!parameter inputs via namelist convention. !(1) Use ' ' (single quotes) for chars; !(2) integer values are fine for real vars/arrays; !(3) if multiple entries for a parameter are found, the last one wins - please avoid this !(4) array inputs follow column major (like FORTRAN) and can spill to multiple lines !(5) space allowed before/after '=' &CORE !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ! Core (mandatory) parameters; no defaults !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ! Pre-processing option. Useful for checking grid violations. ipre = 0 !Pre-processor flag (1: on; 0: off) ! Baroclinic/barotropic option. If ibc=0 (baroclinic model), ibtp is not used. ibc = 1 !Baroclinic option ibtp = 0 rnday = 3 !total run time in days dt = 150. !Time step in sec ! Grid for WWM (USE_WWM) msc2 = 24 !same as msc in .nml ... for consitency check between SCHISM and WWM mdc2 = 30 !same as mdc in .nml ! Define # of tracers in tracer modules (if enabled) ntracer_gen = 2 !user defined module (USE_GEN) ntracer_age = 4 !age calculation (USE_AGE). Must be =2*N where N is # of age tracers sed_class = 5 !SED3D (USE_SED) eco_class = 27 !EcoSim (USE_ECO): must be between [25,60] ! Global output controls nspool = 24 !output step spool ihfskip = 144 !stack spool; every ihfskip steps will be put into 1_*, 2_*, etc... / &OPT !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ! Optional parameters. The values shown below are default unless otherwise noted !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ !----------------------------------------------------------------------- ! 2nd pre-proc flag. If ipre2/=0, code will output some diagnotic outputs and stop. ! These outputs are: drag coefficients (Cdp) !----------------------------------------------------------------------- ipre2 = 0 ! Starting time start_year = 2021 start_month = 08 start_day = 04 start_hour = 18 utc_start = 0 !double !----------------------------------------------------------------------- ! Coordinate option: 1: Cartesian; 2: lon/lat (hgrid.gr3=hgrid.ll in this case, ! and orientation of element is outward of earth) !----------------------------------------------------------------------- ics = 2 !Coordinate option !----------------------------------------------------------------------- ! Hotstart option. 0: cold start; 1: hotstart with time reset to 0; 2: ! continue from the step in hotstart.nc !----------------------------------------------------------------------- ihot = 1 !----------------------------------------------------------------------- ! Equation of State type used ! ieos_type=0: UNESCO 1980 (nonlinear); =1: linear function of T ONLY, i.e. ! \rho=eos_b+eos_a*T, where eos_a<=0 in kg/m^3/C !----------------------------------------------------------------------- ieos_type = 0 ieos_pres = 0 !used only if ieos_type=0. 0: without pressure effects eos_a = -0.1 !needed if ieos_type=1; should be <=0 eos_b = 1001. !needed if ieos_type=1 !----------------------------------------------------------------------- ! Main ramp option !----------------------------------------------------------------------- nramp = 0 !ramp-up option (1: on; 0: off) dramp = 1. !needed if nramp=1; ramp-up period in days nrampbc = 0 !ramp-up flag for baroclinic force drampbc = 4. !not used if nrampbc=0 !----------------------------------------------------------------------- ! Method for momentum advection. 0: ELM; 1: upwind (not quite working yet) !----------------------------------------------------------------------- iupwind_mom = 0 !----------------------------------------------------------------------- ! Methods for computing velocity at nodes. ! If indvel=0, conformal linear shape function is used; if indvel=1, averaging method is used. ! For indvel=0, a stabilization method is needed (see below). !----------------------------------------------------------------------- indvel = 0 !default: 1 !----------------------------------------------------------------------- ! 2 stabilization methods, mostly for indvel=0. ! (1) Horizontal viscosity option. ihorcon=0: no viscosity is used; =1: Lapacian; ! =2: bi-harmonic. If ihorcon=1, horizontal viscosity _coefficient_ (<=1/8, related ! to diffusion number) is given in hvis_coef0, and the diffusion # ! is problem dependent; [0.001-1/8] seems to work well. ! If ihorcon=2, diffusion number is given by hvis_coef0 (<=0.025). ! If indvel=1, no horizontal viscosity is needed. ! (2) Shapiro filter (see below) ! ! For non-eddying regime applications (nearshore, estuary, river), two easiest options are: ! (1) indvel=1, ishapiro=ihorcon=0, and any choices of inter_mom; ! (2) indvel=0, ishapiro=1 (shapiro0=0.5), ihorcon=inter_mom=0. ! For applications that include eddying regime, refer to the manual. !----------------------------------------------------------------------- ihorcon = 2 hvis_coef0 = 0.025 !const. diffusion # if ihorcon/=0; <=0.025 for ihorcon=2, <=0.125 for ihorcon=1 ! cdh = 0.01 !needed only if ihorcon/=0; land friction coefficient - not active yet !----------------------------------------------------------------------- ! 2nd stabilization method via Shapiro filter. This should normally be used ! if indvel=ihorcon=0. To transition between eddying/non-eddying regimes, use ! indvel=0, ihorcon/=0, and ishapiro=-1 (shapiro.gr3). !----------------------------------------------------------------------- ishapiro = -1 !on/off flag. Default: 0 shapiro0 = 0.5 !Shapiro filter strength, needed only if ishapiro=1; max is 0.5 niter_shap = 1 !needed of ishapiro/=0 - # of iterations with Shapiro filter. Suggested: 1 !----------------------------------------------------------------------- ! Implicitness factor (0.5=h2_bcc (i.e. like Z) or uses const extrap ! (i.e. like terrain-following) if h<=h1_bcc(h1_bcc !----------------------------------------------------------------------- ! Hannah-Wright-like ratio & depth used to account for under-resolution ! in a b-clinic model. Used only if ibc=0 and iunder_deep/=0. ! The b-clinic force at prism centers is calculated with a reconstruction ! method in horizontal that has a stencil of an element and its adjacent elements. ! If the depths change is too much between the elem and its adjacent elem ! the under-resolution occurs (with steep bottom slope) and b-clinic force ! needs to be zeroed out below the (higher) bottom, specifically, if ! max(2 depths)>=hw_depth and abs(diff(2 depths))>=hw_ratio*max(2 depths). !----------------------------------------------------------------------- hw_depth = 1.e6 !threshold depth in [m] hw_ratio = 0.5 !ratio !----------------------------------------------------------------------- ! Hydraulic model option. If ihydraulics/=0, hydraulics.in ! is required. This option cannot be used with non-hydrostatic model. !----------------------------------------------------------------------- ihydraulics = 0 !----------------------------------------------------------------------- ! Point sources/sinks option (0: no; 1: on). If =1, needs source_sink.in (list of elements), ! vsource,th, vsink.th, and msource.th. Source/sinks can be specified at an elem more ! than once, and the code will accumulate the volumes, but for mass conc, one of ! the specified values will be taken (no summation). !----------------------------------------------------------------------- if_source = 1 nramp_ss = 0 !needed if if_source=1; ramp-up flag for source/sinks dramp_ss = 3 !needed if if_source=1; ramp-up period in days !----------------------------------------------------------------------- ! Horizontal diffusivity option. if ihdif=1, horizontal diffusivity is given in hdif.gr3 !----------------------------------------------------------------------- ihdif = 0 !----------------------------------------------------------------------- ! Bottom friction. ! nchi=0: drag coefficients specified in drag.gr3; nchi=-1: Manning's ! formulation (even for 3D prisms) with n specified in manning.gr3. ! nchi=1: bottom roughness (in meters) specified in rough.gr3 (and in this case, negative ! or 0 depths in rough.gr3 indicate time-independent Cd, not roughness!). ! Cd is calculated using the log law, when dzb>=dzb_min; when dzb=2, TVD or WENO method is used ! on an element/prism if the total depth (at all nodes of the elem.)>=h_tvd and the flag in ! tvd.prop = 1 for the elem. (tvd.prop is required in this case); ! otherwise upwind is used for efficiency. ! itr_met=3 (horizontal TVD) or 4 (horizontal WENO): implicit TVD in the vertical dimension. ! Also if itr_met==3 and h_tvd>=1.e5, some parts of the code are bypassed for efficiency ! Controls for WENO are not yet in place !----------------------------------------------------------------------- itr_met = 1 !Default: 1 h_tvd = 5. !used only if itr_met>=2; cut-off depth (m) !If itr_met=3 or 4, need the following 2 tolerances of convergence. The convergence !is achieved when sqrt[\sum_i(T_i^s+1-T_i^s)^2]<=eps1_tvd_imp*sqrt[\sum_i(T_i^s)^2]+eps2_tvd_imp eps1_tvd_imp = 1.e-4 !suggested value is 1.e-4, but for large suspended load, need to use a smaller value (e.g. 1.e-9) eps2_tvd_imp = 1.e-14 !Optional hybridized ELM transport for efficiency ielm_transport = 1 !1: turn on. Used only with itr_met>=3 max_subcyc = 10 !used only if ielm_transport/=0. Max # of subcycling per time step in transport allowed !if itr_met = 4, the following parameters are needed !if itr_met=4 and ipre=1, diagnostic outputs are generated for weno accuracy and stencil quality, ! see subroutine weno_diag in src/Hydro/misc_subs.F90 for details ip_weno = 2 !order of accuracy: 0- upwind; 1- linear polynomial, 2nd order; 2- quadratic polynomial, 3rd order courant_weno=0.5 !Courant number for weno transport nquad = 2 !number of quad points on each side, nquad= 1 or 2 ntd_weno = 1 !order of temporal discretization: (1) Euler (default); (3): 3rd-order Runge-Kutta (only for benchmarking) epsilon1 = 1.e-3 !coefficient for 2nd order weno smoother epsilon2 = 1.e-5 !1st coefficient for 3rd order weno smoother (larger values are more prone to numerical dispersion !, 1.e-10 should be fairly safe, recommended values: 1.e-8 ~ 1.e-6 (from the real applications so far) i_prtnftl_weno = 0 !option for writing nonfatal errors on invalid temp. or salinity for density: (0) off; (1) on. !Inactive at the moment: epsilon3 = 1.e-25 !2nd coefficient for 3rd order weno smoother (inactive at the moment) !Elad filter has not been implemented yet; preliminary tests showed it might not be necessary ielad_weno = 0 !ielad, if ielad=1, use ELAD method to suppress dispersion (inactive at the moment) small_elad = 1.e-4 !small (inactive at the moment) !----------------------------------------------------------------------- ! Atmos. option. nws=3 is reserved for coupling with atmospheric model. ! If nws=0, no atmos. forcing is applied. If nws=1, atmos. ! variables are read in from wind.th. If nws=2, atmos. variables are ! read in from sflux_ files. ! If nws=4, ascii format is used for wind and atmos. pressure at each node (see source code). ! If nws>0, 'iwindoff' can be used to scale wind speed (with windfactor.gr3). ! ! Stress calculation: ! If nws=2, ihconsv=1 and iwind_form=0, the stress is calculated from heat exchange ! routine; ! Otherwise if iwind_form=-1, the stress is calculated from Pond & Pichard formulation; ! if iwind_form=1, Hwang (2018) formulation (Cd tapers off at high wind). ! If WWM is enabled and icou_elfe_wwm>0 and iwind_form=-2, stress is overwritten by WWM. ! In all cases, if USE_ICE the stress in ice-covered portion is calculated by ICE routine. !----------------------------------------------------------------------- nws = 2 wtiminc = 150. !time step for atmos. forcing. Default: same as dt nrampwind = 0 !ramp-up option for atmos. forcing drampwind = 1. !needed if nrampwind/=0; ramp-up period in days ! iwindoff = 0 !needed only if nws/=0; '1': needs windfactor.gr3 iwind_form = -1 !needed if nws/=0 !If impose_net_flux/=0 and nws=2, read in net _surface_ heat flux as var 'dlwrf' !(Downward Long Wave) in sflux_rad (solar radiation is still used separately), !and if PREC_EVAP is on, also read in net P-E as 'prate' (Surface Precipitation Rate) in sflux_prc. impose_net_flux = 0 !----------------------------------------------------------------------- ! Heat and salt exchange. isconsv=1 needs ihconsv=1; ihconsv=1 needs nws=2. ! If isconsv=1, need to compile with precip/evap module turned on. !----------------------------------------------------------------------- ihconsv = 0 !heat exchange option isconsv = 0 !evaporation/precipitation model ! Min total water depth for applying heat/salt exchange (i.e. off if the local water depth 0) !----------------------------------------------------------------------- ! Sponge layer for elevation and vel. ! If inu_elev=0, no relaxation is applied to elev. ! If inu_elev=1, relax. constants are specified in elev_nudge.gr3 ! and applied to eta=0 (thus a depth=0 means no relaxation). ! Similarly for inu_uv (with input uv_nudge.gr3) !----------------------------------------------------------------------- inu_elev = 0 inu_uv = 0 !----------------------------------------------------------------------- ! Nudging options for tracers. If inu_[MOD]=0, no nudging is used. If inu_tr=1, ! nudge to initial condition according to relaxation constants specified. ! If inu_tr=2, nudge to values in [MOD]_nu.nc (with step 'step_nu_tr'). ! The relaxation constants = [horizontal relax (specified in [MOD]_nudge.gr3) + ! vertical relax] times dt, where vertical relax is a linear function of ! vnh[1,2] and vnf[1,2], and [MOD] are tracer model names. ! Code will ignore junk values (<=-99) inside [MOD]_nu.nc, so 1 way to avoid ! nudging for a tracer is to set its nudged values to -9999 !----------------------------------------------------------------------- inu_tr(1) = 0 !T inu_tr(2) = 0 !S inu_tr(3) = 0 !GEN inu_tr(4) = 0 !Age inu_tr(5) = 0 !SED3D inu_tr(6) = 0 !EcoSim inu_tr(7) = 0 !ICM inu_tr(8) = 0 !CoSINE inu_tr(9) = 0 !FIB inu_tr(10) = 0 !TIMOR inu_tr(11) = 0 !FABM vnh1 = 400 !vertical nudging depth 1 vnf1 = 0. !vertical relax \in [0,1] vnh2 = 500 !vertical nudging depth 2 (must >vnh1) vnf2 = 0. !vertical relax step_nu_tr = 86400. !time step [sec] in all [MOD]_nu.nc (for inu_[MOD]=2) !----------------------------------------------------------------------- ! Cut-off depth for cubic spline interpolation near bottom when computing horizontal gradients ! e.g. using hgrad_nodes() (radiation stress, and gradients of qnon and qhat in non-hydro model). ! If depth > h_bcc1 ('deep'), ! a min. (e.g. max bottom z-cor for the element) is imposed in the spline and so a more ! conservative method is used without extrapolation beyond bottom; ! otherwise constant extrapolation below bottom is used. !----------------------------------------------------------------------- h_bcc1 = 100. !h_bcc1 !----------------------------------------------------------------------- ! Dimensioning parameters for inter-subdomain btrack. ! If error occurs like 'bktrk_subs: overflow' or 'MAIN: nbtrk > mxnbt' ! gradually increasing these will solve the problem !----------------------------------------------------------------------- s1_mxnbt = 0.5 s2_mxnbt = 3.5 !----------------------------------------------------------------------- ! Flag for harmonic analysis for elevation. If used , need to turn on cpp flags ! in Makefile first. Otherwise set it to 0. !----------------------------------------------------------------------- iharind = 0 !----------------------------------------------------------------------- ! Conservation check option. If iflux=1, some fluxes are computed ! in regions specified in fluxflag.prop (regional number from -1 to an arbitrary integer). ! in output flux.dat, positive means flux from region n to region n-1 (n>=1) ! output file flux.dat need to be saved before continuing hotstart !----------------------------------------------------------------------- iflux = 0 !----------------------------------------------------------------------- ! Test flags for debugging. These flags should be turned off normally. !----------------------------------------------------------------------- ! Williamson test #5 (zonal flow over an isolated mount); if ! on, ics must =2 !----------------------------------------------------------------------- izonal5 = 0 !"0" - no test; otherwise on !----------------------------------------------------------------------- ! Rotating Gausshill test with stratified T,S (1: on; 0: off) ! Surface T,S read in from *.ic; code generates stratification !----------------------------------------------------------------------- ibtrack_test = 0 !----------------------------------------------------------------------- ! Rouse profile test (1: on; 0: off) ! If on, must turn on USE_TIMOR !----------------------------------------------------------------------- irouse_test = 0 !----------------------------------------------------------------------- ! Flag to choose FIB model for bacteria decay (used with USE_FIB) ! flag_fib = 1 - Constant decay rate (/day) in .gr3 format ! (kkfib_1.gr3 and kkfib_2.gr3) ! flag_fib = 2 - Decay rate computed from Canteras et al., 1995 ! flag_fib = 3 - Decay rate computed from Servais et al., 2007 !---------------------------------------------------------------------- flag_fib = 1 !---------------------------------------------------------------------- ! Marsh model parameters (only if USE_MARSH is on) !---------------------------------------------------------------------- slr_rate = 120. !sea-level rise rate in mm/yr, times morphological acceleration if used !---------------------------------------------------------------------- ! Vegetation model ! If isav=1, need 3 extra inputs: (1) sav_D.gr3 (depth is stem diameter in meters); ! (2) sav_N.gr3 (depth is # of stems per m^2); ! (3) sav_h.gr3 (height of canopy in meters). ! If one of these depths=0 at a node, the code will set all to 0. ! If USE_MARSH is on and isav=1, all .gr3 must have constant depths! !---------------------------------------------------------------------- isav = 0 !on/off flag !---------------------------------------------------------------------- ! Coupling step with ICE module. !---------------------------------------------------------------------- nstep_ice = 1 !call ice module every nstep_ice steps of SCHISM !---------------------------------------------------------------------- ! Specify level #'s if age module is invoked (USE_AGE), for 1st half of tracers only !---------------------------------------------------------------------- level_age = 9, -999 !defauly: -999 (all levels) !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ! Physical constants !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ !----------------------------------------------------------------------- ! Earth's radii at pole and equator (to define an ellipsoid) !----------------------------------------------------------------------- rearth_pole = 6378206.4 rearth_eq = 6378206.4 !----------------------------------------------------------------------- ! Specific heat of water (C_p) in J/kg/K !----------------------------------------------------------------------- shw = 4184.d0 !----------------------------------------------------------------------- ! Reference water density for Boussinesq approximation !----------------------------------------------------------------------- rho0 = 1000.d0 !kg/m^3 !----------------------------------------------------------------------- ! Fraction of vertical flux closure adjustment applied at surface, then subtracted ! from all vertical fluxes. This is currently done for T,S only ! 0.0 <= vclose_surf_frac < 1.0 ! 1: fully from surface (i.e. no correction as before); 0: fully from bottom !----------------------------------------------------------------------- vclose_surf_frac=1.0 !----------------------------------------------------------------------- ! Option to enforce strict mass conservation for each tracer model (only works with itr_met=3,4) ! At moment the scheme has not accounted for bottom 'leaking' (e.g. in SED), ! so iadjust_mass_consv0(5) must =0 !----------------------------------------------------------------------- iadjust_mass_consv0(1)=0 !T iadjust_mass_consv0(2)=0 !S iadjust_mass_consv0(3)=0 !GEN iadjust_mass_consv0(4)=0 !AGE iadjust_mass_consv0(5)=0 !SED3D (code won't allow non-0 for this module) iadjust_mass_consv0(6)=0 !EcoSim iadjust_mass_consv0(7)=0 !ICM iadjust_mass_consv0(8)=0 !CoSiNE iadjust_mass_consv0(9)=0 !Feco iadjust_mass_consv0(10)=0 !TIMOR iadjust_mass_consv0(11)=0 !FABM / &SCHOUT !----------------------------------------------------------------------- ! Output section - all optional. Values shown are default unless otherwise stated. !----------------------------------------------------------------------- ! Option for hotstart outputs !----------------------------------------------------------------------- nhot = 1 !1: output *_hotstart every 'hotout_write' steps nhot_write = 144 !must be a multiple of ihfskip if nhot=1 !----------------------------------------------------------------------- ! Station output option. If iout_sta/=0, need output skip (nspool_sta) and ! a station.in. If ics=2, the cordinates in station.in must be in lon., lat, ! and z (positive upward; not used for 2D variables). !----------------------------------------------------------------------- iout_sta = 1 nspool_sta = 12 !needed if iout_sta/=0; mod(nhot_write,nspool_sta) must=0 !----------------------------------------------------------------------- ! Global output options ! The variable names that appear in nc output are shown in {} !----------------------------------------------------------------------- iof_hydro(1) = 1 !0: off; 1: on - elev. [m] {elev} iof_hydro(2) = 0 !air pressure [Pa] {air_pressure} iof_hydro(3) = 0 !air temperature [C] {air_temperature} iof_hydro(4) = 0 !Specific humidity [-] {specific_humidity} iof_hydro(5) = 0 !solar (shortwave) radiation [W/m/m] {solar_radiation} iof_hydro(6) = 0 !sensible flux (positive upward) [W/m/m] {sensible_flux} iof_hydro(7) = 0 !latent heat flux (positive upward) [W/m/m] {latent_heat} iof_hydro(8) = 0 !upward longwave radiation (positive upward) [W/m/m] {upward_longwave} iof_hydro(9) = 0 !downward longwave radiation (positive downward) [W/m/m] {downward_longwave} iof_hydro(10) = 0 !total flux=-flsu-fllu-(radu-radd) [W/m/m] {total_heat_flux} iof_hydro(11) = 0 !evaporation rate [kg/m/m/s] {evaporation} iof_hydro(12) = 0 !precipitation rate [kg/m/m/s] {precipitation} iof_hydro(13) = 0 !Bottom stress vector [kg/m/s^2(Pa)] {bottom_stress} iof_hydro(14) = 0 !wind velocity vector [m/s] {wind_speed} iof_hydro(15) = 0 !wind stress vector [m^2/s/s] {wind_stress} iof_hydro(16) = 0 !depth-averaged vel vector [m/s] {dahv} iof_hydro(17) = 0 !vertical velocity [m/s] {vertical_velocity} iof_hydro(18) = 0 !water temperature [C] {temp} iof_hydro(19) = 0 !water salinity [PSU] {salt} iof_hydro(20) = 0 !water density [kg/m^3] {water_density} iof_hydro(21) = 0 !eddy diffusivity [m^2/s] {diffusivity} iof_hydro(22) = 0 !eddy viscosity [m^2/s] {viscosity} iof_hydro(23) = 0 !turbulent kinetic energy {TKE} iof_hydro(24) = 0 !turbulent mixing length [m] {mixing_length} iof_hydro(25) = 1 !horizontal vel vector [m/s] {hvel} iof_hydro(26) = 0 !horizontal vel vector defined @side [m/s] {hvel_side} iof_hydro(27) = 0 !vertical vel. @elem [m/s] {wvel_elem} iof_hydro(28) = 0 !T @prism centers [C] {temp_elem} iof_hydro(29) = 0 !S @prism centers [PSU] {salt_elem} iof_hydro(30) = 0 !Barotropic pressure gradient force vector (m.s-2) @side centers {pressure_gradient} !----------------------------------------------------------------------- ! Outputs from optional modules. Only uncomment these if the USE_* is on !----------------------------------------------------------------------- ! Outputs from WWM (USE_WWM must be on in Makefile) !----------------------------------------------------------------------- ! iof_wwm(1) = 1 !sig. height (m) {WWM_1} ! iof_wwm(2) = 1 !Mean average period (sec) - TM01 {WWM_2} ! iof_wwm(3) = 1 !Zero down crossing period for comparison with buoy (s) - TM02 {WWM_3} ! iof_wwm(4) = 1 !Average period of wave runup/overtopping - TM10 {WWM_4} ! iof_wwm(5) = 1 !Mean wave number (1/m) {WWM_5} ! iof_wwm(6) = 1 !Mean wave length (m) {WWM_6} ! iof_wwm(7) = 1 !Mean average energy transport direction (degr) - MWD in NDBC? {WWM_9} ! iof_wwm(8) = 1 !Mean directional spreading (degr) {WWM_10} ! iof_wwm(9) = 1 !Discrete peak period (sec) - Tp {WWM_11} ! iof_wwm(10) = 1 !Continuous peak period based on higher order moments (sec) {WWM_12} ! iof_wwm(11) = 1 !Peak phase vel. (m/s) {WWM_13} ! iof_wwm(12) = 1 !Peak n-factor {WWM_14} ! iof_wwm(13) = 1 !Peak group vel. (m/s) {WWM_15} ! iof_wwm(14) = 1 !Peak wave number {WWM_16} ! iof_wwm(15) = 1 !Peak wave length {WWM_17} ! iof_wwm(16) = 1 !Peak (dominant) direction (degr) {WWM_18} ! iof_wwm(17) = 1 !Peak directional spreading {WWM_19} ! iof_wwm(18) = 1 !Discrete peak direction (radian?) {WWM_20} ! iof_wwm(19) = 1 !Orbital vel. (m/s) {WWM_21} ! iof_wwm(20) = 1 !RMS Orbital vel. (m/s) {WWM_22} ! iof_wwm(21) = 1 !Bottom excursion period (sec?) {WWM_23} ! iof_wwm(22) = 1 !Bottom wave period (sec) {WWM_24} ! iof_wwm(23) = 1 !Uresell number based on peak period {WWM_25} ! iof_wwm(24) = 0 !Friction velocity (m/s?) {WWM_26} ! iof_wwm(25) = 1 !Charnock coefficient {WWM_27} ! iof_wwm(26) = 1 !Rougness length {WWM_28} ! iof_wwm(27) = 1 !WWM_energy vector {WWM_energy_dir} ! iof_wwm(28) = 1 !Wave force vector (m.s-2) computed by wwm @side centers and whole levels {wave_force} !----------------------------------------------------------------------- ! Tracer module outputs. In most cases, actual # of outputs depends on # of tracers used !----------------------------------------------------------------------- ! Outputs for user-defined tracer module (USE_GEN) !----------------------------------------------------------------------- ! iof_gen(1) = 1 !1st tracer {GEN_1} ! iof_gen(2) = 1 !2nd tracer {GEN_2} !----------------------------------------------------------------------- ! Outputs for (age). Indices from "1" to "ntracer_age/2"; [days] !----------------------------------------------------------------------- ! iof_age(1) = 1 {AGE_1} ! iof_age(2) = 1 {AGE_2} !----------------------------------------------------------------------- ! Specific outputs in SED3D (USE_SED must be on in Makefile; ! otherwise these are not needed) !----------------------------------------------------------------------- ! iof_sed(1) = 1 !bottom depth _change_ from init. condition (m) {SED_depth_change} ! iof_sed(2) = 1 ! Bed median grain size in the active layer (mm) {SED_D50} ! iof_sed(3) = 1 ! Bottom shear stress (Pa) {SED_bed_stress} ! iof_sed(4) = 1 ! Bottom roughness lenghth (mm) {SED_bed_roughness} ! iof_sed(5) = 1 !total suspended concentration (g/L) {SED_TSC} ! iof_sed(6) = 1 ! total bed thickness @elem (m) {bed_thickness} ! iof_sed(7) = 1 ! total bed age over all layers @elem (sec) {bed_age} ! iof_sed(8) = 1 ! Sediment transport roughness length @elem (m) (z0st_elem) {z0st} ! iof_sed(9) = 1 !current-ripples roughness length @elem (m) (z0cr_elem) {z0cr} ! iof_sed(10) = 1 !sand-waves roughness length (m) @elem (z0sw_elem) {z0sw} ! iof_sed(11) = 1 !wave-ripples roughness length @elem (m) (z0wr_elem) {z0wr} ! Example of using 2 classes ! iof_sed(12) = 1 !conc. of 1st class (one output need by each class) [g/L] {SED3D_1} ! iof_sed(13) = 1 !Bedload transport rate vector (kg.m-1.s-1) for 1st tracer (one output need by tracer) {SED_bdld_1} ! iof_sed(14) = 1 !Bed fraction 1st tracer (one output need by each class) [-] {SED_bedfrac_1} ! iof_sed(15) = 1 !conc. of 2nd class {SED3D_2} ! iof_sed(16) = 1 !Bedload transport of 2nd class {SED_bdld_2} ! iof_sed(17) = 1 !Bed fraction of 2nd class {SED_bedfrac_3} !----------------------------------------------------------------------- ! EcoSim outputs !----------------------------------------------------------------------- ! iof_eco(1) = 1 {ECO_1} !----------------------------------------------------------------------- ! ICM outputs !----------------------------------------------------------------------- ! iof_icm(1) = 1 !Chlorophyll {ICM_Chl} ! iof_icm(2) = 1 !PH values (ICM_PH on) {ICM_pH} ! iof_icm(3) = 1 !ICM primary production @elem [gC/m^3/day] {ICM_PrmPrdt} ! iof_icm(4) = 1 !ICM totoal inorganic nitrogen (DIN) @elem [gN/m^3] {ICM_DIN} ! iof_icm(5) = 1 !ICM paticulate organic nitrogen (PON) @elem [gN/m^3] {ICM_PON} !! sediment flux @elem ! iof_icm(6) = 1 !ICM bed sediment flux arrays: SED_BENDOC (output name:ICM_SED_BENDOC) @elem [gC/(m^2 day)] {ICM_SED_BENDOC} ! iof_icm(7) = 1 !ICM bed sediment flux arrays: SED_BENNH4 (output name:ICM_SED_BENNH4) @elem [gC/(m^2 day)] {ICM_SED_BENNH4} ! iof_icm(8) = 1 !ICM bed sediment flux arrays: SED_BENNO3 (output name:ICM_SED_BENNO3)@elem [gC/(m^2 day)] {ICM_SED_BENNO3} ! iof_icm(9) = 1 !ICM bed sediment flux arrays: SED_BENPO4 (output name:ICM_SED_BENPO4) @elem [gC/(m^2 day)] {ICM_SED_BENPO4} ! iof_icm(10) = 1 !ICM bed sediment flux arrays: SED_BENCOD (output name:ICM_SED_BENCOD) @elem [gC/(m^2 day)] {ICM_SED_BENCOD} ! iof_icm(11) = 1 !ICM bed sediment flux arrays: SED_BENDO (output name:ICM_SED_BENDO) @elem [gC/(m^2 day)] {ICM_SED_BENDO} ! iof_icm(12) = 1 !ICM bed sediment flux arrays: SED_BENSA (output name:ICM_SED_BENSA) @elem [gC/(m^2 day)] {ICM_SED_BENSA} !! sav @elem ! iof_icm(13) = 1 !ICM SAV leaf biomass @elem [gC/m^3] (k=1 is surface) {ICM_lfsav} ! iof_icm(14) = 1 !ICM SAV stem biomass @elem [gC/m^3] {ICM_stsav} ! iof_icm(15) = 1 !ICM SAV root biomass @elem [gC/m^3] {ICM_rtsav} ! iof_icm(16) = 1 !ICM SAV total leaf biomass @elem [gC/m^2] {ICM_tlfsav} ! iof_icm(17) = 1 !ICM SAV total stem biomass @elem [gC/m^2] {ICM_tstsav} ! iof_icm(18) = 1 !ICM SAV total root biomass @elem [gC/m^2] {ICM_trtsav} ! iof_icm(19) = 1 !ICM SAV canopy height @elem [m] {ICM_hcansav} !! sediment conc @elem ! iof_icm(20) = 1 !bottom NH4 conc {ICM_CNH4} ! iof_icm(21) = 1 !bottom NO3 conc {ICM_CNH3} ! iof_icm(22) = 1 !bottom P conc {ICM_CPIP} ! iof_icm(23) = 1 !bottom Si conc {ICM_CPOS} ! iof_icm(24) = 1 !bottom CH4 conc {ICM_CCH4} ! iof_icm(25) = 1 !bottom SO4 conc {ICM_CSO4} ! iof_icm(26) = 1 !bottom H2S conc {ICM_CH2S} ! iof_icm(27) = 1 !bottom PON g1 conc {ICM_SEDPON1} ! iof_icm(28) = 1 !bottom PON g2 conc {ICM_SEDPON2} ! iof_icm(29) = 1 !bottom PON g3 conc {ICM_SEDPON3} ! iof_icm(30) = 1 !bottom POP g1 conc {ICM_SEDPOP1} ! iof_icm(31) = 1 !bottom POP g2 conc {ICM_SEDPOP2} ! iof_icm(32) = 1 !bottom POP g3 conc {ICM_SEDPOP3} ! iof_icm(33) = 1 !bottom POC g1 conc {ICM_SEDPOC1} ! iof_icm(34) = 1 !bottom POC g2 conc {ICM_SEDPOC2} ! iof_icm(35) = 1 !bottom POC g3 conc {ICM_SEDPOC3} ! iof_icm(36) = 1 !erosion flux H2S {ICM_EROH2S} ! iof_icm(37) = 1 !ersoion flux LPOC {ICM_EROLPOC} ! iof_icm(38) = 1 !ersoion flux RPOC {ICM_ERORPOC} !! water column rates @elem ! iof_icm(39) = 1 !DO consumption {ICM_DO_consumption} ! iof_icm(40) = 1 !PB growth #1 {ICM_GP1} ! iof_icm(41) = 1 !PB growth #2 {ICM_GP2} ! iof_icm(42) = 1 !PB growth #3 {ICM_GP3} ! water column foundamental tracers @nodes ! iof_icm(43) = 0 !Zoo. #1 {ICM_1} ! iof_icm(44) = 0 !Zoo. #2 {ICM_2} ! iof_icm(45) = 1 !phyto #1 {ICM_3} ! iof_icm(46) = 1 !phyto #2 {ICM_4} ! iof_icm(47) = 1 !phyto #3 {ICM_5} ! iof_icm(48) = 1 !RPOC {ICM_6} ! iof_icm(49) = 1 !LPOC {ICM_7} ! iof_icm(50) = 1 !DOC {ICM_8} ! iof_icm(51) = 1 !RPON {ICM_9} ! iof_icm(52) = 1 !LPON {ICM_10} ! iof_icm(53) = 1 !DON {ICM_11} ! iof_icm(54) = 1 !NH4 {ICM_12} ! iof_icm(55) = 1 !NO3 {ICM_13} ! iof_icm(56) = 1 !RPOP {ICM_14} ! iof_icm(57) = 1 !LPOP {ICM_15} ! iof_icm(58) = 1 !DOP {ICM_16} ! iof_icm(59) = 1 !PO4t {ICM_17} ! iof_icm(60) = 0 !Si- biogenic {ICM_18} ! iof_icm(61) = 0 !available Si {ICM_19} ! iof_icm(62) = 1 !COD: Chemical oxygen demand {ICM_20} ! iof_icm(63) = 1 !DO {ICM_21} !! following requires ICM_PH on ! iof_icm(64) = 1 !TIC {ICM_22} ! iof_icm(65) = 1 !ALK {ICM_23} ! iof_icm(66) = 1 !CA {ICM_24} ! iof_icm(67) = 1 !CACO3 {ICM_25} !----------------------------------------------------------------------- ! CoSINE outputs !----------------------------------------------------------------------- ! iof_cos(1) = 1 ! {COS_1} ! iof_cos(2) = 1 ! {COS_2} ! iof_cos(3) = 1 ! {COS_3} ! iof_cos(4) = 1 ! {COS_4} ! iof_cos(5) = 1 ! {COS_5} ! iof_cos(6) = 1 ! {COS_6} ! iof_cos(7) = 1 ! {COS_7} ! iof_cos(8) = 1 ! {COS_8} ! iof_cos(9) = 1 ! {COS_9} ! iof_cos(10) = 1 ! {COS_10} ! iof_cos(11) = 1 ! {COS_11} ! iof_cos(12) = 1 ! {COS_12} ! iof_cos(13) = 1 ! {COS_13} !----------------------------------------------------------------------- ! Fecal indicating bacteria module !----------------------------------------------------------------------- ! iof_fib(1) = 1 ! {FIB_1} !----------------------------------------------------------------------- ! Specific outputs in SED2D (USE_SED2D must be on in Makefile; ! otherwise these are not needed) !----------------------------------------------------------------------- ! iof_sed2d(1) = 1 !bottom depth _change_ from init. condition (m) {SED2D_depth_change} ! iof_sed2d(2) = 1 !drag coefficient used in transport formulae SED2D_Cd{} ! iof_sed2d(3) = 1 !Courant number (b.qtot.dt / h.dx) {SED2D_cflsed} ! iof_sed2d(4) = 1 !Top layer d50 (m) {SED2D_d50} ! iof_sed2d(5) = 1 !total transport rate vector (kg/m/s) {SED2D_total_transport} ! iof_sed2d(6) = 1 !suspended tranport rate vector (kg/m/s) {SED2D_susp_load} ! iof_sed2d(7) = 1 !bedload transport rate vector (kg/m/s) {SED2D_bed_load} ! iof_sed2d(8) = 1 !time averaged total transport rate vector (kg/m/s) {SED2D_average_transport} ! iof_sed2d(9) = 1 !bottom slope vector (m/m); negative uphill {SED2D_bottom_slope} ! iof_sed2d(10) = 1 !Total roughness length @elem (m) (z0eq) {z0eq} ! iof_sed2d(11) = 1 !current-ripples roughness length @elem (m) (z0cr) {z0cr} ! iof_sed2d(12) = 1 !sand-waves roughness length @elem (m) (z0sw) {z0sw} ! iof_sed2d(13) = 1 !wave-ripples roughness length @elem (m) (z0wr) {z0wr} !----------------------------------------------------------------------- ! marsh flags (USE_MARSH on) !----------------------------------------------------------------------- ! iof_marsh(1) = 1 ! {marsh_flag} !----------------------------------------------------------------------- ! Ice module outputs (if USE_ICE is on) !----------------------------------------------------------------------- ! iof_ice(1)= 1 !ice advective velcoity vector [m/s] {ICE_velocity} ! iof_ice(2)= 1 !strain rate @ elem [1/sec] {ICE_strain_rate} ! iof_ice(3)= 1 !net heat flux to ocean (>0 warm up SST) [W/m/m] {ICE_net_heat_flux} ! iof_ice(4)= 1 !net fresh water flux to ocean (>0 freshens up SSS) [kg/s/m/m] {ICE_fresh_water_flux} ! iof_ice(5)= 1 !ice temperature [C] at air-ice interface {ICE_top_T} ! iof_ice(6)= 1 !ice volume [m] {ICE_tracer_1} ! iof_ice(7)= 1 !ice concentration [-] {ICE_tracer_2} ! iof_ice(8)= 1 !snow volume [m] {ICE_tracer_3} !----------------------------------------------------------------------- ! Analysis module outputs (USE_ANALYSIS) !----------------------------------------------------------------------- iof_ana(1) = 0 !x-component of \nabla air_pres /\rho_0 [m/s/s] {ANA_air_pres_grad_x} iof_ana(2) = 0 !y-component of \nabla air_pres /\rho_0 [m/s/s] {ANA_air_pres_grad_y} iof_ana(3) = 0 !\alpha*g*\nabla \Psi [m/s/s] (gradient of tidal potential) {ANA_tide_pot_grad_x} iof_ana(4) = 0 !\alpha*g*\nabla \Psi [m/s/s] {ANA_tide_pot_grad_y} iof_ana(5) = 0 !\nabla \cdot (\mu \nabla u) [m/s/s] (horizontal viscosity) {ANA_hor_viscosity_x} iof_ana(6) = 0 !\nabla \cdot (\mu \nabla u) [m/s/s] {ANA_hor_viscosity_y} iof_ana(7) = 0 !-g/rho0* \int_z^\eta dr_dx dz [m/s/s] (b-clinic gradient) {ANA_bclinic_force_x} iof_ana(8) = 0 !-g/rho0* \int_z^\eta dr_dy dz [m/s/s] {ANA_bclinic_force_y} iof_ana(9) = 0 !d (\nu du/dz)/dz [m/s/s] - no vegetation effects (vertical viscosity) {ANA_vert_viscosity_x} iof_ana(10) = 0 !d (\nu dv/dz)/dz [m/s/s] - no vegetation effects {ANA_vert_viscosity_y} iof_ana(11) = 0 !(u \cdot \nabla) u [m/s/s] (momentum advection) {ANA_mom_advection_x} iof_ana(12) = 0 !(u \cdot \nabla) u [m/s/s] {ANA_mom_advection_y} iof_ana(13) = 0 !gradient Richardson number [-] {ANA_Richardson} iof_ana(14) = 1 !min time step at each element over all !subcycles in horizontal transport solver [s] {ANA_transport_min_dt_elem} /