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SEDIMENT TRANSPORT MODULE USER GUIDE

1. BCOND_ TRA indicate that the boundary data for tracer 3 and tracer 4 are specified in data files The location of this data file bnd_ocean ts is indicated by the 3 highlighted line BOUNDARY 0 NAMI north BOUNDARYO TYP ul BOUNDARYO BCOND_ NOR CUSTOM BOUNDARYO CUSTOM ul uv_to_ul home mgdata dent c2_mgs run6 coarse uv_n nc BOUNDARYO BCOND_ TAN CLAMPD Gl Gl 21 BOUNDARYO CUSTOM u2 uv to u2 home mgdata dent c2 mgs run6 coarse uv_t nc BOUNDARYO BCOND ELE NOTHIN BOUNDARYO BCOND TRA ALL NOGRAD BOUNDARYO BCOND TRAQ FILEIN BOUNDARYO BCOND TRA1 FILEIN BOUNDARYO BCOND TRA2 NOGRAD BOUNDARYO BCOND_TRA3 FILEIN UPSTRM BOUNDARYO BCOND_TRA4 FILEIN UPSTRM BOUNDARYO BCOND VZ NOGRAD BOUNDARYO BCOND_ KZ NOGRAD BOUNDARYO DATA home mgproja dent st_meco ctd_stationl ne home mgproja sedi_mgf huon 3d bnd_ocean ts BOUNDARYO INVERSE BAROMETER FALSE BOUNDARYO POINTS 2 53 12 53 13 An example of the open sea boundary data file bnd_ocean ts is given below COLUMNS 3 COLUMN1 name Time COLUMN1 long name Time COLUMN1 units days since 2001 06 01 00 00 00 10 COLUMN1 missing value 999 COLUMN1 f1i11 value 0 0 COLUMN2 name Sand COLUMN2 long name Sand COLUMN2 units kg s l COLUMN2 missing value 999 COLUMN2 fill value 35 COLUMN3 name Silt COLUMN3 long name Silt COLUMN3 units kg s l COLUMN3 missing value 999 COLUMN
2. 0 01 TRACER fill_value_sed 600 Spatially varying fields of the initial sediment deposits can be specified through the interpolation of observations Observations must be stored in an ASCII file for instance init_deposit txt file with the first and second columns representing longitude and latitude of the sampling site respectively and the rest columns showing observed concentrations TRACER data_sed init_deposit txt TRACER interp_type linear The data file format is the same as that used for boundary data see section 8 1 The interpolation type is given by the key TRACER interp_type Constraints If the concentration units for sediments and dissolved tracers differ from kg m 3 then the model assumes that the concentration is given in mg m 3 except for sediment attached pollutants Concentration of the sediment attached tracers must be given as some activity per unit volume Activity m 3 rather than per unit mass It is recommended to keep initial concentration of all sediment fractions within the reasonable bounds so that to insure that initial porosity of sediments exceeds 0 but is lower than 1 Benthic layer of MECOSED must always include some sediment particles In applications with a high energy environment it is recommended to include in MECOSED a sediment class 16 representing heavy particles eg gravel fraction that would form a baseline un erodible substrate underlying fine sediments EMS typically does
3. K J Parslow M Herzfeld P Sakov J Andrewartha amp U Rosebrock 2005 Biogeochemical Modelling of the D Entrecasteaux Channel and Huon Estuary Technical Report CSIRO Marine amp Atmospheric Research 113 p 24
4. not resolve bed load transport layer Z coordinate grids produce step like representation of bathymetry Hence the developed 3 d sediment module is particularly suitable for simulating transport of only fine sediments If the sediment flocculation is on the salinity field must be specified in both benthic and pelagic layers eg TRACER type WATER SEDIMENT 7 3 Settling velocity Settling velocity of the particulate tracer is given by TRACER4 svel 0 001 Default is 0 This parameter specifies settling velocity of the individual sediment grains When sediments flocculate the settling velocity of the flocs is estimated through the flocculation model and the largest of the two the settling velocity of the individual grains and the settling velocity of the flocs is used to settle sediment particles 7 4 Cohesive sediment MECOSED employs two different formulations for sediment resuspension on cohesive and non cohesive sediment bed A particular sediment resuspension regime could be specified by assigning zero non cohesive or unit cohesive value to cohesive flag TRACER4 cohesive 1 Default value is cohesive 7 5 Resuspension deposition Resuspension and deposuition of any particular tracer is controlled by resuspend and deposit flags TRACER4 resuspend 1 TRACER4 deposit 1 Default is resuspend and deposit If both resuspend and deposit flags are off then there is neither
5. on observations in the Brisbane estuary and Moreton Bay see 10 formula 5 4 in the MECOSED science manual The parameter FLOC_PRM1 in this case represents settling velocity of the individual sediment grains in m s 1 All flocculation modes involve scaling of the settling velocity by the water salinity so that there is no flocculation when the water salinity is less than 0 1 ppm The flocculation of a particular sediment fraction is controlled by additional tracer specific parameter TRACER floc which is described in section 7 8 Constraints FLOC1 and FLOC4 options require salinity to be included in the list of the hydrodynamic model variables 6 9 Consolidation Consolidation of sediments is activated by CONSOLIDATE 1 If this indicator is on then the model requires also data on final minimal porosity of sediments FINPOR_SED non dimensional and typical time scale of the sediment bed consolidation CONSOLRATE in days FINPOR_SED 0 3 CONSOLRATE 5 e 0 The default option is no consolidation CONSOLIDATE 0 Constraints We have never used consolidation option in our case studies An option CONSOLIDATE 0 is recommended 6 10 Biodiffusion Biological activity of the benthic layers is given by the parameter BIODENS 100 0 which prescribes the number of standard animals per square metre of sediments Maximum depth for the biological activity in meters is specified as MAXBIODEPTH 0 2 Diffusion coefficients for b
6. zero volume tracers so that any transient instabilities in biogeochemical model simulations do not blow away the sediment layer TRACER Particulate Dissolved partic 1 dissof 1 Volumetric Zero volume particles particles caicvol 1 calevol 0 Fig 7 1 MECOSED tracers Every MECOSED tracer must be specified as either particulate tracer TRACER4 partic 1 or dissolved tracer TRACER4 dissol 1 15 The volumetric tracer can be specified using the following string TRACER4 calcvol 1 Default value for calcvol is zero and the traces is considered as having zero volume of constituting particles If the flag calcvol is on volumetric tracer then the tracer is not allowed to attach to any sediment fraction adsorb 0 7 2 Initial concentrations Initial concentration of each sediment fraction is specified individually for each tracer in a tracer description filed To indicate that a particular tracer is present in both water column and sediments a type indicator must be added to the tracer description list TRACER type WATER SEDIMENT Then the concentration units are specified by TRACER units kg m 3 This is followed by valid range of the concentrations in water and in sediments TRACER valid_range_wc 0 1000 TRACER valid_range_sed 0 3000 Finally the initial concentrations of the tracer in water and in sediments is specified by TRACER fill_value_we
7. 3 f1i1l1 value 35 lel3 0 0 0 01 lel13 0 0 0 01 9 FILE INVENTORY The sediment model file inventory is shown in table 9 1 MecoSed initialisation routine yd2sed c Data flow from EMS to mecosed Sed2hyd c Data flow from mecosed to EMS Bottom boundary layer model Vertical transport in water column and sediment bed 22 8s Sediments h Include file for mecosed structures Table 9 1 MECOSED file inventory 23 REFERENCES Herzfeld M Waring J Parslow J Margvelashvili N Sakov P Andrewartha J 2008 SHOC Sparse Hydrodynamic Ocean Code Science manual CSIRO internal document 121 p Herzfeld M Waring J R 2008 SHOC Sparse Hydrodynamic Ocean Code User s manual CSIRO internal document 128 p Herzfeld M 2006 An alternative coordinate system for solving finite difference ocean models Ocean Modelling 14 174 196 Margvelashvili N 2003 MECOSED Model for Estuarine and Coastal Sediment Transport Scientific Manual CMAR internal document 46 p Margvelashvili N 2009 Stretched Eulerian coordinate model of coastal sediment transport Computers and Geosciences 35 1167 1176 Murray A G Parslow J S 1997 Port Phillip Bay Integrated model Final Report Port Phillip Bay Environment Study Technical Report No 44 Melbourne Walker S J Sherwood C R 1997 A transport model of Port Phillip Bay CSIRO Division of Oceanography Technical Report 39 59 p Wild Allen
8. CER4 adsorbkd 20 And the adsorption rate constant in days is given by TRACER4 adsorbrate 1 MECOSED employs first order kinetic reaction to simulate sorption desorption reactions between particulate and dissolved fractions of the sediment reactive tracer equations 7 3 7 4 MECOSED science manual Note that concentrations of the sediment reactive tracers are given as an activity per unit volume rather then per unit mass 7 11 Example for a sediment reactive tracer This section gives an example of the tracer specifications for the sediment reactive tracer TRACER6 name ZNclay TRACER6 long name Zn on clay TRACER6 type WATER SEDIMENT 19 RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC R6 units g m 3 R6 valid_range we 0 le 35 R6 valid_range sed 0 le 35 R6 diagn 0 R6 fill value we 0 0 R6 fill value sed 0 0 R6 dissol 0 R6 partic 1 R6 advect 1 R6 diffuse 1 R6 b dens 2 65e 03 R6 i conc 1 2e 03 R6 decay 0 R6 adsorb 1 R6 carriername Clay R6 dissolvedname ZincDis R6 adsorbkd 20 R6 adsorbrate 1 Vee Pa ce A ge ete A oo a oe A E G A A G A A A A A A A a a A a 7 12 Diagnostic files A number of 3d and 2d diagnostic variables specific to sediment processes can be added to the stream of the model output by specifying extra diagnostic tracers in the parameter file The diagnostic tracer is identified by the key TRACER diagn 1 The 3d diag
9. CSS1 3 options have never been tested in real world applications An option CSSO or CSS4 is recommended 6 7 Critical deposition stresses Critical shear stress of cohesive sediment deposition in N m is given by CSS_DEP 0 3 In a default mode cohesive sediments are always allowed to settle on the sediment bed e g CSS_DEP inf 6 8 Flocculation A number of options is currently available in MECOSED to calculate cohesive sediment flocculation FLOCO FLOC1 FLOC4 A particular option is specified by the key FLOC_MODE FLOC_MODE FLOCO The simplest FLOCO mode assumes that sediments do not flocculate FLOC1 mode predicts mean floc velocities as a function of cohesive sediment concentration FLOC2 and FLOC3 modes are under construction and currently are not available FLOC4 mode is based on empirical formulation for settling velocity of cohesive sediment derived from observations in the Brisbane estuary The default mode is FLOCO i e sediments do not flocculate If the flocculation mode FLOC1 is on FLOC_MODE FLOC1 two additional parameters must be specified FLOC_PRM1 1 FLOC_PRM2 2 Here FLOC_PRM1 is a scaling parameter and FLOC_PRM2 is a power of the exponential term in a power low approximation of the sediment flocculation see formula 5 2 in the MECOSED science manual An option FLOC_MODE FLOC4 FLOC_PRM1 2e 4 makes the model to estimate settling velocity of the sediment flocs using an empirical relationship based
10. EMS ENVIRONMENTAL MODELLING SUITE SEDIMENT TRANSPORT MODULE USER GUIDE i CSIRO MARINE RESEARCH Margvelashvili N Andrewartha J Herzfeld M Parslow J Sakov P Rosebrock U Version 1 0 CSIRO Marine and Atmospheric Research GPO Box 1538 Hobart 7001 31 03 2003 Last updated March 2011 1 INTRODUCTION eee eeeeeee eee teeeeeeeeeseeeeeeeeeeseeeeeeeseseeeeeeess 3 2 EMS STRUCTURE EE 3 3 SEDIMENT BREET EEEE ii 4 4 INSTALLATION AND OPERATION 6 5 THE MODEL SE RTE 6 6 GENERAL MECOSED PARAMETERSG 6 6 1 Activate sediment module AAA 6 6 2 len e ed WEE 6 6 3 leen 7 6 4 UE a a a E Ee 7 6 5 Bottom ICON eege ge 8 6 6 Critical erosion Stress un 9 6 7 Critical deposition stresses a nntcnancnannnaiucanananunads 10 6 87 PIOCCUIANON E 10 E SR ee Ee le Ee DE 11 6 10 Biodiffusion EE 11 6 11 Initialisation diagnostic eneen eege 12 6 12 Maximum thickness of Sediment ceececeeeeeeeeeeeeeeenneeeeeeeees 12 6 138 EECHER ee ee EE 12 6 14 LEE 13 7 TRACER SPECIFIC PARAMETERS 0aiiiaeennneeeennneeererrrnerrrnneerrrrneee 14 Tel MECGOSED EE 15 7 2 Initial concentrations ergeet egg ebdette gie etc deg 16 7 3 Settling velocity ote sali ial aot atl eRe teh es ot Cea 17 7 4 Cohesive SCCUM CIWS EE 17 7 5 HRESUSPENSIOM GSPOS ION ee ee 17 7 6 Sediment grain density EE 17 7 7 Concentration of fresh sediment depnosits enesenn 18 7 8 Flocculation EN bedreet eege 18 7 9 Example of the trace
11. LOCCULATION Modes FLOCO FLOC1 Default FLOCO no flocculation FLOC_MODE FLOC1 PRM1 300 PRM2 3 CONSOLIDATION CONSOLIDATE 0 FINPOR SED 0 4 CONSOLRATE 10 e 0 13 Bottom Boundary Layer model BBL NONLINEAR 1 Bottom Skin roughness m ZO SKIN 0 00003 RIPPLES Default 0 PHYSRIPH 0 03 PHYSRIPL 0 6 BIORIPH 0 005 BIORIPL 0 2 Maximum depth for biological activity m MAXBIODEPTH 0 2 Functional form for bioirrigarion and bioturbation activity as a function of depth Currently can be one of constant linear parabolic gaussian Only the first letter of this parameter is significant BIOSEDPROFILE parabolic Biological activity standard animals per square metre BIODENS 10 0 Diffusion coefficient for bio irrigation of sediments This value is scaled by the amount of biological activity present and also decreases with depth in the sediment according to some fixed profile The value here is the value which would apply at zero depth in the sediment Units are m2 s 1 per animal per m2 BI_DISSOL_KZ 1 0e 9 BI_DISSOL KZ I 1 0e 9 Diffusion coefficient for bio turbation of sediments This value is scaled by the amount of biological activity present and also decreases with depth in the sediment according to some fixed profile The value here is the value which would apply at zero depth in the sediment Units are m2 s 1 per
12. SO The simplest CSSO mode assumes constant critical shear stress The value of this constant can be specified as CSS_ER 0 25 The default value of the critical erosion stress is 0 2 Nim In CSS1 CSS2 CSS3 modes critical shear stress is calculated as a function of the sediment bed compactness using empirical formulations 5 5 5 6 and 5 7 respectively see MECOSED scientific manual Note that CSS1 3 options typically imply that the sediment porosity varies with time due to consolidation processes An option CSS4 specifies the critical shear stress of erosion that varies with the sediment depth The shear stress values must be specified using the key CSS_ER An example is given below CSS_ER 4 0 2 0 3 0 5 0 7 The corresponding depth levels in m are given by the key CSS_ER_DEPTH CSS_ER_DEPTH 4 0 0 002 0 1 0 2 In this example the critical shear stress of erosion is 0 2 N m 2 for sediments allocated below 0 and above 0 002 m depth The critical shear stress is 0 3 for sediments below 0 002 and above 0 1 m depth and so on Note than the number following CSS_ER and CSS_ER_DEPTH keys now specifies the number of the sediment layers with a distinct critical shear stress value Critical erosion stress for non cohesive sediments is calculated as a quarter of the sediment settling velocity The reference height for the reference velocity is specified at seven Nikuradze roughness heights 7 30 ZO_SKIN Constraints
13. animal per m2 BT_PARTIC KZ 1 0e 10 BT_PARTIC KZ I 1 0e 12 HEHEHE EE EEE HEE EE EEE HEE EE EEE EH EEE EE EEE HEE HE HE EEEE HE EH EE FH HEHEH Activate Waves DO WAVES YES WAVES_DT 1 hour WAVE VARS YES WAVES BOT STRESS VERT MIX 7 TRACER SPECIFIC PARAMETERS 14 Apart from the general model parameters each tracer of EMS has its own set of the tracer specific parameters A general guideline for tracer specification in EMS can be found in Herzfeld and Waring 2008 This chapter describes tracer parameters specific to MECOSED 7 1 MECOSED tracers MECOSED calculates transport of two basic types of tracers particulate and dissolved fig 7 1 Particulate tracers represent either volumetric particles or zero volume tracers Volumetric particles settle due to gravity force and change porosity in water column and in sediment bed The concentration of volumetric particles is limited by free volume available in water column or in sediment bed Zero volume particles are assumed to occupy zero volume in space A typical example of zero volume tracer is a sediment attached tracer pollutant As any particulate tracer the sediment attached tracer undergoes settling and resuspension deposition in water column and bioturbation consolidation in sediments but unlike to sediments it does not change porosity of the sediment layer It is recommended to treat also biogeochemical reaction variables as
14. e tss TRACER7 type WATER SEDIMENT TRACER7 units kg m 3 TRACER7 valid range wc 0 let 35 TRACER7 valid_ range sed 0 le 35 TRACER7 fill value we 0 0 TRACER7 fill value_sed 0 0 TRACER7 advect 0 TRACER7 diffuse 0 TRACER7 diagn 1 TRACER8 name ustrcw_skin TRACER8 long name ustrcw_skin TRACER8 type BENTHIC TRACER8 units m s l TRACER8 valid range wc 0 let 35 TRACER8 valid_ range sed 0 le 35 TRACER8 fill value we 0 0 TRACER8 fill value_sed 0 0 TRACER8 advect 0 TRACER8 diffuse 0 TRACER8 diagn 1 An extra diagnostics can be inferred from the model output through the development of customised processing scripts interrogating netcdf files produced by the model tracers in sediments in the output files are identified by suffix sed added to the tracer name 8 BOUNDARY CONDITIONS MECOSED assumes no sediment fluxes through the water surface at the bottom of the benthic layer and at the lateral land boundaries To specify sediment concentrations at the open sea lateral boundaries data file must be provided and referenced to in the list of the boundary condition specifications For more details on open boundary specification for tracers please refer to SHOC manual Herzfeld and Waring 2008 8 1 Example of a boundary condition This section includes an example of the boundary conditions for hydrodynamic and sediment variables at the open sea boundary Features relevant to MECOSED are highlighted in bold The parameters BCOND TRA3 and
15. es only horizontal diffusion and updates water velocities and 3 d advection of tracers in water column 3 D hydrodynamics i Pelagic layer NS 0 D biogeochemical reactions econ Es Interface routines me z Benthic layer 1 D sediment model Fig 2 1 Schematic structure of EMS 3 SEDIMENT PROCESSES Sediment module of EMS is based on a 1 d vertical model of coastal and estuarine sediment transport MECOSED Margvelashvili 2008 The model was intended as an improvement to the transport simulation capabilities of a 3 d coastal hydrodynamic water quality model MECO developed at CSIRO Division of Marine Research Walker amp Sherwood 1997 MECOSED simulates vertical transport of particulate dissolved and sediment bound tracers in water column and in sediment bed Fig 3 1 Resuspension Deposition Bioturbation ko Consolidation Bioturbation SEDIMENT BED Fig 3 1 Key sediment processes in MECOSED Sediment transport The sediment transport module of MECOSED solves advection diffusion equations for the mass conservation of suspended and bottom sediments taking into account bottom exchanges through the resuspension and deposition Suspended particles undergo turbulent mixing and settling due to gravity force Displacement of particles in sediment bed is driven by bioturbation and consolidation The bioturbation is represented by local diffusion Empirical formulas are used to parameterise sediment c
16. io turbation BT_PARTIC_KZ in m2 s and bio irrigation BI_DISSOL_KZ in m2 s of sediments are scaled by the amount of biological activity present m2 s per animal m2 and also decrease with depth in sediment bed 11 according to some fixed profile Diffusion coefficients in the sediment bed are specified as follows BI_DISSOL_KZ 1 0e 10 BT_PARTIC_KZ 1 0e 10 Diffusion coefficients across sediment water interface are given by BI_DISSOL_KZ I 1 0e 12 BT_PARTIC_KZ I 1 0e 12 Functional form of the scaling profile for bioirrigarion and bioturbation activity as a function of depth is prescribed by one of the following strings constant linear parabolic gaussian BIOSEDPROFILE _ parabolic 6 11 Initialisation diagnostic key The key VERBOSE_SED 1 downloads sedlog txt file containing sediment initialisation diagnostics The default option is no diagnostics 6 12 Maximum thickness of sediments The maximum thickness of sediments can be specified by MAX_THICK_SED 2 There is no feedback in EMS from the sediment processes to the hydrodynamic model so that any changes in the sediment thickness do not translate into the corresponding changes of the water depth An implicit assumption underlying this approximation is that changes in the sediment thickness are small compared to the water depth This assumption can be violated particularly during long term simulations To avoid unrealistic situations where the sediment thic
17. kness exceeds the water depth we introduce the parameter MAX_THICK_SED Sediment particles are not allowed to settle on the seabed in areas where the sediment thickness has reached the maximum predefined value 6 13 Wave input Wave input is represented by the amplitude of the near bottom wave orbital velocities m s 1 wave period s and wave direction degrees The direction angle is given as 12 degrees Cartesian referenced to the West East direction counter clockwise The wave data are updated at time intervals given by WAVE_VARS_INPUT_DT WAVE_VARS_INPUT_DT 1 hour The wave data source file is specified through the key WAVE_VARS WAVE_VARS waves nc The default option is no waves 6 14 Example Examp le of EMS parameter file section that specifies general parameters of the sediment model is given below it it FE aE aE TE AE AE AE FE aE aE AE AE E aE aE a ae a aaa aaa aaa aaa FEF Sediments VERBOSE SED 1 Sediment layers thickness NSEDLAYERS 3 0 005 0 015 0 1 9 Activate sediment process Default 0 DO SEDIMENTS 1 CEL CRITICAL STRESSES tical shear stress of cohesive bed erosion N m 2 Modes CSS0 CSS1 CSS2 CSS3 Default CSS0 css_er 0 2 CSS_ER_MODE CSSO CSS_ER 0 05 Critical shear stress of cohesive sediment deposition N m 2 css FLOC FLOC Default CSS_DEP inf DEP 0 3 F
18. nd application manual for EMS hydrodynamics can be found in Herzfeld et al 2002 Herzfeld and Waring 2008 2 EMS STRUCTURE A general structure of EMS is illustrated in fig 2 1 A 3 d hydrodynamic model is coupled to 1 d sediment transport model via a number of interface routines During every simulation time step these routines interrogate EMS inquiring for hydrodynamic variables plus benthic data to initialise the 1 d sediment model and to update forcing data The sediment model then solves 1 d vertical advection diffusion equations for every column of the numerical grid Within every grid column the model solves equations for turbulent mixing in water column and bioturbation in sediments and simulates sediment settling erosion deposition and consolidation of sediments plus vertical transport of the dissolved and sediment attached tracers Updated profiles are stored in 3 d arrays of EMS representing benthic and pelagic layers One way to think of the sediment module is that of a sewing machine coupling benthic and pelagic layers together in a single integrated system Once the hydrodynamic and sediment transport steps are complete EMS proceeds with the biogeochemical model updating concentrations of biogeochemical variables in benthic and pelagic cells When the sediment model is on vertical diffusion and settling in a coupled benthic pelagic system is handled by the sediment model routines The hydrodynamic model in this case simulat
19. nostic variables specific to sediments are tss total suspended sediment concentration in water and in sediments svel floc settling velocity of the sediment flocs in water column and velocity of consolidating particles in sediments porosity porosity in water and porosity in sediments cohsed cohesive sediment fraction given as a mass percentage of cohesive sediments relative to the total mass of either suspended or bottom sediments A particular 3 d variable is identified by its name for example tss Note that the sediment settling velocity is estimated in the model as the largest of the settling velocity of individual grains and the settling velocity of flocs so that if there are no flocs present svel_floc 0 sediments still settle due to gravity force acting on the individual sediment grains Porosity in water column is always assumed to be equal to 1 All 3d diagnostic variables must be specified as of WATER SEDIMENT type 2d diagnostic variables include ustrew_ skin bottom shear stress velocity m s 1 depth sed sediment thickness m dzactive thickness of the top active layer of sediments m hripple ripple height m Tripple ripple length m All 2d diagnostic variables must be specified as of BENTHIC type 20 An example bellow illustrates specification of the 3d and 2d diagnostic variables TRACER7 name tss TRACER7 long nam
20. ohesive 1 R4 calcvol 1 R4 floc 1 R4 resuspend 1 R4 deposit 1 HHA HAH HAH RHAH AHAHAHAHA RA AA A A A a a H A E E A E A A les A A A A A A A A o A ae 18 7 10 Sorption desorption Any particulate partic 1 zero volume calcvol 0 tracer in MECOSED can be attached to any other particulate partic 1 volumetric calcvol 1 tracer by specifying adsorb flag 1 if adsorbed 0 if not adsorbed TRACER4 adsorb 1 and indicating the name of the sediment class carrying this particular adsorbed tracer TRACER4 carriername Clay The above strings indicate that the tracers N4 is attached adsorbed to the tracer called Clay The tracer Clay must represent some particulate volumetric tracer To simulate sorption desorption exchange between particulate and dissolved fractions of the sediment reactive tracer the user ought to indicate the corresponding dissolved fraction and specify sorption parameters The dissolved fraction of the sediment reactive tracer is identified by the parameter dissolvedname indicating the name of the dissolved tracer TRACER4 dissolvedname ZincDis The above strings indicate that the sediment reactive tracer N4 attached to the sediment tracer Clay has the dissolved counterpart ZincDis An equilibrium distribution constant for the desorbed and adsorbed fractions of the sediment reactive tracer is specified by the parameter adsorbkd in m3 kg TRA
21. onsolidation Cohesive sediments are either eroded or deposited depending on bottom shear stress and critical shear stress of the sediment resuspension and deposition A concept of equilibrium sediment distribution is utilized to parameterize erosion deposition of non cohesive particles Dissolved transport The module of the dissolved transport solves advection diffusion equations of the mass conservation of tracers dissolved in water column and in sediment bed Dissolved tracers undergo turbulent mixing in water column and diffusion in sediments Transport in water is coupled with benthic processes through the diffusion across water and sediments and through the water entrainment expulsion during resuspension deposition or consolidation events Sediment bound tracers The sediment bound tracer is analogous to a hydrophobic contaminant e g organic chemical heavy metal or radionuclide that adsorb to fine grained sediment particles The model solves advection diffusion equations for the mass conservation of the sediment bound tracers in water column and in sediment bed Sorption exchange between solid and liquid phases is calculated using the concept of the equilibrium distribution To simulate degradable pollutants the model also incorporates first order decay reaction Bottom boundary layer Bottom friction under combined wave current flow is calculated from bottom boundary layer model On cohesive sediment bed constant physical ro
22. r specific D ramelerg 18 7 10 Sorption desorption EE 19 7 11 Example for a sediment reactive racer 19 142 DIGQMOSIC INES EE 20 8 BOUNDARY CONDITIONS cece cere eee eeeceeeeeeeeeeeeeeeeeeeeaaees 21 8 1 Example of a boundary Condition ccccceeeeeeeeeeeeeeeeeeeeeneeeeeeees 21 9 FILE INVENTORY ee 22 PEPER ENCES EE EE EE 24 1 INTRODUCTION EMS is a general purpose modelling package that simulates three dimensional flow transport and biogeochemical reactions in surface water The model has been developed at CSIRO Marine and Atmospheric Division and tested and refined through a number of applications around the Australian coast EMS comprises hydrodynamic sediment transport and biogeochemical reaction modules Hydrodynamics of EMS is based on a 3 d nonlinear nonstationary hydrostatic approximation model SHOC Herzfeld 2008 The sediment model solves mass balance equations for sediment concentrations in a coupled benthic and pelagic layers taking into account bottom exchanges Margvelashvili 2008 Hydrodynamic and sediment models provide physical settings to biogeochemical model which updates concentration of biogeochemical variables in water column and in sediments Murrey and Parslow 1997 Wild Allen et al 2005 This report is designed to assist the user in operating sediment module of EMS Theoretical and computational aspects of the sediment transport formulation are given in Margvelashvili 2003 Scientific background a
23. resuspension nor deposition of particles across water and sediments Note that unless diffusion fluxes across water and sediments is switched off see section on 6 10 on Biodiffusion benthic and pelagic layers in this case are not fully decoupled 7 6 Sediment grain density 17 Density of sediment grains kg m3 is specified by TRACER4 b_dense 2 65e 03 The sediment grain density along with the mass concentration and the grid cell volume is used to calculate the seabed porosity 7 7 Concentration of fresh sediment deposits Concentration of fresh sediment deposits kg m3 is given by TRACER4 1_conc 1 2e 03 This parameter is used to estimate the volume of water trapped in sediments during the deposition event 7 8 Flocculation key Flocculation of individual tracers can be switched on or off with the following flag TRACER4 floc 1 Default is 0 no flocculation 7 9 Example of the tracer specific parameters This section shows an example of the tracer specifications for sediment particles RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC RAC R4 name Silt R4 long name Silt fraction R4 type WATER SEDIMENT R4 units kg m 3 R4 valid_range we 0 le 35 R4 valid_ range sed 0 le 35 R4 diagn 0 R4 fill value_we 0 0 R4 fill value_sed 600 0 R4 dissol 0 R4 partic 1 R4 advect 1 R4 diffuse 1 R4 decay 0 R4 b dens 2 65e 03 R4 i conc 1 2e 03 R4 svel 0 2e 3 R4 c
24. studies and remains largely untested We recommend to use CALC_RIPPLES 0 and have the ripple dimension prescribed as the model input data 6 5 Bottom friction Two options are available in MECOSED to estimate bottom friction One is based on nonlinear Grant and Madsen model Madsen 1994 which is activated by BBL_NONLINEAR 1 The model requires wave current data and bottom roughness as an input The bottom roughness is computed as a sum of the skin roughness and the roughness due to ripples see section 6 4 The wave current data must be provided from the hydrodynamic module An alternative option for calculating bottom friction is based on a linear bottom boundary model activated by BBL_NONLINEAR 0 With this option the bottom friction is approximated as a sum of the current friction over the ripples and the wave friction over the sediments grains There is no interaction between waves and currents The bedform roughness is used to estimate friction of currents over the ripples and the skin roughness is used to estimate wave friction over the individual sediment grains The default option for bottom boundary layer model is Grant and Madsen model BBL_NONLINEAR 1 6 6 Critical erosion stress Five options CSSO CSS1 CSS2 CSS3 CSS4 are available in MECOSED to estimate critical shear stress on a cohesive sediment bed A particular option can be specified using the key CSS_ER_MODE An example is given below Cas ER MODE CS
25. the ripple height and length in meters on sandy sediments respectively The development of such ripples is associated with the physical processes waves and currents The BIORIPH and BIORIPL parameters provide dimension of ripples on a cohesive seabed where ripples development is typically associated with the biological reworking of the benthic layer PHYSRIPH 0 02 PHYSRIPL 0 6 BIORIPH 0 005 BIORIPL 0 2 Unless the ripple dimension is simulated the model takes the largest out of the PHYSRIPH and the BIORIPH as a representative ripple height and the largest out of the PHYSRIPL and the BIRIPL as a representative ripple length Once the ripple dimension is specified MECOSED proceeds with estimating bottom roughness due to ripples according to Grant and Madsen 1982 formula In a wave dominated environment simulation of the ripple dimension can be activated by CALC_RIPPLES 1 In this case the model estimates the ripple height and length based on Wakramanayake 1993 model Ripples are estimated only over sandy sediments On a cohesive bed ripple dimension is specified as an input data from the parameter file see description of BIORIPH and BIORIPL parameters above The default option for estimating ripples is do not estimate the ripple dimension CALC_RIPPLES 0 In this case the ripple dimension must be specified in a parameter file Constraints An option for ripple calculation CALC RIPPLES 1 has never been used in our case
26. ts The developed model is particularly suitable for representing fine sediment dynamics 4 INSTALLATION AND OPERATION All installation and operation procedures required by the sediment module are covered by EMS installation requirements and can be found in SHOC user manual Herzfeld and Waring 2008 5 THE MODEL SET UP All input data for the sediment model are stored in a single ASCII parameter file This file contains comments key words and values and its contents completely describe a particular model implementation and run parameters Data structure and parameter file format are exactly the same as used by the hydrodynamic module Herzfeld and Waring 2008 In a typical application the development of the sediment model follows the development of the hydrodynamic model Throughout this document we assume that the hydrodynamic step is complete and parameter file of the hydrodynamic model is available otherwise refer to SHOC manual describing the hydrodynamic model set up Herzfeld and Waring 2008 To set up the sediment model the hydrodynamic model parameter file must be augmented with the sediment variables The sediment data and parameters can be broadly classified into initialisation data boundary data parameters specific to a particular sediment tracer and general sediment parameters Detailed description of this data is given in the next chapter The output variables from the sediment module are handled by EMS infrastruct
27. ughness associated with biogenic bed forms is specified On non cohesive sediment bed the total physical roughness is assumed to be composed of two components one due to skin friction over the sediment grains and another due to form drag over the ripples Ripples in a wave dominated environment are either calculated or specified as the model input data Under combined waves and currents and in a current dominated flow the bed forms must be specified as the model input data Numerical solution The numerical grid for sediment variables in the water column coincides with the numerical grid of the hydrodynamic model Within the bottom sediments horizontal resolution of the model follows the resolution in water column In vertical direction the model utilises stretched sediment thickness adapted grid which allows for high vertical resolution of the top sediments throughout the simulation The sediment model can run in a mode fully coupled to the hydrodynamic model and in a transport mode when the sediment transport is simulated off line using pre calculated velocities and diffusion coefficients The model benefits from high order numerical schemes developed in EMS Curvilinear grids provide refined resolution in areas with high spatial gradients The model capabilities also involve multiply nesting of the modelling domains nested numerical grids which gives a very high resolution in areas of a particular interest at a relatively low computational cos
28. ure routines 6 GENERAL MECOSED PARAMETERS 6 1 Activate sediment module The sediment module of EMS is activated by adding the following command to EMS parameter file DO_SEDIMENTS 1 The default option is do not activate the sediment code DO_SEDIMENTS 0 6 2 Numerical grid The numerical grid for sediment variables in the water column coincides with the numerical grid of the hydrodynamic model Numerical grid in sediments is defined by specifying initial thickness of every sediment layer in meters starting from the top layer An example of the sediment grid data is given below NSEDLA YERS 4 0 01 0 03 0 07 0 14 Here NSEDLAYER parameter gives the number of sediment layers while the column underneath lists the thickness of each layer sequentially starting from the top layer The top layer of the numerical grid represents an active layer of sediments and its thickness remains constant throughout the simulation The thickness of the underlaying layers varies with time in response to sediment resuspension deposition and consolidation Constraints Numerical grid in sediments must include at least two sediment layers 6 3 Skin roughness Bottom skin roughness in meters associated with individual sediment grains is specified by ZO_SKIN 0 00001 The value of the skin roughness can be estimated as a median grain size Nikuradze roughness height divided by 30 6 4 Ripples Parameters PHYSRIPH PHYSRIPL prescribe

SEDIMENT TRANSPORT MODULE USER GUIDE

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