sediment.in

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Sediment Model Input Script - sediment.in

The sediment.in file sets the parameters for sediment output. The name of this file is set by the SPARNAM keyword in the roms.in file. This standard input ASCII file is organized in several sections as shown below, with links to more detailed explanation where required.


Note Notice: Detailed information about ROMS input script file syntax can be found here.

Note Notice: A default sediment.in input script is provided in the User/External subdirectory. Also there are several sediment input scripts in the ROMS/External subdirectory which are used in the distributed test cases. They are usually named sediment_app.in where app is the lowercase of the test case CPP option.


Sediment Model Control Switches

  • Switch is used to control sediment model computation within nested and/or multiple connected grids, [1:Ngrids] values are expected.
    Lsediment == T

Tracer Advection Schemes

  • Set horizontal and vertical advection schemes for biological tracers. A different advection scheme is allowed for each tracer. For example, a positive-definite (monotonic) algorithm can be activated for salinity and biological tracers, while a different one is set for temperature.
    Keyword Advection Algorithm

    A4 4th-order Akima (horizontal/vertical)
    C2 2nd-order centered differences (horizontal/vertical)
    C4 4th-order centered differences (horizontal/vertical)
    HSIMT 3th-order HSIMT with TVD limiter (horizontal/vertical)
    MPDATA recursive flux corrected MPDATA (horizontal/vertical)
    SPLINES parabolic splines reconstruction (only vertical)
    SU3 split third-order upstream (horizontal/vertical)
    U3 3rd-order upstresm-bias (only horizontal)
    The user has the option of specifying the full Keyword or the first two letters, regardless if using uppercase or lowercase. If nested grids, specify values for each grid. For more details please read the roms.in Tracer Advection Schemes section. [1:NBT,Ngrids] values are expected.
    Hadvection == HSIMT  ! idsed(:), compact

    Vadvection == HSIMT  ! idsed(:), compact

Lateral Open Boundary Conditions Parameters

  • The lateral boundary conditions are entered with a keyword. A value is expected for each boundary segment per nested grid for each state variable. The sediment tracer variables (cohesive and non-cohesive) require [1:4,1:NCS+NNS,Ngrids] values. If specifying every tracer, enter first 1:NCS cohesive sediment entries followed by 1:NNS non-cohesive sediment entries. The boundary order is: 1=west, 2=south, 3=east, and 4=north. That is, anticlockwise starting at the western boundary.

    The keyword is case insensitive and usually has three characters. However, it is possible to have compound keywords, if applicable. For example, the keyword RadNud implies radiation boundary condition with nudging. This combination is usually used in active/passive radiation conditions.

    NoteNotice: It is possible to specify the lateral boundary conditions for all biological tracers in a compact form with a single entry. If so, all the biological tracers are assumed to have the same boundary condition as the single entry.
    ! Keyword Lateral Boundary Condition Type
    !
    ! Cla Clamped _____N_____ j=Mm
    ! Clo Closed | 4 |
    ! Gra Gradient | |
    ! Nes Nested 1 W E 3
    ! Nud Nudging | |
    ! Per Periodic |_____S_____|
    ! Rad Radiation 2 j=1
    ! i=1 i=Lm
    ! W S E N
    ! e o a o
    ! s u s r
    ! t t t t
    ! h h
    !
    ! 1 2 3 4

    LBC(isTvar) == Per Clo Per Clo  ! idsed(:), compact
  • Adjoint-based algorithms can have different lateral boundary conditions keywords.
    ad_LBC(isTvar) == Per Clo Per Clo  ! idsed(:), compact

General Sediment Bed Model Controls

  • Depositional bed layer thickness (m) criteria to create a new layer. If deposition exceeds this value, then a new layer is created, [1:Ngrids] values are expected.
    NEWLAYER_THICK == 0.01d0

Bed Layer and Bottom Sediment Parameters

  • Logical switches to activate writing of bed layer and bottom sediment fields into history output NetCDF file(s), [1:Ngrids] values are expected.
Hout(ithck) == T  ! bed_thickness sediment layer thickness
Hout(iaged) == T  ! bed_age sediment layer age
Hout(iporo) == T  ! bed_porosity sediment layer porosity
Hout(idiff) == F  ! bed_biodiff biodiffusivity

Hout(ids50) == T  ! grain_diameter mean grain diameter
Hout(idens) == T  ! grain_density mean grain density
Hout(iwsed) == T  ! settling_vel mean settling velocity
Hout(itauc) == T  ! erosion_stress critical erosion stress
Hout(irlen) == T  ! ripple_length ripple length
Hout(irhgt) == T  ! ripple_height ripple height
Hout(ibwav) == T  ! bed_wave_amp wave excursion amplitude
Hout(izdef) == T  ! Zo_def default bottom roughness
Hout(izapp) == T  ! Zo_app apparent bottom roughness
Hout(izNik) == T  ! Zo_Nik Nikuradse bottom roughness
Hout(izbio) == T  ! Zo_bio biological bottom roughness
Hout(izbfm) == T  ! Zo_bedform bed form bottom roughness
Hout(izbld) == T  ! Zo_bedload bed load bottom roughness
Hout(izwbl) == T  ! Zo_wbl wave bottom roughness
Hout(iactv) == T  ! active_layer_thickness active layer thickness
Hout(ishgt) == T  ! saltation saltation height
  • Logical switches to activate writing of bed layer and bottom sediment fields into quicksave output NetCDF file(s), [1:Ngrids] values are expected.
Qout(ithck) == F  ! bed_thickness sediment layer thickness
Qout(iaged) == F  ! bed_age sediment layer age
Qout(iporo) == F  ! bed_porosity sediment layer porosity
Qout(idiff) == F  ! bed_biodiff biodiffusivity

Qout(ids50) == F  ! grain_diameter mean grain diameter
Qout(idens) == F  ! grain_density mean grain density
Qout(iwsed) == F  ! settling_vel mean settling velocity
Qout(itauc) == F  ! erosion_stress critical erosion stress
Qout(irlen) == F  ! ripple_length ripple length
Qout(irhgt) == F  ! ripple_height ripple height
Qout(ibwav) == F  ! bed_wave_amp wave excursion amplitude
Qout(izdef) == F  ! Zo_def default bottom roughness
Qout(izapp) == F  ! Zo_app apparent bottom roughness
Qout(izNik) == F  ! Zo_Nik Nikuradse bottom roughness
Qout(izbio) == F  ! Zo_bio biological bottom roughness
Qout(izbfm) == F  ! Zo_bedform bed form bottom roughness
Qout(izbld) == F  ! Zo_bedload bed load bottom roughness
Qout(izwbl) == F  ! Zo_wbl wave bottom roughness
Qout(iactv) == F  ! active_layer_thickness active layer thickness
Qout(ishgt) == F  ! saltation saltation height


Non-cohesive Sediment Parameters

There are NNS non-cohesive (sand) sediment tracers per nested grid in ROMS. Therefore, [1:NNS,1:Ngrids] values are expected for these parameters.

  • Median sediment grain diameter (mm).
    SAND_SD50 == 1.0d0
  • Sediment concentration (kg/m3).
    SAND_CSED == 0.0d0
  • Sediment grain density (kg/m3).
    SAND_SRHO == 2650.0d0
  • Particle settling velocity (mm/s).
    SAND_WSED == 1.0d0
  • Surface erosion rate (kg/m2/s).
    SAND_ERATE == 5.0d-4
  • Porosity (nondimensional): Vwater/(Vwater+Vsed). Its values range between 0 and 1.
    SAND_POROS == 0.5d0
  • Lateral, constant, harmonic/biharmonic horizontal diffusion of tracer for the nonlinear model and adjoint-based algorithms.
    SAND_TNU2 == 0.0d0  ! m2/s
    SAND_TNU4 == 0.0d0  ! m4/s

    ad_SAND_TNU2 == 0.0d0  ! m2/s
    ad_SAND_TNU4 == 0.0d0  ! m4/s
  • Logical switches to increase horizontal diffusivity of noncohesive sediment trace in specific areas of the application domain (like sponge areas) for the desired grid.
    SAND_Sponge == F
  • Vertical mixing coefficients for tracers in nonlinear model and basic state scale factor in adjoint-based algorithms.
    SAND_AKT_BAK == 5.0d-6  ! m2/s
    SAND_AKT_fac == 1.0d0  ! nondimensional
  • Nudging/relaxation time scales, inverse scales will be computed internally.
    SAND_TNUDG == 0.0d0  ! days
  • Morphological time scale factor (greater than or equal to 1.0). A value of 1.0 has no scale effect.
    SAND_MORPH_FAC == 1.0d0  ! nondimensional
  • Logical switch to specify which variables to consider on tracers point Sources/Sinks (like river runoff). [1:NCS,Ngrids] values expected.
SAND_Ltsrc == F
  • Logical switches to specify which variables to process for tracers climatology: [1:NCS,Ngrids] values expected.
SAND_Ltclm == F
  • Logical switches to nudge the desired noncohesive sediment tracer climatology field. If not analytical climatology fields, users need to turn on the logical switches above to process the fields from the climatology NetCDF file that are needed for nudging.
    SAND_Tnudge == F
  • Logical switches to activate writing of non-cohesive sediment into output history file.
Hout(idsand) == T  ! sand_01, ... suspended concentration
Hout(iSfrac) == T  ! sandfrac_01, ... bed layer fraction
Hout(iSmass) == T  ! sandmass_01, ... bed layer mass
Hout(iSUbld) == T  ! bedload_Usand_01, ... bed load at U-points
Hout(iSVbld) == T  ! bedload_Vsand_01, ... bed load at V-points
  • Logical switches to activate writing of non-cohesive sediment into output quicksave file.
Qout(idsand) == F  ! sand_01, ... suspended concentration
Qout(iSsand) == F  ! sand_01_sur, ... surface concentration
Qout(iSfrac) == F  ! sandfrac_01, ... bed layer fraction
Qout(iSmass) == F  ! sandmass_01, ... bed layer mass
Qout(iSUbld) == F  ! bedload_Usand_01, ... bed load at U-points
Qout(iSVbld) == F  ! bedload_Vsand_01, ... bed load at V-points
  • Logical switches to activate writing of time-averaged, non-cohesive sediment fields into averages output file.
Aout(idsand) == T  ! sand_01, ... suspended concentration

Aout(iSTTav) == T  ! sand_01_2, ... quadratic <t*t> tracer terms
Aout(iSUTav) == T  ! u_sand_01, ... quadratic <u*t> tracer terms
Aout(iSVTav) == T  ! v_sand_01, ... quadratic <v*t> tracer terms
Aout(SHUTav) == T  ! Huon_sand_01, ... tracer volume flux, <Huon*t>
Aout(SHVTav) == T  ! Hvom_sand_01, ... tracer volume flux, <Hvom*t>

Aout(iSUbld) == T  ! bedload_Usand_01, ... bed load at U-points
Aout(iSVbld) == T  ! bedload_Vsand_01, ... bed load at V-points
  • Logical switches to activate writing of time-averaged, non-cohesive sediment diagnostic terms into output diagnostics file.
Dout(STrate) == T  ! sand_01_rate, ... time rate of change
Dout(SThadv) == T  ! sand_01_hadv, ... horizontal total advection
Dout(STxadv) == T  ! sand_01_xadv, ... horizontal XI-advection
Dout(STyadv) == T  ! sand_01_yadv, ... horizontal ETA-advection
Dout(STvadv) == T  ! sand_01_vadv, ... vertical advection
Dout(SThdif) == T  ! sand_01_hdiff, ... horizontal total diffusion
Dout(STxdif) == T  ! sand_01_xdiff, ... horizontal XI-diffusion
Dout(STydif) == T  ! sand_01_ydiff, ... horizontal ETA-diffusion
Dout(STsdif) == T  ! sand_01_sdiff, ... horizontal S-diffusion
Dout(STvdif) == T  ! sand_01_vdiff, ... vertical diffusion

Suspended Cohesive Sediment Parameters

There are NCS cohesive (mud) sediment tracers per nested grid in ROMS. Therefore, [1:NCS,1:Ngrids] values are expected for these parameters.

  • Median sediment grain diameter (mm).
    MUD_SD50 == 0.01d0 0.005d0
  • Sediment concentration (kg/m3).
    MUD_CSED == 0.0d0 0.0d0
  • Sediment grain density (kg/m3).
    MUD_SRHO == 2650.0d0 2400.0d0
  • Particle settling velocity (mm/s).
    MUD_WSED == 0.1d0 0.01d0
  • Surface erosion rate (kg/m2/s).
    MUD_ERATE == 5.0d-4 5.0d-4
  • Critical shear for erosion and deposition (N/m2).
    MUD_TAU_CE == 0.1d0 0.1d0
    MUD_TAU_CD == 0.1d0 0.1d0
  • Porosity (nondimensional): Vwater/(Vwater+Vsed). Its values range between 0 and 1.
    MUD_POROS == 0.9d0 0.9d0
  • Lateral, constant, harmonic/biharmonic horizontal diffusion of tracer for the nonlinear model and adjoint-based algorithms.
    MUD_TNU2 == 0.0d0 0.0d0  ! m2/s
    MUD_TNU4 == 0.0d0 0.0d0  ! m4/s

    ad_MUD_TNU2 == 0.0d0 0.0d0  ! m2/s
    ad_MUD_TNU4 == 0.0d0 0.0d0  ! m4/s
  • Logical switches to increase horizontal diffusivity of cohesive sediment trace in specific areas of the application domain (like sponge areas) for the desired grid.
    MUD_Sponge == F F
  • Vertical mixing coefficients for tracers in nonlinear model and basic state scale factor in adjoint-based algorithms.
    MUD_AKT_BAK == 5.0d-6 5.0d-6  ! m2/s
    MUD_AKT_fac == 2*1.0d0  ! nondimensional
  • Nudging/relaxation time scales, inverse scales will be computed internally.
    MUD_TNUDG == 0.0d0 0.0d0  ! days
  • Morphological time scale factor (greater than or equal to 1.0). A value of 1.0 has no scale effect.
    MUD_MORPH_FAC == 1.0d0 1.0d0  ! nondimensional
  • Logical switch to specify which variables to consider on tracers point Sources/Sinks (like river runoff). [1:NCS,Ngrids] values expected.
MUD_Ltsrc == F F
  • Logical switches to specify which variables to process for tracers climatology: [1:NCS,Ngrids] values expected.
MUD_Ltclm == F F
  • Logical switches to nudge the desired cohesive sediment tracer climatology field. If not analytical climatology fields, users need to turn on the logical switches above to process the fields from the climatology NetCDF file that are needed for nudging.
    MUD_Tnudge == F F
  • Logical switches to activate writing of cohesive sediment into output history file.
Hout(idmud) == T  ! mud_01, ... suspended concentration
Hout(iMfrac) == T  ! mudfrac_01, ... bed layer fraction
Hout(iMmass) == T  ! mudmass_01, ... bed layer mass
Hout(iMUbld) == T  ! bedload_Umud_01, ... bed load at U-points
Hout(iMVbld) == T  ! bedload_Vmud_01, ... bed load at V-points
  • Logical switches to activate writing of cohesive sediment into output quicksave file.
Qout(idmud) == F  ! mud_01, ... suspended concentration
Qout(iSmud) == F  ! mud_01_sur, ... surface concentration
Qout(iMfrac) == F  ! mudfrac_01, ... bed layer fraction
Qout(iMmass) == F  ! mudmass_01, ... bed layer mass
Qout(iMUbld) == F  ! bedload_Umud_01, ... bed load at U-points
Qout(iMVbld) == F  ! bedload_Vmud_01, ... bed load at V-points
  • Logical switches to activate writing of time-averaged, cohesive sediment fields into averages output file.
Aout(idmud) == T  ! mud_01, ... suspended concentration

Aout(iMTTav) == T  ! mud_01_2, ... quadratic <t*t> tracer terms
Aout(iMUTav) == T  ! u_mud_01, ... quadratic <u*t> tracer terms
Aout(iMVTav) == T  ! v_mud_01, ... quadratic <v*t> tracer terms
Aout(MHUTav) == T  ! Huon_mud_01, ... tracer volume flux, <Huon*t>
Aout(MHVTav) == T  ! Hvom_mud_01, ... tracer volume flux, <Hvom*t>

Aout(iMUbld) == T  ! bedload_Umud_01, ... bed load at U-points
Aout(iMVbld) == T  ! bedload_Vmud_01, ... bed load at V-points
  • Logical switches to activate writing of time-averaged, cohesive sediment diagnostic terms into output diagnostics file.
Dout(MTrate) == T  ! mud_01_rate, ... time rate of change
Dout(MThadv) == T  ! mud_01_hadv, ... horizontal total advection
Dout(MTxadv) == T  ! mud_01_xadv, ... horizontal XI-advection
Dout(MTyadv) == T  ! mud_01_yadv, ... horizontal ETA-advection
Dout(MTvadv) == T  ! mud_01_vadv, ... vertical advection
Dout(MThdif) == T  ! mud_01_hdiff, ... horizontal total diffusion
Dout(MTxdif) == T  ! mud_01_xdiff, ... horizontal XI-diffusion
Dout(MTydif) == T  ! mud_01_ydiff, ... horizontal ETA-diffusion
Dout(MTsdif) == T  ! mud_01_sdiff, ... horizontal S-diffusion
Dout(MTvdif) == T  ! mud_01_vdiff, ... vertical diffusion
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