng)]])
 :'''pointer =''' [[mod_grid.F|GRID(ng)%]]'''Hz'''
-:'''tangent =''' <span class="red">tl_Hz</span>
+:'''tangent =''' <span class="TangentColor">tl_Hz</span>
-:'''adjoint =''' <span class="purple">ad_Hz</span>
+:'''adjoint =''' <span class="AdjointColor">ad_Hz</span>
 :'''units =''' meter
 :'''grid =''' &rho;-points
-:'''CPP =''' [[SOLVE3D]]
+:'''option =''' [[Options#SOLVE3D | SOLVE3D]]
 :'''routine =''' [[set_depths.F]]
 ==<span class="alphabet">I</span>==
+;<span id="IAD"></span>IAD
+:Adjoint initial conditions input NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''IAD'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' IADNAME
+:'''input =''' [[roms.in]]
+;<span id="idbio"></span>idbio
+:Identification indexes for biological tracer variables, [[#t|t]](:,:,:,:,idbio(:)).
+:'''dimension =''' '''idbio'''([[#NBT|NBT]])
+:'''option =''' [[Options#BIOLOGY | BIOLOGY]]
+:'''routine =''' [[mod_scalars.F]]
+;<span id="idsed"></span>idsed
+:Identification indexes for biological tracer variables, [[#t|t]](:,:,:,:,idsed(:)).
+:'''dimension =''' '''idsed'''([[#NST|NST]])
+:'''option =''' [[Options#SEDIMENT | SEDIMENT]]
+:'''routine =''' [[mod_scalars.F]]
+;<span id="ieast"></span>ieast
+:Index of eastern boundary.
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+;<span id="Iend"></span>Iend
+:Non-overlapping upper bound tile index in the '''i'''-direction. Its value depends on the tile rank (sub-domain partition).
+:'''routine =''' [[tile.h]], [[get_tile.F]]
+;<span id="inert"></span>inert
+:Identification indexes for inert tracer variables, [[#t|t]](:,:,:,:,inert(:)).
+:'''dimension =''' '''inert'''([[#NPT|NPT]])
+:'''option =''' [[Options#T_PASSIVE | T_PASSIVE]]
+:'''routine =''' [[mod_scalars.F]]
+;<span id="INI"></span>INI
+:Nonlinear initial conditions input NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''INI'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' ININAME
+:'''input =''' [[roms.in]]
+;<span id="inorth"></span>inorth
+:Index of northern boundary.
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+;<span id="IRP"></span>IRP
+:Representer initial conditions input NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''IRP'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' IRPNAME
+:'''input =''' [[roms.in]]
+;<span id="isFsur"></span>isFsur
+:Assimilation state variable index for free-surface.
+:'''value =''' 1
+:'''routine =''' [[mod_ncparam.F]]
+;<span id="isalt"></span>isalt
+:Tracer identification index for salinity, [[#t|t]](:,:,:,:,isalt).
+:'''routine =''' [[mod_scalars.F]]
+;<span id="isouth"></span>isouth
+:Index of southern boundary.
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+;<span id="Istr"></span>Istr
+:Non-overlapping lower bound tile index in the '''i'''-direction. Its value depends on the tile rank (sub-domain partition).
+:'''routine =''' [[tile.h]], [[get_tile.F]]
+;<span id="isTvar"></span>isTvar
+:Assimilation state variable indices for tracers.
+:'''dimension =''' '''isTvar'''([[#MT|MT]])
+:'''routine =''' [[mod_ncparam.F]]
+;<span id="isUbar"></span>isUbar
+:Assimilation state variable index for 2D U-momentum.
+:'''value =''' 2
+:'''routine =''' [[mod_ncparam.F]]
+;<span id="isVbar"></span>isVbar
+:Assimilation state variable index for 2D V-momentum.
+:'''value =''' 3
+:'''routine =''' [[mod_ncparam.F]]
+;<span id="isUvel"></span>isUvel
+:Assimilation state variable index for 3D U-momentum.
+:'''value =''' 4
+:'''routine =''' [[mod_ncparam.F]]
+;<span id="isVvel"></span>isVvel
+:Assimilation state variable index for 3D V-momentum.
+:'''value =''' 5
+:'''routine =''' [[mod_ncparam.F]]
+;<span id="itemp"></span>itemp
+:Tracer identification index for potential temperature, [[#t|t]](:,:,:,:,itemp).
+:'''routine =''' [[mod_scalars.F]]
+;<span id="ITL"></span>ITL
+:Tangent linear initial conditions input NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''ITL'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' ITLNAME
+:'''input =''' [[roms.in]]
+;<span id="iwest"></span>iwest
+:Index of western boundary.
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
 ==<span class="alphabet">J</span>==
+;<span id="Jend"></span>Jend
+:Non-overlapping upper bound tile index in the '''j'''-direction. Its value depends on the tile rank (sub-domain partition).
+:'''routine =''' [[tile.h]], [[get_tile.F]]
+;<span id="Jstr"></span>Jstr
+:Non-overlapping lower bound tile index in the '''j'''-direction. Its value depends on the tile rank (sub-domain partition).
+:'''routine =''' [[tile.h]], [[get_tile.F]]
+<section begin=Jwtype />;<span id="Jwtype"></span>[[Jwtype]]
+:Jerlov water type: an integer value from 1 to 5.
+:'''option = '''
+:'''routine =''' [[mod_mixing.F]]
+:'''keyword =''' WTYPE
+:'''input =''' [[roms.in]]<section end=Jwtype />
 ==<span class="alphabet">K</span>==
+;<span id="KendS"></span>KendS
+:Ending vertical level of the 3D adjoint state variables whose sensitivity is required. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''KendS'''([[#Ngrids|Ngrids]])
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' KendS
+:'''input =''' [[roms.in]]
+;<span id="KstrS"></span>KstrS
+:Starting vertical level of the 3D adjoint state variables whose sensitivity is required. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''KstrS'''([[#Ngrids|Ngrids]])
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' KstrS
+:'''input =''' [[roms.in]]
 ==<span class="alphabet">L</span>==
-;<span id="LBi"></span>'''LBi'''
+;<span id="Larvae_size0"></span>Larvae_size0
-:Array lower bound dimension in the '''i'''-direction.
+:Initial planktonic larvae size in terms of length (um). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Larvae_size0'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Larvae_size0
+:'''input =''' [[behavior_oyster.in]]
+;<span id="Larvae_GR0"></span>Larvae_GR0
+:Initial planktonic larvae growth rate (um/day). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Larvae_GR0'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' Larvae_GR0
+:'''input =''' [[behavior_oyster.in]]
+;<span id="LBC"></span>LBC
+:Lateral boundary conditions.
+:'''dimension =''' '''LBC'''(4,[[#nLBCvar|nLBCvar]],[[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_param.F]]
+:'''keyword =''' LBC
+:'''input =''' [[bio_Fennel.in]], [[ecosim.in]], [[nemuro.in]], [[npzd_Franks.in]], [[npzd_iron.in]], [[npzd_Powell.in]], [[roms.in]]
+;<span id="LBi"></span>LBi
+:Array lower bound dimension in the '''i'''-direction. In serial and shared-memory applications its value is <span class="blue">LBi</span>&nbsp;=&nbsp;-2 for East-West periodic grids or <span class="blue">LBi</span>&nbsp;=&nbsp;0 for non-periodic grids . In distributed-memory its value is a function of the tile partition, <span class="blue">LBi</span>&nbsp;=&nbsp;[[#Istr|Istr]]&nbsp;-&nbsp;[[#NghostPoints|NghostPoints]].
+:'''option =''' [[Options#LOWER_BOUND_I | LOWER_BOUND_I]]
+:'''routine =''' [[get_bounds.F]], [[get_tile.F]]
-;<span id="LBj"></span>'''LBj'''
+;<span id="LBj"></span>LBj
-:Array lower bound dimension in the '''j'''-direction.
+:Array lower bound dimension in the '''j'''-direction. In serial and shared-memory applications its value is <span class="blue">LBj</span>&nbsp;=&nbsp;-2 for North-South periodic grids or <span class="blue">LBj</span>&nbsp;=&nbsp;0 for non-periodic grids . In distributed-memory its value is a function of the tile partition, <span class="blue">LBj</span>&nbsp;=&nbsp;[[#Jstr|Jstr]]&nbsp;-&nbsp;[[#NghostPoints|NghostPoints]].
+:'''option =''' [[Options#LOWER_BOUND_J | LOWER_BOUND_J]]
+:'''routine =''' [[get_bounds.F]], [[get_tile.F]]
+;<span id="LcycleADJ"></span>LcycleADJ
+:Logical switch(s) (T/F) used to recycle time records in output adjoint file. [[#Ngrids|Ngrids]] values are expected. If TRUE, only the latest two re-start time records are maintained. If FALSE, all adjoint fields are saved every [[#nADJ|nADJ]] time-steps without recycling.
+:'''dimension =''' '''LcycleADJ'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LcycleADJ
+:'''input =''' [[roms.in]]
+;<span id="LcycleRST"></span>LcycleRST
+:Logical switch(s) (T/F) used to recycle time records in output re-start file. [[#Ngrids|Ngrids]] values are expected. If TRUE, only the latest two re-start time records are maintained. If FALSE, all re-start fields are saved every [[#nRST|nRST]] time-steps without recycling. The re-start fields are written at all levels in double precision unless the [[Options#RST_SINGLE|RST_SINGLE]] [[C_Preprocessor|CPP option]] is activated.
+:'''dimension =''' '''LcycleRST'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#PERFECT_RESTART|PERFECT_RESTART]], [[Options#RST_SINGLE|RST_SINGLE]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LcycleRST
+:'''input =''' [[roms.in]]
+;<span id="LcycleTLM"></span>LcycleTLM
+:Logical switch(s) (T/F) used to recycle time records in output tangent linear file. [[#Ngrids|Ngrids]] values are expected. If TRUE, only the latest two re-start time records are maintained. If FALSE, all tangent linear fields are saved every [[#nTLM|nTLM]] time-steps without recycling.
+:'''dimension =''' '''LcycleTLM'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LcycleTLM
+:'''input =''' [[roms.in]]
+;<span id="LdefNRM"></span>LdefNRM
+:Logical switch(s) (T/F) used to create new normalization NetCDF file for:
+::<div class="box">LdefNRM(1,:)   initial conditions error covariance<br />LdefNRM(2,:)   model error covariance<br />LdefNRM(3,:)   boundary conditions error covariance<br />LdefNRM(4,:)   surface forcing error covariance</div>
+:The computation of the correlation normalization coefficients is very expensive and needs to be computed only once for a particular application provided that grid, land/sea masking (if any), and decorrelation scales (see [[Variables#HdecayM|HdecayM]], [[Variables#VdecayM|VdecayM]], [[Variables#TdecayM|TdecayM]], [[Variables#HdecayI|HdecayI]], [[Variables#VdecayI|VdecayI]], [[Variables#HdecayB|HdecayB]], [[Variables#VdecayB|VdecayB]], [[Variables#HdecayF|HdecayF]]) remain the same.  The user can use this switch in conjunction with the [[Variables#CnormM|CnormM]], [[Variables#CnormI|CnormI]], [[Variables#CnormB|CnormB]], [[Variables#CnormF|CnormF]] switches to compute each coefficient separately. The normalization NetCDF file only needs to be created once and simultaneous runs can write to the same file.  If using this approach, compute the normalization factors with the [[Options#CORRELATION|CORRELATION]] CPP-option and not [[Options#I4DVAR|I4DVAR]], [[Options#RBL4DVAR|RBL4DVAR]] or [[Options#R4DVAR|R4DVAR]].
+:'''dimension =''' '''LdefNRM'''(4, [[#Ngrids|Ngrids]])
+:'''option =''' [[Options#I4DVAR|I4DVAR]], [[Options#RBL4DVAR|RBL4DVAR]], [[Options#R4DVAR|R4DVAR]], [[Options#CORRELATION|CORRELATION]]
+:'''routine =''' [[correlation.h]], [[mod_scalars.F]], [[read_asspar.F]]
+:'''keyword =''' LdefNRM
+:'''input =''' [[s4dvar.in]]
+;<span id="ldefout"></span>ldefout
+:Logical switch(s) (T/F) used to create new output files when initializing from a re-start file, |[[#nrrec|nrrec]]|&nbsp;>&nbsp;0. [[#Ngrids|Ngrids]] values are expected. If TRUE and applicable, a new history, average, diagnostic and station files are created during the initialization stage. If FALSE and applicable, data is appended to existing history, average, diagnostic and station files.  See also parameters [[#ndefHIS|ndefHIS]], [[#ndefAVG|ndefAVG]] and [[#ndefDIA|ndefDIA]].
+:'''dimension =''' '''ldefout'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#PERFECT_RESTART|PERFECT_RESTART]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LDEFOUT
+:'''input =''' [[roms.in]]
+;<span id="levbfrc"></span>levbfrc
+:Shallowest level to apply bottom momentum stress as a body-force. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''levbfrc'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#BODYFORCE|BODYFORCE]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LEVBFRC
+:'''input =''' [[roms.in]]
+;<span id="levsfrc"></span>levsfrc
+:Deepest level to apply surface momentum stress as a body-force. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''levsfrc'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#BODYFORCE|BODYFORCE]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LEVSFRC
+:'''input =''' [[roms.in]]
+;<span id="Lfloats"></span>Lfloats
+:Logical switch(s) (T/F) used to control the computation of floats trajectories within nested and/or multiple connected grids. [[#Ngrids|Ngrids]] values are expected. By default this switch is set to TRUE in [[mod_scalars.F]] for all grids when the [[C Preprocessor|CPP option]] [[Options#FLOATS|FLOATS]] is activated.  The '''user''' can control which grids to process by turning on/off this switch.
+:'''dimension =''' '''Lfloats'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' Lfloats
+:'''input =''' [[floats.in]]
+;<span id="LhessianEV"></span>LhessianEV
+:Switch (T/F) to compute approximated Hessian eigenpairs in the Lanzos conjugate gradient algorithm.
+:'''routine =''' [[cgradient.F]], [[congrad.F]], [[mod_fourdvar.F]], [[read_asspar.F]], [[rpcg_lanczos.F]]
+:'''keyword =''' LhessianEV
+:'''input =''' [[s4dvar.in]]
+;<span id="LhotStart"></span>LhotStart
+:Switch (T/F) to activate hot start in weak-constraint (R4DVAR and RBL4DVAR) algorithms of subsequent outer loops.
+:'''routine =''' [[ad_congrad.F]], [[congrad.F]], [[mod_fourdvar.F]], [[read_asspar.F]], [[tl_congrad.F]]
+:'''keyword =''' LhotStart
+:'''input =''' [[s4dvar.in]]
+;<span id="Lm"></span>Lm
+:Number of interior grid points in the &xi;-direction. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Lm'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_param.F]]
+:'''keyword =''' Lm
+:'''input =''' [[roms.in]]
+;<span id="Lm2CLM"></span>Lm2CLM
+:Logical switch(s) (T/F) used to process 2D momentum ([[Variables#ubar|ubar]], [[Variables#vbar|vbar]]) climatology. The [[C Preprocessor|CPP option]] [[Options#M2CLIMATOLOGY|M2CLIMATOLOGY]] is now '''obsolete''' and replaced with these switches to facilitate nesting applications. Currently, '''CLIMA(ng)%ubarclm''' and '''CLIMA(ng)%vbarclm''' are used for sponges and nudging. If using tidal forcing, the climatological values are adjusted to include tides.
+:'''dimension =''' '''Lm2CLM'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' Lm2CLM
+:'''input =''' [[roms.in]]
+;<span id="Lm3CLM"></span>Lm3CLM
+:Logical switch(s) (T/F) used to process 3D momentum ([[Variables#u|u]], [[Variables#v|v]]) climatology. The [[C Preprocessor|CPP option]] [[Options#M3CLIMATOLOGY|M3CLIMATOLOGY]] is now '''obsolete''' and replaced with these switches to facilitate nesting applications. Currently, '''CLIMA(ng)%uclm''' and '''CLIMA(ng)%vclm''' are used for sponges and nudging.
+:'''dimension =''' '''Lm3CLM'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' Lm3CLM
+:'''input =''' [[roms.in]]
+;<span id="LNM_depth"></span>LNM_depth
+:Level of no motion depth (m; positive) used to compute the balanced free-surface contribution in the error covariance balance operator. It is only relevant when [[#LNM_flag|LNM_flag]]=1, [[#balance|balance(isFsur)]]=T, and [[Options#ZETA_ELLIPTIC|ZETA_ELLIPTIC]] is '''NOT''' activated. It is used to integrate the non-hydrostatic equation. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''LNM_depth'''([[#Ngrids|Ngrids]])
+:'''units =''' meters
+:'''routine =''' [[ad_balance.F]], [[mod_scalars.F]], [[read_asspar.F]], [[tl_balance.F]]
+:'''keyword =''' LNM_depth
+:'''input =''' [[s4dvar.in]]
+;<span id="LNM_flag"></span>LNM_flag
+:Level of no motion integration flag used to used to compute the balanced free-surface contribution:
+::<span class="blue">LNM_flag</span> = 0,  integrate from local bottom to the surface
+::<span class="blue">LNM_flag</span> = 1,  integrate from LNM_depth to surface or integrate from local bottom if shallower than [[#LNM_depth|LNM_depth]]
+:'''routine =''' [[ad_balance.F]], [[mod_scalars.F]], [[read_asspar.F]], [[tl_balance.F]]
+:'''keyword =''' LNM_flag
+:'''input =''' [[s4dvar.in]]
+;<span id="LnudgeM2CLM"></span>LnudgeM2CLM
+:Logical switch(s) (T/F) used to activate the nudging of 2D momentum climatology. The [[C Preprocessor|CPP option]] [[Options#M2CLM_NUDGING|M2CLM_NUDGING]] is now '''obsolete''' and replaced with these switches to facilitate nesting applications.<br /><br />Users also need '''turn on''' (set to '''T''') the logical switch [[Variables#Lm2CLM|Lm2CLM]] to process the required 2D momentum climatology data. This data can be set with analytical functions ([[Options#ANA_M2CLIMA|ANA_M2CLIMA]]) or read from input climatology NetCDF files(s).<br /><br />The nudging coefficients ('''CLIMA(ng)%M2nudgcof''') can be set with analytical functions in [[ana_nudgcoef.h]] using [[C Preprocessor|CPP option]] [[Options#ANA_NUDGCOEF|ANA_NUDGCOEF]]. Otherwise it will be read from NetCDF file [[Variables#NUD|NUDNAME]].
+:'''dimension =''' '''LnudgeM2CLM'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LnudgeM2CLM
+:'''input =''' [[roms.in]]
+;<span id="LnudgeM3CLM"></span>LnudgeM3CLM
+:Logical switch(s) (T/F) used to activate the nudging of 3D momentum climatology. The [[C Preprocessor|CPP option]] [[Options#M3CLM_NUDGING|M3CLM_NUDGING]] is now '''obsolete''' and replaced with these switches to facilitate nesting applications.<br /><br />Users also need '''turn on''' (set to '''T''') the logical switch [[Variables#Lm3CLM|Lm3CLM]] to process the required 3D momentum climatology data. This data can be set with analytical functions ([[Options#ANA_M3CLIMA|ANA_M3CLIMA]]) or read from input climatology NetCDF files(s).<br /><br />The nudging coefficients ('''CLIMA(ng)%M3nudgcof''') can be set with analytical functions in [[ana_nudgcoef.h]] using [[C Preprocessor|CPP option]] [[Options#ANA_NUDGCOEF|ANA_NUDGCOEF]]. Otherwise it will be read from NetCDF file [[Variables#NUD|NUDNAME]].
+:'''dimension =''' '''LnudgeM3CLM'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LnudgeM3CLM
+:'''input =''' [[roms.in]]
+;<span id="LnudgeTCLM"></span>LnudgeTCLM
+:Logical switch(s) (T/F) used to activate the nudging of active and inert tracer climatology variables. These switches also control which tracer variables to nudge. The [[C Preprocessor|CPP option]] [[Options#TCLM_NUDGING|TCLM_NUDGING]] is now '''obsolete''' and replaced with these switches to facilitate nesting applications.<br /><br />Only [[Variables#NAT|NAT]] active tracers (temperature, salinity) and [[Variables#NPT|NPT]] inert tracers need to be specified here.<div class="box">[[Variables#LnudgeTCLM|LnudgeTCLM]](itemp,ng)     for temperature (itemp=1)<br />[[Variables#LnudgeTCLM|LnudgeTCLM]](isalt,ng)     for salinity    (isalt=2)<br />[[Variables#LnudgeTCLM|LnudgeTCLM]](NAT+1,ng)     for inert tracer 1<br />...                      ...<br />[[Variables#LnudgeTCLM|LnudgeTCLM]](NAT+NPT,ng)   for inert tracer NPT</div>Other biological and sediment tracers switches are specified in their respective input scripts.<br /><br />Users also need '''turn on''' (set to '''T''') the logical switch [[Variables#LtracerCLM|LtracerCLM]] to process the required 3D tracer climatology data. This data can be set with analytical functions ([[Options#ANA_TCLIMA|ANA_TCLIMA]]) or read from input climatology NetCDF files(s).<br /><br />The nudging coefficients ('''CLIMA(ng)%Tnudgcof''') can be set with analytical functions in [[ana_nudgcoef.h]] using [[C Preprocessor|CPP option]] [[Options#ANA_NUDGCOEF|ANA_NUDGCOEF]]. Otherwise it will be read from NetCDF file [[Variables#NUD|NUDNAME]].
+:'''dimension =''' '''LnudgeTCLM'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LnudgeTCLM
+:'''input =''' [[bio_Fennel.in]], [[ecosim.in]], [[nemuro.in]], [[npzd_Franks.in]], [[npzd_iron.in]], [[npzd_Powell.in]], [[roms.in]]
+;<span id="Lprecond"></span>Lprecond
+:Switch (T/F) to activate preconditioning in the I4DVAR algorithm. Two types of Limited-Memory preconditioners (LMP) are available [[Bibliography#TshimangaJ_2008a|Tshimanga et al., (2008)]]: Spectral and Ritz.
+::If <span class="blue">Lprecond</span>=T and [[#Lritz|Lritz]]=F,  Spectral LMP
+::If <span class="blue">Lprecond</span>=T and [[#Lritz|Lritz]]=T,  Ritz LMP
+:'''routine =''' [[ad_congrad.F]], [[cgradient.F]], [[congrad.F]], [[mod_fourdvar.F]], [[read_asspar.F]], [[rpcg_lanczos.F]], [[tl_congrad.F]]
+:'''keyword =''' Lprecond
+:'''input =''' [[s4dvar.in]]
+;<span id="Lritz"></span>Lritz
+:Switch to activate either Ritz Limited-Memory Preconditioner (T) or spectral Limited-Memory Preconditioner (F) in the I4DVAR algorithm using eigenpairs approximation for the Hessian matrix.  The accuracy of the Hessian eigenvectors ([[#HevecErr|HevecErr]]) can be used to fine tune the minimization. That is, [[#HevecErr|HevecErr]] can be used to control the number of eigenvalues of the preconditioning Hessian matrix. See [[Bibliography#TshimangaJ_2008a|Tshimanga et al., (2008)]] for details.
+:'''routine =''' [[cgradient.F]], [[congrad.F]], [[mod_fourdvar.F]], [[read_asspar.F]], [[rpcg_lanczos.F]]
+:'''keyword =''' Lritz
+:'''input =''' [[s4dvar.in]]
+;<span id="LrstGST"></span>LrstGST
+:Logical switch(s) (T/F) used to restart GST analysis. If TRUE, the check pointing data is read in from the GST restart NetCDF file.  If FALSE and applicable, the check pointing GST data is saved and overwritten every [[#nGST|nGST]] iterations of the algorithm.
+:'''dimension ='''
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LcycleTLM
+:'''input =''' [[roms.in]]
+;<span id="Lsediment"></span>Lsediment
+:Logical switch(s) (T/F) used to control sediment model computation within nested and/or multiple connected grids. [[#Ngrids|Ngrids]] values are expected. By default this switch is set to TRUE in [[mod_scalars.F]] for all grids when the [[C Preprocessor|CPP option]] [[Options#SEDIMENT|SEDIMENT]] is activated.  The '''user''' can control which grids to process by turning on/off this switch.
+:'''dimension =''' '''Lsediment'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#SEDIMENT|SEDIMENT]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' Lsediment
+:'''input =''' [[sediment.in]]
+;<span id="LsshCLM"></span>LsshCLM
+:Logical switch(s) (T/F) used to process sea-surface height climatology. The [[C Preprocessor|CPP option]] [[Options#ZCLIMATOLOGY|ZCLIMATOLOGY]] is now '''obsolete''' and replaced with these switches to facilitate nesting applications. Currently, the sea-surface height climatology, '''CLIMA(ng)%ssh''', is '''not''' used but is kept for future use.<br /><br />The nudging of SSH on the free-surface governing equation (vertically integrated continuity equation) is '''not''' allowed because it violates mass/volume conservation. Recall that the time rate of change of free-surface is computed from the divergence of [[Variables#ubar|ubar]] and [[Variables#vbar|vbar]].  If such a nudging term is required, it needs to be specified on the momentum equations for ([[Variables#u|u]],[[Variables#v|v]]) and/or ([[Variables#ubar|ubar]],[[Variables#vbar|vbar]]). If done on ([[Variables#u|u]],[[Variables#v|v]]) only, its effects enter the 2D momentum equations via the residual vertically integrated forcing term.
+:'''dimension =''' '''LsshCLM'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LsshCLM
+:'''input =''' [[roms.in]]
+<section begin=Lstate />;<span id="Lstate"></span>[[Lstate]]
+:Logical switches (T/F) to specify the adjoint state variables whose sensitivity is required. [[Variables#Ngrids|Ngrids]] values are expected for each state variable.
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' Lstate
+:'''input =''' [[roms.in]]<section end=Lstate />
+;<span id="Lstations"></span>Lstations
+:Logical switch(s) (T/F) used to control the writing of station data within nested and/or multiple connected grids. [[#Ngrids|Ngrids]] values are expected. By default this switch is set to TRUE in [[mod_scalars.F]] for all grids when the [[C Preprocessor|CPP option]] [[Options#STATIONS|STATIONS]] is activated.  The '''user''' can control which grids to process by turning on/off this switch.
+:'''dimension =''' '''Lstations'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#STATIONS|STATIONS]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' Lstations
+:'''input =''' [[stations.in]]
+;<span id="LtracerCLM"></span>LtracerCLM
+:Logical switch(s) (T/F) used to process active and inert climatology tracer variables. The [[C Preprocessor|CPP option]] [[Options#TCLIMATOLOGY|TCLIMATOLOGY]] is now '''obsolete''' and replaced with these switches to facilitate nesting applications. Currently, '''CLIMA(ng)%tclm''' is used for horizontal mixing, sponges, and nudging.<br /><br />Only [[Variables#NAT|NAT]] active tracers (temperature, salinity) and [[Variables#NPT|NPT]] inert tracers need to be specified here.<div class="box">[[Variables#LtracerCLM|LtracerCLM]](itemp,ng)     for temperature (itemp=1)<br />[[Variables#LtracerCLM|LtracerCLM]](isalt,ng)     for salinity    (isalt=2)<br />[[Variables#LtracerCLM|LtracerCLM]](NAT+1,ng)     for inert tracer 1<br />...                      ...<br />[[Variables#LtracerCLM|LtracerCLM]](NAT+NPT,ng)   for inert tracer NPT</div>Other biological and sediment tracers switches are specified in their respective input scripts.<br /><br /> These switches also control which climatology tracer fields (especially passive tracers) need to be processed so we may reduce the memory allocation for the '''CLIMA(ng)%tclm''' array.
+:'''dimension =''' '''LtracerCLM'''([[#MT|MT]],[[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LtracerCLM
+:'''input =''' [[bio_Fennel.in]], [[ecosim.in]], [[nemuro.in]], [[npzd_Franks.in]], [[npzd_iron.in]], [[npzd_Powell.in]], [[roms.in]]
+;<span id="LtracerSponge"></span>LtracerSponge
+:Logical switch(s) (T/F) to increase/decrease horizontal diffusivity in specific areas of the domain. It can be used to specify sponge areas with larger horizontal mixing coefficients for damping of high frequency noise due to open boundary conditions or nesting. The [[C Preprocessor|CPP option]] [[Options#SPONGE|SPONGE]] is now obsolete and replaced with these switches to facilitate or not sponge areas over a particular nested grid.<br /><br />The horizontal mixing distribution is specified in [[ini_hmixcoef.F]] as:<div class="box">diff2(i,j,itrc) = [[Variables#diff_factor|diff_factor]](i,j) * diff2(i,j,itrc)<br />diff4(i,j,itrc) = [[Variables#diff_factor|diff_factor]](i,j) * diff4(i,j,itrc)</div>The variable [[Variables#diff_factor|diff_factor]] can be read from the grid NetCDF file. Alternately, the horizontal viscosity in the sponge area can be set-up with analytical functions in [[ana_sponge.h]] using CPP [[Options#ANA_SPONGE|ANA_SPONGE]] when the  '''LuvSponge''' is turned ON for a particular grid.
+:'''dimension =''' '''LtracerSponge'''([[Variables#MT|MT]],[[Variables#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LtracerSponge
+:'''input =''' [[roms.in]]
+<section begin=LtracerSrc />;<span id="LtracerSrc"></span>[[LtracerSrc]]
+:Logical switch(s) (T/F) used to activate tracers point Sources/Sinks (like river runoff) and to specify which tracer variables to consider. Only [[Variables#NAT|NAT]] active tracers (temperature, salinity) and [[Variables#NPT|NPT]] inert tracers need to be specified here.
+:'''dimension =''' '''LtracerSrc'''([[Variables#MT|MT]],[[Variables#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LtracerSrc
+:'''input =''' [[bio_Fennel.in]], [[ecosim.in]], [[nemuro.in]], [[npzd_Franks.in]], [[npzd_iron.in]], [[npzd_Powell.in]], [[roms.in]]
+:Other biological and sediment tracers switches are activated in their respective input scripts.
+:In nesting applications, turn on only the grids that require activation and processing of tracers point Sources/Sinks.<section end=LtracerSrc />
+;<span id="LuvSponge"></span>LuvSponge
+:Logical switch(s) (T/F) to increase/decrease horizontal viscosity in specific areas of the domain. It can be used to specify sponge areas with larger horizontal mixing coefficients for damping of high frequency noise due to open boundary conditions or nesting. The [[C Preprocessor|CPP option]] [[Options#SPONGE|SPONGE]] is now obsolete and replaced with these switches to facilitate or not sponge areas over a particular nested grid.<br /><br />The horizontal mixing distribution is specified in [[ini_hmixcoef.F]] as:<div class="box">visc2_r(i,j) = [[Variables#visc_factor|visc_factor]](i,j) * visc2_r(i,j)<br />visc4_r(i,j) = [[Variables#visc_factor|visc_factor]](i,j) * visc4_r(i,j)</div>The variable [[Variables#visc_factor|visc_factor]] can be read from the grid NetCDF file. Alternately, the horizontal viscosity in the sponge area can be set-up with analytical functions in [[ana_sponge.h]] using CPP [[Options#ANA_SPONGE|ANA_SPONGE]] when the switch '''LuvSponge''' is turned '''ON''' for a particular grid.
+:'''dimension =''' '''LuvSponge'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LuvSponge
+:'''input =''' [[roms.in]]
+;<span id="LuvSrc"></span>LuvSrc
+:Logical switch(s) (T/F) used to activate momentum horizontal transport points Sources/Sinks. Usually it is used to turn on/off river runoff transport ([[#u|u]] or [[#v|v]] variables) in an application. In nesting applications, turn on only the grids that require activation and processing of momentum point Sources/Sinks.
+:'''dimension =''' '''LuvSrc'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LuvSrc
+:'''input =''' [[roms.in]]
+;<span id="LwSrc"></span>LwSrc
+:Logical switch(s) (T/F) used to activate mass points Sources/Sinks. Usually it is used to turn on/off volume vertical influx ([[#w|w]]) in an application. In nesting applications, turn on only the grids that require activation and processing of mass influx point Sources/Sinks.
+:'''dimension =''' '''LwSrc'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' LwSrc
+:'''input =''' [[roms.in]]
+;<span id="LwrtNRM"></span>LwrtNRM
+:Logical switch(s) (T/F) to write out correlation normalization factors for:
+::<div class="box">LwrtNRM(1,:)   initial conditions error covariance<br />LwrtNRM(2,:)   model error covariance<br />LwrtNRM(3,:)   boundary conditions error covariance<br />LwrtNRM(4,:)   surface forcing error covariance</div>
+:If TRUE, these factors computed and written to [[Variables#NRMnameI|NRMnameI]], [[Variables#NRMnameM|NRMnameM]], [[Variables#NRMnameB|NRMnameB]], and [[Variables#NRMnameF|NRMnameF]] NetCDF files, respectively. If FALSE, they are read from [[Variables#NRMname|NRMname]] NetCDF file.
+:'''dimension =''' '''LwrtNRM'''(4, [[#Ngrids|Ngrids]])
+:'''option =''' [[Options#I4DVAR|I4DVAR]], [[Options#RBL4DVAR|RBL4DVAR]], [[Options#R4DVAR|R4DVAR]], [[Options#CORRELATION|CORRELATION]]
+:'''routine =''' [[correlation.h]], [[mod_scalars.F]], [[normalization.F]], [[read_asspar.F]]
+:'''keyword =''' LwrtNRM
+:'''input =''' [[s4dvar.in]]
 ==<span class="alphabet">M</span>==
+;<span id="M2nudg"></span>M2nudg
+:Nudging time scale for 2D momentum. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''M2nudg'''([[#Ngrids|Ngrids]])
+:'''units =''' days
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' M2NUDG
+:'''input =''' [[roms.in]]
+;<span id="M3nudg"></span>M3nudg
+:Nudging time scale for 3D momentum. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''M3nudg'''([[#Ngrids|Ngrids]])
+:'''units =''' days
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' M3NUDG
+:'''input =''' [[roms.in]]
+;<span id="MaxIterGST"></span>MaxIterGST
+:Maximum number of GST algorithm iterations.
+:'''dimension ='''
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' MaxIterGST
+:'''input =''' [[roms.in]]
+;<span id="ml_depth"></span>ml_depth
+:Mixed-layer depth (m; positive) in [[#deltaS_b|deltaS_b]] smoothing coefficient. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''ml_depth'''([[#Ngrids|Ngrids]])
+:'''units =''' meters
+:'''routine =''' [[ad_balance.F]], [[mod_scalars.F]], [[read_asspar.F]], [[tl_balance.F]]
+:'''keyword =''' ml_depth
+:'''input =''' [[s4dvar.in]]
+;<span id="Mm"></span>Mm
+:Number of interior grid points in the &eta;-direction. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Mm'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_param.F]]
+:'''keyword =''' Mm
+:'''input =''' [[roms.in]]
+;<span id="morph_fac"></span>morph_fac
+:Morphological scale factor for cohesive and non-cohesive sediment.
+:'''dimension =''' '''morph_fac'''([[#NST|NST]],[[#Ngrids|Ngrids]])
+:'''option = ''' [[Options#SEDIMENT|SEDIMENT]]
+:'''routine =''' [[mod_sediment.F]]
+:'''keywords =''' MUD_MORPH_FAC, SAND_MORPH_FAC
+:'''input =''' [[sediment.in]]
+;<span id="MyAppCPP"></span>MyAppCPP
+:C-preprocessing flag to define the specific configuration. In versions up to 2.3 this flag was one of the predefined model applications that headed the [[cppdefs.h]] file. You '''must''' make the value of <span class="blue">MyAppCPP</span> consistent with variable <span class="blue">ROMS_APPLICATION</span> in the [[build_Script|build script]] or [[makefile]] if you are not using [[build_Script|build.sh]] or [[build_Script|build.bash]]. ROMS converts the <span class="blue">ROMS_APPLICATION</span> variable to lowercase to determine the name of the file to include.
+:'''keyword =''' MyAppCPP
+:'''input =''' [[roms.in]]
+;<span id="MT"></span>MT
+:The maximum number of tracers between all nested grids. Basically the sum of all [[Variables#NT|NT]].
 ==<span class="alphabet">N</span>==
-;<span id="N"></span>'''N'''
+;<span id="N"></span>N
-:Number of vertical levels for each nested grid.
+:Number of vertical levels for each nested grid. [[#Ngrids|Ngrids]] values are expected.
-:'''dimension =''' '''N([[#Ngrids|Ngrids]])
+:'''dimension =''' '''N'''([[#Ngrids|Ngrids]])
 :'''routine =''' [[mod_param.F]]
+:'''keyword =''' N
+:'''input =''' [[roms.in]]
-;<span id="Ngrids"></span>'''Ngrids'''
+;<span id="NAT"></span>NAT
-:Number of nested and/or connected grids to solve.
+:Number of active tracer-type variables. Usually, it has a value of two for potential temperature and salinty.
+:'''option =''' [[Options#SOLVE3D | SOLVE3D]]
 :'''routine =''' [[mod_param.F]]
+:'''keyword =''' NAT
+:'''input =''' [[roms.in]]
-;<span id="NAT"></span>'''NAT'''
+;<span id="nADJ"></span>nADJ
-:Number of active tracer-type variables. Usually, it has a value of two for potential temperature and salinty.
+:Number of time-steps between writing fields into adjoint model file. [[#Ngrids|Ngrids]] values are expected.
-:'''CPP =''' [[SOLVE3D]]
+:'''dimension =''' '''nADJ'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NADJ
+:'''input =''' [[roms.in]]
+;<span id="nAVG"></span>nAVG
+:Number of time-steps between writing time-averaged data into averages file.  Averaged date is written for all fields. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''nAVG'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NAVG
+:'''input =''' [[roms.in]]
+;<span id="Nbed"></span>Nbed
+:Number of sediment bed layers.
 :'''routine =''' [[mod_param.F]]
+:'''keyword =''' Nbed
+:'''input =''' [[roms.in]]
-;<span id="NBT"></span>'''NBT'''
+;<span id="Nbico"></span>Nbico
+:Number of iterations in the biconjugate gradient algorithm used to solve the elliptic equation for sea surface height in the error covariance balance operator. We need as many iterations are required to decrease the error value of the reference free-surface to 1E-8 or smaller. In some applications Nbico=200 will do the job. [[#Ngrids|Ngrids]] values are expected.
+:{{warning}}'''Warning:''' Be aware that there are 4 arrays that are allocated with this parameter and its value may be constrained by available memory:<div class="box">[[#FOURDVAR|FOURDVAR]]([[#ng|ng]]) % [[#p_r2d|p_r2d]] ([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],<span class="blue">Nbico</span>([[#ng|ng]]))<br />[[#FOURDVAR|FOURDVAR]]([[#ng|ng]]) % [[#r_r2d|r_r2d]] ([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],<span class="blue">Nbico</span>([[#ng|ng]]))<br />[[#FOURDVAR|FOURDVAR]]([[#ng|ng]]) % [[#bp_r2d|bp_r2d]] ([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],<span class="blue">Nbico</span>([[#ng|ng]]))<br />[[#FOURDVAR|FOURDVAR]]([[#ng|ng]]) % [[#br_r2d|br_r2d]] ([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],<span class="blue">Nbico</span>([[#ng|ng]]))</div>All the iteration values are needed in the backward stepping of the adjoint.
+:'''dimension =''' '''Nbico'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[ad_balance.F]], [[mod_fourdvar.F]], [[mod_param.F]], [[read_asspar.F]], [[tl_balance]], [[zeta_balance.F]]
+:'''keyword =''' Nbico
+:'''input =''' [[s4dvar.in]]
+;<span id="NBT"></span>NBT
 :Number of biological tracer-type variables.
-:'''CPP =''' [[BIOLOGY]]
+:'''option =''' [[Options#BIOLOGY | BIOLOGY]]
 :'''routine =''' [[mod_param.F]]
+:'''keyword =''' NBT
+:'''input =''' [[biology.in]]
-;<span id="NCT"></span>'''NCS'''
+;<span id="NCS"></span>NCS
 :Number of cohesive (mud) sediment tracer-type variables.
-:'''CPP =''' [[SEDIMENT]]
+:'''option =''' [[Options#SEDIMENT|SEDIMENT]]
 :'''routine =''' [[mod_param.F]]
+:'''keyword =''' NCS
+:'''input =''' [[roms.in]]
+<section begin=NCV />;<span id="NCV"></span>[[Eigenproblem Parameters|NCV]]
+:Number of eigenvectors to compute for the Lanczos/Arnoldi problem. <span class="blue">NCV</span> must be greater than [[Variables#NEV|NEV]].
+:'''option ='''
+:'''routine =''' [[mod_storage.F]]
+:'''keyword =''' NCV
+:'''input =''' [[roms.in]]<section end=NCV />
+;<span id="ndefADJ"></span>ndefADJ
+:Number of time-steps between the creation of new adjoint file. If <span class="blue">ndefADJ</span>&nbsp;=&nbsp;0, the model will only process one adjoint file.  This feature is useful for long simulations when output NetCDF files get too large; it creates a new file every <span class="blue">ndefADJ</span> time-steps. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''ndefADJ'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NDEFADJ
+:'''input =''' [[roms.in]]
+;<span id="ndefAVG"></span>ndefAVG
+:Number of time-steps between the creation of new average file. If <span class="blue">ndefAVG</span>&nbsp;=&nbsp;0, the model will only process one average file.  This feature is useful for long simulations when average files get too large; it creates a new file every <span class="blue">ndefAVG</span> time-steps. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''ndefAVG'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NDEFAVG
+:'''input =''' [[roms.in]]
+;<span id="ndefDIA"></span>ndefDIA
+:Number of time-steps between the creation of new time-averaged diagnostics file.  If <span class="blue">ndefDIA</span>&nbsp;=&nbsp;0, the model will only process one diagnostics file.  This feature is useful for long simulations when diagnostics files get too large; it creates a new file every <span class="blue">ndefDIA</span> time-steps. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''ndefDIA'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NDEFDIA
+:'''input =''' [[roms.in]]
+;<span id="ndefHIS"></span>ndefHIS
+:Number of time-steps between the creation of new history file. If <span class="blue">ndefHIS</span>&nbsp;=&nbsp;0, the model will only process one history file. This feature is useful for long simulations when history files get too large; it creates a new file every <span class="blue">ndefHIS</span> time-steps. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''ndefHIS'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NDEFHIS
+:'''input =''' [[roms.in]]
+;<span id="ndefTLM"></span>ndefTLM
+:Number of time-steps between the creation of new tangent linear file. If <span class="blue">ndefTLM</span>&nbsp;=&nbsp;0, the model will only process one tangent linear file.  This feature is useful for long simulations when output NetCDF files get too large; it creates a new file every <span class="blue">ndefTLM</span> time-steps. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''ndefTLM'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NDEFTLM
+:'''input =''' [[roms.in]]
+;<span id="nDIA"></span>nDIA
+:Number of time-steps between writing time-averaged diagnostics data into diagnostics file. Averaged date is written for all fields. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''nDIA'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NDIA
+:'''input =''' [[roms.in]]
+;<span id="ndtfast"></span>ndtfast
+:Number of barotropic time-steps between each baroclinic time step. If only 2D configuration, <span class="blue">ndtfast</span> should be unity since there is no need to split time-stepping.
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NDTFAST
+:'''input =''' [[roms.in]]
+;<span id="NestLayers"></span>NestLayers
+:Number of grid nesting layers. This parameter is used to allow refinement and composite grid combinations as shown for the [[Nested_Grids#Nested_Grids_Classes|Refinement and Partial Boundary Composite Sub-Classes]]. In non-nesting applications, set NestLayers = 1.
+:'''option ='''
+:'''routine =''' [[mod_param.F]]
+:'''keyword =''' NestLayers
+:'''input =''' [[roms.in]]
+<section begin=NEV />;<span id="NEV"></span>[[Eigenproblem Parameters|NEV]]
+:Number of eigenvalues to compute for the Lanczos/Arnoldi problem.  Notice that the model memory requirement increases substantially as '''NEV''' increases.  The GST requires '''NEV'''+1 copies of the model state vector.  The memory requirements are decreased in distributed-memory applications.
+:'''option ='''
+:'''routine =''' [[mod_storage.F]]
+:'''keyword =''' NEV
+:'''input =''' [[roms.in]]<section end=NEV />
+<!--
+;<span id="NextraObs"></span>NextraObs
+:Number of extra-observation classes to consider in addition to those associated with the state variables (one-to-one correspondence). They are used in observation operators that require more that one state variable to evaluate  extra-observation type like HF radials, travel time, pressure, etc.
+:In any application, the number of observation types is computed as:
+::[[#NobsVar|NobsVar]]([[#ng|ng]]) = [[#NstateVar|NstateVar]]([[#ng|ng]]) + <span class="blue">NextraObs</span>
+:If not processing extra-observation classes, set <span class="blue">NextraObs</span> to zero.
+:'''routine =''' [[mod_fourdvar.F]], [[read_asspar.F]]
+:'''keyword =''' NextraObs
+:'''input =''' [[s4dvar.in]]
+-->
+;<span id="nFfiles"></span>nFfiles
+:Number of forcing NetCDF files. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''nFfiles'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' NFFILES
+:'''input =''' [[roms.in]]
+;<span id="nFLT"></span>nFLT
+:Number of time-steps between writing data into floats file ([[#FLTname|FLTname]]). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''nFLT'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NFLT
+:'''input =''' [[roms.in]]
+;<span id="Nfloats"></span>Nfloats
+:Number of floats to release in each nested grid. Value(s) are used to dynamically allocate the arrays in the [[Options#FLOATS|FLOATS]] array structure. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Nfloats'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]]
+:'''routine =''' [[mod_floats.F]] [[init_param.F]]
+:'''keyword =''' NFLOATS
+:'''input =''' [[floats.in]]
+;<span id="NGCname"></span>NGCname
+:Input nested grids contact points information file name. This NetCDF file is currently generated using script <span class="red">matlab/grid/contact.m</span> from the ROMS Matlab repository.  The nesting information is not trivial and this Matlab scripts is quite complex. See [[Nested_Grids]] and [[Grid_Processing_Scripts]] for more information.
+:'''option =''' [[Options#NESTING|NESTING]]
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' NGCNAME
+:'''input =''' [[roms.in]]
+;<span id="NghostPoints"></span>NghostPoints
+:Number of ghost points in the halo region used in distributed-memory configurations.
+:'''option =''' [[Options#GHOST_POINTS | GHOST_POINTS]]
+:'''routine =''' [[mod_param.F]]
+;<span id="Ngrids"></span>Ngrids
+:Number of nested and/or multiple connected grids to solve.
+:'''routine =''' [[mod_param.F]]
+;<span id="nGST"></span>nGST
+:Number of GST iterations between storing of check pointing data into NetCDF file. The restart data is always saved if [[#MaxIterGST|MaxIterGST]] is reached without convergence. It is also saved when convergence is achieved. It is always a good idea to save the check pointing data at regular intervals so there is a mechanism to recover from an unexpected interruption in this very expensive computation. The check pointing data can be also be used to recompute the Ritz vectors by changing some of the parameters, like convergence criteria ([[#Ritz_tol|Ritz_tol]]) and number of Arnoldi iterations (iparam(3)).
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NGST
+:'''input =''' [[roms.in]]
+;<span id="nHIS"></span>nHIS
+:Number of time-steps between writing fields into history file. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''nHIS'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NHIS
+:'''input =''' [[roms.in]]
+;<span id="Nimpact"></span>Nimpact
+:If observations impact or observations sensitivity, set the 4D-Var outer loop to consider in the computation of the observations impact or observation sensitivity. It must be less than or equal to [[#Nouter|Nouter]]. This facilitates the computations with multiple outer loop 4D-Var applications.  The observation analysis needs to be computed separately for each outer loop.  The full analysis for all outer loops is combined offline.
+:'''routine =''' [[mod_fourdvar.F]], [[obs_sen_i4dvar_analysis.h]], [[obs_sen_rbl4dvar_analysis.h]], [[read_asspar.F]]
+:'''keyword =''' Nimpact
+:'''input =''' [[s4dvar.in]]
+;<span id="ninfo"></span>ninfo
+:Number of time-steps between printing of single line information to standard output.  It also determines the interval between the computation of global energy diagnostics. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''ninfo'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NINFO
+:'''input =''' [[roms.in]]
+;<span id="Ninner"></span>Ninner
+:Maximum number of 4DVAR inner loop iterations.
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' Ninner
+:'''input =''' [[roms.in]]
+<section begin=Nintervals />;<span id="Nintervals"></span>[[Nintervals]]
+:Number of time interval divisions for stochastic optimals computations. It must be a multiple of [[Variables#ntimes|ntimes]].
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' Nintervals
+:'''input =''' [[roms.in]]<section end=Nintervals />
+;<span id="nLBCvar"></span>nLBCvar
+:Number of lateral boundary condition variables.
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
-;<span id="NNS"></span>'''NNS'''
+;<span id="Nmethod"></span>Nmethod
+:Correlation normalization method:
+::[0]  Exact, very expensive
+::[1]  Approximated, randomization
+:[[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Nmethod'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_fourdvar.F]], [[nomalization.F]], [[read_asspar.F]]
+:'''keyword =''' Nmethod
+:'''input =''' [[s4dvar.in]]
+;<span id="NNS"></span>NNS
 :Number of non-cohesive (sand) sediment tracer-type variables.
-:'''CPP =''' [[SEDIMENT]]
+:'''option =''' [[Options#SEDIMENT | SEDIMENT]]
 :'''routine =''' [[mod_param.F]]
+:'''keyword =''' NNS
+:'''input =''' [[roms.in]]
+;<span id="nOBC"></span>nOBC
+:Number of time-steps between 4DVAR adjustment of open boundary fields. [[#Ngrids|Ngrids]] values are expected. In strong constraint 4DVAR, it is possible to adjust open boundaries at other time intervals in addition to initial time.  This parameter is used to store the appropriate number of open boundary records in the output history NetCDF files: 1&nbsp;+&nbsp;[[#ntimes|ntimes]]&nbsp;/&nbsp;<span class="blue">nOBC</span> records. <span class="blue">nOBC</span> must be a factor of [[#ntimes|ntimes]] or greater than [[#ntimes|ntimes]]. If <span class="blue">nOBC</span>&nbsp;>&nbsp;[[#ntimes|ntimes]], only one record is stored in the NetCDF files and the adjustment is for constant forcing with constant correction. This parameter is only relevant in 4DVAR when activating [[Options#ADJUST_BOUNDARY|ADJUST_BOUNDARY]].
+:'''dimension =''' '''nOBC'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NOBC
+:'''input =''' [[roms.in]]
+;<span id="Nouter"></span>Nouter
+:Maximum number of 4DVAR outer loop iterations.
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' Nouter
+:'''input =''' [[roms.in]]
+;<span id="NpostI"></span>NpostI
+:If weak constraint 4DVar (RBL4DVAR or R4DVAR), set number of iterations in the Lanczos algorithm used to estimate the posterior analysis error covariance matrix.
+:'''routine =''' [[mod_fourdvar.F]], [[posterior.F]], [[read_asspar.F]]
+:'''keyword =''' NpostI
+:'''input =''' [[s4dvar.in]]
+;<span id="NPT"></span>NPT
+:Number of inert tracer-type variables. Currently, an inert passive tracer is one that it is only advected and diffused. Other processes are ignored. These tracers include, for example, dyes, pollutants, oil spills, etc.
+:'''option =''' [[Options#T_PASSIVE | T_PASSIVE]]
+:'''routine =''' [[mod_param.F]]
+:'''keyword =''' NPT
+:'''input =''' [[roms.in]]
+;<span id="Nrandom"></span>Nrandom
+:Number of iterations to compute correlation normalization factors using the randomization approach of [[Bibliography#FisherM_1995a|Fisher and Courtier (1995)]]. A large number is required to be statistically meaningful and achieve zero expectation mean and unit variance, approximately. These factors ensure that the error covariance diagonal elements are equal to unity.
+:'''routine =''' [[nomalization.F]], [[read_asspar.F]]
+:'''keyword =''' Nrandom
+:'''input =''' [[s4dvar.in]]
+;<span id="NritzEV"></span>NritzEV
+:If preconditioning, specify number of eigenpairs to use. If zero, use [[#HevecErr|HevecErr]] parameter to determine the number of converged eigenpairs.
+:'''routine =''' [[cgradient.F]], [[congrad.F]], [[mod_fourdvar.F]], [[read_asspar.F]], [[rpcg_lanczos.F]]
+:'''keyword =''' NritzEV
+:'''input =''' [[s4dvar.in]]
+;<span id="nrrec"></span>nrrec
+:Switch(s) to indicate re-start from a previous solution. [[#Ngrids|Ngrids]] values are expected. Use <span class="blue">nrrec</span>&nbsp;=&nbsp;0 for new solutions. In a re-start solution, <span class="blue">nrrec</span> is the time index of the re-start NetCDF file assigned for initialization.  If <span class="blue">nrrec</span> is negative (say <span class="blue">nrrec</span>&nbsp;=&nbsp;-1), the model will re-start from the most recent time record. That is, the initialization record is assigned internally. Notice that it is also possible to re-start from a history or time-averaged NetCDF file.  If a history or time-averaged NetCDF file is used for re-start, it must contain all the necessary primitive variables at all levels.
+:'''dimension =''' '''nrrec'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#PERFECT_RESTART|PERFECT_RESTART]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NRREC
+:'''input =''' [[roms.in]]
+;<span id="nRST"></span>nRST
+:Number of time-steps between writing of re-start fields. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''nRST'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#PERFECT_RESTART|PERFECT_RESTART]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NRST
+:'''input =''' [[roms.in]]
+;<span id="nSFF"></span>nSFF
+:Number of time-steps between 4DVAR adjustment of surface forcing fluxes. [[#Ngrids|Ngrids]] values are expected. In strong constraint 4DVAR, it is possible to adjust surface forcing at other time intervals in addition to initial time.  This parameter is used to store the appropriate number of surface forcing records in the output history NetCDF files: 1&nbsp;+&nbsp;[[#ntimes|ntimes]]&nbsp;/&nbsp;<span class="blue">nSFF</span> records. <span class="blue">nSFF</span> must be a factor of [[#ntimes|ntimes]] or greater than [[#ntimes|ntimes]]. If <span class="blue">nSFF</span>&nbsp;>&nbsp;[[#ntimes|ntimes]], only one record is stored in the NetCDF files and the adjustment is for constant forcing with constant correction. This parameter is only relevant in 4DVAR when activating either [[Options#ADJUST_STFLUX|ADJUST_STFLUX]] or [[Options#ADJUST_WSTRESS|ADJUST_WSTRESS]].
+:'''dimension =''' '''nSFF'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NSFF
+:'''input =''' [[roms.in]]
-;<span id="NST"></span>'''NST'''
+;<span id="NSperiodic"></span>NSperiodic
+:North-South periodic boundary condition.
+:'''dimension =''' '''NSperiodic'''([[#Ngrids|Ngrids]])
+:'''option = '''
+;<span id="NST"></span>NST
 :Number of sediment tracer-type variables, NST=[[#NCS|NCS]]+[[#NCS|NNS]].
-:'''CPP =''' [[SEDIMENT]]
+:'''option =''' [[Options#SEDIMENT | SEDIMENT]]
 :'''routine =''' [[mod_param.F]]
-;<span id="NT"></span>'''NT'''
+;<span id="nSTA"></span>nSTA
+:Number of time-steps between writing data into stations file. Station data is written at all levels. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''nSTA'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#STATIONS|STATIONS]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NSTA
+:'''input =''' [[roms.in]]
+;<span id="Nstation"></span>Nstation
+:Number of stations to process in each nested grid. Value(s) are used to dynamically allocate the station arrays. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Nstation'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#STATIONS|STATIONS]]
+:'''routine =''' [[mod_param.F]]
+:'''keyword =''' NSTATION
+:'''input =''' [[stations.in]]
+;<span id="NT"></span>NT
 :Total number of tracer-type variables for each nested grid. Currently, NT=[[#NAT|NAT]]+[[#NPT|NPT]]+[[#NST|NST]]+[[#NBT|NBT]].
-:'''dimension =''' '''NT([[#Ngrids|Ngrids]])
+:'''dimension =''' '''NT'''([[#Ngrids|Ngrids]])
-:'''CPP =''' [[SOLVE3D]]
+:'''option =''' [[Options#SOLVE3D | SOLVE3D]]
 :'''routine =''' [[mod_param.F]]
+:'''input =''' [[roms.in]] (derived from [[#NAT|NAT]]+[[#NPT|NPT]]+[[#NST|NST]]+[[#NBT|NBT]])
+<section begin=NtileI />;<span id="NtileI"></span>[[NtileI]]
+:Number of domain partitions in the I-direction (&xi;-coordinate). It must be equal to or greater than one. [[Variables#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''NtileI'''([[Variables#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_param.F]]
+:'''keyword =''' NtileI
+:'''input =''' [[roms.in]]<section end=NtileI />
+<section begin=NtileJ />;<span id="NtileJ"></span>[[NtileJ]]
+:Number of domain partitions in the J-direction (&eta;-coordinate). It must be equal to or greater than one. [[Variables#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''NtileJ'''([[Variables#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_param.F]]
+:'''keyword =''' NtileJ
+:'''input =''' [[roms.in]]<section end=NtileJ />
+<section begin=ntimes />;<span id="ntimes"></span>[[ntimes]]
+:Total number time-steps in current run. If 3D configuration, ntimes is the total of baroclinic time-steps.  If only 2D configuration, ntimes  is the total of barotropic time-steps.
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NTIMES
+:'''input =''' [[roms.in]]<section end=ntimes />
+<section begin=ntimes_ana />;<span id="ntimes_ana"></span>[[ntimes_ana]]
+:Total number time-steps for computing observations impacts interval during the analysis cycle. It is only used when [[Options#RBL4DVAR_FCT_SENSITIVITY|RBL4DVAR_FCT_SENSITIVITY]] is activated.
+:'''option =''' [[Options#RBL4DVAR_FCT_SENSITIVITY|RBL4DVAR_FCT_SENSITIVITY]]
+:'''routine =''' [[mod_fourdvar.F]], [[obs_sen_rbl4dvar_forecast.h]]
+:'''keyword =''' NTIMES_ANA
+:'''input =''' [[roms.in]]<section end=ntimes_ana />
+<section begin=ntimes_fct />;<span id="ntimes_fct"></span>[[ntimes_fct]]
+:Total number of timesteps for computing observations impacts interval during the forecast cycle. It is only used when [[Options#RBL4DVAR_FCT_SENSITIVITY|RBL4DVAR_FCT_SENSITIVITY]] is activated.
+:'''option =''' [[Options#RBL4DVAR_FCT_SENSITIVITY|RBL4DVAR_FCT_SENSITIVITY]]
+:'''routine =''' [[mod_fourdvar.F]], [[obs_sen_rbl4dvar_forecast.h]]
+:'''keyword =''' NTIMES_FCT
+:'''input =''' [[roms.in]] <section end=ntimes_fct />
+;<span id="nTLM"></span>nTLM
+:Number of time-steps between writing fields into tangent linear model file. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''nTLM'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NTLM
+:'''input =''' [[roms.in]]
+;<span id="ntsAVG"></span>ntsAVG
+:Starting time-step for the accumulation of output time-averaged data. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''ntsAVG'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NTSAVG
+:'''input =''' [[roms.in]]
+;<span id="ntsDIA"></span>ntsDIA
+:Starting time-step for the accumulation of output time-averaged diagnostics data. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''ntsDIA'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NTSDIA
+:'''input =''' [[roms.in]]
+;<span id="NUD"></span>NUD
+:Input nudging coefficients file(s).
+:'''dimension =''' '''NUD([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#NESTING|NESTING]]
+:'''routine =''' [[read_phypar.F]], [[get_nudgcoef.F]]
+:'''keyword =''' NUDNAME
+:'''input =''' [[roms.in]]
+;<span id="Nuser"></span>Nuser
+:Number of generic user parameters to consider (integer). This integer and the number of values in [[#user|USER]] must be the same.
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' NUSER
+:'''input =''' [[roms.in]]
+;<span id="NV"></span>NV
+:Maximum number of variables in information arrays. Currently, 500.
+:'''option ='''
+:'''routine =''' [[mod_ncparam.F]]
+:'''input =''' [[roms.in]]
+;<span id="Nvct"></span>Nvct
+:Parameter to process the <span class="blue">Nvct</span> eigenvector of the stabilized representer matrix when computing array modes (here, <span class="blue">Nvct</span>=[[#Ninner|Ninner]] is the most important while <span class="blue">Nvct</span>=1 is the least important) OR cut-off parameter for the clipped analysis to disregard potentially unphysical array modes (that is, all the eigenvectors < <span class="blue">Nvct</span> are disregarded).
+:'''option = '''
+:'''routine =''' [[mod_fourdvar.F]], [[inp_par.F]]
+:'''keyword =''' Nvct
+:'''input =''' [[s4dvar.in]]
 ==<span class="alphabet">O</span>==
+;<span id="obcfac"></span>obcfac
+:Factor between passive (outflow) and active (inflow) open boundary conditions.  The nudging time scales for the active (inflow) conditions are obtained by multiplying the passive values by <span class="blue">obcfac</span>. If <span class="blue">obcfac</span>&nbsp;>&nbsp;1, nudging on inflow is stronger than on outflow (recommended). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''obcfac'''([[#Ngrids|Ngrids]])
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' OBCFAC
+:'''input =''' [[roms.in]]
+;<span id="OIFA"></span>OIFA
+:Input forcing filename at observation locations for computing observations impacts during the analysis-forecast cycle when the forecast is initialized with the 4D-Var analysis.
+:'''dimension ='''
+:'''option = '''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' OIFnameA
+:'''input =''' [[s4dvar.in]]
+;<span id="OIFB"></span>OIFB
+:Input forcing filename at observation locations for computing observations impacts during the analysis-forecast cycle when the forecast is initialized with the 4D-Var background.
+:'''dimension ='''
+:'''option = '''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' OIFnameB
+:'''input =''' [[s4dvar.in]]
 ==<span class="alphabet">P</span>==
+;<span id="pros"></span>poros
+:Porosity for cohesive and non-cohesive sediment.
+:'''dimension =''' '''poros'''([[#NST|NST]],[[#Ngrids|Ngrids]])
+:'''option = ''' [[Options#SEDIMENT|SEDIMENT]]
+:'''routine =''' [[mod_ocean.F]], [[mod_sediment.F]]
+:'''keywords =''' MUD_POROS, SAND_POROS
+:'''input =''' [[sediment.in]]
 ==<span class="alphabet">Q</span>==
@@ Line 93: / Line 1,893: @@
 ==<span class="alphabet">R</span>==
-;<span id="rho"></span>'''rho'''
+;<span id="R0"></span>R0
+:Background density value used in Linear Equation of State. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''R0'''([[#Ngrids|Ngrids]])
+:'''units =''' kilograms meters<sup>-3</sup>
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' R0
+:'''input =''' [[roms.in]]
+;<span id="rdrg"></span>rdrg
+:Linear bottom drag coefficient used in the computation of momentum stress. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''rdrg'''([[#Ngrids|Ngrids]])
+:'''units =''' meters seconds<sup>-1</sup>
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' RDRG
+:'''input =''' [[roms.in]]
+;<span id="rdrg2"></span>rdrg2
+:Quadratic bottom drag coefficient used in the computation of momentum stress. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''rdrg2'''([[#Ngrids|Ngrids]])
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' RDRG2
+:'''input =''' [[roms.in]]
+;<span id="rho"></span>rho
 :''In situ'' density anomaly computed as a function of potential temperature, salinity, and depth.
-::<math>\,\sigma(\xi,\eta,s) = \rho(\xi,\eta,s) - 1000</math>.
+::<math>\sigma(\xi,\eta,s) = \rho(\xi,\eta,s) - 1000</math>.
 :'''dimension =''' '''rho'''([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],[[#N|N(ng)]])
 :'''pointer =''' [[mod_ocean.F|OCEAN(ng)%]]'''rho'''
-:'''tangent =''' <span class="red">tl_rho</span>
+:'''tangent =''' <span class="TangentColor">tl_rho</span>
-:'''adjoint =''' <span class="purple">ad_rho</span>
+:'''adjoint =''' <span class="AdjointColor">ad_rho</span>
 :'''units =''' kilogram meter<sup>-3</sup>
 :'''grid =''' &rho;-points
-:'''CPP = ''' [[SOLVE3D]], [[NONLIN_EOS]]
+:'''option = ''' [[Options#SOLVE3D | SOLVE3D]], [[Options#NONLIN_EOS | NONLIN_EOS]]
 :'''routine =''' [[rho_eos.F]]
 :It can computed using a linear or nonlinear equation of state. The nonlinear equation of state is based on [[Bibliography#JackettDR_1995a | Jackett and McDougall (1992)]] polynomial expressions.
+;<span id="rho0"></span>rho0
+:Mean density used when the Boussinesq approximation is inferred.
+:'''units =''' kilograms meters<sup>-3</sup>
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' RHO0
+:'''input =''' [[roms.in]]
+;<span id="Ritz_tol"></span>Ritz_tol
+:Relative accuracy of the Ritz values computed in the GST analysis.
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' Ritz_tol
+:'''input =''' [[roms.in]]
+;<span id="Rscheme"></span>Rscheme
+:Random number generation scheme if randomization:
+::[1]  Gaussian distributed deviates, numerical recipes
+:[[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Rscheme'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[nomalization.F]], [[read_asspar.F]], [[white_noise.F]]
+:'''keyword =''' Rscheme
+:'''input =''' [[s4dvar.in]]
+;<span id="RST"></span>RST
+:Restart NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''RST'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' RSTNAME
+:'''input =''' [[roms.in]]
 ==<span class="alphabet">S</span>==
+;<span id="S0"></span>S0
+:Background salinity (nondimensional) constant used in Linear Equation of State. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''S0'''([[#Ngrids|Ngrids]])
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' S0
+:'''input =''' [[roms.in]]
+;<span id="Scoef"></span>Scoef
+:Saline contraction coefficient in Linear Equation of State. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Scoef'''([[#Ngrids|Ngrids]])
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' SCOEF
+:'''input =''' [[roms.in]]
+;<span id="Sd50"></span>Sd50
+:Median grain diameter for cohesive and non-cohesive sediment.
+:'''dimension =''' '''Sd50'''([[#NST|NST]],[[#Ngrids|Ngrids]])
+:'''units =''' millimeters
+:'''option = ''' [[Options#SEDIMENT|SEDIMENT]]
+:'''routine =''' [[mod_ncparam.F]], [[mod_ocean.F]], [[mod_sediment.F]]
+:'''keywords =''' MUD_SD50, SAND_SD50
+:'''input =''' [[sediment.in]]
+;<span id="settle_size"></span>settle_size
+:Planktonic larvae settlement size (um). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''settle_size'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' settle_size
+:'''input =''' [[behavior_oyster.in]]
+;<span id="sink_base"></span>sink_base
+:Larval sinking exponential factor (mm/s) for larval sinking rate (mm/s), as a function of larval size (um). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''sink_base'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' sink_base
+:'''input =''' [[behavior_oyster.in]]
+;<span id="sink_rate"></span>sink_rate
+:Sinking exponential rate factor (1/um) for larval sinking rate (mm/s), as a function of larval size (um). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''sink_rate'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' sink_rate
+:'''input =''' [[behavior_oyster.in]]
+;<span id="sink_size"></span>sink_size
+:Larval size (um) for mean exponential sinking for larval sinking rate (mm/s), as a function of larval size (um). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''sink_size'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' sink_size
+:'''input =''' [[behavior_oyster.in]]
+;<span id="slope_Sdec"></span>slope_Sdec
+:Coefficient {d} due to decreasing salinity. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''slope_Sdec'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' slope_Sdec
+:'''input =''' [[behavior_oyster.in]]
+;<span id="slope_Sinc"></span>slope_Sinc
+:Coefficient {c} due to increasing salinity. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''slope_Sinc'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' slope_Sinc
+:'''input =''' [[behavior_oyster.in]]
+;<span id="SO_decay"></span>SO_decay
+:Stochastic optimals time decorrelation scale assumed for red noise processes. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''SO_decay'''([[#Ngrids|Ngrids]])
+:'''units =''' days
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' SO_decay
+:'''input =''' [[roms.in]]
+<section begin=SO_sdev />;<span id="SO_sdev"></span>[[SO_sdev]]
+:Stochastic optimals surface forcing standard deviation for dimensionalization.
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' SO_sdev
+:'''input =''' [[roms.in]]
+<section begin=SOstate />;<span id="SOstate"></span>[[SOstate]]
+:Logical switches (T/F) to specify the state surface forcing variables whose stochastic optimals are required.
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' SOstate
+:'''input =''' [[roms.in]]<section end=SOstate />
+<section begin=Sout />;<span id="Sout"></span>[[Sout]]
+:Set of switches that determine what fields are written to the stations output file ([[Variables#STAname|STAname]]).
+:'''dimension =''' '''Sout'''([[Variables#NV|NV]],[[Variables#Ngrids|Ngrids]])
+:'''option = ''' [[Options#STATIONS|STATIONS]]
+:'''routine =''' [[mod_ncparam.F]]
+:'''keyword =''' Sout
+:'''input =''' [[stations.in]]<section end=Sout />
+;<span id="sparnam"></span>sparnam
+:Input sediment transport parameters ([[sediment.in]]) file name.
+:'''option = ''' [[Options#SEDIMENT|SEDIMENT]]
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' SPARNAM
+:'''input =''' [[roms.in]]
+;<span id="sposnam"></span>sposnam
+:Input initial stations positions ([[stations.in]]) file name.
+:'''option = ''' [[Options#STATIONS|STATIONS]]
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' SPOSNAM
+:'''input =''' [[roms.in]]
+;<span id="Srho"></span>Srho
+:Sediment grain density for cohesive and non-cohesive sediment.
+:'''dimension =''' '''Srho'''([[#NST|NST]],[[#Ngrids|Ngrids]])
+:'''units =''' kilograms meter<sup>-3</sup>
+:'''option = ''' [[Options#SEDIMENT|SEDIMENT]]
+:'''routine =''' [[mod_sediment.F]]
+:'''keywords =''' MUD_SRHO, SAND_SRHO
+:'''input =''' [[sediment.in]]
+;<span id="SSF"></span>SSF
+: River runoff data. This file is separated from the regular forcing files to allow manipulations over nested grids. A particular nesting grid may or may not have Sources/Sinks forcing. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''SSF'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#TS_SOURCE|TS_SOURCE]]
+:'''routine =''' [[read_phypar.F]]
+:'''keyword =''' SSFNAME
+:'''input =''' [[roms.in]]
+:For example, in an application with 3 nested grids but with river forcing in grids 1 and 3 we would have:<div class="box">    [[#LuvSrc|LuvSrc]] == T F T<br />[[#LtracerSrc|LtracerSrc]] == 2*T 2*F 2*T<br /><br />   [[#SSFNAME|SSFNAME]] == my_rivers_grid1.nc \<br />              my_rivers_grid2.nc \<br />              my_rivers_grid3.nc</div>Here, <span class="forestGreen">my_rivers_grid2.nc</span> is a dummy name that will never be processed in ROMS because the logical switches are FALSE in the second grid.
+;<span id="STA"></span>STA
+:Stations output NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''STA'''([[#Ngrids|Ngrids]])
+:'''option = '''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' STANAME
+:'''input =''' [[roms.in]]
+;<span id="swim_DL"></span>swim_DL
+:Larval size J-axis increment for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius).
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' swim_DL
+:'''input =''' [[behavior_oyster.in]]
+;<span id="swim_DT"></span>swim_DT
+:Temperature I-axis increment for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius).
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' swim_DT
+:'''input =''' [[behavior_oyster.in]]
+;<span id="swim_Im"></span>swim_Im
+:Number of values in larval size I-axix for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius).
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' swim_Im
+:'''input =''' [[behavior_oyster.in]]
+;<span id="swim_Jm"></span>swim_Jm
+:Number of values in temperature J-axis for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius).
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' swim_Jm
+:'''input =''' [[behavior_oyster.in]]
+;<span id="swim_L0"></span>swim_L0
+:Starting value for temperature I-axis for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius).
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' swim_
+:'''input =''' [[behavior_oyster.in]]
+;<span id="swim_Sdec"></span>swim_Sdec
+:Fraction active {f} due to decreasing salinity for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''swim_Sdec'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' swim_Sdec
+:'''input =''' [[behavior_oyster.in]]
+;<span id="swim_Sinc"></span>swim_Sinc
+:Fraction active {d} due to increasing salinity for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''swim_Sinc'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' swim_Sinc
+:'''input =''' [[behavior_oyster.in]]
+;<span id="swim_T0"></span>swim_T0
+:Starting value for larval size J-axis for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius).
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' swim_T0
+:'''input =''' [[behavior_oyster.in]]
+;<span id="swim_table"></span>swim_table
+:Look-up table, '''swim_table'''(58,24) for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius).
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' swim_table
+:'''input =''' [[behavior_oyster.in]]
+;<span id="swim_Tmax"></span>swim_Tmax
+:Maximum swimming time fraction for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''swim_Tmax'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' swim_Tmax
+:'''input =''' [[behavior_oyster.in]]
+;<span id="swim_Tmin"></span>swim_Tmin
+:Minimum swimming time fraction for planktonic larvae swimming speed (mm/s) as a function of larval size (um) and temperature (Celsius). [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''swim_Tmin'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' swim_Tmin
+:'''input =''' [[behavior_oyster.in]]
+;<span id="sz_alpha"></span>sz_alpha
+:Surface flux from wave dissipation used in the various formulations of surface turbulent kinetic energy flux in the GLS. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''sz_alpha'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' SZ_ALPHA
+:'''input =''' [[roms.in]]
 ==<span class="alphabet">T</span>==
-;<span id="t"></span>'''t'''
+;<span id="t"></span>t
-:Tracer-type variables, <math>\,T(\xi,\eta,s,t,itrc)</math>.
+:Tracer-type variables, <math>T(\xi,\eta,s,t,itrc)</math>.
 :'''dimension =''' '''t'''([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],[[#N|N(ng)]],3,[[#NT|NT(ng)]])
 :'''pointer =''' [[mod_ocean.F|OCEAN(ng)%]]'''t'''
-:'''tangent =''' <span class="red">tl_t</span>
+:'''tangent =''' <span class="TangentColor">tl_t</span>
-:'''adjoint =''' <span class="purple">ad_t</span>
+:'''adjoint =''' <span class="AdjointColor">ad_t</span>
 :'''grid =''' &rho;-points
-:'''CPP =''' [[SOLVE3D]]
+:'''option =''' [[Options#SOLVE3D | SOLVE3D]]
 :'''routine =''' [[step3d_t.F]]
@@ Line 128: / Line 2,215: @@
 ! CPP
 |-
-| [[itemp|itemp]]
+| [[#itemp|itemp]]
 | Potential temperature
 | Celsius
-| [[SOLVE3D]]
+| [[Options#SOLVE3D|SOLVE3D]]
 |-
 | [[#isalt|isalt]]
 | Salinity
 | None
-| [[SALINITY]]
+| [[Options#SALINITY|SALINITY]]
 |-
 | [[#inert|inert(1:NPT)]]
 | [[#NPT|NPT]] inert tracers
 | kilogram meter<sup>-3</sup>
-| [[T_PASSIVE]]
+| [[Options#T_PASSIVE|T_PASSIVE]]
 |-
 | [[#idsed|idsed(1:NST)]]
 | [[#NST|NST]] sediment tracers
 | kilogram meter<sup>-3</sup>
-| [[SEDIMENT]]
+| [[Options#SEDIMENT|SEDIMENT]]
 |-
-| [[idbio|idbio(1:NBT)]]
+| [[#idbio|idbio(1:NBT)]]
 | [[#NBT|NBT]] biology tracers
 | millimole meter<sup>-3</sup>
-| [[BIOLOGY]]
+| [[Options#BIOLOGY|BIOLOGY]]
 |-
 |}
-==<span class="alphabet">U</span>==
+;<span id="T0"></span>T0
+:Background potential temperature constant used in Linear Equation of State. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''T0'''([[#Ngrids|Ngrids]])
+:'''units =''' Celsius
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' T0
+:'''input =''' [[roms.in]]
+;<span id="tau_cd"></span>tau_cd
+:Kinematic critical shear for deposition of cohesive and non-cohesive sediment. This is ignored for cohesive sediment.
+:'''dimension =''' '''tau_cd'''([[#NST|NST]],[[#Ngrids|Ngrids]])
+:'''units =''' Newton meter<sup>-2</sup>
+:'''option = ''' [[Options#SEDIMENT|SEDIMENT]]
+:'''routine =''' [[mod_sediment.F]]
+:'''keywords =''' MUD_TAU_CD, SAND_TAU_CD
+:'''input =''' [[sediment.in]]
+;<span id="tau_ce"></span>tau_ce
+:Kinematic critical shear for erosion of cohesive and non-cohesive sediment.
+:'''dimension =''' '''tau_ce'''([[#NST|NST]],[[#Ngrids|Ngrids]])
+:'''units =''' Newton meter<sup>-2</sup>
+:'''option = ''' [[Options#SEDIMENT|SEDIMENT]]
+:'''routine =''' [[mod_sediment.F]]
+:'''keywords =''' MUD_TAU_CE, SAND_TAU_CE
+:'''input =''' [[sediment.in]]
+;<span id="Tcoef"></span>Tcoef
+:Thermal expansion coefficient in Linear Equation of State. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Tcoef'''([[#Ngrids|Ngrids]])
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' TCOEF
+:'''input =''' [[roms.in]]
+;<span id="Tcline"></span>Tcline
+:Width of surface or bottom boundary layer in which higher vertical resolution is required during stretching. [[#Ngrids|Ngrids]] values are expected. <span class="red">WARNING:</span> Users need to experiment with [[#theta_b|theta_b]], [[#theta_s|theta_s]] and <span class="blue">Tcline</span>. We have found out that the model goes unstable with high values of [[#theta_s|theta_s]].  In steep and very tall topography, it is recommended to use [[#theta_s|theta_s]]&nbsp;&lt;&nbsp;3.0.
+:'''dimension =''' '''Tcline'''([[#Ngrids|Ngrids]])
+:'''units =''' meters
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' TCLINE
+:'''input =''' [[roms.in]]
+;<span id="theta_b"></span>theta_b
+:S-coordinate bottom control parameter, (0&nbsp;&lt;&nbsp;<span class="blue">theta_b</span>&nbsp;&lt;&nbsp;1). [[#Ngrids|Ngrids]] values are expected. <span class="red">WARNING:</span> Users need to experiment with <span class="blue">theta_b</span>, [[#theta_s|theta_s]] and [[#Tcline|Tcline]]. We have found out that the model goes unstable with high values of [[#theta_s|theta_s]].  In steep and very tall topography, it is recommended to use [[#theta_s|theta_s]]&nbsp;&lt;&nbsp;3.0.
+:'''dimension =''' '''theta_b'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' THETA_B
+:'''input =''' [[roms.in]]
+;<span id="theta_s"></span>theta_s
+:S-coordinate surface control parameter, (0&nbsp;&lt;&nbsp;<span class="blue">theta_s</span>&nbsp;&lt;&nbsp;20). [[#Ngrids|Ngrids]] values are expected. <span class="red">WARNING:</span> Users need to experiment with [[#theta_b|theta_b]], <span class="blue">theta_s</span> and [[#Tcline|Tcline]]. We have found out that the model goes unstable with high values of <span class="blue">theta_s</span>.  In steep and very tall topography, it is recommended to use <span class="blue">theta_s</span>&nbsp;&lt;&nbsp;3.0.
+:'''dimension =''' '''theta_s'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' THETA_S
+:'''input =''' [[roms.in]]
+;<span id="TIDE"></span>TIDE
+: Input tidal forcing file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''TIDE'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[read_phypar.F]]
+:'''keyword =''' TIDENAME
+:'''input =''' [[roms.in]]
+;<section begin=tide_start />;<span id="tide_start"></span>[[tide_start]]
+:Reference time origin for tidal forcing. This is the time used when processing input tidal model data. It is needed in routine [[set_tides.F]] to compute the correct phase lag with respect ROMS/TOMS initialization time.
+:'''option ='''
+:'''units =''' days
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' TIDE_START
+:'''input =''' [[roms.in]]<section end=tide_start />
+<section begin=time_ref />;<span id="time_ref"></span>[[time_ref]]
+:Reference time (yyyymmdd.f) used to compute relative time: elapsed time interval since reference-time.
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' TIME_REF
+:'''input =''' [[roms.in]]<section end=time_ref />
+;<span id="title"></span>title
+:Title of model run.
+:'''keyword =''' TITLE
+:'''input =''' [[roms.in]]
+;<span id="tkenu2"></span>tkenu2
+:Lateral harmonic constant mixing coefficient for turbulent closure variables. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''tkenu2'''([[#Ngrids|Ngrids]])
+:'''units =''' meters<sup>2</sup> second<sup>-1</sup>
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' TKENU2
+:'''input =''' [[roms.in]]
+;<span id="tkenu4"></span>tkenu4
+:Lateral biharmonic constant mixing coefficient for turbulent closure variables. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''tkenu4'''([[#Ngrids|Ngrids]])
+:'''units =''' meters<sup>4</sup> second<sup>-1</sup>
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' TKENU4
+:'''input =''' [[roms.in]]
+;<span id="tl_LBC"></span>tl_LBC
+:Lateral boundary conditions for tangent linear model.
+:'''dimension =''' '''tl_LBC'''(4,[[#nLBCvar|nLBCvar]],[[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_param.F]]
+;<span id="tl_M2diff"></span>tl_M2diff
+:If weak constraint 4DVar and the [[Options#RPM_RELAXATION|RPM_RELAXATION]] flag is activated, this coefficient is used to relax 2D momentum in the representer tangent linear solution to the previous outer loop linearized trajectory during the Picard iterations. The user may turn off relaxation by setting this to zero. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''tl_M2diff'''([[#Ngrids|Ngrids]])
+:'''units =''' meters<sup>2</sup> second<sup>-1</sup>
+:'''routine =''' [[mod_scalars.F]], [[read_asspar.F]], [[rp_step2d_LF_AM3.h]]
+:'''keyword =''' tl_M2diff
+:'''input =''' [[s4dvar.in]]
+;<span id="tl_M3diff"></span>tl_M3diff
+:If weak constraint 4DVar and the [[Options#RPM_RELAXATION|RPM_RELAXATION]] flag is activated, this coefficient is used to relax 3D momentum in the representer tangent linear solution to the previous outer loop linearized trajectory during the Picard iterations. The user may turn off relaxation by setting this to zero. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''tl_M3diff'''([[#Ngrids|Ngrids]])
+:'''units =''' meters<sup>2</sup> second<sup>-1</sup>
+:'''routine =''' [[ad_uv3drelax.F]], [[mod_scalars.F]], [[read_asspar.F]], [[rp_uv3drelax.F]], [[tl_uv3drelax.F]]
+:'''keyword =''' tl_M3diff
+:'''input =''' [[s4dvar.in]]
+;<span id="tl_Tdiff"></span>tl_Tdiff
+:If weak constraint 4DVar and the [[Options#RPM_RELAXATION|RPM_RELAXATION]] flag is activated, this coefficient is used to relax tracer type variables diffusion in the representer tangent linear solution to the previous outer loop linearized trajectory during the Picard iterations. The user may turn off relaxation by setting this to zero. [[#MT|MT]] values are expected.
+:'''dimension =''' '''tl_Tdiff'''([[#NT|NT]],[[#Ngrids|Ngrids]])
+:'''units =''' meters<sup>2</sup> second<sup>-1</sup>
+:'''routine =''' [[ad_t3drelax.F]], [[mod_scalars.F]], [[read_asspar.F]], [[rp_t3drelax.F]], [[tl_t3drelax.F]]
+:'''keyword =''' tl_Tdiff
+:'''input =''' [[s4dvar.in]]
+;<span id="TLF"></span>TLF
+:Impulse tangent linear forcing output NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''TLF'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' TLFNAME
+:'''input =''' [[roms.in]]
+;<span id="TLM"></span>TLM
+:Tangent linear history output NetCDF file name. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''TLM'''([[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' TLMNAME
+:'''input =''' [[roms.in]]
+;<span id="tnu2"></span>tnu2
+:Lateral harmonic constant mixing coefficient for tracer type variables. If variable horizontal diffusion is activated, <span class="blue">tnu2</span> is the mixing coefficient for the largest grid-cell in the domain.
+:'''dimension =''' '''tnu2'''([[#MT|MT]],[[#Ngrids|Ngrids]])
+:'''units =''' meter<sup>2</sup> second<sup>-1</sup>
+:'''option = ''' [[Options#SEDIMENT|SEDIMENT]], [[Options#BIOLOGY|BIOLOGY]]
+:'''routine =''' [[mod_mixing.F]], [[mod_scalars.F]]
+:'''keywords =''' MUD_TNU2, SAND_TNU2, TNU2
+:'''input =''' [[biology.in]], [[sediment.in]]
+;<span id="tnu4"></span>tnu4
+:Square root lateral biharmonic constant mixing coefficient for tracer type variables. If variable horizontal diffusion is activated, <span class="blue">tnu4</span> is the mixing coefficient for the largest grid-cell in the domain.
+:'''dimension =''' '''tnu4'''([[#MT|MT]],[[#Ngrids|Ngrids]])
+:'''units =''' meter<sup>4</sup> second<sup>-1</sup>
+:'''option = ''' [[Options#SEDIMENT|SEDIMENT]], [[Options#BIOLOGY|BIOLOGY]]
+:'''routine =''' [[mod_mixing.F]], [[mod_scalars.F]]
+:'''keywords =''' MUD_TNU4, SAND_TNU4, TNU4
+:'''input =''' [[biology.in]], [[sediment.in]]
+;<span id="Tnudg"></span>Tnudg
+:Inverse time-scale for nudging tracers at open boundaries and sponge areas.
+:'''dimension =''' '''Tnudg'''([[#MT|MT]],[[#Ngrids|Ngrids]])
+:'''option = ''' [[Options#SEDIMENT|SEDIMENT]], [[Options#BIOLOGY|BIOLOGY]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keywords =''' MUD_TNUDG, SAND_TNUDG, TNUDG
+:'''input =''' [[biology.in]], [[sediment.in]]
+;<span id="turb_ambi"></span>turb_ambi
+:Ambient turbidity level, {turb}, (g/l) for turbidity effects on planktonic larvae growth. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''turb_ambi'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' turb_ambi
+:'''input =''' [[behavior_oyster.in]]
+;<span id="turb_axis"></span>turb_axis
+:Turbidity linear axis crossing {c} for turbidity effects on planktonic larvae growth. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''turb_axis'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' turb_axis
+:'''input =''' [[behavior_oyster.in]]
+;<span id="turb_base"></span>turb_base
+:Turbidity base factor, {b}, (g/l) for turbidity effects on planktonic larvae growth. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''turb_base'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' turb_base
+:'''input =''' [[behavior_oyster.in]]
+;<span id="turb_crit"></span>turb_crit
+:Critical turbidity value (g/l) for turbidity effects on planktonic larvae growth. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''turb_crit'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' turb_crit
+:'''input =''' [[behavior_oyster.in]]
+;<span id="turb_mean"></span>turb_mean
+:Turbidity mean, {turb0}, (g/l) for turbidity effects on planktonic larvae growth. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''turb_mean'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' turb_mean
+:'''input =''' [[behavior_oyster.in]]
+;<span id="turb_rate"></span>turb_rate
+:Turbidity rate, {beta}, (1/(g/l)) for turbidity effects on planktonic larvae growth. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''turb_rate'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' turb_rate
+:'''input =''' [[behavior_oyster.in]]
+;<span id="turb_size"></span>turb_size
+:Minimum larvae size (um) affected by tubidity for turbidity effects on planktonic larvae growth. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''turb_size'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' turb_size
+:'''input =''' [[behavior_oyster.in]]
-;<span id="UBi"></span>'''UBi'''
+;<span id="turb_slop"></span>turb_slop
-:Array upper bound dimension in the '''i'''-direction.
+:Turbidity linear slope, {m}, (1/(g/l)) for turbidity effects on planktonic larvae growth. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''turb_slop'''([[#Ngrids|Ngrids]])
+:'''option =''' [[Options#FLOATS|FLOATS]], [[Options#FLOAT_OYSTER|FLOAT_OYSTER]]
+:'''routine =''' [[oyster_floats.h]], [[oyster_floats_def.h]], [[oyster_floats_inp.h]], [[oyster_floats_mod.h]], [[oyster_floats_wrt.h]]
+:'''keyword =''' turb_slop
+:'''input =''' [[behavior_oyster.in]]
-;<span id="UBj"></span>'''UBj'''
+==<span class="alphabet">U</span>==
-:Array upper bound dimension in the '''j'''-direction.
-;<span id="u"></span>'''u'''
+;<span id="u"></span>u
-:Total momentum component in the &xi;-direction, <math>\,u(\xi,\eta,s,t)</math>.
+:Total momentum component in the <math>\xi</math>-direction, <math>u(\xi,\eta,s,t)</math>.
 :'''dimension =''' '''u'''([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],[[#N|N(ng)]],2)
 :'''pointer =''' [[mod_ocean.F|OCEAN(ng)%]]'''u'''
-:'''tangent =''' <span class="red">tl_u</span>
+:'''tangent =''' <span class="TangentColor">tl_u</span>
-:'''adjoint =''' <span class="purple">ad_u</span>
+:'''adjoint =''' <span class="AdjointColor">ad_u</span>
 :'''units =''' meter second<sup>-1</sup>
 :'''grid =''' u-points
-:'''CPP =''' [[SOLVE3D]]
+:'''option =''' [[Options#SOLVE3D | SOLVE3D]]
 :'''routine =''' [[step3d_uv.F]]
-;<span id="ubar"></span>'''ubar'''
+;<span id="ubar"></span>ubar
-:Vertically-integrated momentum component in the &xi;-direction, <math>\bar u(\xi,\eta,t)</math>.
+:Vertically-integrated momentum component in the <math>\xi</math>-direction, <math>\bar u(\xi,\eta,t)</math>.
-::<math>\bar u = \frac{1}{D} \int_{-h}^{\zeta} u\,H_z\,dz</math>
+::<math display="block">\bar u = \frac{1}{D} \int_{-h}^{\zeta} u\,H_z\,dz</math>
 :'''dimension =''' '''ubar'''([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],3)
 :'''pointer =''' [[mod_ocean.F|OCEAN(ng)%]]'''ubar'''
-:'''tangent =''' <span class="red">tl_ubar</span>
+:'''tangent =''' <span class="TangentColor">tl_ubar</span>
-:'''adjoint =''' <span class="purple">ad_ubar</span>
+:'''adjoint =''' <span class="AdjointColor">ad_ubar</span>
 :'''units =''' meter second<sup>-1</sup>
 :'''grid =''' u-points
 :'''routine =''' [[step2d.F]]
+;<span id="UBi"></span>UBi
+:Array upper bound dimension in the '''i'''-direction. In serial and shared-memory applications its value is govern by the value of UPPER_BOUND_I.  In distributed-memory its value is a function of the tile partition, '''UBi'''=[[#Iend|Iend]]+[[#NghostPoints|NghostPoints]].
+:'''option =''' [[Options#UPPER_BOUND_I|UPPER_BOUND_I]]
+:'''routine =''' [[get_bounds.F]], [[get_tile.F]]
+;<span id="UBj"></span>UBj
+:Array upper bound dimension in the '''j'''-direction. In serial and shared-memory applications its value is govern by the value of UPPER_BOUND_J.  In distributed-memory its value is a function of the tile partition, '''UBj'''=[[#Jend|Jend]]+[[#NghostPoints|NghostPoints]].
+:'''option =''' [[Options#UPPER_BOUND_J|UPPER_BOUND_J]]
+:'''routine =''' [[get_bounds.F]], [[get_tile.F]]
+;<section begin=user />;<span id="user"></span>[[user]]
+:Generic User parameters, <span class="blue">NUSER</span> values are expected.
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' USER
+:'''input =''' [[roms.in]]<section end=user />
+;<span id="USRname"></span>USRname
+:USER's input generic file name.
+:'''routine =''' [[mod_iounits.F]]
+:'''keyword =''' USRNAME
+:'''input =''' [[roms.in]]
 ==<span class="alphabet">V</span>==
-;<span id="v"></span>'''v'''
+;<span id="v"></span>v
-:3D momentum component in the &eta;-direction, <math>\,v(\xi,\eta,s,t)</math>.
+:3D momentum component in the &eta;-direction, <math>v(\xi,\eta,s,t)</math>.
 :'''dimension =''' '''v'''([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],[[#N|N(ng)]],2)
 :'''pointer =''' [[mod_ocean.F|OCEAN(ng)%]]'''v'''
-:'''tangent =''' <span class="red">tl_u</span>
+:'''tangent =''' <span class="TangentColor">tl_u</span>
-:'''adjoint =''' <span class="purple">ad_u</span>
+:'''adjoint =''' <span class="AdjointColor">ad_u</span>
 :'''units =''' meter second<sup>-1</sup>
 :'''grid =''' v-points
-:'''CPP =''' [[SOLVE3D]]
+:'''option =''' [[Options#SOLVE3D|SOLVE3D]]
 :'''routine =''' [[step3d_uv.F]]
-;<span id="vbar"></span>'''vbar'''
+;<span id="varname"></span>varname
+:Input variable information file name. This file needs to be processed first so all information arrays can be initialized properly. The default file is at ROMS/External/[[varinfo.dat]].
+:'''keyword =''' VARNAME
+:'''input =''' [[roms.in]]
+;<span id="vbar"></span>vbar
 :Vertically-integrated momentum component in the &eta;-direction, <math>\bar v(\xi,\eta,t)</math>.
-::<math>\bar v = \frac{1}{D} \int_{-h}^{\zeta} v\,H_z\,dz</math>
+::<math display="block">\bar v = \frac{1}{D} \int_{-h}^{\zeta} v\,H_z\,dz</math>
 :'''dimension =''' '''vbar'''([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],3)
 :'''pointer =''' [[mod_ocean.F|OCEAN(ng)%]]'''vbar'''
-:'''tangent =''' <span class="red">tl_vbar</span>
+:'''tangent =''' <span class="TangentColor">tl_vbar</span>
-:'''adjoint =''' <span class="purple">ad_vbar</span>
+:'''adjoint =''' <span class="AdjointColor">ad_vbar</span>
 :'''units =''' meter second<sup>-1</sup>
 :'''grid =''' v-points
 :'''routine =''' [[step2d.F]]
+;<span id="Vgamma"></span>Vgamma
+:Vertical stability and accuracy factor (< 1) used to scale the time-step of the convolution operator below its theoretical limit. Notice that four values are needed for <span class="blue">Vgamma</span> to facilitate the error covariance modeling for:
+::[1] initial conditions
+::[2] model
+::[3] boundary conditions
+::[4] surface forcing
+:'''dimension =''' '''Vgamma'''(4)
+:'''routine =''' [[metrics.F]], [[mod_netcdf.F]], [[mod_scalars.F]], [[read_asspar.F]]
+:'''keyword =''' Vgamma
+:'''input =''' [[s4dvar.in]]
+;<span id="visc2"></span>visc2
+:Lateral harmonic constant mixing coefficient for momentum. [[#Ngrids|Ngrids]] values are expected. If variable horizontal viscosity is activated, <span class="blue">visc2</span> is the mixing coefficient for the largest grid-cell in the domain.
+:'''dimension =''' '''visc2'''([[#Ngrids|Ngrids]])
+:'''units =''' meters<sup>2</sup> second<sup>-1</sup>
+:'''option = '''
+:'''routine =''' [[mod_mixing.F]], [[mod_scalars.F]]
+:'''keyword =''' VISC2
+:'''input =''' [[roms.in]]
+;<span id="visc2"></span>visc4
+:Lateral biharmonic constant mixing coefficient for momentum. [[#Ngrids|Ngrids]] values are expected. If variable horizontal viscosity is activated, <span class="blue">visc4</span> is the mixing coefficient for the largest grid-cell in the domain.
+:'''dimension =''' '''visc4'''([[#Ngrids|Ngrids]])
+:'''units =''' meters<sup>4</sup> second<sup>-1</sup>
+:'''option = '''
+:'''routine =''' [[mod_mixing.F]], [[mod_scalars.F]]
+:'''keyword =''' VISC4
+:'''input =''' [[roms.in]]
+;<span id="VolCons"></span>VolCons
+:Lateral open boundary edge volume conservation switch for the nonlinear model. This is usually activated with radiation boundary conditions to enforce global mass conservation. Notice that these switches should not be activated if tidal forcing enabled.
+:'''dimension =''' '''VolCons'''(4,[[#Ngrids|Ngrids]])
+:'''option ='''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' VolCons
+:'''input =''' [[roms.in]]
+;<span id="Vstretching"></span>Vstretching
+:Selects the vertical stretching function, C(s). [[#Ngrids|Ngrids]] values are expected. Possible values are:
+::'''1''' - Original function in ROMS from the very beginning from [[Bibliography#SongY_1994a | Song and Haidvogel (1994)]]
+::'''2''' - ''A. Shchepetkin'' function from UCLA-ROMS
+::'''3''' - ''R. Geyer'' function for shallow sediment applications
+::'''4''' - ''A. Shchepetkin'' improved double stretching
+::'''5''' - ''Souza et al.'' quadratic Legendre polynomial function that allows higher resolution near the surface
+:See [[Vertical S-coordinate]] for more information.
+:'''dimension =''' '''Vstretching'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' Vstretching
+:'''input =''' [[roms.in]]
+;<span id="Vtransform"></span>Vtransform
+:Selects the vertical transform equation. [[#Ngrids|Ngrids]] values are expected. Possible values are:
+::'''1''' - Original formulation that has been in ROMS since 1999 described in [[Bibliography#ShchepetkinAF_2005a | Shchepetkin and McWilliams (2005)]]
+::'''2''' - New formulation developed by ''A. Shchepetkin''
+:See [[Vertical S-coordinate]] for more information.
+:'''dimension =''' '''Vtransform'''([[#Ngrids|Ngrids]])
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' Vtransform
+:'''input =''' [[roms.in]]
 ==<span class="alphabet">W</span>==
-;<span id="W"></span>'''W'''
+;<span id="W"></span>W
-:Terrain-following, vertical velocity component, <math>\,\Omega(\xi,\eta,s)\,Hz/mn</math>.
+:Terrain-following, vertical velocity component, <math>\Omega(\xi,\eta,s)\,H_z/mn</math>.
 :'''dimension =''' '''W'''([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],[[#N|0:N(ng)]])
 :'''pointer =''' [[mod_ocean.F|OCEAN(ng)%]]'''W'''
-:'''tangent =''' <span class="red">tl_W</span>
+:'''tangent =''' <span class="TangentColor">tl_W</span>
-:'''adjoint =''' <span class="purple">ad_W</span>
+:'''adjoint =''' <span class="AdjointColor">ad_W</span>
 :'''units =''' meter<sup>3</sup> second<sup>-1</sup>
 :'''sign = ''' positive downwards (downwelling), negative upwards (upwelling)
 :'''grid =''' w-points
-:'''CPP =''' [[SOLVE3D]]
+:'''option =''' [[Options#SOLVE3D | SOLVE3D]]
 :'''routine =''' [[omega.F]]
-;<span id="wvel"></span>'''wvel'''
+;<span id="Wsed"></span>Wsed
-:True vertical velocity component, <math>\,w(\xi,\eta,s)</math>. It is computed only for output purposes.
+:Particle settling velocity for cohesive and non-cohesive sediment.
+:'''dimension =''' '''Wsed'''([[#NST|NST]],[[#Ngrids|Ngrids]])
+:'''option = ''' [[Options#SEDIMENT|SEDIMENT]]
+:'''routine =''' [[mod_ncparam.F]], [[mod_ocean.F]], [[mod_sediment.F]]
+:'''keywords =''' MUD_WSED, SAND_WSED
+:'''input =''' [[sediment.in]]
+;<span id="wvel"></span>wvel
+:True vertical velocity component, <math>w(\xi,\eta,s)</math>. It is computed only for output purposes.
 :'''dimension =''' '''wvel'''([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],[[#N|0:N(ng)]])
 :'''pointer =''' [[mod_ocean.f|OCEAN(ng)%]]'''wvel'''
@@ Line 230: / Line 2,645: @@
 :'''sign = ''' positive downwards (downwelling), negative upwards (upwelling
 :'''grid =''' w-points
-:'''CPP =''' [[SOLVE3D]]
+:'''option =''' [[Options#SOLVE3D | SOLVE3D]]
 :'''routine =''' [[wvelocity.F]]
@@ Line 239: / Line 2,654: @@
 ==<span class="alphabet">Z</span>==
-;<span id="zeta"></span>'''zeta'''
+;<span id="zeta"></span>zeta
-:Free-surface, <math>\,\zeta(\xi,\eta,t)</math>.
+:Free-surface, <math>\zeta(\xi,\eta,t)</math>.
 :'''dimension =''' '''zeta'''([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],3)
 :'''pointer =''' [[mod_ocean.F|OCEAN(ng)%]]'''zeta'''
-:'''tangent =''' <span class="red">tl_zeta</span>
+:'''tangent =''' <span class="TangentColor">tl_zeta</span>
-:'''adjoint =''' <span class="purple">ad_zeta</span>
+:'''adjoint =''' <span class="AdjointColor">ad_zeta</span>
 :'''units =''' meter
 :'''grid =''' &rho;-points
 :'''routine =''' [[step2d.F]]
-;<span id="z_r"></span>'''z_r'''
+;<span id="z_r"></span>z_r
-:Actual depths of variables at &rho;-points, <math>\,Z_r(\xi,\eta,s)</math>.
+:Actual depths of variables at &rho;-points, <math>Z_r(\xi,\eta,s)</math>.
 :'''dimension =''' '''z_r'''([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],[[#N|N(ng)]])
 :'''pointer =''' [[mod_grid.f|GRID(ng)%]]'''z_r'''
@@ Line 256: / Line 2,671: @@
 :'''sign =''' negative downwards
 :'''grid =''' &rho;-points
-:'''CPP =''' [[SOLVE3D]]
+:'''option =''' [[Options#SOLVE3D | SOLVE3D]]
 :'''routine =''' [[set_depths.F]]
-;<span id="z_w"></span>'''z_w'''
+;<span id="z_w"></span>z_w
-:Actual depths of variables at w-points, <math>\,Z_w(\xi,\eta,s)</math>.
+:Actual depths of variables at w-points, <math>Z_w(\xi,\eta,s)</math>.
 :'''dimension =''' '''z_w'''([[#LBi|LBi]]:[[#UBi|UBi]],[[#LBj|LBj]]:[[#UBj|UBj]],[[#N|0:N(ng)]])
 :'''pointer =''' [[mod_grid.F|GRID(ng)%]]'''z_w'''
@@ Line 266: / Line 2,681: @@
 :'''sign =''' negative downwards
 :'''grid =''' w-points
-:'''CPP =''' [[SOLVE3D]]
+:'''option =''' [[Options#SOLVE3D | SOLVE3D]]
 :'''routine =''' [[set_depths.F]]
-&nbsp;
+;<span id="Znudg"></span>Znudg
+:Nudging time scale for free-surface. [[#Ngrids|Ngrids]] values are expected.
-&nbsp;
+:'''dimension =''' '''Znudg'''([[#Ngrids|Ngrids]])
+:'''units =''' days
-&nbsp;
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
-&nbsp;
+:'''keyword =''' ZNUDG
+:'''input =''' [[roms.in]]
-&nbsp;
-&nbsp;
-&nbsp;
-&nbsp;
-&nbsp;
-&nbsp;
-&nbsp;
-&nbsp;
-&nbsp;
-&nbsp;
+;<span id="Zob"></span>Zob
+:Bottom roughness used in the computation of momentum stress. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Zob'''([[#Ngrids|Ngrids]])
+:'''units =''' meters
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' Zob
+:'''input =''' [[roms.in]]
-&nbsp;
+;<span id="Zos"></span>Zos
+:Surface roughness used in the computation of momentum stress. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''Zos'''([[#Ngrids|Ngrids]])
+:'''units =''' meters
+:'''option = '''
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' Zos
+:'''input =''' [[roms.in]]
-&nbsp;
+;<span id="zos_hsig_alpha"></span>zos_hsig_alpha
+:Roughness from wave amplitude used in the various formulations of surface turbulent kinetic energy flux in the GLS. [[#Ngrids|Ngrids]] values are expected.
+:'''dimension =''' '''zos_hsig_alpha'''([[#Ngrids|Ngrids]])
+:'''option = ''' [[GLS_MIXING]]
+:'''routine =''' [[mod_scalars.F]]
+:'''keyword =''' ZOS_HSIG_ALPHA
+:'''input =''' [[roms.in]]