cppdefs.h

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/*
** include file "cppdefs.h"
**
** git $id$
********************************************************** hernan g. arango ***
** copyright(c) 2002-2025 the roms group                                    **
**   licensed under a mit/x style license                                    **
**   see license_roms.md                                                     **
*******************************************************************************
**                                                                           **
** the following is short description of all available cpp options.          **
**                                                                           **
** options associated with momentum equations:                               **
**                                                                           **
**   the default horizontal advection is 3rd-order upstream bias for         **
**   3d momentum and 4th-order centered for 2d momentum. the default         **
**   vertical advection is 4th-order centered for 3d momentum. If this       **
**   is the case, no flags for momentum advection need to be activated.      **
**                                                                           **
**   the 3rd-order upstream split advection(uv_u3adv_split) can be used     **
**   to correct for the spurious mixing of the advection operator in         **
**   terrain-following coordinates. If this is the case, the advection       **
**   operator is split in advective and viscosity components and several     **
**   internal flags are activated in "globaldefs.h".  notice that            **
**   horizontal and vertical advection of momentum is 4th-order centered     **
**   plus biharmonic viscosity to correct for spurious mixing. the total     **
**   time-dependent horizontal mixing coefficient are computed in            **
**   "hmixing.F".                                                            **
**                                                                           **
**   warning:  Use the splines vertical advection option (uv_sadvection)     **
**             only in idealized, high vertical resolution applications.     **
**                                                                           **
** uv_adv                  to turn on or off advection terms                 **
** uv_cor                  to turn on or off coriolis term                   **
** uv_u3adv_split          if 3rd-order upstream split momentum advection    **
** uv_c2advection          to turn on or off 2nd-order centered advection    **
** uv_c4advection          to turn on or off 4th-order centered advection    **
** uv_sadvection           to turn on or off splines vertical advection      **
** uv_vis2                 to turn on or off harmonic horizontal mixing      **
** uv_vis4                 to turn on or off biharmonic horizontal mixing    **
** uv_smagorinsky          to turn on or off smagorinsky-like viscosity      **
** uv_drag_grid            if spatially varying bottom friction parameters   **
** uv_logdrag              to turn on or off logarithmic bottom friction     **
** uv_ldrag                to turn on or off linear bottom friction          **
** uv_qdrag                to turn on or off quadratic bottom friction       **
** omega_implicit          to add adaptive implicit vertical advection       **
** splines_vvisc           if splines reconstruction of vertical viscosity   **
**                                                                           **
** option for barotropic kernel time-stepping algorithm. currently, the      **
** default is the legacy predictor/corrector lf-am3 scheme. see shchepetkin  **
** and mcwilliams(2005, 2009) for details. the efficient and accurate       **
** forward-backward ab3-am4 kernel will become the default soon.             **
**                                                                           **
** step2d_corilis          to add coriolis to barotropic kernel in 3d set-up **
** step2d_fb_lf_am3        lf-am3 scheme but with forward-backward feedback  **
** step2d_fb_ab3_am4       forward-backward ab3-am4 scheme                   **
**                                                                           **
** option to not allow the bottom stress components to change the direction  **
** of bottom momentum(change sign of velocity components.                   **
**                                                                           **
** limit_bstress           to limit the magnitude of bottom stress           **
**                                                                           **
** options associated with tracers equations:                                **
**                                                                           **
** ts_dif2                 to turn on or off harmonic horizontal mixing      **
** ts_dif4                 to turn on or off biharmonic horizontal mixing    **
** ts_smagorinsky          to turn on or off smagorinsky-like diffusion      **
** ts_fixed                if diagnostic run, no evolution of tracers        **
** t_passive               if inert passive tracers(dyes, etc)              **
** age_mean                if computing mean age of inert passive tracers    **
** nonlin_eos              if using nonlinear equation of state              **
** qcorrection             if net heat flux correction                       **
** salinity                if having salinity                                **
** scorrection             if freshwater flux correction                     **
** solar_source            if solar radiation source term                    **
** splines_vdiff           if splines reconstruction of vertical diffusion   **
** srelaxation             if salinity relaxation as a freshwater flux       **
** wtype_grid              to turn on spatially varying jerlov water type    **
**                                                                           **
** option to suppress further surface cooling if the sst is at freezing      **
** point or below and the net surface heat flux is cooling:                  **
**                                                                           **
** limit_stflx_cooling use to suppress sst cooling below freezing point      **
**                                                                           **
** options for mpdata 3d advection: hadvection(itrc,ng)%MPDATA and           **
**                                  vadvection(itrc,ng)%MPDATA switches      **
**                                                                           **
** ts_mpdata_limit         to limit upwind corrector fluxes for stability    **
**                                                                           **
** pressure gradient algorithm options:                                      **
**                                                                           **
**   If no option is selected, the pressure gradient term is computed using  **
**   standard density jacobian algorithm. notice that there are two quartic  **
**   pressure jacobian options. they differ on how the weno reconciliation   **
**   step is done and in the monotonicity constraining algorithms.           **
**                                                                           **
** dj_gradps               if splines density jacobian(shchepetkin, 2000)   **
** pj_gradp                if finite volume pressure jacobian(lin,1997)     **
** pj_gradpq2              if quartic 2 pressure jacobian(shchepetkin,2000) **
** pj_gradpq4              if quartic 4 pressure jacobian(shchepetkin,2000) **
** wj_gradp                if weighted density jacobian(song,1998)          **
**                                                                           **
** atm_press               to impose atmospheric pressure onto sea surface   **
** press_compensate        to compensate for boundary without atm pressure   **
**                                                                           **
** options for surface fluxes formulation using atmospheric boundary layer   **
** (fairall et al, 1996):                                                    **
**                                                                           **
**   there are three ways to provide longwave radiation in the atmospheric   **
**   boundary layer: (1) compute the net longwave radiation internally using **
**   the berliand(1952) equation(longwave) as function of air temperature, **
**   sea surface temperature, relative humidity, and cloud fraction;         **
**   (2) provide(read) longwave downwelling radiation only  and then add    **
**   outgoing longwave radiation(longwave_out) as a function of the model   **
**   sea surface temperature; (3) provide net longwave radiation(default).  **
**                                                                           **
** bulk_fluxes             if bulk fluxes computation                        **
** cool_skin               if cool skin correction                           **
** longwave                if computing net longwave radiation               **
** longwave_out            if computing outgoing longwave radiation          **
** eminusp                 if computing e-p                                  **
** wind_minus_current      if compute effective wind by removing current     **
**                                                                           **
** options for wave roughness formulation in bulk fluxes:                    **
**                                                                           **
** coare_taylor_yelland    if taylor and yelland(2001) relation             **
** coare_oost              if oost et al. (2002) relation                    **
** drennan                 if drennan(2003) relation                        **
** deepwater_waves         if deep water waves approximation                 **
**                                                                           **
** options for shortwave radiation:                                          **
**                                                                           **
**   the shortwave radiation can be computed using the global albedo         **
**   equation with a cloud correction. alternatively, input shortwave        **
**   radiation data computed from averaged data (with snapshots greater      **
**   or equal than 24 hours) can be modulated by the local diurnal cycle     **
**   which is a function longitude, latitude and day-of-year.                **
**                                                                           **
** albedo                  if albedo equation for shortwave radiation        **
** diurnal_srflux          to impose shortwave radiation local diurnal cycle **
**                                                                           **
** model configuration options:                                              **
**                                                                           **
** solve3d                 if solving 3d primitive equations                 **
** curvgrid                if curvilinear coordinates grid                   **
** masking                 if land/sea masking                               **
** bodyforce               if applying stresses as bodyforces                **
** profile                 if time profiling                                 **
** averages                if writing out nlm time-averaged data             **
** averages_detide         if writing out nlm time-averaged detided fields   **
** ad_averages             if writing out adm time-averaged data             **
** rp_averages             if writing out tlm time-averaged data             **
** tl_averages             if writing out adm time-averaged data             **
** diagnostics_bio         if writing out biological diagnostics             **
** diagnostics_uv          if writing out momentum diagnostics               **
** diagnostics_ts          if writing out tracer diagnostics                 **
** iceshelf                if including ice shelf cavities                   **
** single_precision        if single precision arithmetic numerical kernel   **
** spherical               if analytical spherical grid                      **
** stations                if writing out station data                       **
** stations_cgrid          if extracting data at native c-grid               **
**                                                                           **
** options for lagrangian drifters:                                          **
**                                                                           **
** floats                  to activate simulated lagrangian drifters         **
** float_oyster            to activate oyster model behavior in floats       **
** float_sticky            to reflect/stick floats that hit surface/bottom   **
** float_vwalk             if vertical random walk                           **
** vwalk_forward           if forward time stepping vertical random walk     **
**                                                                           **
** options for analytical fields configuration:                              **
**                                                                           **
**    any of the analytical expressions are coded in "analytical.F".         **
**                                                                           **
** ana_biology             if analytical biology initial conditions          **
** ana_bpflux              if analytical bottom passive tracers fluxes       **
** ana_bsflux              if analytical bottom salinity flux                **
** ana_btflux              if analytical bottom temperature flux             **
** ana_cloud               if analytical cloud fraction                      **
** ana_diag                if customized diagnostics                         **
** ana_dqdsst              if analytical surface heat flux sensitivity to sst**
** ana_drag                if analytical spatially varying drag parameters   **
** ana_fsobc               if analytical free-surface boundary conditions    **
** ana_grid                if analytical model grid set-up                   **
** ana_humidity            if analytical surface air humidity                **
** ana_initial             if analytical initial conditions                  **
** ana_m2clima             if analytical 2d momentum climatology             **
** ana_m2obc               if analytical 2d momentum boundary conditions     **
** ana_m3clima             if analytical 3d momentum climatology             **
** ana_m3obc               if analytical 3d momentum boundary conditions     **
** ana_mask                if analytical land/sea masking                    **
** ana_nudgcoef            if analytical climatology nudging coefficients    **
** ana_pair                if analytical surface air pressure                **
** ana_passive             if analytical inert tracers initial conditions    **
** ana_perturb             if analytical perturbation of initial conditions  **
** ana_psource             if analytical point sources/sinks                 **
** ana_rain                if analytical rain fall rate                      **
** ana_sediment            if analytical sediment initial fields             **
** ana_smflux              if analytical surface momentum stress             **
** ana_spflux              if analytical surface passive tracers fluxes      **
** ana_spinning            if analytical time-varying rotation force         **
** ana_sponge              if analytical enhanced viscosity/diffusion sponge **
** ana_srflux              if analytical surface shortwave radiation flux    **
** ana_ssflux              if analytical surface salinity flux               **
** ana_ssh                 if analytical sea surface height                  **
** ana_sss                 if analytical sea surface salinity                **
** ana_sst                 if analytical sea surface temperature, sst        **
** ana_stflux              if analytical surface net heat flux               **
** ana_tair                if analytical surface air temperature             **
** ana_tclima              if analytical tracers climatology                 **
** ana_tobc                if analytical tracers boundary conditions         **
** ana_vmix                if analytical vertical mixing coefficients        **
** ana_winds               if analytical surface winds                       **
** ana_wwave               if analytical wind induced waves                  **
**                                                                           **
** options for horizontal mixing of momentum:                                **
**                                                                           **
** visc_grid               to scale viscosity coefficient by grid size       **
** mix_s_uv                if mixing along constant s-surfaces               **
** mix_geo_uv              if mixing on geopotential(constant z) surfaces   **
**                                                                           **
** options for horizontal mixing of tracers:                                 **
**                                                                           **
** diff_grid               to scale diffusion coefficients by grid size      **
** mix_s_ts                if mixing along constant s-surfaces               **
** mix_geo_ts              if mixing on geopotential(constant z) surfaces   **
** mix_iso_ts              if mixing on epineutral(constant rho) surfaces   **
** ts_mix_clima            if diffusion of tracer perturbation(t-tclm)      **
** ts_mix_max_slope        if maximum slope in epineutral diffusion          **
** ts_mix_min_strat        if minimum stratification in epineutral diffusion **
** ts_mix_stability        if weighting diffusion between two time levels    **
**                                                                           **
** options for vertical turbulent mixing scheme of momentum and tracers      **
** (activate only one closure):                                              **
**                                                                           **
** bvf_mixing              if brunt-vaisala frequency mixing                 **
** gls_mixing              if generic length-scale mixing closure            **
** my25_mixing             if mellor/yamada level-2.5 closure                **
** lmd_mixing              if large et al. (1994) interior closure           **
**                                                                           **
** limit_vdiff             to impose an upper limit on vertical diffusion    **
** limit_vvisc             to impose an upper limit on vertical viscosity    **
**                                                                           **
** options for the generic length-scale closure(warner et al., 2005):       **
**                                                                           **
**   the default horizontal advection is third-order upstream bias.  the     **
**   default vertical advection is 4th-order centered advection.             **
**                                                                           **
** canuto_a                if canuto a-stability function formulation        **
** canuto_b                if canuto b-stability function formulation        **
** charnok                 if charnock surface roughness from wind stress    **
** craig_banner            if craig and banner wave breaking surface flux    **
** kantha_clayson          if kantha and clayson stability function          **
** k_c2advection           if 2nd-order centered advection                   **
** k_c4advection           if 4th-order centered advection                   **
** n2s2_horavg             if horizontal smoothing of buoyancy/shear         **
** ri_splines              if splines reconstruction for vertical sheer      **
** zos_hsig                if surface roughness from wave amplitude          **
** tke_wavediss            if wave breaking surface flux from wave amplitude **
**                                                                           **
** options for the mellor/yamada level 2.5 closure:                          **
**                                                                           **
**   the default horizontal advection is third-order upstream bias.  the     **
**   default vertical advection is 4th-order centered advection.             **
**                                                                           **
** n2s2_horavg             if horizontal smoothing of buoyancy/shear         **
** kantha_clayson          if kantha and clayson stability function          **
** k_c2advection           if 2nd-order centered advection                   **
** k_c4advection           if 4th-order centered advection                   **
** ri_splines              if splines reconstruction for vertical sheer      **
**                                                                           **
** options for the large et al. (1994) k-profile parameterization mixing:    **
** mixing:                                                                   **
**                                                                           **
** lmd_bkpp                if bottom boundary layer kpp mixing               **
** lmd_convec              to add convective mixing due to shear instability **
** lmd_ddmix               to add double-diffusive mixing                    **
** lmd_nonlocal            if nonlocal transport                             **
** lmd_rimix               to add diffusivity due to shear instability       **
** lmd_shapiro             if shapiro filtering boundary layer depth         **
** lmd_skpp                if surface boundary layer kpp mixing              **
** ri_splines              if splines reconstruction for richardson number   **
**                                                                           **
** options in the k-profile parameterization to activate smoothing of        **
** richardson number, if ri_splines is not activated:                        **
**                                                                           **
** ri_horavg               if horizontal richardson number smoothing         **
** ri_veravg               if vertical   richardson number smoothing         **
**                                                                           **
** options for meinte blass bottom boundary layer closure:                   **
**                                                                           **
**   the options mb_z0bl and mb_z0rip should be activated concurrently.      **
**                                                                           **
** mb_bbl                  if meinte blaas bbl closure                       **
** mb_calc_znot            if computing bottom roughness internally          **
** mb_calc_ub              if computing bottom orbital velocity internally   **
** mb_z0bio                if biogenic bedform roughness for ripples         **
** mb_z0bl                 if bedload roughness for ripples                  **
** mb_z0rip                if bedform roughness for ripples                  **
**                                                                           **
** options for styles and glenn(2000) bottom boundary layer closure:        **
**                                                                           **
** sg_bbl                  if styles and glenn(2000) bbl closure            **
** sg_calc_znot            if computing bottom roughness internally          **
** sg_calc_ub              if computing bottom orbital velocity internally   **
** sg_logint               if logarithmic interpolation of(ur,vr)           **
**                                                                           **
** options for the sherwood/signell/warner bottom boundary layer closure:    **
**                                                                           **
** ssw_bbl                 if sherwood et al. bbl closure                    **
** ssw_calc_znot           if computing bottom roughness internally          **
** ssw_logint              if logarithmic interpolation of(ur,vr)           **
** ssw_logint_wbl          if wave boundary layer height for ur,vr elevation **
** ssw_logint_direct       if user height for ur,vr elevation                **
** ssw_calc_ub             if computing bottom orbital velocity internally   **
** ssw_form_drag_cor       to activate form drag coefficient                 **
** ssw_zobio               if biogenic bedform roughness from ripples        **
** ssw_zobl                if bedload roughness for ripples                  **
** ssw_zorip               if bedform roughness from ripples                 **
**                                                                           **
** lateral boundary conditions options:                                      **
**                                                                           **
** implicit_nudging        if implicit nudging term in momentum radiation    **
** radiation_2d            if tangential phase speed in radiation conditions **
**                                                                           **
** options for tidal forcing at open boundaries:                             **
**                                                                           **
**   the tidal data is processed in terms of tidal components, classified by **
**   period. the tidal forcing is computed for the full horizontal grid. If  **
**   requested, the tidal forcing is added to the processed open boundary    **
**   data.                                                                   **
**                                                                           **
**   both tidal elevation and tidal currents are required to force the model **
**   properly. however, if only the tidal elevation is available, the tidal  **
**   currents at the open boundary can be estimated by reduced physics. only **
**   the pressure gradient, coriolis, and surface and bottom stresses terms  **
**   are considered at the open boundary. see "u2dbc_im.F" or "v2dbc_im.F"   **
**   for details. notice that there is an additional option(fsobc_reduced)  **
**   for the computation of the pressure gradient term in both flather or    **
**   reduced physics conditions(*_m2flather, *_m2reduced).                  **
**                                                                           **
** ssh_tides               if imposing tidal elevation                       **
** uv_tides                if imposing tidal currents                        **
** ramp_tides              if ramping(over one day) tidal forcing           **
** tide_generating_forces  adds tide generation forces to pressure gradient  **
** fsobc_reduced           if ssh data and reduced physics conditions        **
** add_fsobc               to add tidal elevation to processed obc data      **
** add_m2obc               to add tidal currents  to processed obc data      **
**                                                                           **
** roms driver options:                                                      **
**                                                                           **
** adm_driver                 if generic adjoint model                       **
** ad_sensitivity             if adjoint sensitivity                         **
** aft_eigenmodes             if adjoint finite time eingenmodes             **
** array_modes                if 4d-var representer matrix array modes       **
** clipping                   if r4d-var representer matrix clipping analysis**
** correlation                if background-error correlation model          **
** ensemble                   if ensemble prediction                         **
** evolved_lcz                if 4d-var evolved hessian singular vectors     **
** forcing_sv                 if forcing singular vectors driver             **
** ft_eigenmodes              if finite time eingenmodes: normal modes       **
** hessian_fsv                if hessian forcing singular vectors            **
** hessian_so                 if hessian stochastic optimals                 **
** hessian_sv                 if hessian singular vectors                    **
** inner_product              if tangent/adjoint inner product check         **
** i4dvar                     if incremental 4d-var data assimilation        **
** i4dvar_ana_sensitivity     if i4d-var observations sensitivity            **
** initialize_automatic       to initialize automatic arrays in step2d       **
** jedi                       if using joint effort for da integration       **
** lcz_final                  if computing 4d-var hessian singular vectors   **
** opt_observations           if optimal observations                        **
** opt_perturbation           if optimal perturbations, singular vectors     **
** picard_test                if representer tangent linear model test       **
** pseudospectra              if pseudospectra of tangent linear resolvant   **
** rbl4dvar                   if weak constraint rbl4d-var data assimilation **
** rbl4dvar_ana_sensitivity   if rbl4d-var analysis observation sensitivity  **
** rbl4dvar_fct_sensitivity   if rbl4d-var forecast observation sensitivity  **
** rpm_driver                 if generic representers model                  **
** r_symmetry                 if representer matrix symmetry test            **
** r4dvar                     if r4d-var data assimilation                   **
** r4dvar_ana_sensitivity     if r4d-var analysis observation sensitivity    **
** sanity_check               if tangent/adjoint codes sanity check          **
** so_semi                    if stochastic optimals driver, semi-norm       **
** so_trace                   if stochastic optimals, randomized trace       **
** split_i4dvar               if split i4d-var data assimilation             **
** split_rbl4dvar             if split rbl4d-var data assimilation           **
** split_r4dvar               if split r4d-var data assimilation             **
** split_sp4dvar              if split sp4d-var data assimilation            **
** sp4dvar                    if saddle-point 4d-var data assimilation       **
** stochastic_opt             if stochastic optimals                         **
** tlm_check                  if tangent linear model linearization check    **
** tlm_driver                 if generic tangent linear model driver         **
**                                                                           **
** options associated with tangent linear, representer and adjoint models:   **
**                                                                           **
** ad_impulse              to force adjoint model with intermittent impulses **
** ad_output_state         to write full adjoint state by adding time levels **
** adjust_boundary         if including boundary conditions in 4dvar state   **
** adjust_stflux           if including surface tracer flux in 4dvar state   **
** adjust_wstress          if including wind-stress in 4dvar state           **
** array_modes_split       to separate analysis due to ic, forcing, and obc  **
** balance_operator        if error covariance multivariate balance term     **
** beofs_only              if computing eofs of background error covariance  **
** bgqc                    if background quality control of observations     **
** bnorm                   if background norm hessian singular vectors       **
** celerity_write          if writing radiation celerity in forward file     **
** clipping_split          to separate analysis due to ic, forcing, and obc  **
** compute_mld             to compute mixed layer depth for background error **
** dataless_loops          if testing convergence of picard iterations       **
** enkf_restart            if writting restart fields for enkf               **
** forward_fluxes          if using nlm trajectory surface fluxes            **
** forward_mixing          if processing forward vertical mixing coefficient **
** forward_write           if writing out forward solution, basic state      **
** forward_read            if reading in  forward solution, basic state      **
** forward_rhs             if processing forward right-hand-side terms       **
** geopotential_hconv      if horizontal convolutions along geopotentials    **
** impact_inner            to write observations impacts for each inner loop **
** implicit_vconv          if implicit vertical convolution algorithm        **
** impulse                 if processing adjoint impulse forcing             **
** minres                  if minimal residual method for 4dvar minimization **
** multiple_tlm            if multiple tlm history files in 4dvar            **
** nlm_outer               if nonlinear model as basic state in outer loop   **
** obs_impact              if observation impact to 4dvar data assimilation  **
** obs_impact_split        to separate impact due to ic, forcing, and obc    **
** posterior_eofs          if posterior analysis error covariance eofs       **
** posterior_error_f       if final posterior analysis error covariance      **
** posterior_error_i       if initial posterior analysis error covariance    **
** prior_bulk_fluxes       if imposing prior nlm surface fluxes              **
** recompute_4dvar         if recomputing 4dvar in analysis algorithms       **
** remove_lapack_gotos     to replace gotos in customized lapack routines    **
** rpcg                    if restricted b-preconditioned lanczos solver     **
** rpm_relaxation          if picard iterations, diffusive relaxation of rpm **
** skip_nlm                to skip running nlm, reading nlm trajectory       **
** so_semi_white           to activate so semi norm white/red noise processes**
** std_model               if background error standard deviation modeling   **
** stoch_opt_white         to activate so white/red noise processes          **
** splines_vconv           to activate implicit splines vertical convolution **
** time_conv               if weak-constraint 4d-var time convolutions       **
** vconvolution            to add vertical correlation to 3d convolution     **
** verification            if writing out solution at observation locations  **
** weak_nointerp           if not time interpolation in weak 4d-var forcing  **
** zeta_elliptic           if ssh elliptic equation in balance operator      **
**                                                                           **
** option for processing the full grid range(interior and boundary points)  **
** of the state vector in variational data assimilation and generalized      **
** stability theory analysis. otherwise, only interior points are processed. **
**                                                                           **
** full_grid               to consider both interior and boundary points     **
**                                                                           **
** fennel et al. (2006) biology model options:                               **
**                                                                           **
** bio_fennel              if fennel et al. (2006) nitrogen-based model      **
** bio_sediment            to restore fallen material to the nutrient pool   **
** carbon                  to add carbon constituents                        **
** denitrification         to add denitrification processes                  **
** ocmip_oxygen_sc         if o2 schmidt number from keeling et al. (1998)   **
** oxygen                  to add oxygen dynamics                            **
** pco2air_data            if pco2 climatology from laurent et al. (2017)    **
** pco2air_secular         if pco2 time-depedent evolution                   **
** rw14_c02_sc             if co2 schmidt number from wanninkhof(2014)      **
** rw14_oxygen_sc          if o2  schmidt number from wanninkhof(2014)      **
** po4                     if phytoplanckton growth limitef by phosphorus    **
** river_don               if don non-sinking source from rivers             **
** talk_nonconserv         if nonconservative computation of alkalinity      **
**                                                                           **
** hypoxia ecosysten model options:                                          **
**                                                                           **
** hypoxia_srm             if hypoxia simple respiration model               **
** ocmip_oxygen_sc         if o2 schmidt number from keeling et al. (1998)   **
**                                                                           **
** npzd biology model options:                                               **
**                                                                           **
** npzd_franks             if npzd biology model, franks et al. (1986)       **
** npzd_iron               if npzd biology model with iron limitation        **
** npzd_powell             if npzd biology model, powell et al. (2006)       **
** iron_limit              if fe limitation on phytoplankton growth          **
** iron_relax              if nudging fe over the shelf, h <= fehmin         **
**                                                                           **
** bio-optical ecosim model options:                                         **
**                                                                           **
** ecosim                  if bio-optical ecosim model                       **
** bio_optical             to compute underwater spectral light properties   **
**                                                                           **
** nemuro lower trophic level ecosystem model options:                       **
**                                                                           **
**    need to choose a zooplankton grazing option(holling_grazing or        **
**    ivlev_explicit). the default implicit ivlev algorithm does not         **
**    work yet.                                                              **
**                                                                           **
** nemuro                  if nemuro ecosystem model.                        **
** bio_sediment            to restore fallen material to the nutrient pool   **
** holling_grazing         if holling-type s-shaped curve grazing(implicit) **
** ivlev_explicit          if ivlev explicit grazing algorithm               **
**                                                                           **
** red tide biological model options:                                        **
**                                                                           **
** red_tide                if red tide biological model.                     **
**                                                                           **
** sediment transport model options:                                         **
**                                                                           **
** sediment                to activate sediment transport model              **
** bedload_mpm             to activate meyer-peter-mueller bed load          **
** bedload_soulsby         to activate soulsby wave/current bed load         **
** cohesive_bed            to activate cohesive bed model                    **
** floc_turb_diss          dissipation for flocculation based on turbulence  **
** floc_bbl_diss           dissipation for flocs from bottom boundary layer  **
** mixed_bed               to activate mixed bed behavior                    **
** noncohesive_bed1        original bed model of warner et al 2008, default  **
** noncohesive_bed2        modified bed model of sherwood et al              **
** sed_biodiff             to activate sediment biodiffusivity               **
** sed_defloc              flocculation decomposition in sediment bed        **
** sed_dens                to activate sediment to affect equation of state  **
** sed_flocs               flocculation model of verney et al., 2011         **
** sed_morph               to allow bottom model elevation to evolve         **
** sed_tau_cd_const        constant critical stress for deposition           **
** sed_tau_cd_lin          linear critical stress for deposition             **
** suspload                to activate suspended load transport              **
**                                                                           **
** wave effoct on currents(wec) and shallow water options:                  **
**                                                                           **
** bottom_streaming    activate wave enhanced bottom streaming               **
** roller_svendsen     activate wave roller based on svendsen                **
** roller_mono         activate wave roller for monchromatic waves           **
** roller_reniers      activate wave roller based on reniers                 **
** surface_streaming   activate wave enhanced surface streaming              **
** wave_mixing         activate enhanced vertical viscosity mixing from waves**
** wdiss_churthor      activate wave dissipation from church/thorton.        **
** wdiss_gamma         activate wave dissipation when using inwave           **
** wdiss_roelvink      activate wave dissipation roelvink when using inwave  **
** wdiss_thorguza      activate wave dissipation from thorton/guza.          **
** wdiss_wavemod       activate wave dissipation from a wave model           **
** wec_vf              activate wave-current stresses from uchiyama et al.   **
** wet_dry             activate wetting and drying                           **
**                                                                           **
** options for grid nesting:                                                 **
**                                                                           **
** nesting                 to activate grid nesting: composite/refinement    **
** nesting_debug           to check mass fluxes conservation in refinement   **
** no_correct_tracer       to avoid two-way correction of boundary tracer    **
** one_way                 if one-way nesting in refinement grids            **
** refine_boundary         fine-to-coarse averaging at coarse grid boundary  **
** time_interp_flux        time interpolate coarse mass flux instead persist **
**                                                                           **
** options for coupling to other earth system models(esm) via the earth     **
** modeling framework(esmf) or modeling coupling toolkit(mct) libraries.   **
** If coupling with esmf library, it uses the national unified operational   **
** prediction capability(nuopc) layer "cap" files to facilitate exchanges   **
** with other esm components.                                                **
**                                                                           **
** esmf_lib                if coupling with the esmf/nuopc library           **
** mct_lib                 if coupling with the mct library                  **
**                                                                           **
** cice_coupling           if coupling to cice sea ice model                 **
** coamps_coupling         if coupling to coamps atmospheric model           **
** data_coupling           if coupling to DATA model                         **
** exclude_sponge          if excluding sponge point in export fields        **
** frc_coupling            if forcing from atmopheric or Data model          **
** refdif_coupling         if coupling to refdit wave model                  **
** regcm_coupling          if coupling to regcm atmospheric model            **
** swan_coupling           if coupling to swan wave model                    **
** time_interp             if importing snapshots for time interpolation     **
** wam_coupling            if coupling to wam wave model                     **
** wrf_coupling            if coupling to wrf atmospheric model              **
** wrf_timeavg             if time-averaged fields over coupling interval    **
**                                                                           **
** nearshore and shallow water model options:                                **
**                                                                           **
** wet_dry                 to activate wetting and drying                    **
**                                                                           **
** mpi communication options:  the routines "mp_assemble" (used in nesting), **
**                             "mp_collect" (used in netcdf i/o and 4d-var), **
** and "mp_reduce" (used in global reductions) are coded in "distribution.F" **
** by either using low-level("mpi_isend" and "mpi_irecv") or high-level     **
** ("mpi_allgather" and "mpi_allreduce") mpi calls. the default is to use    **
** the low-level mpi  calls. the options for routine "mp_boundary" (used to  **
** process lateral open boundary conditions is either "mpi_allgather" or     **
** "mpi_allreduce" (default).                                                **
**                                                                           **
** the user needs to be aware that the choice of these mpi communication     **
** routines it will affect performance issue. in some computers, the         **
** low-level are either slower or faster than the high-level mpi library     **
** calls. it depends on the computer(cluster) set-up. some vendors provide  **
** native mpi libraries fine-tuned for the computer architecture. the        **
** user needs to find which function option performs better by carrying on   **
** benchmarks. we provides the following choices:                            **
**                                                                           **
** assemble_allgather  use "mpi_allgather" in "mp_assemble"                  **
** assemble_allreduce  use "mpi_allreduce" in "mp_assemble"                  **
**                                                                           **
** boundary_allgather  use "mpi_allgather" in "mp_boundary"                  **
**                                                                           **
** collect_allgather   use "mpi_allgather" in "mp_collect"                   **
** collect_allreduce   use "mpi_allreduce" in "mp_collect"                   **
**                                                                           **
** reduce_allgather    use "mpi_allgather" in "mp_reduce"                    **
** reduce_allreduce    use "mpi_allreduce" in "mp_reduce"                    **
**                                                                           **
** netcdf input/output options:                                              **
**                                                                           **
** checksum                to report checksum when processing i/o            **
** check_open_files        to report number opened/closed/created files      **
** deflate                 to set compression netcdf-4/hdf5 format files     **
** hdf5                    to create netcdf-4/hdf5 format files              **
** metadata_report         to report/dump yaml metadata dictionary           **
** no_lbc_att              to not check nlm_lbc global attribute on restart  **
** no_read_ghost           to not include ghost points during read/scatter   **
** no_write_grid           if not writing grid arrays                        **
** out_double              if writing double precision output fields         **
** output_stats            to report netcdf output fields statistics         **
** parallel_io             if parallel i/o via hdf5 or pnetcdf libraries     **
** perfect_restart         to include perfect restart variables              **
** pio_lib                 to include parallel-io from the pio library       **
** pnetcdf                 if parallel i/o with pnetcdf(classic format)     **
** positive_zero           to impose positive zero in ouput data             **
** read_water              if only reading water points data                 **
** regrid_shapiro          to apply shapiro filter to regridded data         **
** roms_stdout             to write standard output into the 'log.roms' file **
** rst_single              if writing single precision restart fields        **
** write_water             if only writing water points data                 **
**                                                                           **
** option to process 3d data by levels(2d slabs) to reduce memory needs in  **
** distributed-memory configurations. this option is convenient for large    **
** problems on nodes with limited memory.                                    **
**                                                                           **
** inline_2dio             if processing 3d io level by level                **
**                                                                           **
** sea-ice modeling options:                                                 **
**                                                                           **
** ice_model               to activate sea-ice model                         **
** ice_thermo              if thermodynamic component                        **
** ice_mk                  if mellor-kantha thermodynamics(only choice)     **
** ice_alb_ec92            if albedo computation from ebert and curry        **
** ice_momentum            if momentum component                             **
** ice_mom_bulk            if alternate ice-water stress computation         **
** ice_evp                 if elastic-viscous-plastic rheology               **
** ice_advect              if advection of ice tracers                       **
** ice_smolar              if mpdata advection scheme                        **
** ice_upwind              if upwind advection scheme                        **
** ice_bulk_fluxes         if ice part of bulk flux computation              **
** ice_convsnow            if conversion of flooded snow to ice              **
** ice_strength_quad       if quadratic ice strength, a function of thickness**
** no_scorrection_ice      if no salinity correction under the ice           **
** outflow_mask            if hibler style outflow cells                     **
**                                                                           **
** option to avoid writing current date and cpp options to netcdf file       **
** headers. this is used to compare serial and parallel solutions where      **
** the unix command "diff" is used between netcdf files. it will only        **
** tell us that the binary files are different or not. finding the           **
** parallel bug is complete different story.                                 **
**                                                                           **
** debugging           use to activate parallel debugging switch             **
**                                                                           **
*******************************************************************************
*******************************************************************************
*******************************************************************************
**                                                                           **
** idealized test problems:                                                  **
**                                                                           **
** basin               big bad basin example                                 **
** benchmark           benchmark tests(small, medium, big grids)            **
** bio_toy             one-dimension (vertical) biology toy                  **
** bl_test             boundary layers test                                  **
** channel             periodic channel, optimal perturbations test          **
** canyon              coastal form stress canyon test                       **
** channel_neck        channel with a constriction                           **
** coupling_test       two-way atmosphere-ocean coupling test                **
** dogbone             idealize nesting grids(composite/refinement) test    **
** double_gyre         idealized double-gyre example                         **
** estuary_test        test estuary for sediment                             **
** flt_test            float tracking example                                **
** grav_adj            gravitational adjustment example                      **
** inlet_test          test inlet application                                **
** kelvin              kelvin wave test                                      **
** lab_canyon          lab canyon, polar coordinates example                 **
** lake_jersey         lake jersey nesting test Case                         **
** lake_signell        lake signell sediment test Case                       **
** lmd_test            test for lmd and kpp                                  **
** overflow            gravitational/overflow example                        **
** riverplume1         river plume example 1                                 **
** riverplume2         river plume example 2 (hyatt and signell)             **
** seamount            seamount example                                      **
** sed_test1           suspended sediment test in a channel                  **
** sed_toy             one-dimension (vertical) sediment toy                 **
** shoreface           shore face planar beach test Case                     **
** soliton             equatorial rossby wave example                        **
** test_chan           sediment test channel Case                            **
** test_head           sediment test headland Case                           **
** upwelling           upwelling example(default)                           **
** weddell             idealized weddell sea shelf application               **
** windbasin           linear wind-driven constant coriolis basin            **
**                                                                           **
** climatological applications: (see www.myroms.org/datasets)                **
**                                                                           **
** damee_4             north atlantic damee application, 3/4 degree          **
**                                                                           **
** selected realistic applications:                                          **
**                                                                           **
** adria02             adriatic sea application                              **
** nj_bight            new jersey bight application                          **
** wc13                california current system, 1/3 degree resolution      **
**                                                                           **
*******************************************************************************
*******************************************************************************
*******************************************************************************
**                                                                           **
**  the user needs to choose either a pre-defined application or his/her     **
**  own application. the application cpp flag to run is activated in the     **
**  makefile. for example, to activate the upwelling example(upwelling)     **
**  set:                                                                     **
**                                                                           **
**    roms_application ?= upwelling                                          **
**                                                                           **
**  in the makefile. roms will include the associated header file located    **
**  in the roms/include directory. the application header file name is the   **
**  lowercase value of roms_application with the .h extension and passed     **
**  as roms_header definition during  c-preprocessing.  for example, the     **
**  upwelling test problem includes the "upwelling.h" header file:           **
**                                                                           **
**    roms_header="upwelling.h"                                              **
**                                                                           **
**  If building a new application, choose an unique cpp flag for it and      **
**  create its associated include file(*.h) to specify the appropriate      **
**  configuration options.                                                   **
**                                                                           **
*******************************************************************************
*/
 
#if defined ROMS_HEADER
# include ROMS_HEADER
#else
   cppdefs - choose an appropriate roms application.
#endif
 
/*
**  include internal cpp definitions.
*/
 
#include "globaldefs.h"