rompy.schism.namelists.param.PARAM#

pydantic model rompy.schism.namelists.param.PARAM[source]#

This file was auto generated from a schism namelist file on 2023-11-20. The full contents of the namelist file are shown below providing associated documentation for the objects:

!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. ! Values can be separated by commas or spaces. !(5) space allowed before/after ‘=’

&CORE !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ! Core (mandatory) parameters; no defaults !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ! Pre-processing option. Useful for checking grid errors etc. Need to use 1 ! core only for compute (plus necessary scribe cores). Under scribe I/O, the ! code (the scribe part) will hang but the outputs will be there. Just kill ! the job.

ipre = 0 !Pre-processor flag (1: on; 0: off)

! Baroclinic/barotropic option. If ibc=0 (baroclinic model), ibtp is not used.
ibc = 0 !Baroclinic option ibtp = 1

rnday = 30 !total run time in days dt = 100. !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 = 36 !output step spool ihfskip = 864 !stack spool; every ihfskip steps will be put into 1_*, 2_*, etc…

/

&OPT !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ! Optional parameters. The values shown below are default unless otherwise noted !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ !———————————————————————– ! Optional offline partitioning using NO_PARMETIS. If on, need partition.prop (like global_to_local.prop). !———————————————————————–

!———————————————————————– ! 2nd pre-proc flag. If ipre2/=0, code will output some diagnotic outputs and stop. ! These outputs are: drag coefficients (Cdp) !———————————————————————–

ipre2 = 0

!———————————————————————– ! Option to only solve tracer transport (and bypass most b-tropic solver) ! Usage: turn the flag on (‘1’ or ‘2’) and turn on your tracer modules and make sure ! (1) your inputs are consistent with the original hydro-only run (with additional tracers ! of course); (2) hydro-only run results are in hydro_out/schout*.nc, which must ! have ‘hvel_side’ (not normal hvel), ‘elev’, ‘diffusivity’, ‘temp_elem’, ‘salt_elem’ (for ! new scribe outputs, use corresponding files/var names); (3) dt above is ! multiple of _output_ step used in the original hydro-only run ! (as found in in hydro_out/schout*.nc); e.g. dt = 1 hour. (4). When itransport_only=2, ! additional variables (‘totalSuspendedLoad’,’sedBedStress’) are needed. ! Hotstart should work also, but you’d probably not use an aggressively large dt especially ! when air-sea exchange is involved. !———————————————————————–

itransport_only = 0

!———————————————————————– ! Option to add self-attracting and loading tide (SAL) into tidal potential ! (usually for basin-scale applications). ! If iloadtide=0, no SAL. ! If iloadtide=1, needs inputs: loadtide_[FREQ].gr3, ! where [FREQ] are freq names (shared with tidal potential, in upper cases) ! and the _two_ ‘depths’ inside are amplitude (m) and phases (degrees behind GMT), ! interpolated from global tide model (e.g. FES2014). In this option, SAL is ! lumped into tidal potential so it shares some parameters with tidal potential ! in bctides.in (cut-off depth, frequencies). ! If iloadtide=2 or 3, use a simple scaling for gravity approach (in this option, ! SAL is applied everywhere and does not share parameters with tidal potential). ! For iloadtide=2, a const scaling (1-loadtide_coef) is used; for iloadtide=3, the scaling is ! dependent on depth (Stepanov & Hughes 2004) with max of loadtide_coef. !———————————————————————–

iloadtide = 0 loadtide_coef = 0.1 !only used if iloadtide=2,3 (for ‘3’, the default should be 0.12)

! Starting time
start_year = 2000 !int start_month = 1 !int start_day = 1 !int start_hour = 0 !double utc_start = 8 !double

!———————————————————————– ! Coordinate option: 1: Cartesian; 2: lon/lat (hgrid.gr3=hgrid.ll in this case, ! and orientation of element is outward of earth) ! Notes for lon/lat: make sure hgrid.ll and grid in sflux are consistent in ! longitude range! !———————————————————————–

ics = 1 !Coordinate option

!———————————————————————– ! Hotstart option. 0: cold start; 1: hotstart with time reset to 0; 2: ! continue from the step in hotstart.nc !———————————————————————–

ihot = 0

!———————————————————————– ! Equation of State type used ! ieos_type=0: UNESCO 1980 (nonlinear); =1: linear function of T ONLY, i.e. !

ho=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 = 1 !ramp-up option (1: on; 0: off)

dramp = 1. !ramp-up period in days for b.c. etc (no ramp-up if <=0)

! nrampbc = 0 !ramp-up flag for baroclinic force: drampbc = 0. !ramp-up period in days for baroclinic force

!———————————————————————– ! 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

!———————————————————————– ! 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), an easiest option is: ! indvel=0, ishapiro=1 (shapiro0=0.5), ihorcon=inter_mom=0. ! For applications that include eddying regime, refer to the manual. !———————————————————————–

ihorcon = 0 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=0. ishapiro=0: off; =1: constant filter strength in shapiro0; =-1: ! variable filter strength specified in shapiro.gr3; =2: variable filter strength specified ! as a Smagorinsky-like filter, with the coefficient specified in shapiro.gr3. ! To transition between eddying/non-eddying regimes, use ! indvel=0, ihorcon/=0, and ishapiro=-1 (requiring shapiro.gr3) or 2 (Smagorinsky-like filter). !———————————————————————–

ishapiro = 1 !options niter_shap = 1 !needed if ishapiro/=0: # of iterations with Shapiro filter !shapiro0: Shapiro filter strength, needed only if ishapiro=1 !If ishapiro=1, shapiro0 is the filter strength (max is 0.5). !If ishapiro=2, the coefficient in tanh() is specified in shapiro.gr3. Experiences so far suggest 100 to 1.e3 !If ishapiro=-1, the filter strength is directly read in from shapiro.gr3 shapiro0 = 0.5 !needed only if ishapiro=1

!———————————————————————– ! Implicitness factor (0.5<thetai<=1). !———————————————————————–

thetai = 0.6

!———————————————————————– ! If WWM is used, set coupling/decoupling flag ‘icou_elfe_wwm’. ! No effects if USE_WWM is distabled in Makefile. ! Note that all these parameters must be present in this file (even when not used). ! 0: no elevation and no currents in wwm, no wave force in SCHISM (but wave turbulecne, WBL etc are still in SCHISM); ! 1: full coupled (elevation, vel, and wind are all passed to WWM); ! 2: elevation and currents in wwm, no wave force in SCHISM; ! 3: no elevation and no currents in wwm, wave force in SCHISM; ! 4: elevation but no currents in wwm, wave force in SCHISM; ! 5: elevation but no currents in wwm, no wave force in SCHISM; ! 6: no elevation but currents in wwm, wave force in SCHISM; ! 7: no elevation but currents in wwm, no wave force in SCHISM; ! If WWM is used and RADFLAG=’VOR’ in wwminput.nml, some parameters (fwvor_*) ! are added to take into account (1) or not (0) the different terms in vortex ! force expression. ! To get SCHISM-only result withno feedback from WWM, compile without WWM. !———————————————————————–

icou_elfe_wwm = 0 nstep_wwm = 1 !call WWM every this many time steps iwbl = 0 !wave boundary layer formulation (used only if USE_WMM and

!icou_elfe_wwm/=0 and nchi=1. If icou_elfe_wwm=0, set iwbl=0): !1-modified Grant-Madsen formulation; 2-Soulsby (1997)

hmin_radstress = 1. !min. total water depth used only in radiation stress calculation [m]

! nrampwafo = 0 !ramp-up option for the wave forces (1: on; 0: off)

drampwafo = 0. !ramp-up period in days for the wave forces (no ramp-up if <=0) turbinj = 0.15 !% of depth-induced wave breaking energy injected in turbulence

!(default: 0.15 (15%), as proposed by Feddersen, 2012)

turbinjds = 1.0 !% of wave energy dissipated through whitecapping injected in turbulence

!(default: 1 (100%), as proposed by Paskyabi et al. 2012)

alphaw = 0.5 !for itur=4scaling parameter for the surface roughness z0s = alphaw*Hm0.

!If negative z0s = abs(alphaw) e.g. z0s=0.2 m (Feddersen and Trowbridge, 2005): ! Vortex Force terms (off/on:0/1)

fwvor_advxy_stokes = 1 ! –> Stokes drift advection (xy), Coriolis fwvor_advz_stokes = 1 ! –> Stokes drift advection (z) , Coriolis fwvor_gradpress = 1 ! –> Pressure term fwvor_breaking = 1 ! –> Wave breaking fwvor_streaming = 1 ! –> Wave streaming (works with iwbl /= 0) fwvor_wveg = 0 ! –> Wave dissipation by vegetation acceleration term fwvor_wveg_NL = 0 ! –> Non linear intrawave vegetation force (see Dean and Bender, 2006 or van Rooijen et al., 2016 for details) cur_wwm = 0 ! Coupling current in WWM

! 0: surface layer current ! 1: depth-averaged current ! 2: computed according to Kirby and Chen (1989)

wafo_obcramp = 0 ! Ramp on wave forces at open boundary (1: on / 0: off): ! –> this option requires the input file wafo_ramp.gr3 ! which defines the ramp value (between 0 and 1) ! at nodes over the whole domain

!———————————————————————– ! Bed deformation option (0: off; 1: vertical deformation only; 2: 3D bed deformation). ! If imm=1, bdef.gr3 is needed; if imm=2, user needs to update depth info etc ! in the code (not working for ics=2 yet). !———————————————————————–

imm = 0 ibdef = 10 !needed if imm=1; # of steps used in deformation

!———————————————————————– ! Reference latitude for beta-plane approximation when ncor=1 (not used if ics=2) !———————————————————————–

slam0 = -124 !lon - not really used sfea0 = 45 !lat

!———————————————————————– ! Option to deal with under resolution near steep slopes in deeper depths ! 0: use h[12,_bcc below; /=0: use hw_* below !———————————————————————–

iunder_deep = 0

!———————————————————————– ! Baroclinicity calculation in off/nearshore with iunder_deep=ibc=0. ! The ‘below-bottom’ gradient ! is zeroed out if h>=h2_bcc (i.e. like Z) or uses const extrap ! (i.e. like terrain-following) if h<=h1_bcc(<h2_bcc) (and linear ! transition in between based on local depth) !———————————————————————–

h1_bcc = 50. ![m] h2_bcc = 100. ![m]; >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: ASCII inputs; -1: netcdf). ! If =1, needs source_sink.in (list of elements), ! vsource,th, vsink.th, and msource.th (the source/sink values must be single precision). ! If =-1, all info is in source.nc ! and each type of volume/mass source/sink can have its own time step and ! # of records. ! Source/sinks can be specified at an elem more ! than once, and the code will accumulate the volumes; for mass conc, ! values are applied at _net_ source elem (no summation for conc).

! meth_sink: options to treat sinks @ dry elem: no speacial treatment if meth_sink=0; ! zero out sink if the elem is dry if meth_sink=1 ! If USE_NWM_BMI is on with if_source/=0, some parts of the reading and some b.c. will be bypassed (but the inputs ! will still be needed). !———————————————————————–

if_source = 0

! nramp_ss = 1 !needed if if_source=1; ramp-up flag for source/sinks: dramp_ss = 2 !needed if if_source/=0; ramp-up period in days for source/sinks (no ramp-up if <=0) meth_sink = 1 !options to treat sinks @ dry elem

!———————————————————————- ! Specify vertical level to inject source concentration for each tracer _module_. ! Code will extrapolate below bottom/above surface unless level 0 is specified. In ! the latter case, the incoming tracer mass will be distributed across all vertical layers - ! this approach works best in shallow waters. ! NOTE: AGE module has its own way of injecting age tracers, so make sure the age concentrations ! are all -9999. in msource.th so as to not interfere! !———————————————————————-

lev_tr_source(1) = -9 !T lev_tr_source(2) = -9 !S lev_tr_source(3) = -9 !GEN lev_tr_source(4) = -9 !AGE: set -9999. in msource’s AGE section lev_tr_source(5) = -9 !SED3D lev_tr_source(6) = -9 !EcoSim lev_tr_source(7) = -9 !ICM lev_tr_source(8) = -9 !CoSINE lev_tr_source(9) = -9 !Feco lev_tr_source(10) = -9 !TIMOR lev_tr_source(11) = -9 !FABM lev_tr_source(12) = -9 !DVD

!———————————————————————- ! Specify level #’s if age module is invoked (USE_AGE), for 1st half of tracers only !———————————————————————-

level_age = 9, -999 !default: -999 (all levels)

!———————————————————————– ! 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<dzb_min, ! Cd=Cdmax, where Cdmax=Cd(dzb=dzb_min). ! If iwbl/=0, nchi must =1. !———————————————————————–

nchi = 0 dzb_min = 0.5 !needed if nchi=1; min. bottom boundary layer thickness [m].

! dzb_decay = 0. !needed if nchi=1; a decay const. [-]. should =0: hmin_man = 1. !needed if nchi=-1: min. depth in Manning’s formulation [m]

!———————————————————————– ! Coriolis. If ncor=-1, specify “rlatitude” (in degrees); if ncor=0, ! specify Coriolis parameter in “coricoef”; if ncor=1, model uses ! lat/lon in hgrid.ll for beta-plane approximation if ics=1, and in this case, ! the latitude specified in CPP projection (‘sfea0’) is used. If ncor=1 and ics=2, ! Coriolis is calculated from local latitude, and ‘sfea0’ is not used. !———————————————————————–

ncor = 0 !should usually be 1 if ics=2 rlatitude = 46 !if ncor=-1 coricoef = 0 !if ncor=0

!———————————————————————– ! Elevation initial condition flag for cold start only. For hotstart, set this to 0 ! (and elev will be read in from hotstart.nc). ! If ic_elev=1, elev.ic (in *.gr3 format) is needed ! to specify the initial elevations; otherwise elevation is initialized to 0 everywhere !———————————————————————–

ic_elev = 0

!———————————————————————– ! Elevation boundary condition ramp-up flag. =0: ramp up from 0; =1: ramp up from ! elev. values read in from elev.ic or hotstart.nc - if neither is present, from 0. ! This flag is mainly used to start the simulation from non-zero elev. ! The ramp-up period is ‘dramp’ (so if dramp=0, full strength is applied). !———————————————————————–

nramp_elev = 0

!———————————————————————– ! Optional inverse barometric effects on the elev. b.c. ! If inv_atm_bnd=1, the elev.’s at boundary are corrected by the difference ! between the actual atmos. pressure and a reference pressure (prmsl_ref below) !———————————————————————–

inv_atm_bnd = 0 !0: off; 1: on prmsl_ref = 101325. !reference atmos. pressure on bnd [Pa]

!———————————————————————– ! Initial condition for T,S. This value only matters for ihot=0 (cold start). ! If flag_ic(1:2)=1, the initial T,S field is read in from temp.ic and salt.ic (horizontally varying). ! If flag_ic(1:2)=2, the initial T,S field is read in from ts.ic (vertical varying). ! If ihot=0 && flag_ic(1:2)=2 || ibcc_mean=1, ts.ic is used for removing mean density profile. ! flag_ic(1) must =flag_ic(2) !———————————————————————–

flag_ic(1) = 1 !T flag_ic(2) = 1 !S

! initial conditions for other tracers. ! 1: needs inputs [MOD]_hvar_[1,2,…].ic (‘1…’ is tracer id); format of each file is similar to salt.ic; ! i.e. horizontally varying i.c. is used for each tracer. ! 2: needs [MOD]_vvar_[1,2,…].ic. Format of each file (for each tracer in tis MOD) is similar to ts.ic ! (i.e. level #, z-coord., tracer value). Verically varying i.c. is used for each tracer. ! 0: model sets own i.c. (EcoSim; TIMOR)

flag_ic(3) = 1 !GEN (user defined module)

! flag_ic(4) = 1 !Age i.c. flag set inside code: flag_ic(5) = 1 !SED3D flag_ic(6) = 1 !EcoSim flag_ic(7) = 1 !ICM flag_ic(8) = 1 !CoSINE flag_ic(9) = 1 !FIB flag_ic(10) = 1 !TIMOR flag_ic(11) = 1 !FABM flag_ic(12) = 0 !DVD (must=0)

!———————————————————————– ! Settling vel [m/s] for GEN module (positive downward) !———————————————————————–

gen_wsett = 0 !1.e-4

!———————————————————————– ! Mean T,S profile option. If ibcc_mean=1 (or ihot=0 and flag_ic(1)=2), mean profile ! is read in from ts.ic, and will be removed when calculating baroclinic force. ! No ts.ic is needed if ibcc_mean=0. !———————————————————————–

ibcc_mean = 0

!———————————————————————– ! Max. horizontal velocity magnitude, used mainly to prevent problem in ! bulk aerodynamic module !———————————————————————–

rmaxvel = 5.

!———————————————————————– ! Following parameters control backtracking !———————————————————————– !———————————————————————– ! min. vel for invoking btrack and for abnormal exit in quicksearch !———————————————————————–

velmin_btrack = 1.e-4

!———————————————————————– ! Nudging factors for starting side/node - add noise to avoid underflow ! The starting location is nudged to: old*(1-btrack_nudge)+btrack_nudge*centroid ! Suggested value: btrack_nudge=9.013e-3 !———————————————————————–

btrack_nudge= 9.013e-3

!———————————————————————– ! Behavior when trajectory hits open bnd. If ibtrack_openbnd=0, slide with ! tangential vel; otherwise, stop and exit btrack !———————————————————————– ! ibtrack_openbnd = 1 !hardwired

!———————————————————————– ! Wetting and drying. ! - if ihhat=1, hat{H} is made non-negative to enhance robustness near ! wetting and drying; if ihhat=0, no retriction is imposed for this quantity. ! - inunfl=0 is used for normal cases and inunfl=1 is used for more accurate wetting ! and drying if grid resolution is sufficiently fine. ! - if shorewafo=1, we impose radiation stress R_s = g*grad(eta) (balance between radiation stress ! gradients and the barotropic gradients) at the numerical shoreline (boundary between ! dry and wet elements). This option ensures that the shallow depth in dry elements does not ! create unphysical and very high wave forces at the shoreline (advised for morphodynamics runs). !———————————————————————–

ihhat = 1 inunfl = 0 h0 = 0.01 !min. water depth for wetting/drying [m] shorewafo = 0 !Matters only if USE_WWM

!———————————————————————– ! Solver options ! USE_PETSC controls the solver type. If it’s diabled, the default JCG ! solver is used. If it’s enabled, use PetSc lib. Some of the parameters ! have different meanings under these 2 options. Also with PetSc one can ! use cmd line options to choose solver etc. !———————————————————————–

moitn0 = 50 !output spool for solver info; used only with JCG mxitn0 = 1500 !max. iteration allowed rtol0 = 1.e-12 !error tolerance

!———————————————————————– ! Advection (ELM) option. If nadv=1, backtracking is done using Euler method; ! nadv=2, using 2nd order Runge-Kutta; if nadv=0, advection in momentum ! is turned off/on in adv.gr3 (the depths=0,1, or 2 also control methods ! in backtracking as above). dtb_max/min are the max/min steps allowed - ! actual step is calculated adaptively based on local gradient. !———————————————————————–

nadv = 1 dtb_max = 30. !in sec dtb_min = 10.

!———————————————————————– ! If inter_mom=0, linear interpolation is used for velocity at foot of char. line. ! If inter_mom=1 or -1, Kriging is used, and the choice of covariance function is ! specified in ‘kr_co’. If inter_mom=1, Kriging is applied to whole domain; ! if inter_mom=-1, the regions where Kriging is used is specified in krvel.gr3 ! (depth=0: no kriging; depth=1: with kriging). !———————————————————————–

inter_mom = 0 kr_co = 1 !not used if inter_mom=0

!———————————————————————– ! Tracer transport method. TVD or WENO method requires tvd.prop. ! 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; 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 = 3 h_tvd = 5. !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 = 0 !1: turn on 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-15 !coefficient for 2nd order weno smoother (larger values are more prone to numerical dispersion) epsilon2 = 1.e-10 !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. Use nws=2 and USE_ATMOS 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=-1 (requires USE_PAHM), use Holland parametric wind model (barotropic only with wind and atmos. pressure). ! In this case, the Holland model is called every step so wtiminc is not used. An extra ! input file is needed: hurricane-track.dat, in addition to a few parameters below. ! ! Stress calculation: ! If nws=2, ihconsv=1 and iwind_form=0, the stress is calculated from heat exchange ! routine; in this case USE_ATMOS cannot be on. ! 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 or -3, stress is overwritten by WWM: ! If iwind_form=-2, stress=rho_air*ufric^2; scaled by rho_water ! If iwind_form=-3, the stress is calculated according to the param. of Donelan et al. (1993) based on the wave age. ! In all cases, if USE_ICE the stress in ice-covered portion is calculated by ICE routine. !———————————————————————–

nws = 0 wtiminc = 150. !time step for atmos. forcing. Default: same as dt

! nrampwind = 1 !ramp-up option for atmos. forcing

drampwind = 1. !ramp-up period in days for wind (no ramp-up if <=0) iwindoff = 0 !needed only if nws/=0; ‘1’: needs windfactor.gr3 iwind_form = 1 !needed if nws/=0 model_type_pahm=10 !only used if nws=-1: hurricane model type (1: Holland; 10: GAHM)

!If IMPOSE_NET_FLUX is on 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.

!———————————————————————– ! Heat and salt exchange using Zeng’s (default) or Fairall (USE_BULK_FAIRALL) scheme. ! isconsv=1 needs ihconsv=1; ihconsv=1 needs nws=2. ! If isconsv=1, need to compile with precip/evap module turned on. ! If at least one of ihconsv and isconsv is set to 1, ! locally turning off air-sea exchange in shallow waters (<0.25 m) is recommended. ! Options for locally turning off heat/salt exchange are specified by ! i_hmin_airsea_ex, i_hmin_salt_ex respectively: ! 0: not turned off locally; ! 1: locally turned off, based on grid depth, i.e., ! off when the local grid depth (z in hgrid) < hmin_airsea_ex or hmin_salt_ex; ! 2 (recommended): locally turned off, based on local total water depth, i.e., ! off when the local total water depth < hmin_airsea_ex or hmin_salt_ex, ! hmin_airsea_ex, hmin_salt_ex: ! 0.2 m is recommended for both “1” and “2” !———————————————————————–

ihconsv = 0 !heat exchange option isconsv = 0 !evaporation/precipitation model i_hmin_airsea_ex = 2 ! no effect if ihconsv=0 hmin_airsea_ex = 0.2 ![m], no effect if ihconsv=0 i_hmin_salt_ex = 2 ! no effect if isconsv=0 hmin_salt_ex = 0.2 ![m], no effect if isconsv=0 iprecip_off_bnd = 0 !if /=0, precip will be turned off near land bnd

!———————————————————————– ! Turbulence closure. !———————————————————————–

itur = 3 !Default: 0 dfv0 = 1.e-2 !needed if itur=0 dfh0 = 1.e-4 !needed if itur=0 mid = ‘KL’ !needed if itur=3,5. Use KE if itur=5 stab = ‘KC’ !needed if itur=3 or 5. Use ‘GA’ if turb_met=’MY’; otherwise use ‘KC’. xlsc0 = 0.1 !needed if itur=3 or 5. Scale for surface & bottom mixing length (>0)

!———————————————————————– ! Sponge layer for elevation and vel. ! If inu_elev=0, no relaxation is applied to elev. ! If inu_elev=1, relax. constants (in 1/sec, i.e. relax*dt<=1) 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) + or x ! 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. ‘nu_sum_mult’ decides ! ‘+’ or ‘x’ in the calculation of final relax. ! 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 inu_tr(12) = 0 !DVD (must=0)

nu_sum_mult=1 !1: final relax is sum of horizontal&vertical; 2: product 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 USE_HA ! in Makefile, and input harm.in. Otherwise set it to 0. Hotstart ihot=2 is not working with HA ! Outputs are harme_* and use combine_outHA to combine. !———————————————————————–

iharind = 0

!———————————————————————– ! Conservation check option. If iflux/=0, some fluxes are computed ! in regions specified in fluxflag.prop (regional number from -1 to an arbitrary integer) ! in output flux.out, positive means flux from region n to region n-1 (n>=1). ! Output file flux.out will be appended on ihot=2. ! iflux=1: basic output; =2: more elaborate outputs !———————————————————————–

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 4 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); ! (4) sav_cd.gr3 (drag coefficient). ! 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

!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ! 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 iadjust_mass_consv0(12)=0 !DVD (must=0)

! For ICM, impose mass conservation for depths larger than a threshold by considering prism ! volume change from step n to n+1. rinflation_icm is the max ratio btw H^{n+1} and H^n allowed.

h_massconsv = 2. ![m] rinflation_icm = 1.e-3

&SCHOUT !———————————————————————– ! Output section - all optional. Values shown are default unless otherwise stated, ! and default for most global outputs is off !———————————————————————–

!———————————————————————– ! Main switch to control netcdf. If =0, SCHISM won’t output nc files ! at all (useful for other programs like ESMF to output) !———————————————————————–

nc_out = 1

!———————————————————————– ! UGRID option for _3D_ outputs under scribed IO (out2d*.nc always has meta ! data info). If iof_ugrid/=0, 3D outputs will also have UGRID metadata (at ! the expense of file size). !———————————————————————–

iof_ugrid = 0

!———————————————————————– ! Option for hotstart outputs !———————————————————————–

nhot = 0 !1: output *_hotstart every ‘nhot_write’ steps nhot_write = 8640 !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 = 0 nspool_sta = 10 !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] {elevation} 2D iof_hydro(2) = 0 !air pressure [Pa] {airPressure} 2D iof_hydro(3) = 0 !air temperature [C] {airTemperature} 2D iof_hydro(4) = 0 !Specific humidity [-] {specificHumidity} 2D iof_hydro(5) = 0 !Net downward solar (shortwave) radiation after albedo [W/m/m] {solarRadiation} 2D iof_hydro(6) = 0 !sensible flux (positive upward) [W/m/m] {sensibleHeat} 2D iof_hydro(7) = 0 !latent heat flux (positive upward) [W/m/m] {latentHeat} 2D iof_hydro(8) = 0 !upward longwave radiation (positive upward) [W/m/m] {upwardLongwave} 2D iof_hydro(9) = 0 !downward longwave radiation (positive downward) [W/m/m] {downwardLongwave} 2D iof_hydro(10) = 0 !total flux=-flsu-fllu-(radu-radd) [W/m/m] {totalHeat} 2D iof_hydro(11) = 0 !evaporation rate [kg/m/m/s] {evaporationRate} 2D iof_hydro(12) = 0 !precipitation rate [kg/m/m/s] {precipitationRate} 2D iof_hydro(13) = 0 !Bottom stress vector [kg/m/s^2(Pa)] {bottomStressX,Y} 2D vector iof_hydro(14) = 0 !wind velocity vector [m/s] {windSpeedX,Y} 2D vector iof_hydro(15) = 0 !wind stress vector [m^2/s/s] {windStressX,Y} 2D vector iof_hydro(16) = 0 !depth-averaged vel vector [m/s] {depthAverageVelX,Y} 2D vector iof_hydro(17) = 0 !vertical velocity [m/s] {verticalVelocity} 3D iof_hydro(18) = 0 !water temperature [C] {temperature} 3D iof_hydro(19) = 0 !water salinity [PSU] {salinity} 3D iof_hydro(20) = 0 !water density [kg/m^3] {waterDensity} 3D iof_hydro(21) = 0 !vertical eddy diffusivity [m^2/s] {diffusivity} 3D iof_hydro(22) = 0 !vertical eddy viscosity [m^2/s] {viscosity} 3D iof_hydro(23) = 0 !turbulent kinetic energy {turbulentKineticEner} 3D iof_hydro(24) = 0 !turbulent mixing length [m] {mixingLength} 3D

! iof_hydro(25) = 1 !z-coord {zCoordinates} 3D - this flag should be on for visIT etc: iof_hydro(26) = 1 !horizontal vel vector [m/s] {horizontalVelX,Y} 3D vector iof_hydro(27) = 0 !horizontal vel vector defined @side [m/s] {horizontalSideVelX,Y} 3D vector iof_hydro(28) = 0 !vertical vel. @elem [m/s] {verticalVelAtElement} 3D iof_hydro(29) = 0 !T @prism centers [C] {temperatureAtElement} 3D iof_hydro(30) = 0 !S @prism centers [PSU] {salinityAtElement} 3D iof_hydro(31) = 0 !Barotropic pressure gradient force vector (m.s-2) @side centers {pressure_gradient} 2D vector

!———————————————————————– ! Outputs from optional modules. Only uncomment these if the USE_* is on !———————————————————————– !———————————————————————– ! Outputs from DVD (USE_DVD must be on in Makefile) !———————————————————————– ! iof_dvd(1) = 1 !num mixing for S (PSU^2/s) {DVD_1} 3D elem

!———————————————————————– ! Outputs from WWM (USE_WWM must be on in Makefile) !———————————————————————– ! iof_wwm(1) = 0 !sig. height (m) {sigWaveHeight} 2D ! iof_wwm(2) = 0 !Mean average period (sec) - TM01 {meanWavePeriod} 2D ! iof_wwm(3) = 0 !Zero down crossing period for comparison with buoy (s) - TM02 {zeroDowncrossPeriod} 2D ! iof_wwm(4) = 0 !Average period of wave runup/overtopping - TM10 {TM10} 2D ! iof_wwm(5) = 0 !Mean wave number (1/m) {meanWaveNumber} 2D ! iof_wwm(6) = 0 !Mean wave length (m) {meanWaveLength} 2D ! iof_wwm(7) = 0 !Mean average energy transport direction (degr) - MWD in NDBC? {meanWaveDirection} 2D ! iof_wwm(8) = 0 !Mean directional spreading (degr) {meanDirSpreading} 2D ! iof_wwm(9) = 0 !Discrete peak period (sec) - Tp {peakPeriod} 2D ! iof_wwm(10) = 0 !Continuous peak period based on higher order moments (sec) {continuousPeakPeriod} 2D ! iof_wwm(11) = 0 !Peak phase vel. (m/s) {peakPhaseVel} 2D ! iof_wwm(12) = 0 !Peak n-factor {peakNFactor} 2D ! iof_wwm(13) = 0 !Peak group vel. (m/s) {peakGroupVel} 2D ! iof_wwm(14) = 0 !Peak wave number {peakWaveNumber} 2D ! iof_wwm(15) = 0 !Peak wave length {peakWaveLength} 2D ! iof_wwm(16) = 0 !Peak (dominant) direction (degr) {dominantDirection} 2D ! iof_wwm(17) = 0 !Peak directional spreading {peakSpreading} 2D ! iof_wwm(18) = 0 !Discrete peak direction (radian?) {discretePeakDirectio} 2D ! iof_wwm(19) = 0 !Orbital vel. (m/s) {orbitalVelocity} 2D ! iof_wwm(20) = 0 !RMS Orbital vel. (m/s) {rmsOrbitalVelocity} 2D ! iof_wwm(21) = 0 !Bottom excursion period (sec?) {bottomExcursionPerio} 2D ! iof_wwm(22) = 0 !Bottom wave period (sec) {bottomWavePeriod} 2D ! iof_wwm(23) = 0 !Uresell number based on peak period {UresellNumber} 2D ! iof_wwm(24) = 0 !Friction velocity (m/s?) {frictionalVelocity} 2D ! iof_wwm(25) = 0 !Charnock coefficient {CharnockCoeff} 2D ! iof_wwm(26) = 0 !Rougness length {rougnessLength} 2D

! iof_wwm(27) = 0 !Roller energy dissipation rate (W/m²) @nodes {Drol} 2D ! iof_wwm(28) = 0 !Total wave energy dissipation rate by depth-induced breaking (W/m²) @nodes {wave_sbrtot} 2D ! iof_wwm(29) = 0 !Total wave energy dissipation rate by bottom friction (W/m²) @nodes {wave_sbftot} 2D ! iof_wwm(30) = 0 !Total wave energy dissipation rate by whitecapping (W/m²) @nodes {wave_sdstot} 2D ! iof_wwm(31) = 0 !Total wave energy dissipation rate by vegetation (W/m²) @nodes {wave_svegtot} 2D ! iof_wwm(32) = 0 !Total wave energy input rate from atmospheric forcing (W/m²) @nodes {wave_sintot} 2D ! iof_wwm(33) = 0 !WWM_energy vector {waveEnergyDirX,Y} 2D vector

! iof_wwm(34) = 0 !Vertical Stokes velocity (m.s-1) @sides and whole levels {stokes_wvel} 3D ! iof_wwm(35) = 0 !Wave force vector (m.s-2) computed by wwm @side centers and whole levels {waveForceX,Y} 3D vector

! iof_wwm(36) = 0 !Horizontal Stokes velocity (m.s-1) @nodes and whole levels {stokes_hvel} 3D vector ! iof_wwm(37) = 0 !Roller contribution to horizontal Stokes velocity (m.s-1) @nodes and whole levels {roller_stokes_hvel} 3D vector

!———————————————————————– ! 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) = 0 !1st tracer {GEN_1} 3D ! iof_gen(2) = 0 !2nd tracer {GEN_2} 3D

!———————————————————————– ! Outputs for (age). Indices from “1” to “ntracer_age/2”; [days] !———————————————————————– ! iof_age(1) = 0 !{AGE_1} 3D ! iof_age(2) = 0 !{AGE_2} 3D

!———————————————————————– ! Specific outputs in SED3D (USE_SED must be on in Makefile; ! otherwise these are not needed) !———————————————————————– ! iof_sed(1) = 0 ! total bed thickness @elem (m) {sedBedThickness} 2D ! iof_sed(2) = 0 ! total bed age over all layers @elem (sec) {sedBedAge} 2D ! iof_sed(3) = 0 ! Sediment transport roughness length @elem (m) (sedTransportRough) {z0st} 2D ! iof_sed(4) = 0 !current-ripples roughness length @elem (m) (sedRoughCurrentRippl) {z0cr} 2D ! iof_sed(5) = 0 !sand-waves roughness length (m) @elem (z0sw_elem) {sedRoughSandWave} 2D ! iof_sed(6) = 0 !wave-ripples roughness length @elem (m) (z0wr_elem) {sedRoughWaveRipple} 2D

! iof_sed(7) = 0 !bottom depth _change_ from init. condition (m) {sedDepthChange} 2D ! iof_sed(8) = 0 ! Bed median grain size in the active layer (mm) {sedD50} 2D ! iof_sed(9) = 0 ! Bottom shear stress (Pa) {sedBedStress} 2D ! iof_sed(10) = 0 ! Bottom roughness lenghth (mm) {sedBedRoughness} 2D ! iof_sed(11) = 0 ! sediment porosity in the top layer (-) {sedPorocity} 2D ! iof_sed(12) = 0 ! erosion flux for suspended transport (kg/m/m/s) {sedErosionalFlux} 2D ! iof_sed(13) = 0 ! deposition flux for suspended transport (kg/m/m/s) {sedDepositionalFlux} 2D ! iof_sed(14) = 0 ! Bedload transport rate vector due to wave acceleration (kg/m/s) {sedBedloadTransportX,Y} 2D vector

! Example of using 2 classes ! iof_sed(15) = 0 !Bedload transport rate _vector_ (kg.m-1.s-1) for 1st tracer (one output per class) {sedBedload[X,Y]_1} 2D vector ! iof_sed(16) = 0 !Bedload transport of 2nd class {sedBedFraction_[X,Y]_2} 2D vector ! iof_sed(17) = 0 !Bed fraction 1st tracer (one output per class) [-] {sedBedFraction_1} 2D ! iof_sed(18) = 0 !Bed fraction of 2nd class {sedBedFraction_2} 2D

! iof_sed(19) = 0 !conc. of 1st class (one output need by each class) [g/L] {sedConcentration_1} 3D ! iof_sed(20) = 0 !conc. of 2nd class {sedConcentration_2} 3D

! iof_sed(21) = 0 !total suspended concentration (g/L) {totalSuspendedLoad} 3D

!———————————————————————– ! EcoSim outputs !———————————————————————– ! iof_eco(1) = 0 {ECO_1} 3D

!———————————————————————– ! ICM outputs !———————————————————————– ! !core Module ! iof_icm_core(1) = 1 !PB1 ! iof_icm_core(2) = 1 !PB2 ! iof_icm_core(3) = 1 !PB3 ! iof_icm_core(4) = 1 !RPOC ! iof_icm_core(5) = 1 !LPOC ! iof_icm_core(6) = 1 !DOC ! iof_icm_core(7) = 1 !RPON ! iof_icm_core(8) = 1 !LPON ! iof_icm_core(9) = 1 !DON ! iof_icm_core(10) = 1 !NH4 ! iof_icm_core(11) = 1 !NO3 ! iof_icm_core(12) = 1 !RPOP ! iof_icm_core(13) = 1 !LPOP ! iof_icm_core(14) = 1 !DOP ! iof_icm_core(15) = 1 !PO4 ! iof_icm_core(16) = 1 !COD ! iof_icm_core(17) = 1 !DOX ! ! !silica module ! iof_icm_silica(1) = 1 !SU ! iof_icm_silica(2) = 1 !SA ! ! !zooplankton module ! iof_icm_zb(1) = 1 !ZB1 ! iof_icm_zb(2) = 1 !ZB2 ! ! !pH model ! iof_icm_ph(1) = 1 !TIC ! iof_icm_ph(2) = 1 !ALK ! iof_icm_ph(3) = 1 !CA ! iof_icm_ph(4) = 1 !CACO3 ! ! !CBP model ! iof_icm_cbp(1) = 1 !SRPOC ! iof_icm_cbp(2) = 1 !SRPON ! iof_icm_cbp(3) = 1 !SRPOP ! iof_icm_cbp(4) = 1 !PIP ! ! !SAV model ! iof_icm_sav(1) = 1 !stleaf: total leaf biomass @elem [gC/m^2] ! iof_icm_sav(2) = 1 !ststem: total stem biomass @elem [gC/m^2] ! iof_icm_sav(3) = 1 !stroot: total root biomass @elem [gC/m^2] ! iof_icm_sav(4) = 1 !sht: canopy height @elem [m] ! ! !VEG model ! iof_icm_veg(1) = 1 !vtleaf1: leaf biomass group 1 [gC/m^2] ! iof_icm_veg(2) = 1 !vtleaf2: leaf biomass group 2 [gC/m^2] ! iof_icm_veg(3) = 1 !vtleaf3: leaf biomass group 3 [gC/m^2] ! iof_icm_veg(4) = 1 !vtstem1: stem biomass group 1 [gC/m^2] ! iof_icm_veg(5) = 1 !vtstem2: stem biomass group 2 [gC/m^2] ! iof_icm_veg(6) = 1 !vtstem3: stem biomass group 3 [gC/m^2] ! iof_icm_veg(7) = 1 !vtroot1: root biomass group 1 [gC/m^2] ! iof_icm_veg(8) = 1 !vtroot2: root biomass group 2 [gC/m^2] ! iof_icm_veg(9) = 1 !vtroot3: root biomass group 3 [gC/m^2] ! iof_icm_veg(10) = 1 !vht1: canopy height group 1 [m] ! iof_icm_veg(11) = 1 !vht2: canopy height group 2 [m] ! iof_icm_veg(12) = 1 !vht3: canopy height group 3 [m] ! ! !SFM model ! iof_icm_sed(1) = 1 !bPOC1 (g.m-3) ! iof_icm_sed(2) = 1 !bPOC2 (g.m-3) ! iof_icm_sed(3) = 1 !bPOC3 (g.m-3) ! iof_icm_sed(4) = 1 !bPON1 (g.m-3) ! iof_icm_sed(5) = 1 !bPON2 (g.m-3) ! iof_icm_sed(6) = 1 !bPON3 (g.m-3) ! iof_icm_sed(7) = 1 !bPOP1 (g.m-3) ! iof_icm_sed(8) = 1 !bPOP2 (g.m-3) ! iof_icm_sed(9) = 1 !bPOP3 (g.m-3) ! iof_icm_sed(10) = 1 !bNH4 (g.m-3) ! iof_icm_sed(11) = 1 !bNO3 (g.m-3) ! iof_icm_sed(12) = 1 !bPO4 (g.m-3) ! iof_icm_sed(13) = 1 !bH2S (g.m-3) ! iof_icm_sed(14) = 1 !bCH4 (g.m-3) ! iof_icm_sed(15) = 1 !bPOS (g.m-3) ! iof_icm_sed(16) = 1 !bSA (g.m-3) ! iof_icm_sed(17) = 1 !bstc: surface transfer coeff. (m/day) ! iof_icm_sed(18) = 1 !bSTR: benthic stress (day) ! iof_icm_sed(19) = 1 !bThp: consective days of hypoxia (day) ! iof_icm_sed(20) = 1 !bTox: consective days of oxic condition after hypoxia (day) ! iof_icm_sed(21) = 1 !SOD (g.m-2.day-1) ! iof_icm_sed(22) = 1 !JNH4 (g.m-2.day-1) ! iof_icm_sed(23) = 1 !JNO3 (g.m-2.day-1) ! iof_icm_sed(24) = 1 !JPO4 (g.m-2.day-1) ! iof_icm_sed(25) = 1 !JSA (g.m-2.day-1) ! iof_icm_sed(26) = 1 !JCOD (g.m-2.day-1) ! ! !Benthic Algae model ! iof_icm_ba(1) = 1 !BA (g[C].m-2) ! ! !ICM Debug Outputs (need coding, for developers) ! iof_icm_dbg(1) = 1 !2D ICM debug variables ! iof_icm_dbg(2) = 1 !3D ICM debug variables

!———————————————————————– ! CoSINE outputs: all 3D !———————————————————————– ! iof_cos(1) = 0 !NO3 (uM) ! iof_cos(2) = 0 !SiO4(uM) ! iof_cos(3) = 0 !NH4 (uM) ! iof_cos(4) = 0 !S1 (uM) ! iof_cos(5) = 0 !S2 (uM) ! iof_cos(6) = 0 !Z1 (uM) ! iof_cos(7) = 0 !Z2 (uM) ! iof_cos(8) = 0 !DN (uM) ! iof_cos(9) = 0 !DSi (uM) ! iof_cos(10) = 0 !PO4 (uM) ! iof_cos(11) = 0 !DOX (uM) ! iof_cos(12) = 0 !CO2 (uM) ! iof_cos(13) = 0 !ALK (uM)

!———————————————————————– ! Fecal indicating bacteria module !———————————————————————– ! iof_fib(1) = 0 ! {FIB_1} 3D

!———————————————————————– ! Specific outputs in SED2D (USE_SED2D must be on in Makefile; ! otherwise these are not needed) - not implemented yet !———————————————————————– ! iof_sed2d(1) = 0 !bottom depth _change_ from init. condition (m) {SED2D_depth_change} ! iof_sed2d(2) = 0 !drag coefficient used in transport formulae SED2D_Cd{} ! iof_sed2d(3) = 0 !Courant number (b.qtot.dt / h.dx) {SED2D_cflsed} ! iof_sed2d(4) = 0 !Top layer d50 (m) {SED2D_d50} ! iof_sed2d(5) = 0 !total transport rate vector (kg/m/s) {SED2D_total_transport} ! iof_sed2d(6) = 0 !suspended tranport rate vector (kg/m/s) {SED2D_susp_load} ! iof_sed2d(7) = 0 !bedload transport rate vector (kg/m/s) {SED2D_bed_load} ! iof_sed2d(8) = 0 !time averaged total transport rate vector (kg/m/s) {SED2D_average_transport} ! iof_sed2d(9) = 0 !bottom slope vector (m/m); negative uphill {SED2D_bottom_slope} ! iof_sed2d(10) = 0 !Total roughness length @elem (m) (z0eq) {z0eq} ! iof_sed2d(11) = 0 !current-ripples roughness length @elem (m) (z0cr) {z0cr} ! iof_sed2d(12) = 0 !sand-waves roughness length @elem (m) (z0sw) {z0sw} ! iof_sed2d(13) = 0 !wave-ripples roughness length @elem (m) (z0wr) {z0wr}

!———————————————————————– ! marsh flags (USE_MARSH on) !———————————————————————– ! iof_marsh(1) = 0 ! {marshFlag} 2D elem

!———————————————————————– ! Ice module outputs (if USE_ICE is on) !———————————————————————– ! iof_ice(1)= 0 !divergence @ elem (‘Delta’) [1/sec] {iceStrainRate} 2D ! iof_ice(2)= 0 !ice advective velcoity vector [m/s] {iceVelocityX,Y} 2D vector ! iof_ice(3)= 0 !net heat flux to ocean (>0 warm up SST) [W/m/m] {iceNetHeatFlux} 2D ! iof_ice(4)= 0 !net fresh water flux to ocean (>0 freshens up SSS) [kg/s/m/m] {iceFreshwaterFlux} 2D ! iof_ice(5)= 0 !ice temperature [C] at air-ice interface {iceTopTemperature} 2D

! iof_ice(6)= 0 !ice volume [m] {iceTracer_1} 2D ! iof_ice(7)= 0 !ice concentration [-] {iceTracer_2} 2D ! iof_ice(8)= 0 !snow volume [m] {iceTracer_3} 2D

!———————————————————————– ! Analysis module outputs (USE_ANALYSIS) !———————————————————————– ! iof_ana(1) = 0 !min time step at each element over all subcycles in horizontal transport solver [s] {minTransportTimeStep} 2D ! iof_ana(2) = 0 !x-component of

abla air_pres / ho_0 [m/s/s] {airPressureGradientX} 2D

! iof_ana(3) = 0 !y-component of

abla air_pres / ho_0 [m/s/s] {airPressureGradientY} 2D

! iof_ana(4) = 0 !lpha*g*

abla Psi [m/s/s] (gradient of tidal potential) {tidePotentialGradX} 2D: ! iof_ana(5) = 0 !lpha*g*
abla Psi [m/s/s] {tidePotentialGradY} 2D: ! iof_ana(6) = 0 !

abla cdot (mu abla u) [m/s/s] (horizontal momentum mixing) {horzontalViscosityX} 3D side

! iof_ana(7) = 0 !

abla cdot (mu abla v) [m/s/s] {horzontalViscosityY} 3D side

! iof_ana(8) = 0 !-g/rho0* int_z^eta dr_dx dz [m/s/s] (b-clinic gradient) {baroclinicForceX} 3D side ! iof_ana(9) = 0 !-g/rho0* int_z^eta dr_dy dz [m/s/s] {baroclinicForceY} 3D side ! iof_ana(10) = 0 !d (

u du/dz)/dz [m/s/s] - no vegetation effects (vertical momentum mixing) {verticalViscosityX} 3D side: ! iof_ana(11) = 0 !d (
u dv/dz)/dz [m/s/s] - no vegetation effects {verticalViscosityY} 3D side: ! iof_ana(12) = 0 !(u cdot
abla) u [m/s/s] (momentum advection) {mommentumAdvectionX} 3D side: ! iof_ana(13) = 0 !(u cdot
abla) u [m/s/s] {mommentumAdvectionY} 3D side: ! iof_ana(14) = 0 !gradient Richardson number [-] {gradientRichardson} 3D /

Fields:

core (rompy.schism.namelists.param.CORE)
opt (rompy.schism.namelists.param.OPT)
schout (rompy.schism.namelists.param.SCHOUT)
vertical (rompy.schism.namelists.param.VERTICAL)

field core: CORE = CORE(ipre=0, ibc=0, ibtp=1, rnday=30, dt=100.0, msc2=24, mdc2=30, ntracer_gen=2, ntracer_age=4, sed_class=5, eco_class=27, nspool=36, ihfskip=864)#

field opt: OPT = OPT(ipre2=0, itransport_only=0, iloadtide=0, loadtide_coef=0.1, start_year=2000, start_month=1, start_day=1, start_hour=0, utc_start=8, ics=1, ihot=0, ieos_type=0, ieos_pres=0, eos_a=-0.1, eos_b=1001.0, dramp=1.0, drampbc=0.0, iupwind_mom=0, indvel=0, ihorcon=0, hvis_coef0=0.025, ishapiro=1, niter_shap=1, shapiro0=0.5, thetai=0.6, icou_elfe_wwm=0, nstep_wwm=1, iwbl=0, hmin_radstress=1.0, drampwafo=0.0, turbinj=0.15, turbinjds=1.0, alphaw=0.5, fwvor_advxy_stokes=1, fwvor_advz_stokes=1, fwvor_gradpress=1, fwvor_breaking=1, fwvor_streaming=1, fwvor_wveg=0, fwvor_wveg_NL=0, cur_wwm=0, wafo_obcramp=0, imm=0, ibdef=10, slam0=-124, sfea0=45, iunder_deep=0, h1_bcc=50.0, h2_bcc=100.0, hw_depth='1.e6', hw_ratio=0.5, ihydraulics=0, if_source=0, dramp_ss=2, meth_sink=1, lev_tr_source__1=-9, lev_tr_source__2=-9, lev_tr_source__3=-9, lev_tr_source__4=-9, lev_tr_source__5=-9, lev_tr_source__6=-9, lev_tr_source__7=-9, lev_tr_source__8=-9, lev_tr_source__9=-9, lev_tr_source__10=-9, lev_tr_source__11=-9, lev_tr_source__12=-9, level_age=[9, -999], ihdif=0, nchi=0, dzb_min=0.5, hmin_man=1.0, ncor=0, rlatitude=46, coricoef=0, ic_elev=0, nramp_elev=0, inv_atm_bnd=0, prmsl_ref=101325.0, flag_ic__1=1, flag_ic__2=1, flag_ic__3=1, flag_ic__5=1, flag_ic__6=1, flag_ic__7=1, flag_ic__8=1, flag_ic__9=1, flag_ic__10=1, flag_ic__11=1, flag_ic__12=0, gen_wsett=0, ibcc_mean=0, rmaxvel=5.0, velmin_btrack='1.e-4', btrack_nudge='9.013e-3', ihhat=1, inunfl=0, h0=0.01, shorewafo=0, moitn0=50, mxitn0=1500, rtol0='1.e-12', nadv=1, dtb_max=30.0, dtb_min=10.0, inter_mom=0, kr_co=1, itr_met=3, h_tvd=5.0, eps1_tvd_imp='1.e-4', eps2_tvd_imp='1.e-14', ielm_transport=0, max_subcyc=10, ip_weno=2, courant_weno=0.5, nquad=2, ntd_weno=1, epsilon1='1.e-15', epsilon2='1.e-10', i_prtnftl_weno=0, epsilon3='1.e-25', ielad_weno=0, small_elad='1.e-4', nws=0, wtiminc=150.0, drampwind=1.0, iwindoff=0, iwind_form=1, model_type_pahm=10, ihconsv=0, isconsv=0, i_hmin_airsea_ex=2, hmin_airsea_ex=0.2, i_hmin_salt_ex=2, hmin_salt_ex=0.2, iprecip_off_bnd=0, itur=3, dfv0='1.e-2', dfh0='1.e-4', mid="'KL'", stab="'KC'", xlsc0=0.1, inu_elev=0, inu_uv=0, inu_tr__1=0, inu_tr__2=0, inu_tr__3=0, inu_tr__4=0, inu_tr__5=0, inu_tr__6=0, inu_tr__7=0, inu_tr__8=0, inu_tr__9=0, inu_tr__10=0, inu_tr__11=0, inu_tr__12=0, nu_sum_mult=1)#

field schout: SCHOUT = SCHOUT(nc_out=1, iof_ugrid=0, nhot=0, nhot_write=8640, iout_sta=0, nspool_sta=10, iof_hydro__1=1, iof_hydro__2=0, iof_hydro__3=0, iof_hydro__4=0, iof_hydro__5=0, iof_hydro__6=0, iof_hydro__7=0, iof_hydro__8=0, iof_hydro__9=0, iof_hydro__10=0, iof_hydro__11=0, iof_hydro__12=0, iof_hydro__13=0, iof_hydro__14=0, iof_hydro__15=0, iof_hydro__16=0, iof_hydro__17=0, iof_hydro__18=0, iof_hydro__19=0, iof_hydro__20=0, iof_hydro__21=0, iof_hydro__22=0, iof_hydro__23=0, iof_hydro__24=0, iof_hydro__26=1, iof_hydro__27=0, iof_hydro__28=0, iof_hydro__29=0, iof_hydro__30=0, iof_hydro__31=0)#

field vertical: VERTICAL = VERTICAL(vnh1=400, vnf1=0.0, vnh2=500, vnf2=0.0, step_nu_tr=86400.0, h_bcc1=100.0, s1_mxnbt=0.5, s2_mxnbt=3.5, iharind=0, iflux=0, izonal5=0, ibtrack_test=0, irouse_test=0, flag_fib=1, slr_rate=120.0, isav=0, nstep_ice=1, rearth_pole=6378206.4, rearth_eq=6378206.4, shw='4184.d0', rho0='1000.d0', vclose_surf_frac=1.0, iadjust_mass_consv0__1=0, iadjust_mass_consv0__2=0, iadjust_mass_consv0__3=0, iadjust_mass_consv0__4=0, iadjust_mass_consv0__5=0, iadjust_mass_consv0__6=0, iadjust_mass_consv0__7=0, iadjust_mass_consv0__8=0, iadjust_mass_consv0__9=0, iadjust_mass_consv0__10=0, iadjust_mass_consv0__11=0, iadjust_mass_consv0__12=0, h_massconsv=2.0, rinflation_icm='1.e-3')#

Table of Contents

rompy.schism.namelists.param.PARAM#