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Updating Sediment Model and Friends #24

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6d880c5
Updating sediment algortihms and added Vegetation routines
jcwarner-usgs Nov 22, 2023
87dc081
updating sediment and adding Veg
jcwarner-usgs Nov 22, 2023
143a7e2
Merging latest develop into feature/sediment
hga007 Jan 4, 2024
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Merge branch 'develop' into feature/sediment
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319 changes: 293 additions & 26 deletions ROMS/External/sediment_estuary_test.in
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Original file line number Diff line number Diff line change
Expand Up @@ -142,33 +142,65 @@ ad_LBC(isTvar) == RadNud Clo Cla Clo ! idsed(:), compact

BEDLOAD_COEFF == 0.05d0

! Logical switches (TRUE/FALSE) to activate writing of bed layer parameters
! into HISTORY output files, [1:Ngrids] values 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

! Logical switches (TRUE/FALSE) to activate writing of bed bottom sediment
! parameters into HISTORY output files, [1:Ngrids] values expected.
! Maximum biodiffusivity, [1:Ngrids].

DBMAX == 1.0d-10

! Minimum biodiffusivity, [1:Ngrids].

DBMIN == 1.0d-12

! Depth of maximum biodiffusivity, [1:Ngrids].

DBZS == 0.002d0

! Depth of end of exponential biodiffusivity, [1:Ngrids].

DBZM == 0.08d0

! Depth of minimum biodiffusivity, [1:Ngrids].

DBZP == 0.01d0

! Logical switches (TRUE/FALSE) to activate writing of bed layer
! parameters, [1:Ngrids] values expected.

Hout(ithck) == T ! sediment layer thickness
Hout(iaged) == T ! sediment layer age
Hout(iporo) == T ! sediment layer porosity
Hout(idiff) == T ! biodiffusivity

! Logical switches (TRUE/FALSE) to activate writing of bed
! bottom sediment parameters, [1:Ngrids] values expected.

Hout(isd50) == T ! mean grain diameter
Hout(idens) == T ! mean grain density
Hout(iwsed) == T ! mean settling velocity
Hout(itauc) == T ! critical erosion stress
Hout(irlen) == T ! ripple length
Hout(irhgt) == T ! ripple height
Hout(ibwav) == T ! wave excursion amplitude
Hout(izdef) == T ! default bottom roughness
Hout(izapp) == T ! apparent bottom roughness
Hout(izNik) == F ! Nikuradse bottom roughness
Hout(izbio) == F ! biological bottom roughness
Hout(izbfm) == F ! bed form bottom roughness
Hout(izbld) == F ! bed load bottom roughness
Hout(izwbl) == F ! wave bottom roughness
Hout(iactv) == F ! active layer thickness
Hout(ishgt) == F ! saltation height
Hout(imaxD) == F ! maximum inundation depth
Hout(idnet) == F ! Erosion or deposition
Hout(idoff) == F ! dmix erodibility profile offset
Hout(idslp) == F ! dmix or erodibility slope
Hout(idtim) == F ! erodibility profile restore time
Hout(idbmx) == F ! Bed biodifusivity maximum
Hout(idbmm) == F ! Bed biodifusivity minimum
Hout(idbzs) == F ! Bed biodifusivity zs
Hout(idbzm) == F ! Bed biodifusivity zm
Hout(idbzp) == F ! Bed biodifusivity phi
Hout(idprp) == F ! cohesive behavior

Hout(isd50) == 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) == F ! Zo_Nik Nikuradse bottom roughness
Hout(izbio) == F ! Zo_bio biological bottom roughness
Hout(izbfm) == F ! Zo_bedform bed form bottom roughness
Hout(izbld) == F ! Zo_bedload bed load bottom roughness
Hout(izwbl) == F ! Zo_wbl wave bottom roughness
Hout(iactv) == F ! active_layer_thickness active layer thickness
Hout(ishgt) == F ! saltation saltation height

! Logical switches (TRUE/FALSE) to activate writing of bed layer parameters
! into QUICKSAVE output files, [1:Ngrids] values expected.
Expand Down Expand Up @@ -460,6 +492,131 @@ 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

!------------------------------------------------------------------------------
! Mixed Bed parameters- Transition threshold for cohesive mix
! and non-cohesive behaviors [1:Ngrids] values expected.
!------------------------------------------------------------------------------
! Cohesive transition- Under that value of total mud fraction
! entire bed behaves as a non-cohesive bed

TRANSC == 0.03d0

! Noncohesive transition- Over that value of total mud fraction
! entire bed behaves as a cohesive bed

TRANSN == 0.2d0

!------------------------------------------------------------------------------
! Cohesive/Mixed bed critical shear
! Bed critical shear stress values if cohesive or mixed Bed is active
! These values are applied to the entire bed. [1:Ngrids] values expected.
!------------------------------------------------------------------------------

! Minimum shear for erosion

MUD_TAUCR_MIN == 0.030000d0

! Maximum shear for erosion

MUD_TAUCR_MAX == 5.20d0

! Tau_crit profile slope

MUD_TAUCR_SLOPE == 0.300000d0

! Tau_crit profile offset

MUD_TAUCR_OFF == 1.000000d0

! Tau_crit consolidation rate

MUD_TAUCR_TIME == 28800.0d0

!------------------------------------------------------------------------------
! Flocculation Sediment Parameters.
!------------------------------------------------------------------------------

! Boolean set to .true. if differential settling aggregation

L_ADS == F

! Boolean set to .true. if shear aggregation

L_ASH == T

! Boolean set to .true. if collision-induced fragmentation enable

L_COLLFRAG == F

! Primary particle size (m), typically 4e-6 m

F_DP0 == 0.000004d0

! Floc fractal dimension, typically ranging from 1.6 to 2.6

F_NF == 2.0d0

! Maximum diameter (m)

F_DMAX == 0.0015d0

! Number of fragments by shear erosion, If binary/ternary : 2.0

F_NB_FRAG == 2.0d0

! Flocculation efficiency, ranging from 0 to 1.0

F_ALPHA == 0.35d0

! Shear fragmentation rate

F_BETA == 0.15d0

! For ternary breakup, use 0.5, for binary : 0. (a boolean could be better)

F_ATER == 0.0d0

! Fraction of the shear fragmentation term transfered to shear erosion.
! Ranging from [(0.0 - no erosion to 1.0 - all erosion)]

F_ERO_FRAC == 0.0d0

! Number of fragments induced by shear erosion.

F_ERO_NBFRAG == 2.0d0

! Fragment size class (could be changed to a particle
! size or a particle distribution) (INTEGER)

F_ERO_IV == 1

! Fragmentation rate for collision-induced breakup

F_COLLFRAGPARAM == 0.01d0

! Min concentration below which flocculation processes are not calculated

F_CLIM == 0.001d0

! If .TRUE. sets G(t) to values from Verney et al., 2011 lab experiment

L_TESTCASE == F

!------------------------------------------------------------------------------
! Flocculation Decomposition in Bed Sediment Parameters
! Only #ifdef DEFLOC
!------------------------------------------------------------------------------
!
! Equilibrium fractional class distribution (they should add up to 1).
! There is no check for that
! [1:NCS,1:Ngrids] values expected.

MUD_FRAC_EQ == 0.10d0 0.20d0 0.40d0 0.20d0 0.10d0 0.0d0 0.0d0 0.00d0 0.0d0 0.0d0 0.0d0 0.0d0 0.0d0 0.0d0 0.0d0

! Time scale of flocculation decomposition in bed
! [1:Ngrids] values expected.

MUD_T_DFLOC == 200.0d0
!
! GLOSSARY:
! =========
Expand Down Expand Up @@ -638,6 +795,17 @@ Dout(MTvdif) == T ! mud_01_vdiff, ... vertical diffusion
! layer is created.
!
! BEDLOAD_COEFF Bed load transport rate coefficient.

!
! DBMAX Maximum biodiffusivity
!
! DBMIN Minimum biodiffusivity
!
! DBZS Depth of maximum biodiffusivity
!
! DBZM Depth of end of exponential biodiffusivity
!
! DBZP Depth of minimum biodiffusivity
!
! Logical switches (TRUE/FALSE) to activate writing of bed layer parameters
! into output HISTORY NetCDF file:
Expand Down Expand Up @@ -685,6 +853,29 @@ Dout(MTvdif) == T ! mud_01_vdiff, ... vertical diffusion
!
! Hout(ishgt) Write out saltation height.
!
!
! Hout(imaxD) Maximum inundation depth
!
! Hout(idnet) Erosion or deposition
!
! Hout(idoff) Dmix erodibility profile offset
!
! Hout(idslp) Dmix or erodibility slope
!
! Hout(idtim) Erodibility profile restore time
!
! Hout(idbmx) Bed biodiffusivity maximum
!
! Hout(idbmm) Bed biodiffusivity minimum
!
! Hout(idbzs) Bed biodiffusivity
!
! Hout(idbzm) Bed biodiffusivity
!
! Hout(idbzp) Bed biodiffusivity
!
! Hout(idprp) Cohesive behavior
!
! Logical switches (TRUE/FALSE) to activate writing of bed layer parameters
! into output QUICKSAVE NetCDF file:
!
Expand Down Expand Up @@ -1165,3 +1356,79 @@ Dout(MTvdif) == T ! mud_01_vdiff, ... vertical diffusion
! Dout(MTsdif) Horizontal S-diffusion
! Dout(MTvdif) Vertical diffusion
!
!------------------------------------------------------------------------------
! Mixed Bed parameters- Transition threshold for cohesive mix
! and non-cohesive behaviors, [1:Ngrids] values expected.
!------------------------------------------------------------------------------
!
! TRANSC Cohesive transition- Under that value of total mud fraction
! entire bed behaves as a non-cohesive bed
!
! TRANSN Cohesive transition- Over that value of total mud fraction
! entire bed behaves as a cohesive bed
!
!------------------------------------------------------------------------------
! Cohesive/Mixed bed critical shear
! Bed critical shear stress values if cohesive or mixed Bed is active
! These values are applied to the entire bed, [1:Ngrids] values expected.
!------------------------------------------------------------------------------
!
! MUD_TAUCR_MIN Minimum shear for erosion
!
! MUD_TAUCR_MAX Maximum shear for erosion
!
! MUD_TAUCR_SLOPE Tau_crit profile slope
!
! MUD_TAUCR_OFF Tau_crit profile offset
!
! MUD_TAUCR_TIME Tau_crit consolidation rate
!
!------------------------------------------------------------------------------
! Flocculation Sediment Parameters.
!------------------------------------------------------------------------------
!
! L_ADS Boolean set to .true. if differential settling aggregation
!
! L_ASH Boolean set to .true. if shear aggregation
!
! L_COLLFRAG Boolean set to .true. if collision-induced fragmentation enable
!
! F_DP0 Primary particle size (m), typically 4e-6 m
!
! F_NF Floc fractal dimension, typically ranging from 1.6 to 2.6
!
! F_DMAX Maximum diameter (m)
!
! F_NB_FRAG Number of fragments by shear erosion. If binary/ternary : 2.
!
! F_ALPHA Flocculation efficiency, ranging from 0. to 1.
!
! F_BETA Shear fragmentation rate
!
! F_ATER For ternary breakup, use 0.5, for binary : 0. (a boolean could be better)
!
! F_ERO_FAC Fraction of the shear fragmentation term transfered to shear erosion.
! Ranging from 0. (no erosion) to 1. (all erosion)
!
! F_ERO_NBFRAG Number of fragments induced by shear erosion.
!
! F_ERO_IV Fragment size class (could be changed to a particle
! size or a particle distribution (INTEGER)
!
! F_COLLFRAGPARAM Fragmentation rate for collision-induced breakup
!
! F_CLIM Min concentration below which flocculation processes are not calculated
!
! L_TESTCASE If .TRUE. sets G(t) to values from Verney et al., 2011 lab experiment
!
!------------------------------------------------------------------------------
! Flocculation Decomposition in Bed Sediment Parameters
! Only #ifdef DEFLOC
!------------------------------------------------------------------------------
!
! MUD_FRAC_EQ Equilibrium fractional class distribution (they should add up to 1).
! There is no check for that, [1:NCS,1:Ngrids] values expected.
!
! MUD_T_DFLOC Time scale of flocculation decomposition in bed
! [1:Ngrids] values expected.

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