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Sparse Hydrodynamic Ocean Code V5199 User Manual

1. en to the e levels 20 08 2015 main print information on major general events info print information on minor general events warn non fatal warning information debug print high level debug information trace print low level debug information metric information on time spent in routines for development only Allows smoothing of various fields at initialisation Currently valid fields are CD Bottom roughness U1VH Horizontal viscosity in the el direction U2VH Horizontal viscosity in the e2 direction U1LKH Horizontal diffusivity in the el direction U1KH Horizontal diffusivity in the e2 direction The form of smoothing is SMOOTH_VARS lt name gt n where lt name gt is one of the names above and n is the number of smoothing passes e g SMOOTH_VARS CD 2 U2VH 1 will perform 2 smoothing passes on bottom drag and one pass on e2 horizontal viscosity Allows scaling of various fields at initialisation Valid fields are the same as for SMOOTH_VARS The form of scaling is SCALE_VARS lt name gt s where lt name gt is one of the names above and s is a scaling fraction e g SCALE_VARS CD 1 2 U2VH 0 9 will scale bottom drag by 1 2 and ei horizontal viscosity by 0 9 Records a sequence of runs in the file
2. Geographic rectangular grids Grid Creation Clear Read ASCII Files Read PRM File Xx lt ls 7 10 S Seege j qg RECT flat Grid POLAR sphere Grid CURVILINEAR Grid Draw Erase Points Draw Erase Grid Edit Grid Mask creation Draw Erase Mask Get Ascii Bty Data Get Nedf Bty Data Get Shoo Biy Data Draw Erase Bathy Aad MSL Edit Bathy Decimate Grid Create Clear Patch Draw Partitions Bathymetry loading options Bathy interpolation Edit Partitions Draw Erase Var Edit Variable Save AUTO File Fun SHOC auto Main Menu Quit Figure 14 3 1 PLUM grid generation menu Zoom in on the location the grid is to be constructed for using the icon at the top left of the Plan View screen Click on RECT sphere Grid to generate a spherical geographic rectangular grid Other options are a non geographic grid polar grid or orthogonal curvilinear grid Follow the instructions in the matlab window i e click on the grid centre left and right bottom corners A grid is then created e g Figure 14 3 2 The grid can be rotated relocated or scaled by clicking and dragging the blue dots The number of cells in the x direction is specified by entering x followed by the number of cells in the matlab w
3. Information regarding any initialization data for tracers temp and salt RACERO data profile nc RACER1 data profile nc The open boundaries are automatically generated by SHOC on the basis that any wet cell at the grid extremes or any cell in the grid interior adjacent to an OUTSIDE flagged cell are set to open boundary cells The grid is searched for these occurrences in the following order 1 u1 boundaries on the left hand i 0 or west grid extremities ul boundaries on the right hand i NCE1 or east grid extremities u2 boundaries on the bottom j 0 or south grid extremities u2 boundaries on the top j NCE2 or north grid extremities Interior u1 boundaries from i 0 to i NCI Interior u2 boundaries from j 0 to j NCI Do btoh BRD Ey Jl N If elevation boundary data is present in the parameter file the corresponding boundary is set to be elevation forced otherwise the boundary is set to be passive e g Set the first 3 boundaries found to be elevation forced BOUNDARYO DATA eta_west ts BOUNDARY1 DATA eta_south ts BOUNDARY2 DATA eta_north ts River inputs may be specified at a location using RIVER lt name gt lt lon gt lt lat gt lt flowfile gt Where is the number of the river in a consecutive list lt lon gt is the longitude of the river lt lat gt is the latitude of the river and lt flowfile gt is the name of a file containing the river flow The
4. The default is INTERIOR A better method of implementing the tracer OBC is to use the advection scheme nominated by the user e g VANLEER QUICKEST etc see Section 4 12 to solve the advection equation on the boundary Using these higher order schemes ensures diffusion and dispersion errors are minimised and since the flux form of the equation is solved the solution is conservative This method is denoted TRCONC and similar to the UPSTRM scheme an additional boundary condition must be used to specify the value in this cell see above The default is TRCONC FILEIN where the user must supply a data file containing boundary values If no data are available passive conditions may be specified using eg TRCONC NOGRAD Note that conservation is only achieved and reasonable values computed if the volume is conserved in the boundary cell This requires the velocity forced OBCs to be used Section 4 10 7 20 08 2015 Page 54 of 185 Version 1 00 SHOC User Manual If the total flux of tracer entering the domain at the open boundary is precisely known then this may be specified using the TRF LUX condition Here the prescribed flux is used directly on the boundary face in the solution of the advection equation and all other faces use the nominated advection scheme The specified flux is uniformly distributed over all boundary cells This approach may not be appropriate if the boundary cell becomes dominated by
5. Constituent Doodson Name Number long period LP 55 565 Sa 56 554 Ssa 57955 ERa 58 554 m 65 455 f 13 555 ERm 85 455 93a 934 599 diurnal 201 1253755 Q 135 655 O 145 555 1 1552655 P1 163 555 EN 164 556 K1 1654999 PHI1 167 555 li 175 455 O01 1857939 NU1 195 455 semi diurnal 22 1 227 655 2N2 2395 1355 MU2 2I PL 90 9 N2 245 655 NU2 247 455 2 259959 L2 265 455 T2 272 556 ER 21345995 K2 Se E 285 285 455 Each constituent in the constituent file must be represented by an amplitude in met re with _amp appended to the constituent name from the table above and a phase in degrees with _phase appended to the constituent name A time stamp must also exist in the file for compatibility with the time series file reading libraries although this time value may be anything since it is not used in computations however this does allow time dependent amplitudes and phases if required However the amplitudes and phases must be relative to the local time zone not GMT Note that the spatial extent of the tidal netCDF file must completely encompass the region defined by all cell centres of the model grid An example of a netCDF header for the M2 constituent is given below netcdf tide dimensions t UNLIMITED 1 currently i_centre 20 j_centre 20 variables double t t 20 08 2015 Page 58 of 185 Version 1 00 SHOC User Manual t units seconds since 2
6. RACER name mean_eta RACER long_name ean sea level RACER type WC2D RACER tracerstat mean eta RACER dt 12 hours RACER fill_value_we 0 RACER valid_rang le 10 1e10 RACER advect 0 RACER diffuse 0 TRACER diagn 0 The exposure tracerstat computes the time a nominated tracer s value is above or below a given threshold The units of the exposure are the nominated tracer s units multiplied by days To change the units use the scale_factor e g 7 days for units of lt tracer units gt lt weeks gt This tracerstat is effectively the integral of the tracer when its value is above below 20 08 2015 Page 163 of 185 Version 1 00 SHOC User Manual the threshold The optional dt provided is a time period that the tracer must be below above the threshold in order for the exposure time to be reset to zero The lt exposue_time gt is the name of a tracer in the list that is used to keep track of how many days in the interval dt the tracer is below above the threshold This tracer is required primarily for housekeeping purposes The start time is the time in model days that the exposure computation begins the START_TIME is used as the default if this is absent This allows the exposure tracerstat to operate with restarts The lt threshold gt can be either a number or a tracer in the tracer list The latter option allows a temporally and spatially varying threshold to be supplied The threshold is the value the n
7. Full tracer specification NTRACERS 2 RACERO name salt RACERO long_name Salinity RACERO units psu RACERO fill_ value 35 0 RACERO valid_range 0 40 RACER1 name temp RACER1 long_name Temperatur RACER1L units degrees C RACER1 fill_ value 20 0 RACER1 valid_range 0 40 es e Output files for a grid OutputFiles 1 fileO name out nc Output prefix fileO gridtype standard Standard dumpfile fFileO tstart 0 days Output start time FileO tinc 1 day Output interval fFileO tstop 44 days Output stop time fileO bytespervalu 4 2 shorts 4 floats 8 doubles fFileO vars ALL ALL variables Executing SHOC with the a option will result in the generation of an input netCDF file having a name of the INPUT_FILE name with nc appended and an input prm file template having a name of the INPUT_FILE name with prm appended which may be subsequently modified and executed using the p option see section 2 SHOC will then proceed to run using the automatically generated parameter specification 20 08 2015 Page 134 of 185 Version 1 00 SHOC User Manual 6 Restarts 6 1 Basic restarts The model may be restarted using any standard format netCDF output file see Section 4 31 6 containing ALL variables as the INPUT_FILE In this case the model START_TIME must correspond to one of the dump times in the ne
8. Tangential velocity CLAMPD Elevation FILEIN Tracer 0 salt FILEIN UPSTRM Tracer 1 temp FILEIN UPSTRM Boundary data file 0 home mgproja derwent st_meco east_ets nc Wind forcing from file home mgproja dent wind wind_grid nc Wind speed scale 1 00 Wind speed threshold 1 10 00 Wind speed threshold 2 26 00 Surface drag coefficient 1 0 00114 Surface drag coefficient 2 0 00218 Heat flux calculated Heat flux calculated bulk formulation Bulk scheme Kondo 1975 Reference height for air temperature humidity 4 00 Air temperature file Dome EE EE eg Wet bulb temperature fil home mgproja dent heat_ obs lairport 3hr ts Cloud cover file EE obs airport_3hr ts Atmospheric pressure file home mgproja dent press_m apo ss_grid2 nc No salt flux specified Number of output file dumps 6 Output file 0 home swirll testl1 test_all Output file 1 home swirll testl1 test_sur At every time step the simulation progress is written to file diag txt which is useful to estimate the time remaining for the simulation This file contains the following information Simulation start 0 0000 days 1990 01 01 00 00 00 Simulation stop 400 0000 days 1991 02 05 00 00 00 Simulation time 400 0000 days 1991 02 05 00 00 00 CPU time used this iteration 0 000 sec ean CPU time used iteration 0 000 sec CPU run time ratio 1236051 502146 Elapsed
9. These flags may be assigned to tracers explicitly in the parameter file e g TRACERI1 type WATER HYDRO PROGNOSTIC The above defines a tracer as a 3D hydrodynamic prognostic tracer For auto tracers these flags are set internally The type flag may be interrogated within the code for various purposes The list may also be expanded as required 4 9 8 Tracer filling and filtering It is common that coastlines and bathymetries do not align when interpolating tracers onto a grid from an external file Sometimes the limits of the grid that are to be interpolated onto lie outside the geographic bounds of the file from which the data is interpolated There exist data filling options to set no gradient conditions over cells whose geographic location is outside the 20 08 2015 Page 40 of 185 Version 1 00 SHOC User Manual bounds or over cells that are associated with land in the file from which data is interpolated This can be done for 2D including elevation 3D or sediment tracers and is invoked using TRACER_FILTER FILL Fill all tracers with a no gradient FILL2D Fill only 2D tracers with a no gradient FILL3D Fill only 3D tracers with a no gradient FILLSED Fill only sediment tracers with a no gradient SMOOTH Apply 9 point smoothing filter to filled data SHAPIRO Apply Shapiro filter to filled data SHUMAN Apply Shuman filter to filled data MEDIAN Apply median filter to
10. Additionally a sediment layer structure must be defined for sediments transport to operate e g NSEDLAYERS 4 The number of sediment layers 0 005 Depth in the sediment of the 1 layer face 0 020 Depth in the sediment of the 2 layer face 0 080 Depth in the sediment of the 277 layer face 0 320 Depth in the sediment of the Ain layer face The tracer list must also include a number of sediment fractions with corresponding attributes e g particle size settling velocity etc defined There are also a number of global parameters that must be defined see the Sediment Transport User Guide for a full explanation The sediment transport parameters and tracer attributes can be automated where a set of user defined defaults are used in preference to a fully defined specification in the parameter file This involves defining the tracer sediment classes that are to be used the attributes that will be defined for those tracers and the global parameters used for the sediment transport The sediment tracer classes are defined using SED_VARS lt classl gt lt class2 gt lt class_n gt Where lt class_n gt is the name of the sediment class the user wishes to be include These classes are hardwired into the sediment interface module sediments sediments c and can be expanded as desired Currently the classes consist of Gravel Sand Mud FineSed Dust SHOC will check if the classes defined in S
11. Create Bathy Figure 14 3 1 a list of interpolation methods is listed in the matlab window Enter the interpolation method required In this case a 7 for weighted area is used It is possible that the interpolation scheme will not fill all the cells in the domain In this case click on Create Bathy again and use 6 for inverse distance fill in This may be required to be performed several times The 20 08 2015 Page 168 of 185 Version 1 00 SHOC User Manual resulting interpolated bathymetry is displayed in Figure 14 3 6 Sometimes the interpolation scheme may fail and no cells are interpolated In this case try another interpolation method Bathymetry cells may be manually edited by using the Edit Bathy button File Edit View Scrollback Bookmarks Settings Help 125 E 130 E 135 E 140 E Figure 14 3 2 Geographic rectangular grid of the Great Australian Bight 134E 136 E 138 E Figure 14 3 3 Geographic rectangular grid of the South Australian Gulfs 20 08 2015 Page 169 of 185 Version 1 00 SHOC User Manual TF Plan View lt tracy gt 50x40 1053 2D water cells 136 E 138 E 140 E Figure 14 3 4 Masked image of the South Australian Gulfs 134 E 136 E 138 E 13E 136 E 138E a Database loaded b Decimated and trunca
12. Current 0 2 ms er 0000 11 Jan 2000 08 0 5 E 10 E Current 0 2 ms Sea Level m i 0000 11 Jan 2000 08 0 1134 0 01787 0 07763 0 5 E 10 E Note Fig 4 31 1 a and c utilize slightly different bathymetry i e Fig 4 31 1 is 2 cells narrower in either direction since the walls are not recognized as part of the domain and bathymetry has a step across these walls hence any slight differences in solutions between a and c the general dynamics are the same however 20 08 2015 Page 130 of 185 Version 1 00 SHOC User Manual 5 Automatic setup a option As mentioned in section 3 the parameters outlined in this section may be automatically generated using the a option in following information SHOC In this case the parameter file must contain the The start and stop time of the model simulation period relative to the epoch 01 01 1990 00 00 00 8 by default Relative time specifications here and elsewhere in the parameter file can be specified in seconds minutes hours or days Here the start time corresponds to 1995 02 10 00 00 00 8 and the end time to 1995 03 13 00 00 00 8 START_TIME 1866 days STOP_TIME 1897 days The name of the input and parameter output files The input netCDF file will have nc appended to this name i e test nc and the input parameter file will have prm appended
13. If measurements of shortwave radiation are not available then this parameter may be calculated This requires the specification cloud cover as follows Time series file containing the cloud with units oktas CLOUD cloudiness nc CLOUD_INPUT_DT 10 minutes ALBEDO must not be present if short wave radiation is to be computed by the model Note that if the ecology module is invoked then short wave radiation is input via the LIGHT and ALBEDO_LIGHT parameters which differ from the RADIATION parameters in that the ecology module requires a daily mean short wave radiation which is inadequate for the heat flux calculation The bulk parameters are usually specified at a standard height of 10m If the wet and dry bulb temperatures and wind are not measured at this standard height then the bulk parameters must be scaled from the standard height to the reference height the measurements were taken at The user should therefore supply the reference height of measurements via Reference height of meteorological measurements units m HEATFLUX_REFH 5 10 20 08 2015 Page 73 of 185 Version 1 00 SHOC User Manual If the reference height is absent a height of 10m is assumed A larger reference height results in larger bulk fluxes The sensible heat flux uses a gradient between the air temperature and SST The SST used in this calculation is that predicted by the model The user may submit an alternate file e g
14. Where a to a are fractions whose sum adds up to 1 0 or for default a toa 1 WINDOWS The surface of the domain is then partitioned into windows according to the specified fractions e g if two windows are specified with sizes 0 5 and 0 5 then the surface is split into two equal windows Note that the number of cells in a windows may not be equal if the surface is split into equal sizes since windows with deeper water will contain more cells than windows with shallow water When this option is used the diag txt diagnostic file section 4 32 will contain the amount of CPU time spent in each window Also shown is the actual load balance used i e the prescribed window sizes and the predicted window sizes that are required to achieve equal amounts of CPU time in each window i e an even load balance This load balancing may be automated using Resets window sizes to balance the CPU WINDOW_RESET m Where every m time steps the windows are automatically re generated with sizes that attempt to balance the CPU load The window partitions may be explicitly defined for wINDows 1 windows using WINDOW lt n gt _POINTS where lt n gt is the window number The number of points in the list should be specified followed by a list of the i j locations of the window cells e g Define the first window to contain 2 cells WINDOW1_POINTS 2 21 2 2 Note the Marked facility in jvismeco is a useful tool for extracti
15. http www emg cmar csiro au www en emg software EMS hydrodynamics htm Revision history is available at the same address 20 08 2015 Page 5 of 185 Version 1 00 SHOC User Manual 1 Introduction SHOC Sparse Hydrodynamic Ocean Code is a finite difference hydrodynamic model developed by the Environmental Modelling group at CSIRO Commonwealth Scientific and Industrial Research Organization Division of Marine Research Herzfeld 2006 This model is intended to be a general purpose model applicable to scales ranging from estuaries to regional ocean domains Outputs from the model include three dimensional distributions of velocity temperature salinity density passive tracers mixing coefficients and sea level Inputs required by the model include forcing due to wind atmospheric pressure gradients surface heat and water fluxes and open boundary conditions e g tides SHOC is based on the three dimensional equations of momentum continuity and conservation of heat and salt employing the hydrostatic and Boussinesq assumptions The equations of motion are discretized on a finite difference stencil corresponding to the Arakawa C grid The model uses a curvilinear orthogonal grid in the horizontal and fixed z coordinates in the vertical The z vertical system allows for wetting and drying of surface cells useful for modelling regions such as tidal flats where large areas are periodically dry SHOC has a free surface and uses mod
16. p option the bathymetry used is read from the netCDF file Any bathymetry data and bathymetry manipulation options e g bathymetry limits smoothing etc present in the parameter file are ignored This is because data for all the model variables read from the netCDF file is assumed to correspond to a particular layer configuration over a particular depth range and changing the layer structure or bathymetry range will result in discrepancies between the data read from file and the assumed model geometry Using the a or g option see section 5 and 8 the bathymetry of the area to be modelled is specified by providing a depth value for each horizontal grid cell Thus there are NCE1 NCE2 bathymetry values for each grid They are specified as an array parameter as follows Example depth values for a 3 by 4 grid BATHY 12 KE The values run in order from the bottom left corner of the grid i 0 j 0 with i varying fastest This means that for a single column bathymetry list as in the above example any cell i j is located at position j x NCE1 i 1 in the list Note that the values are depths rather than z coordinate values and hence are usually positive Beware as this can easily cause confusion Negative values are also allowed and signify that the sea bed is above mean sea level Where the sea bed is above ETAMAX see above the cell is taken to be a land cell Values which are deeper than the deepest model layer
17. through the grid s middle 4 7 Vertical grid geometry SHOC is a z or o coordinate model In the z coordinate system each layer height is the same across the whole grid domain The layers are specified by giving the z coordinate of their interfaces relative to mean sea level Because the model z coordinate is positive up with origin at mean sea level this means that layer interface z coordinates are usually negative below the surface For example a model with 5 layers in the vertical extending from 10m depth to the surface and with uniform 2m vertical resolution would be specified as follows t The z coordinates of the model layer interfaces AYERFACES 6 10 0 8 0 6 0 4 0 5220 0 0 Layers need not all have the same thickness but for numerical reasons care should be taken to avoid sudden large changes in layer thickness The top layer need not be at mean sea level An example covering these points is shown below A non uniform vertical grid with 10 layers covering from F 15m depth to 5m above mean sea level AYERFACES 11 EE G s O E E oO ODO O OO CH CH CH e CH Ow WD t The model includes drying and wetting algorithms and the simulated water surface in the model is free to move up and down through the layers The uppermost layer automatically grows thicker as required to incorporate increases in surface elevation up to some maximum height s
18. A unique feature of SHOC is not only its ability to support a myriad of different horizontal grid geometries but also its ability to handle different coordinate systems Currently SHOC supports three coordinate systems e Arbitrary Cartesian e Geographic Latitude Longitude e Geographic Map projected The Cartesian system defines the coordinates on a rectangular plane with no physical association to real locations on the Earth The geographic based coordinate systems however map directly to real world locations For a Latitude Longitude coordinate system all grid metrics are computed on the spheroid while for the map projected coordinate system the metrics are computed on the projected plane The coordinate system is defined using the PROJECTION parameter and applies to ALL windows 20 08 2015 Page 19 of 185 Version 1 00 SHOC User Manual 4 5 1 Defining a Cartesian coordinate system An arbitrary Cartesian coordinate system can be specified by either leaving the PROJECTION blank or by not specifying the parameter at all Please note it is assumed that the XY units are in metres even though they have no real world significance 4 5 2 Defining a latitude longitude coordinate system The Latitude Longitude coordinate system is specified as follows The geographic projections implies that all coordinates should be provided as decimal longitude and latitude PROJECTION geographic Unfortunately at this time n
19. Grid dimension 212z 52 Vertical structure Vertical coordinate system 40 0 30 0 25 0 21 0 18 0 6395 64 0 r 5 4 5 4 0 x 25 Z 1 TSS E 0 3 11 0 2 9 0 Lx 8 0 Ls 7 0 hes 0 0 0 2nd order momentum advection scheme QUICKEST flux form variable grid ltimate filter invoked tracer advection scheme U Free slip Horizontal condition diffusion Horizontal diffusion Horizontal viscosity x direction y direction x direction 2 000 2 000 20 000 20 000 275 01 Horizontal viscosity ean horizontal grid y direction spacing el e2 228 49 Vertical m Surface Backgrou Backgrou Bottom rou ixing scheme me roughness length scale nd diffusivity 1 000e 0 nd viscosity 5 000e 07 ghness length scale 0 0 llor_yamada_2_0 0 100 7 00100 2 0 00e 00 0 00e 00 tracers 0 salt 1 temp Number of Tracer Tracer 00 00 e 01 e 01 Number of open boundaries 2 Boundary 0 west Normal velocity NOGRAD 20 08 2015 Page 125 of 185 Version 1 00 SHOC User Manual Tangential velocity CLAMPD Elevation FILEIN MILLER Tracer 0 salt FILEIN UPSTRM Tracer 1 temp FILEIN UPSTRM Relaxation constant 0 008 hours Boundary data file 0 home mgs dent c2 west_ets nc Boundary 1 east Normal velocity NOGRAD
20. Longitude coordinate variable of a 2d rectangular grid double lon nj ni lon units degrees_east lon coordinate_type longitude 2 coordinate variable double z nj ni Zrunits m zZ coordinate_type 2 Bach record and dimension has a unique T X Y and Z coordinate associated with it The coordinates are stored in lat lon units double salt nrecords nk nj ni salt units practical salinity units salt long_name Salinity salt coordinates t lon lat z D I This a snippet demonstrate how to define a 3d grid with a map projection Australian Map Grid netcdf file dimensions nrecord UNLIMITI ni 10 nj 20 nk 53 ii ei ER variables Time coordinate variable double t nrecords t units seconds since 1990 01 01 00 00 00 10 20 08 2015 Page 154 of 185 Version 1 00 SHOC User Manual Es t coordinate_type TIME X coordinate variable of a 2d rectangular grid double x nj ni xX units m x coordinate_type X X projection proj amg zone 55 Y coordinate variable of a 2d rectangular grid double y nj ni yrunits m y coordinate_type Y y projection proj amg zone 55 2 coordinate variable double z nj ni Zrunits m z coordinate_type 2 Bach record and dimension has a unique T X Y and Z coordinate associated with it The coordinates are stored in AMG units double sa
21. 110 INCLUDE EXCLUDE Case is not important NONLINEAR TRUE CALCDENS no Examples of integer and floating point parameters are NCE1 20 G 9 81 Arrays are entered by giving the keyword and the number of values in the array on the same line followed on the next lines by the array values separated by spaces tabs or new lines Comment lines may not appear in the middle of the list of array values Following are two examples Fills the bathymetry array with four values BATHY 4 0 002 0 0025 0 0026 0 0027 If insufficient data is provided then the last value is used to pad out the array BATHY 4 0 002 Having described the general syntax of the parameters the following sections describe the wide range of parameters needed to specify a particular model application 4 1 Parameter header Most parameter files begin with some comment lines which describe the model application and mandatory parameters which specify the SHOC code version to be used and descriptive string for this run The format is as shown below 20 08 2015 Page 12 of 185 Version 1 00 SHOC User Manual This is the parameter file header It usually describes the model application The code header must be identical to the Version string specified when SHOC is compiled in version c This provides a check that the intended version of the model code is being used at run time
22. 16 etc source cells may be grouped to form a target cell so that the target grid has coarser resolution than the source grid In this case the target grid is defined as a SUBSET of the source grid 3 The target grid is completely different to the source grid An example of this may be a target grid created at higher resolution than the source grid These grids are defined as a SUPERSET To perform transport on multiple grids a SOURCE_GRID must be defined in the parameter file This is simply an input file containing the grid configuration one wishes to use as the source grid The TRANS_DATA files must also be created on the source grid The target grid is assumed to be defined as the grid nominated by the INPUT_FILE in the parameter file These files must be created using the g option An example is as follows INPUT_FILE insna Target grid SOURCE_GRID source nc Source grid The transport model will compare these grids to determine if the relationship is EXACT SUBSET or INEXACT and handle them accordingly From a users perspective the 20 08 2015 Page 145 of 185 Version 1 00 SHOC User Manual differences are that EXACT grids operate the fastest and INEXACT the slowest owing to the amount of interpolation involved between grids 9 2 STREAMLINE mode An intermediate step may be performed to create transport files that contain information regarding the streamline origin rather
23. 1997 p42 Cn The internal wave speed used is that from the INT_WAVE diagnostic If Fr lt 1 flow is sub critical Fr 1 flow is critical Fr gt 1 flow is super critical Note Dyer 1997 p43 states critical flow occurs at Fr 0 33 for continuous stratification ROSSBY_IN Internal Rossby radius m where Ro Cn H n 1 2 3 Gill 1982 eqn 7 5 4 The mode 1 internal Rossby radius is supplied as the diagnostic ROSSBY_EX External Rossby radius m where dee Ro Gill 1982 p 207 H SOUND Speed of sound given by c c S T Z c a T 10 B T 10 T 18 Apel 1887 eqn 7 19 6 S 35 T 18 S 35 z where co 1493 0 amp 3 0 Bo 0 006 Yo 0 04 amp 1 2 amp 0 01 and C 0 0164 This equation is believed to be accurate to within 0 2 ms Sound channels are defined as the depth 20 08 2015 Page 107 of 185 Version 1 00 SHOC User Manual where a change of sign in the sound speed gradient occurs i e where the curvature of the sound profile is equal to zero The vertical representation of all variables in SHOC occupies discrete vertical layers arranged at variable depths usually with higher resolution at the surface and being dependent on maximum water depth Therefore the speed of sound is also only provided at discrete depths In SHOC the sound channels are simply computed from a linear interpolation between two layers where the gradient
24. VORTICITY RELATIVE Relative vorticity s rel vor VORTICITY POTENTIAL Potential vorticity mn e pot_vor VORTICITY TENDENCY Vorticity tendencies GG rv_drvdt rv_nonlin rv_beta rv_strch rv_jebar CV MSC rv_bsc MIXING_SCHEME Mixing length scale m lscale CFL CFL stability criterion s cfl2d cfl3d MOM_TEND Momentum tendencies ms ul_adv ul_hdif ul_vdif ul_btp lt p p ul Cor u2_adv u2_hdif u2_vdif u2_btp 2 Dep UZ Cor HEATF LUX Heat flux components Dim swr lwr shf Int nhf WAVE_VARS Wave variables wave_amp wave_period wave_dir wave_ub ustrcw WAVES Wave bottom drag wave_Cd Wave radiation stress wave_Sxy wave_Syx Brunt Vaisala frequency s brunt_vaisala NT_WAVE Internal wave speed ms int_wave_speed ICHARDSON_GR Gradient Richardson number richardson_gr Flux Richardson number richardson_fl Reynolds number reynolds B I R RICHARDSON_FL REYNOLDS F Kal O C EI Di Interfacial Froude number froude ROSSBY_EX External Rossby radius m rossby_external ROSSBY_IN Internal Rossby radius m rossby_internal SIGMA_T Sigma t o kgm sigma_t SOUND Speed of sound ms sound Sonic layer depth m sonic Sound channels m sound_channel SHEAR_V Vertical shear Le shear_vert BUOY_PROD Buoyancy production me buoy_prod SHEAR_PROD Shear production me shear_p
25. e g PT_Source0O Decay 10 days Size decreases to zero in 10 days PT_Source0 Growth 10 days Size doubles in 10 days When a particle becomes lost the size is reset to PT_Source0 Size A particle threshold size of 10 is hardwired so that if particles decay to sizes less than this threshold they are flagged as lost In order to minimise output file size the age of particles are stored as unsigned bytes with values ranging from 0 to 255 The actual size in floating point precision is scaled to this output range via the parameter SizeLimit e g PT_SizeLimit le 3 If the SizeLimit parameter is present then the size is calculated and scaled size is included in the output file For decaying particles scaling is performed linearly such that a size of SizeLimit is scaled to 255 and a size of zero is scaled to zero For growing particles a size of PT_Source0 Size is scaled to zero and a size of SizeLimit is scaled to 255 These scaled sizes may be plotted as a colour spectrum for all sources Particle sizes are only invoked if SizeLimit is present regardless if sizes are set for individual sources If SizeLimit is present and sizes for individual sources are not then the particle size for each source defaults to zero In this case all particles will always be flagged as lost since the particle size is below the threshold of 10 see above 4 28 5 Settling Particles may be prescribed setting velocities as a function of the source or as a fu
26. i e test prm INPUT_FILE test Grid information see section 4 6 defining the grid layout is mandatory An example is included below PROJECTION geographic GRIDTYPE GEOGRAPHIC_RECTANGULAR NCE1 10 NCE2 20 DLAMBDA 0 01 Long cell interval in aux coords degrees DPHI 0 01 Lat cell interval in aux coords degrees X00 144 3856 Longitude of origin degrees YOO 38 2030 Latitude of origin degrees POLE_LONGITUDE 0 Longitude of false pole degrees POLE_LATITUDE 90 Latitude of false pole degrees Bathymetry example depth values for a 3 by 4 grid BATHY 12 2222 12 3 7 4 23 9 12 0 6 0 25 8 13 7 5 8 27 6 14 2 4 9 The parameter file may then conta the model i e Information regarding pressure A time series file co velocity components respectively and hav Se E He HR HR 20 08 2015 in optional fields specifying the forcing and initialization of any forcing data to be read e g wind ntaining wind East and North which must be called u and v e units of ms l Page 131 of 185 Version 1 00 SHOC User Manual WIND_TS cyc_bobby95 nc How often to read data from the wind file and update the wind field in the model WIND_INPUT_DT 10 minutes A time series file containing the variable pressure with units of Pa PRESSURE cyc_bobby95 nc How often to read the file and update the pressur field in the model PRESSURE_INPUT_DT 10 minutes Update every 10 minutes
27. interior processes i e the boundary cell must behave in a passive manner Again an additional boundary condition must be used to specify the boundary flux and the default condition is TRFLUX FILEIN where the user must supply a data file containing boundary fluxes Note that a positive specified flux implies tracer import regardless of the edge the open boundary occupies If a concentration is known then the flux and input method analogous to TRFLUX may be specified using TRCONF In this case the supplied concentration is multiplied by the volume flux to get the tracer flux that is applied to the face This may be useful for river inputs if the river flow and inflow concentration of a tracer are known The result will be identical to that using TRFLUX with the flux concentration x flow and is provided as an option for convenience 4 10 18 Profile Methods for Tracers The profile methods for tracers allow a depth dependent profile to be constructed given a surface and bottom measurement The surface measurement may be spatially variable and the bottom measurement should correspond to the deepest location on the boundary The DEPROF method scales these measurements to the actual density profile predicted by the model a certain number of cells into the model interior currently hardwired to 5 cells whereas the PROFIL method constructs a synthetic profile consisting of surface mixed layer pycnocline and bottom mixed layer This synthetic p
28. residual This residence time is also listed in the region output timeseries files Additionally the residence time computed using the net flow through the region perimeters i e the sum of incoming and outgoing fluxes is listed in this file under residence_time_net This is the time it would take the residual flow to turn the volume within the region over 20 08 2015 Page 115 of 185 Version 1 00 SHOC User Manual 4 30 19 Diagnostic tracer names The following table lists the tracer names 2D and 3D associated with each diagnostic These names must be used when attempting to output the relevant diag nostic to file Diagnostic name Purpose Tracer names CALC_FLUXES Tracer flux calculation flux_el flux_e2 flux_w flux_kz EAN VEL3D 3D mean velocity ms ulmean u2mean wmean EAN VEL2D 2D mean velocity ms ulav_mean u2av_mean EAN ETA Mean sea level m eta_mean EAN KZ Mean vertical diffusivity ms Kzmean EAN WIND Mean wind Nm or ms wlmean w2mean EAN VOLFLUX 3D mean volume flux m s7 ulvmean u2vmean EAN TS Mean temperature and salinity temp_mean salt_mean IX_LAYER Mixed layer depth m mixed_layer FLUSHING_TR Flushing tracer flush STERIC_HEIGHT Steric height m steric VORTICITY ABSOLUTE Absolute vorticity s abs_vor
29. see section 4 7 signify that the corresponding grid cell is outside the domain of computation of the model denoted OUTSIDE cells This mechanism allows open boundaries to be located at arbitrary positions within the grid Here is the above example again but this time the right hand column of the model is land and the top left cell is outside the computational domain Example depth values for a 3 by 4 grid BATHY 12 22 2 JS 99 23 5 0 20 08 2015 Page 28 of 185 Version 1 00 SHOC User Manual 99 25 8 L37 99 99 99 14 2 399 For convenience some parameters are provided which allow the specification of minimum and maximum depth values as follows All cells will be at least 20m deep BATHYMIN 20 No cell will be more than 2000m deep BATHYMAX 2000 The BATHYMIN and BATHYMAX parameters are optional If present they override values in the BATHY array where necessary The bathymetry can be smoothed using a 9 point low pass convolution filter if required This may be done several times by invoking n is the number of smoothing passes performed SMOOTHING n Alternatively a maximum gradient threshold may be supplied and if the local bathymetry gradient becomes greater than this threshold then the bathymetry is locally smoothed until the gradient becomes less than the threshold This is accomplished by invoking x is the gradient threshold typically 0 07 MAXGRAD x Bathy
30. vandg Van der Grinten wink1 Winkel Global parameters In addition to the projection specific parameters there are also a number of parameters supported by all projections Parameter Description ellps Ellipsoid name see Ellipsoid table below es Eccentricity a Major ellipsoid axis radius b Minor ellipsoid axis radius rf Reverse flattening x_0 False easting automatically specified for the UTM projection y_0 False northing Ellipsoids Supported ellipsoid include Ellipsoid Parameters Description merit a 6378137 0 rf 298 257 MERIT 1983 grs80 a 6378137 0 rf 298 257222 GRS 1980 IUGG 1980 iau76 a 6378140 0 rf 298 257 IAU 1976 airy a 6377563 396 b 6356256 910 Airy 1830 mod_airy a 6377340 189 b 6356036 143 Modified Airy aust_nitl a 6378160 0 rf 298 25 Australian Natl S Amer IAU 64 grs67 a 6378160 0 rf 247 247167 GRS 67 IUGG 1967 bessel a 6377397 155 rf 299 1528128 Bessel 1841 bess_nam a 6377483 865 rf 299 1528128 Bessel 1841 Namibia clrk66 a 6378206 4 b 6356583 8 Clarke 1866 clark66 a 6378206 4 b 6356583 8 Clarke 1866 clrk80 a 6378249 145 rf 293 4663 Clarke 1880 mod everest a 6377276 3452 b 6356075 4133 Everest 1830 hough a 6378270 0 b 6356794 343479 Hough intl a 6378388 0 rf 297 International 1909 Hayford krass a 6378245 0 rf 298 3 Krassovsky 1942 mercury a 6378166 0 b 6356784 283666 Me
31. 0 Horizontal viscosity in u2 equation U2VH 1 50 20 08 2015 Page 83 of 185 Version 1 00 SHOC User Manual Horizontal diffusion for tracers is also included and is invoked by specifying the diffusivities in the x and y directions in the parameter file via Horizontal diffusivity in the x direction mis U1KH 100 Horizontal diffusivity in the y direction mis U2KH 100 The horizontal mixing coefficients may be scaled according to the grid size at each cell This allows reasonable values to be specified for curvilinear grids which encompass a large range of resolutions Scaling of horizontal mixing coefficients is specified by the parameter DIFF_SCALE and may take on the following forms where Ax is the grid size and Ax is the mean grid size DIFF_SCALE NONE No scaling performed DIFF_SCALE LINEAR Linear scaling by Ax AXm DIFF_SCALE NONLIN Non linear scaling by Ax AXm DIFF_SCALE AUTO Grid optimized mixing 0 1 Ax At DIFF_SCALE SMAG Sets smagorinsky 0 1 see below The default scaling is DIFF_SCALE LINEAR If scaling is performed the value set in the parameter file is relative to the mean grid spacing in the e1 and e2 directions mean grid spacing is output in the file setup txt The Smagorinsky diffusion coefficients can be independently invoked on any component of viscosity or diffusivity by setting SMAGORINSKY e Where c is t
32. 156 of 185 Version 1 00 SHOC User Manual 12 Tests A suite of tests has been collected for this model These tests are used to validate the model against analytic solutions or other known simply understood situations They are particularly useful to check the correct operation of the model after modifications to the model code 12 1 No forcing Test 1 is an extremely simple null case test where no forcing is applied to a closed model domain The purpose is to demonstrate that no model variables deviate from their initial values A rectangular grid is used with a horizontal grid of 5 by 10 cells and 5 layers in the vertical having 1m vertical spacing The bathymetry varies and the water is initially vertically Stratified Vertical diffusion of salt and heat is turned off in this case to avoid diffusive changes Each run consists of a 1000 second integration with no externally applied forcing The initial variable values zero elevation zero velocity salinity and temperature should remain unchanged for the duration of the integration 12 2 Ekman Spiral A wind of constant stress and direction is blown over a homogeneous open ocean of constant depth The model uses cyclic open boundaries reflect the open ocean condition and utilizes constant vertical viscosity and linear bottom friction for simplicity According to Kowalik and Murty 1993 p27 the linear resistance coefficient is related to the bottom drag coefficient via r pC h 12
33. CONFIGURATION IN THE TRANSPORT MODE AS THAT SPECIFIED IN THE HYDRODYNAMIC SIMULATION If volume fluxes are used in the hydrodynamic simulation then those same point sources in the transport mode must also use volume fluxes If no volume fluxes are present in the hydrodynamic simulation then do not specify volume fluxes for point sources in the transport mode The FFSL advection scheme is not as diffuse as the semi Lagrangian scheme and it may be desirable to explicitly include horizontal mixing e g DIFF_SCALE LINEAR U1KH 0 455 U2KH 0 940 SMAGORINSKY HA Note that H the DYNAMIC river open boundary is used in the hydrodynamic model Section 4 10 6 then there will be inflow and outflow at the river open boundary in the transport model If a TRCONF tracer open boundary condition is used then the value supplied with the TRCONF OBC rather than the cell interior value will be multiplied by any outflow through the boundary face to get the boundary flux This may result in negative boundary cell tracer concentrations 20 08 2015 Page 149 of 185 Version 1 00 SHOC User Manual 10 Percentile computations ps option SHOC can compute the percentile distributions i e order statistics of temporal records in increments of 5 iles of a time series file using shoc ps prmname The keywords required in the parameter file are P_IFILE Input file This may be ASCII netCDF multi netcdf o
34. FUN GALPERIN Galperin et al 1988 STABILITY_FUNC KANTHA amp CLAYSON Kantha and Clayson 1994 STABILITY FUN POM Mellor 1992 STABILITY FUNC UNK amp ANDERSON unk and Anderson 1948 STABILITY_FUNC ERIFLER amp SCHRIMPF Eifler and Schrimpf 1992 STABILITY FUNC SCHUMANN amp GERZ Schumann and Gerz 1995 4 21 10 Waves The effects of waves can be included in the k e k m and W88 models This requires the DO_WAVES flag to be invoked see Section 4 23 with feedback to vertical mixing i e WAVES VERT_MIX Wave amplitude used for surface length scale in vertical The impact of waves on vertical mixing of momentum follows the Craig and Banner 1994 approach where the constant o and scaling factor for significant wave height are set according to WAVE_ALPHA 100 Wave factor WAVE_HEIGHT_FACT 1 Scaling for significant wave height The default values are those listed above See Jones and Monosmith 2008 for alternative values 4 22 Horizontal mixing SHOC includes horizontal mixing of momentum and tracers by specifying a viscosity and diffusivity value respectively This term is usually included in the momentum equations for stability reasons The parameters are specified as follows Horizontal viscosities are specified separately for the ul and u2 momentum equations but except under special circumstances both values should be the same Horizontal viscosity in ul equation U1VH 1
35. Lock A P MacVean M K 1996 Conservative explicit unrestricted time step multidimensional constancy preserving advection schemes Mon Wea Rev 124 2588 2606 Lin S Rood R B 1996 Multidimensional flux form semi Lagrangian transport schemes Mon Wea Rev 124 2046 2070 Madsen O S 1994 Spectral wave current bottom boundary layer flows in Coastal engineering 1994 Proceedings 24 international conference Coastal engineering Research Council ASCE pp 384 398 Masagutov T F 1981 Calculation of vertical turbulent fluxes in the near water atmospheric layer over the ocean in tropical latitudes Meteor Gidrol 12 61 68 Martinsen E A and H Engedahl 1987 Implementation and testing of a lateral boundary scheme as an open boundary condition in a barotropic ocean model Coastal Eng 11 603 627 Mellor G L and T Yamada 1982 development of a turbulence closure model for geophysical fluid problems Rev Geophys 20 851 875 Mesinger F and A Arakawa 1976 Numerical methods used in atmospheric models GARP Publ Ser No 17 WMO ICSU Muller P 1995 Ertel s potential vorticity theorem in physical oceanography Reviews of Geophysics 33 67 97 Miller M J and A J Thorpe 1981 Radiation conditions for the lateral boundaries of limited area numerical models Q J R Meteorol Soc 107 615 628 Moon I 2005 Impact of a coupled ocean tide circulation system on coastal modelling Ocean Modelling 8
36. The length scale is calculated on a sub set of the grid where the user specifies the length scale of the sub set sz The de correlation length scale is invoked using DECORR_LENGTH lt variable gt sz lt scale gt where lt variable gt may be lt variable gt eta Sea level de correlation length scale ul ul velocity u2 u2 velocity any valid 3D tracer name e g temp salt lt scale gt is a scaling factor for sz e g if lt scale gt km then the sub set size sz is assumed to be in kilometres and output length scales will also be in km The default is metres if lt scale gt is absent e g DECORR_LENGTH temp 1000 Temperature de correlation length scale using sub set size of 1000m 20 08 2015 Page 112 of 185 Version 1 00 SHOC User Manual 4 30 18 Mass Budgets The model domain can be arbitrarily divided into a number of regions for which mass and volume budgets can be computed over a predefined period A netCDF file containing the region partitions usually appended with bnc must first exist These files can be created using the BOX CREATION option in PLUM Instructions for creating regions in PLUM are as follows k Enter PLUM in Matlab 2 Click on GRID CREATION and then Read NETCDF File to read in the Shoc grid information 3 Click on Draw Erase Grid to remove the grid line detail leaving just the bathymetry 4 Return to Main Menu and click on BOX CR
37. Usually set to 7 of the surface layer HMIN 0 01 Specification of the slip condition at solid horizontal boundaries This effectively specifies the tangential velocity value at the land or at any solid vertical face used by the horizontal momentum equations Valid values are LE Full slip condition most commonly used 0 0 Half slip condition 1 0 No slip condition Other values may be accepted by the model but may give unexpected or erroneous results SLIP 1 0 Specification of what constitutes a simulation fatality If ETA is specified the model will exit if absolute sea level is greater than ETAMAX If VEL3D is specified exits occur if 20 08 2015 Page 16 of 185 Version 1 00 SHOC User Manual absolute 3D velocity is greater than VELMAX If VEL2D is specified exits occur if 2D velocity is greater than VELMAX_2D If T S is present temp and salinity are checked for NaN If NAN is present exits occur if ETA VEL3D or VEL2D assume the NaN value The default is ETA NAN with ETAMAX 10 FATAL ETA VEL3D VEL2D ETAMAX 10 VELMAX 5 VELMAX_2D 3 Specifies the quanti runlog file ty of messages information writt Same as l option see Section 2 3 Th Supported may be a subset of the following log_levels main warn info debug trace
38. an easterly direction a Eee aa Er bel Seef T P CHE HEITE Dean eg GE ei bt l rT t p ER EECH ae SPe ares bea REEEARRSSStERHRGEES T oe i ee l I i 7 Shell az Slakteteieielsiste ell UDEODDDOE DOE BLE enee EE 36 37 38 391 40 41 e The default ellipsoid is clark66 and false eastings and northings are 500000E 10000000N for the southern hemisphere and 500000E ON for the northern hemisphere Defined by proj utm zone lt number gt south north zone UTM zone 1 60 south Enabled if for southern hemisphere north Enabled if for northern hemisphere default Australian Map Grid A projection for the Australian region based on the UTM projection but using the gda66 ellipsoid Defined by proj amg zone lt number gt zone UTM zone 1 60 Map Grid of Australia A more recent projection for the Australian region based on the UTM projection but using the gda94 ellipsoid This is the current Australian Standard Projection Defined by proj mga zone lt number gt zone UTM zone 1 60 Lambert Conformal Conic A conformal conic projection where parallels are unequally spaced arcs of concentric circles Merdians are equally
39. approach by default for all depths greater than the deepest mooring at a particular geographic location The optional REF_VALUE and REF_DEPTH operate in a similar manner to the BOT_VALUE except a particular value temperature in this example can be prescribed at the depth REF_DEPTH rather that at the bottom In the absence of a BOT_VALUE all values below the REF_DEPTH are set to the REF_VALUE in preference to those contained in the measured data files moor1 ts and profl nc The reference and bottom options are useful for prescribing the scaling function below depths where no measured data is available but the user has insight into what values are expected at those depths The scaling tracer may be initialised with the OUT_FILE created using the create_scale option and if this file is also used as a reset_file then the scaling tracer may be used to scale the open boundary forcing in a time dependent manner Section 4 11 18 4 9 6 Surface fluxes A 3D tracer defined in the tracer list may have a surface flux prescribed that acts as the upper boundary condition in the vertical diffusion equation see Section 2 5 Science Manual This implies that the tracer is allowed to be vertically diffused The flux tracer is introduced by specifying the name of a valid 2D tracer in the tracer list as follows e g for tracer passive TRACER2 name passive TRACER2 long_name Passive tracer T
40. are included in the parameter file then the momentum tendency corresponding to just that tracer will be calculated This diagnostic will not work in the 2D mode 4 30 11 Tracer Tendencies Tracer tendencies can be saved to 3D diagnostic tracers using TRA_TEND lt tr_name gt where lt tr_name gt is the name of a tracer in the tracer list for which the tendencies are to be computed The units of the tendencies are the same as that of the nominated tracer and the following diagnostic tracers are automatically generated lt tr_name gt _adv advective and horizontal diffusive tendency lt tr_name gt _vdif vertical diffusive tendency lt tr_name gt _ncon non conservative tendency 4 30 12 Selective Momentum Calculations The terms in the 2D and 3D momentum balance i e advection horizontal diffusion vertical diffusion barotropic pressure gradients baroclinic pressure gradients and Coriolis may be selectively omitted from the momentum calculation via the flags U1_OMIT lt string gt U2_OMIT lt string gt U1AV_OMIT lt string gt U2AV_OMIT lt string gt Where lt string gt is a string containing ADVECT HDIFF VDIFF PRESS_BT PRESS_BC or CORIOLIS This facility is useful for diagnosing the source of instability in the model The baroclinic contribution is only omitted from the 2D mode if it is also omitted from the 3D mode 4 30 13 Diagnostic numbers A variety of diagnostic numbers can be comp
41. are output in sparse format Variables output are eta ulmean u2mean wmean temp salt and Kzmean swr is also output if present The mean variables required for output are automatically invoked The default dump increment is 1 hour unless specified using TRANS_DT Note that TRANS_OUTPUT may be used in transport mode when wishing to dump multi grid output for the STREAMLINE mode see below In this case output variables are eta ul u2 temp salt Kz origin p q andr Note that if a list of tracers is generated for the transport mode then the tracers must have unique names e g if eta ul u2 or w are used as tracer names then these will be in conflict with the prognostic variables of those names and output may not be correctly generated ul and u2 will not output to standard files u and v will not output to simple files This is especially relevant when using TRANS_MODE NONE Additionally the following attributes are mandatory in the transport parameter file see Section 4 for a description of these parameters CODEHEADER SHOC default version Code version PARAMETERHEADER Transport model Header text TIMEUNI seconds since 1990 01 01 00 00 00 08 OUTPUT_TIMEUNIT days since 1990 01 01 00 00 00 08 ENUNT metre START_TIME 1866 days STOP_TIME 1897 days DT 1 hour Transport timestep HMIN 0 02 The minimum layer thi
42. be controlled by the VISC_METHOD flag VISC_METHOD NONE No horizontal viscosity LAPLACIAN Full formulation default SIMPLE Simple formulation The horizontal viscosity routine executed is controlled by function pointers allowing relatively straightforward inclusion of biharmonic viscosity if required 4 23 Point sources sinks A SHOC implementation can include an arbitrary number of point sources or sinks of water and tracers These allow the representation of minor inputs of fresh water or perhaps nutrients for example Associated with each point source or sink is a time series file see section 11 1 which specifies inputs in one of two ways If flows of water are associated with the point source then the file must specify time varying flow rates m s and tracer concentrations kg m If no water is associated with the point source then the file specifies tracer input rates i e loads or fluxes in kg s only The file need not specify concentrations or fluxes for all model tracers Values for those tracers not mentioned in the file are assumed to be zero the exception is temperature and salinity which are assumed to be equal to the receiving water values if not specified Sources of momentum may also be directly input as the source sink in this case the u1 or u2 velocity in ms is directly read from file If flows of water are associated with the point source i e flow rates are specified in the t
43. be very sensitive to the wind input data The drag parameterization may be alternatively specified using the following WIND_STRESS_FCTN L amp P Large and Pond 1982 scheme Eqn 21 K W Kitaigorodskii et al 1973 scheme B Bunker 1976 scheme Ko Kondo 1975 scheme 20 08 2015 Page 67 of 185 Version 1 00 SHOC User Manual These alternative schemes also require a reference height in metres to be supplied corresponding to the height where measurements were made e g WIND_STRESS_REFH 10 Reference height in m For Ko the option exists to use the drag coefficient for neutral conditions WIND_STRESS_NEUTRAL YES neutral drag coefficient At the start of a model run wind forcing may be smoothly ramped up from zero over some specified period see RAMPSTART and RAMPEND in section 4 3 This may help to avoid shocks or start up transients in the model Wind inputs are specified as follows A time series file containing wind East and North velocity components which must be called u and v respectively and have units of ms l WIND_TS cyc_bobby95 nc How often to read data from the wind file and update the wind field in the model WIND_INPUT_DT 10 minutes Scale factor applied to the wind speed This makes it easy to do experiments with different wind strengths without having to generate a new wind time series fil WIND_SPEED_SCALE 1 0 Drag law
44. by configure as well as all object files etc If make distclean is used it will be necessary to re run conf configure in order to re build the model The ems packing is stand alone in the sense that once it is installed the user is free to modify any of the libraries or core code without being dependent on external libraries or code Individual components of ems can be compiled by using the makefile in the subdirectories of ems the directory structure of ems is illustrated in Figure 2 1 For example to re make SHOC if it has been modified go to ems model hd and type make 20 08 2015 Page 7 of 185 Version 1 00 SHOC User Manual Figure 2 1 ems directory structure 2 3 Running the model To set up and run SHOC it is necessary to provide a parameter file containing information about the model geometry run parameters and forcing inputs A specially formatted netCDF file is also required that contains the initial values for the model variables over the model grid The netCDF file may be the result of a previous model run or may be generated from the parameter file using the g option see section 8 The parameter file contains essentially all the information needed to describe a particular model implementation and its contents are described in detail in the Model setup section The model may be run in one of two modes The auto configuration mode is invoked via shoc a prmname where prmname is the name of the model auto config
45. can occur This may be invoked using TIDAL_REMOVAL CSR Removal using tide computed from the CSR tide model MEAN Use the long term eta mean as an approximation to the relaxation elevation ETA must be included as a MEAN diagnostic see Section 4 30 2 for this to operate with a MEAN_DT equal to the length of the run Velocity relaxation may be achieved with the same functionality as for elevation In this case any eta_ is replaced with vel_ in the relaxation specification Relaxation is performed every 3D time step for the 3D mode and 2D time step for the 2D mode 4 13 Wind Wind forcing is specified by number of parameters which define an input time series of wind velocity components and drag law coefficients The model implements a general piece wise linear surface drag coefficient see for example Large and Pond 1981 It has the form Cao NV SM C Cy TOE o E V lt V lt V V V V2V Cu where C is the surface drag coefficient V is the wind speed and Ca C Vo and V are specified parameters described below The surface stress Top is then calculated as follows Top Par CVV where Oo is the air density see section 0 and V is the wind velocity vector Note that the above formulation for C implies that the surface stress varies roughly as the cube of the wind speed for speeds between V and V As a result in some applications the model results can
46. depth rather than halocline to compute mean inflow velocity FRESH_FLOWw Surface density of 1000 is used in the internal wave speed calculation rather than actual surface density TRUNC_LAYER Truncate halocline depth to next deepest layer SCALE_MULT Use multiplicative scaling to inflow rather than additive scaling YANKOVSKY_ Method of Yankovsky A E 2000 The cyclonic turning and propagation of buoyant coastal discharge along the sheff J Mar Res 58 585 607 NO_OUTFLOW River flow is delivered with the original unmodified parabolic profile MACREADY Use the river mouth salinity approximation of MacCready and Geyer 2010 Annu Rev Mar Sci 2 35 58 Eq 19 and 16 4 10 7 Forcing with Velocity The standard custom routines may be used to force the open boundary with velocity profiles e g saved from a coarser resolution simulation Since this nesting approach usually uses large scale and fine scale grids having different orientation any velocities saved on the coarse grid for nesting must first be rotated into east and north components u amp v The point array parray netCDF output option will automatically do this These east and north velocity components must be saved on both normal and tangential open boundary faces on the fine scale grid The latitude and longitude of these faces must be supplied in the parray specification and may be retrieved from utilities such as jvismeco or plum m
47. enable resetting for a particular tracer two parameters are required the reset data file an ASCII or netCDF time series file see section 10 and how often to perform the reset Using this option allows the user to effectively force the model with supplied distributions of tracer Data file containing prescribed tracer values RACERO reset_file saltprof nc How often to reset the tracer RACERO reset_dt 1 hour 4 9 4 Tracer Increments for State Variables The value of a tracer subject to resetting may be added to a state variable This procedure is an easy way to update state variables if the reset file is created from a data assimilation process offline The state variable the tracer is added to is specified via Add the tracer values to temperature TRACERO increment TEMP Valid values for state variable increments are TEMP 3D tracer value added to temperature SALT 3D tracer value added to salinity ETA 2D tracer value added to surface elevation 4 9 5 Scaling 20 08 2015 Page 37 of 185 Version 1 00 SHOC User Manual The initial conditions specified for any tracer may be scaled by another tracer s values This is useful for easily manipulating input data without creating a new initialisation files for example when scaling is required to convert to the correct units for tracer input The scaling may either be additive of multiplicative To scale a given tracer e g tracerl name temp the sc
48. evaporation data EVAPORATION_INPUT_DT 10 minutes Evaporation removes fresh water from the model Evaporation can cause numerical problems in the model if the surface layer is very thin as tracer concentrations can increase without 20 08 2015 Page 70 of 185 Version 1 00 SHOC User Manual bound as the surface layer evaporates and the thickness approaches zero This problem will be addressed in future model versions but can usually be avoided by judicious choice of vertical grid geometry Note that evaporation rates are specified in an input time series file This implies that the rates must be obtained by calculation or observation prior to the model run so that the water temperature simulated by the run itself is not directly used as an input to the estimates of evaporation 4 17 Surface heat flux SHOC includes a variety of explicit heat flux parameterizations The options for defining a heat flux are HEA No heat flux included FLUX E HEATEF LUX BULK Computed using bulk method HEATF LUX NET_HEAT Net heat flux supplied via timeseries HEATF LUX SURF_RELAX Surface layer temperature relaxation HEATFLUX INVERSE Heat flux calculated inversely HEATF LUX COMP_HEA Heat flux from RAMS components HEATF LUX COMP_HEAT_MOM Heat flux from MOM4 components The least complex and least realistic surfac
49. file see section 5 These files are vastly simplified versions of the full parameter file In this mode SHOC will internally generate all parameters required for the run write this information to a parameter file generate a netCDF input file and commence the run If the ag option is used then SHOC will not commence the run but will terminate once all input files are created and written In the auto 20 08 2015 Page 8 of 185 Version 1 00 SHOC User Manual mode model parameters are set to fixed default values or are calculated from the bathymetry and grid geometry Alternatively a run may be initiated using an existing complete parameter file and input netCDF file using shoc p prmname where prmname is the name of the model parameter file Model parameters used for the run in this mode are those specified in the parameter file Various diagnostic information about the internal status of SHOC can be obtained using the debug or 1 command line option This option is followed by a sequence of diagnostics types separated by commas e g debug time dump where each type defines a desired diagnostic output By default the output is written to the C standard error Depending on the type requested the diagnostic output may be quite voluminous Some diagnostic types depend on the presence of others SHOC will automatically enable any dependent diagnostics To display the command line arguments and a list of all diagnostic tyoes SHOC s
50. fileO tinc 1 day fileO tstop 44 days 20 08 2015 Page 123 of 185 Version 1 00 SHOC User Manual fileO bytespervalu 4 fileO vars ALL 4 31 8 Customised parameters As discussed in section Error Reference source not found SHOC source code may be customised to suit special circumstances that the standard model does not support The customised source may well define its own parameters and read them from the parameter file In such cases please consult the code directly 4 31 9 Coastlines If using the utility jvismeco you will probably need to specify coastline data unless you are modelling simple test cases or a completely open patch of water These are specified in ASCII files containing 2 columns x and y A file may contain more than one coastline section several islands for example It is preferable that each coastline section forms a closed polygon which does not contain any self intersections Coastline sections are separated by a blank line and or usually one or more comment lines as well An example coastline file is shown below This is an optional comment line This is another comment line OrRrROO CO Olea second coastline section 1 0 11 21 2 0 1 0 You can have as many coastlines as you like in as many files as you like but it is usually convenient to keep all the data in one file 4 31 10 Bathymetric data In order to define the area to be modelled you need to specify the bathymetry o
51. for these effects and an option exists to impose a global fill on the tracer solutions to ensure conservation This method computes the mass 20 08 2015 Page 146 of 185 Version 1 00 SHOC User Manual before advection and the mass after advection accounting for input of mass through the open boundaries and due to source sinks If the scheme is conservative then mass before and after should equal If not then the excess or shortage of mass is distributed over all cells equally This excess shortage mass is usually results in very small multiplicative adjustments to the concentrations in each cell Furthermore the mass adjustment may be computed so that resulting tracer values remain monotonic i e the adjusted concentrations are not greater or less than the local maximum or minimum concentrations FILL METHOD NONE No conservation adjustment GLOBAL Global filling MONOTONIC Global filling ensuring monotonicity The default method is FILL_METHOD MONOTONIC Continuity dictates that total volume in the whole domain at the end of the time step is equal to total volume at the start of the time step plus volume fluxes into the domain Volume is not subject to errors from 1 above so ideally assuming volume fluxes are due to n open boundaries only Vi gt OBC V Any error from 2 can be compensated by adjusting the boundary fluxes by some factor f k yu HI es gt OBC This factor may then be applied to
52. gt tracerstat variance lt tracer gt Standard deviation of 2D or 3D tracer usage RACER lt n gt tracerstat stdev lt tracer gt Correlation coefficient of two 2D or 3D tracers usage RACER lt n gt tracerstat corr lt tracer gt lt tracer gt Covariance of two 2D or 3D tracers usage RACER lt n gt tracerstat cov lt tracer gt lt tracer gt Sum of 2D or 3D tracers usage RACER lt n gt tracerstat sum lt trl gt lt tr2 gt Difference of two 2D or 3D tracers usage RACER lt n gt tracerstat diff lt tracer gt lt tracer gt Maximum tracer value over a given time period Minimum tracer value over a given time period Maximum water column value of a 3D tracer Minimum water column value of a 3D tracer Vertical integral of 3D tracer usage RACER lt n gt tracerstat vint lt 3Dtracer gt Vertical mean of 3D tracer usage RACER lt n gt tracerstat vmean lt 3Dtracer gt The ratio of a series of layers of a 3d tracer usage RACER lt n gt tracerstat vdiff lt 3Dtracer gt lt toprange gt lt botrange gt strict Copy of a tracer usage RACER lt n gt tracerstat copy lt tracer gt integrate the flux over a defined area and time usage RTSTAT lt n gt name section lt 3Dtracer gt lt direction gt Compute the RMS error between two tracers Version 1 00 SHOC User Manual usage TRACER lt n gt tracerstat rmse lt tracerl gt lt tracer2 gt exposure Exposure time of a trac
53. i e if salinity is below 10 psu for a full day then salt_ex_time will contain 1 If for example dt were 1 hour and salinity was below 10 psu for 36 minutes 0 6 hour then salt_ex_time would contain 0 025 days Although not the primary array of interest the exposure time is required by this tracerstat to keep track of the instances when the exposure is reset to zero The salt_ex_time must be zero for a period dt for the exposure to be reset to zero The sectionflux statistic is designed to calculate the integral of the flux of a tracer over a defined spatial area and time interval The spatial area may be a vertical curtain in the e1 z or e2 z plane or a horizontal layer in the e1 e2 plane The spatial area is defined by a list of i j coordinates input via ascii file with an optional top and bottom layer included If the top and bottom layer are not present the section is integrated over the entire water column The user must specify in which direction the flux is to be calculated e g u1 u2 or w it is the users responsibility to ensure this direction is perpendicular to the plane of the section e g a flux in the u1 direction must have a section defined in the vertical e2 z plane or a flux in the w direction must have a section defined in the horizontal e1 e2 plane Note that the section must be defined along constant e1 e2 or z coordinates if the section is defined across e1 e2 or z planes then the spatial integral will nor be co
54. in conjunction with the FILEIN attribute and the time scale of the adjustment in the boundary list eg BOUNDARYO ETA NOTHIN FILEIN BOUNDARYO ADJUST_FLUX 60 seconds BOUNDARYO DATA data_ets nc A default timescale mat be specified by setting ADJUST_FLUX lt 0 this default time scale is given by see Herzfeld and Andrewartha 2011 20 08 2015 Page 48 of 185 Version 1 00 SHOC User Manual A dual time scale may be implemented where the tidal component is relaxed toward using a short time scale and the low frequency component using a longer time scale This is invoked using BOUNDARYO ADJUST_FLUX 60 seconds Long time scale BOUNDARYO ADJUST_TIDE 2 seconds Short time scale Often the short time scale is that of the barotropic time step and the long time scale is the default time scale The velocity forced boundary conditions may specified in a simplified format BOUNDARYO NAME Offshore BOUNDARYO TYPE ul BOUNDARYO BCONDO NESTIWAY data_l nc data_2 nc data_n nc bdry_uv_nor nc bdry_uv_tan nc Where data_ lt n gt nc file containing elevation temperature and salinity data at the cell centre Other tracer data is also required if the tracer OBC is active There must be at least one of these files listed bdry_uv_nor nc file containing east and northward velocity components u v at the normal velocity boundary face bdry_uv_tan nc file containing east and northward veloci
55. interpolation for other values of the absolute difference For the exponential case a function rate exp amp dv I is used where av is the difference between modelled eta and that read from infile nc and amp dv ln tc The relaxation constant will therefore vary spatially and temporally throughout the domain and simulation An example is included below where dv 0 5 m and tc 5 days a N o o CH T T L ol T Relaxation constant days 0 i n 0 1 2 3 4 5 6 7 8 9 10 Sea level difference m A relaxation rate linear in time may be specified using eta_relaxation_time_constant temporal dv tc units dv2 tcz units In this case the relaxation rate is tc units at dv days relative to the TIMEUNIT changing linearly to tc units at dv days then thereafter capped at tc units 20 08 2015 Page 66 of 185 Version 1 00 SHOC User Manual Depth based relaxation methods analogous to tracer relaxation see Section 4 9 2 are also available In these cases the sea level increment is saved to a 2D tracer eta_inc These methods are invoked using eta_relaxation_time_constant depth dv tc units dv tc units eta_relaxation_time_constant exp_depth ap tc units du tcz units eta_relaxation_time_constant cos_depth d tc units d tc units Often the relaxation elevation does not contain tidal variation If the model includes tidal forcing this must be removed before relaxation
56. m zZ coordinate_type Z2 Bach record and dimension has a unique T X Y and Z coordinate associated with it The coordinates are stored in units of m double salt nrecords nk nj ni salt units practical salinity units salt long_name Salinity salt coordinates t x Y 2 D I In the above example the salinity variable represents a four dimensional gridded data object The coordinates variable associates with this the t x y and z coordinate information Note that all dimensions used in the salnity variable are collectively found in the coordinate variables and there are no additional dimensions The optional analytic attribute should be specified for coordinate systems where a simple analytically defintion is possible e g rectangular grids The inclusion of an analytic attribute permits faster and more accurate conversion between coordinate and indice space SHOC currently understands both rotated rectangular and polar grids The attribute should be associated with each coordinate variable To define an analytic attribute for a rectangular grid use the following syntax var analytic rectangular ioff joff ni nj x0 yO dx dy rot ioff I offset within the grid 0 is grid edge 0 5 is centre joff J offset within the grid 0 is grid edge 0 5 is centre ni number of grid points along i dimension one more than number of cells nj number of grid points along j dimension one more t
57. mass fluxes for tracers in the transport model so that the global fill factor is adjusted to reflect extra mass that would need to be added or subtracted if volume conservation were achieved in the domain In practice continuity is not achieved in the 3D model at open boundary locations since velocity and elevation are prescribed independently via OBCs and these OBCs rarely honour continuity e g a radiation condition on elevation is often used with a no gradient condition on normal velocity and zero tangential flow leading to zero divergence but non zero change in elevation This can corrupt the above computation therefore fis computed excluding open boundary cells with boundary fluxes computed at the first interior location to open boundaries The open boundary adjustment is invoked by including OBC_ADJUST in the FILL_METHOD e g for MONOTONIC filling FILL METHOD MONOTONIC OBC_ADJUST If the MONOTONIC transport mode is invoked then a 2D diagnostic variable vol_cons is written to the output files which contains the volume error of each water column expressed as a percentage of total volume in each water column This volume error is the difference between the volume at the end of a time step and the sum of volume at the start of the time step and volume flux divergence into the water column If DIAGNOSE is included in the FILL_METHOD then a time series file containing the mass that must be added or subtracted to the domain for
58. means is reset to zero This may result in inaccurate means when restarting and can be avoided by explicitly setting the time counter to its correct value since the last re setting of the means using MEANS_OFFSET lt time gt e g lt time gt 10 days is the time Since the last reset occurred The default is no calculation of mean quantities If the VEL3D flag is invoked then three additional tracers corresponding to the mean 3D velocity in the e e and z directions must exist These tracers are automatically generated by SHOC when the MEAN flag is invoked but may be over ridden by manually specifying any of the following tracers in the parameter file TRACER name ulmean TRACER long_name ean ul velocity TRACER units ms 1 TRACER diagn 0 TRACER name u2mean TRACER long_name ean u2 velocity TRACER units ms 1 TRACER diagn 0 TRACER name wmean 20 08 2015 Page 99 of 185 Version 1 00 SHOC User Manual RACER long_name Mean w velocity RACER units ms 1 RACER diagn 0 If the FLUX flag is invoked then the mean values of the tracer fluxes section 4 30 1 are calculated for the respective flux tracers hence additional flux tracers must also be specified If the TENDENCY flag is set then the contributions to the momentum balance are averaged for the respective tendency tracers see section 4 30 10 The VEL2D and WIND flags generate means of the 2D velocity and wi
59. nearest wet cell for eta 2D and 3D tracers Output may be filtered before being dumped by using fileO filter avarge3 9 point convolution smoothing filter average5 25 point smoothing filter weighted3 9 point Shapiro filter shapiro3 9 point Shapiro filter weighted5 25 point weighted filter shuman3 9 point Shuman filter highpass3 9 point high pass Laplacian filter Filtering is useful for the update of coarse resolution grids when using 2 way nesting 4 31 7 Multi dumpfiles Dump files may be specified using a system analogous to the multi netcdf input specification Section 4 30 2 in this case a valid text file is specified for Out put Files with the following format OutputFiles df txt Name of the multi dumpfile text file With df txt containing for example multi dumpfile version 1 0 nfiles 2 filed standard txt filel simple txt Each of the text files standard txt and simple txt then contains a list of output files as described in Section 4 30 6 e g In standard txt OutputFiles 2 fileO name out nc fileO type standard FileO tstart 0 days FileO tinc 1 day fFileO tstop 44 days fFileO bytespervalu 4 fileO vars ALL filel name out_surf ne filel type standard fFilel tstart 0 days fFilel tinc 1 day filel tstop 44 days filel bytespervalu 4 filel vars eta temp salt ul u2 In simple txt OutputFiles 1 fileO name out nc fileO type simple fileO tstart 0 days
60. of sound speed changes The gradient of sound speed is computed with a 4 order approximation Where C is the sound speed k is the vertical index and his the layer thickness Layers k and k 1 are identified where dcdk dcdk lt 0 and the sound channel depth D is then given by D d dcdk d _ d dedk _ dcdk where d is the depth of layer k Sonic depth and sound channel depths are provided along with the speed of sound when this diagnostic is invoked SHEAR_V The vertical velocity shear magnitude e 1 defined by ov 4 Ou dz du 3z va BUOY_PROD and SHEAR_PROD These diagnostics are assigned from the closure scheme used where buoyancy production B m s and shear production P m s are defined by e g Burchard et al 1998 eqn 9 P V u dz u dz B K_ N where N is the Brunt Vaisala frequency see above Note that these diagnostics are extracted directly from the mixing scheme used and may differ for different schemes e g some schemes add a correction for internal wave shear to P SPEED_2D Depth averaged current speed ms given by Ul JU U U U SPEED_3D Three dimensional current speed ms 1 given by x u Ju u v v SPEED_SQ Three dimensional current speed squared me given by eae H u U v Tu WIND_CD The momentum drag coefficient given by the function
61. of time series outputs TSPOINTS 2 Parameters for each time series point TSO pname MP1 ts Filename prefix TSO location 319672 69 5758871 98 4 Location X Y 2 TSO dt 1800 seconds Output interval TSO reference surface reference level TSO vars salt temp Tracer variables output TSO type simple Velocity output type TS1 pname MP2 ts TS1 location 319672 69 5758871 98 12 75 TSLedt 0 5 hour TSO reference bottom The reference level is determined by the following TSO reference surface referenced to the free surface TSO reference msl referenced to mean sea level TSO reference bottom referenced to the bottom An output type of simple will cell centre the velocity variables and rotate them onto the east west north south axis A standard type will print the velocity at the cell face relative to the e1 e2 grid orientation i e as they are used by the model The simple type is the default The default value is reference msl If the reference level is surface then output will always occur at the specified depth below the free surface and if the free surface is fluctuating may not always be in the same cell If the reference level is ms1 then output will be the specified depth below the undisturbed sea surface and will always be in the same cell if it is wet Note that the depth below the free surface may change in this case If the reference level is bottom then output is the specified depth above the bottom
62. options Since vertical velocity is a diagnosed quantity computed from the volume fluxes which are accessible in the FFSL transport mode it is possible to reconstruct the vertical velocity distribution This is the recommended approach and is achieved by using CONSERVATION W Enforce w conservation The vertical velocity may be recomputed only if it does not violate the Lipschitz condition by using CONSERVATION W WSTAB Enforce stable w conservation If this occurs then the tracer vol_cons will be assigned the value 1 at that water column Sea level may be similarly recomputed in this case sea level is updated to the computed value if that value and the value in the transport files differ by some threshold currently 1x1 0 m This is invoked using CONSERVATION ETA Enforce N conservation If this occurs then the tracer vol_cons will be assigned the value 2 at that water column If vertical velocity or sea level are re computed enforcing conservation then any water fluxes input via point sources or sinks must be accounted for These cannot be read in during the transport simulation in exactly the same manner as during the hydrodynamic simulation due to differences in time stepping and are therefore also saved to the transport file during the hydrodynamic simulation To minimize file size these volume fluxes are saved to the vertical velocity variable in the transport file if point sources are specif
63. output leO tstart 0 days Output start time rel tinc 1 hour Output interval 15 Page 121 of 185 Version 1 00 SHOC User Manual filel tstop 44 days Output stop time filel bytespervalu 2 Output as shorts filel vars eta salt temo Limited variables These fields are optional if they any are not specified t then the full range is used for that dimension filel i_range 60 70 Cells 60 to 70 along I filel j_range 13 18 Cells 13 to 18 along J filel k_range 0 45 Half water column If the file name is appended with _surf nc then only the topmost layer of the grid dumped to file e g equivalent to lt file k_range 20 20 gt fora 20 layer model If tstart and tstop are absent then these values assume the specified START_TIME and STOP_TIM respectively E The following output intervals are also supported fileO tinc YEARLY Output occurs on 1 Jan every year fileO tinc SEASONAL Output occurs on 1 March for summer 1 June for autumn 1 September for winter 1 December for spring 1 fileO tinc MONTHLY Output occurs on 1 day of the month An option exists to automatically chunk netcdf output DAILY MONTHLY or YEARLY as follows filel name out nc filel chunk DAILY or MONTHLY or YEARLY In the above case there will be multiple output files created with the date stamp as a suffix out_2011 02 01 nce out_2011 02 02 nc Note that there may not necessarily be one f
64. radiation open boundary condition and is invoked using BOUNDARYO BCONDO NEST_FLA ts nc eta nc uvav_nor nc uvav_tan nc Where ts nc is a file containing temperature and salinity data eta ts is a file containing sea level data uvav_nor nc is a file containing normal depth averaged velocity data and uvav_tan nc isa file containing tangential depth averaged velocity data The Flather OBC conforms to the following specification BOUNDARYO BCOND_ELE FLATHR FILEIN GRAVTY BOUNDARYO BCOND_NOR NOGRAD BOUNDARYO BCOND_NOR2D FLATHR CUSTOM BOUNDARYO BCOND_TAN GRAVTY BOUNDARYO salt FILEIN BOUNDARYO temp FILEIN BOUNDARYO STAGGER INFACE BOUNDARYO custom ul uvav_to_ulav uvav_nor nc or u2 BOUNDARYO DATA Lance eta nc A standard open boundary configuration may appear as BOUNDARY O NAMI Offshore BOUNDARYO TYPI ul BOUNDARYO BCONDO NESTIWAY data_l ne bdry_uv_nor ne bdry_uv_tan nc BOUNDARYO BCOND1 RIVER flowfile ts data ts Di D 20 08 2015 Page 62 of 185 Version 1 00 Any additional boundary specification e g INVERSE_BAROM applied to th SHOC User Manual T H T ER NSPONGE_HORZ is also e standard boundary 4 11 Advection Schemes The specification of the advection scheme for tracers is set via the flag TRA_SCHEME in the parameter fi ORDER1 VANLEER ORDER2 ORDER2_UW ORDER4 Q Q Q L Aw Gq H Q KES UI
65. ramp may be applied to the heatflux where zero heatflux is applied before the time specified e g Do not apply a heatflux before 10 days relative to the TIMEUNIT HEATFLUX_RAMP 10 days It is possible to distribute the short wave radiation throughout the water column by specifying an attenuation coefficient SWR_LATTENUATION if this is absent all short wave radiation is included in the surface boundary condition It is possible to partition a fraction of the short wave radiation to be input as the surface boundary condition with the remainder distributed throughout the water column according to the attenuation coefficient This is achieved by specifying a transmission coefficient SWR_TRANSMISSION if this is absent it is assumed all short wave radiation is depth distributed Specify short wave radiation attenuation and transmission parameters SWR_ATTENUATION 0 2 Attenuation SWR_TRANSMISSION 0 5 Fraction for depth distributed swr Attenuation and transmission may be set to standard water classes according to Mellor 1992 e g Set the water type to Type II water WATER_TYPE TYPE TI 20 08 2015 Page 72 of 185 Version 1 00 SHOC User Manual Attenuation and transmission are set according to the table below Water Type Attenuation Transmission 0 037 0 32 IA 0 042 0 31 IB 0 056 0 29 II 0 073 0 26 ll 0 127 0 24 Note that SWR_TRANSMISSION 1 means that all
66. relative to UTC or UTC hours seconds 20 08 2015 Page 151 of 185 Version 1 00 SHOC User Manual All text enclosed within square brackets is optional 11 1 2 Utilities The time series format is well suited for use with standard plotting packages such as gnuplot or Matlab Two Matlab scripts tsheader and tsread have been installed in the Matlab software repository directory home software matlab e tsheader reads the header from a time series file and returns a vector of structures each containing the time series file attributes as fields of the structure e tsread reads the header into a structure and returns a column vector of time s and a matrix of the data records 11 2 NetCDF time series The netCDF file format is commonly used by many research organizations for the storage of time varying gridded data in a manner that it is plaform independent NetCDF also permits the association of attributes with any variable this feature is extensively used by SHOC to describe the units missing values coordinate conventions etc The netCDF library was written by Unidata http Awww unidata ucar edu and can be download from ftp ttp unidata ucar edu pub netcdf netcdf tar Z SHOC requires version 3 or higher All SHOC input output dumpfiles are stored using netCDF 11 2 1 Units Units for netCDF variables are handled the same as for ASCII time series files 11 2 1 1 Coordinate conventions The netCDF library prov
67. see the INSTALL file Note that all packages depend on the udunits and netCDF packages Please ensure that udunits and netCDF have been installed before attempting to compile or install either SHOC or the libraries netCDF and udunits are available from Unidata http www unidata ucar edu SHOC resides in a directory structure called the Environmental Modelling Suite ems which also contains source code for various supporting libraries and the sediment transport and ecology models Once ems is installed on the computer it must be configured During this step a script checks for the presence of external and internal libraries searches for compilers linkers and other utilities required to compile the source code If configure was successful it will generate a makefile which can be used to build the model and related utilities The configure script is run as follows conf configure By default the configure script searches for all architecture independent files e g netCDF libraries in the directory usr local If an alternate path is required use conf configure prefix PATH For a full list of configure s command line options enter configure help Once ems is configured all source code is compiled using make The libraries and executables are installed using the make install command The directories are cleared of object files and executables by using make clean command Additionally make distclean removes any files created
68. setup txt and netCDF output files The sequence is invoked via SEQUENCE n The following field is then printed in the file setup txt and as a global attribute in all output netCDF file Run n If a setup txt file is entered as the input to SEQUENCE and the file contains Run n then the run identifier recorded in the setup txt for the current run is Run n 1 Sets a unique identifier that is tagged in output lt n gt is a floating point number e g 1 1 ID_NUMBER lt n gt Page 17 of 185 Version 1 00 SHOC User Manual Applies a Shapiro filter to selected tendencies FILTERING ADVECT 1 order Shapiro filter applied to momentum advection tendencies Sets the model configuration to be V1562 with previous versions of SHOC Backwards incompatibility may be due to bugfixes in the code or implementation of improved numerics The backwards compatibility is currently defines as COMPATIBLE V1246 Pre v1246 global boundary cells include R_EDGE and F_EDGE OUTSIDE cells V1283 Pre v1283 Numerous bugfixes for multiple windows are not included Refer to Revision History Nov 16 2009 v1283 1331 v1562 Pre v1562 swr added explicitly to the water column V1598 Pre v1598 wtop uses 2D detadt and low order approximations Ul
69. shortwave radiation is depth distributed Alternatively the dual extinction parameterization may be used where separate extinction coefficients are used for the surface and deeper layers A fraction determines the partitioning between surface and deep attenuation Specify dual short wave radiation attenuation parameters SWR_ATTENUATION 2 8 Surface attenuation SWR_ATTENUATION_DEEP 0 04 Deep attenuation SWR_FRACTION 0 58 Fraction for surface attenuation Where short wave radiation penetrates to the bottom it is assumed that all surplus radiation below the sea floor is absorbed into the sea bed with no additional heating of the bottom layer This may be altered using the SWR_BOT_ABSORB flag where a default value of 1 assumes the above while a value of 0 assumes all surplus short wave radiation is input into the bottom layer The reality is that bottom reflectance would supply some heat to the bottom layer and the value SWR_BOT_ABSORB of would be somewhere between 0 and 1 This flag may be used as a tuning parameter e g Specify fraction of surplus radiation input into bottom layer SWR_BOT_ABSORB 0 5 Bottom absorbtion The may be input as a 2 D spatially varying field by supplying a netCDF file as input e g SWR_BOT_ABSORB babs nc 2D varying bottom absorbtion Or a list of ascii values in the parameter file e g for a 2 x 2 grid SWR_BOT_ABSORB 4 2x2 4 values 0 9 0 8 0 0 0 5 List of values
70. spaced radii of the same circles The scale is true along two standard parallels The default ellipsoid is wgs84 and false eastings and northings are OE ON Defined by proj icc lon_0 lt long gt lat_O lt lat gt lat_1 lt lat gt lat_2 lt lat gt Ion D Central meridian lat_O Central latitude lat_1 First standard parallel latitude lat_2 Second standard parallel latitude 20 08 2015 Page 21 of 185 Version 1 00 SHOC User Manual Mercator The Mercator map projection is a cylindrical and conformal map projection where the cylinder is aligned north south It has the properties that all meridians are equally spaced straight lines parallels are unequally spaced closer at the equator and Rhumb lines are down as strait lines The default ellipsoid is wgs84 and false eastings and northings are OE ON Defined by proj merc lon_0 lt long gt Ion 0 Central meridian Other projections SHOC also supports a number of other projections if compiled and linked with the USGS PROJ 4 projection library The list of projections supported by PROJ 4 are described below For a full description of each projection and their arguments please consult the PROJ 4 manual Evenden 1995 Projection Description aea Albers Equal Area aeqd Azimu
71. stored in window_map txt and the spatial distribution of all windows in window_geom txt The more tags Set library log level listed the more messages a messages are printed to fil order of output detail sup print information on majo print information on mino non fatal warning informa print high level debug in D aE rint low level debug inf nformation on time spent for development only Set debug level Supported re printed All e runlog In ported tags are r general events r general events tion Formation ormation in routines debug tags are print all debug information list time unit conversions list model time list next dump list particle resets time time initialisation info slave initialisation info ecology info sediment info 4 4 4 4 master 4 4 shoc g input prm in nc debug init_m init_w shoc p input prm 1 main info warn window_log on It is often useful to run the model as a background process with the output captured into a file How this is done depends on the UNIX shell being used For a csh the following command is sufficient shoc p prmname gt amp 20 08 2015 logfile amp Page 10 of 185 Version 1 00 3 3 1 SHOC User Manual Model setup Setting up a model application There are many steps required to successfully configure SHOC Following are some of t
72. than velocities used to calculate the streamline This approach may increase execution speed since the streamline origin is no longer required to be calculated If multiple grids are used then potentially slow input of velocity information for the source grid may also be avoided The STREAMLINE data files may be created when running the transport mode normally and dumping the variables origin p q and r to SPARSE formatted files Section 4 32 6 This file is then used to specify the TRANS_DATA using the STREAMLINE option Note that these TRANS_DATA input files to the STREAMLINE option cannot be interpolated in space and time and must be read in exactly as written hence the use of the SPARSE data format Note also that this means that if STREAMLINE data files are created the user is locked into using the time step corresponding to that for which the files were created When using the STREAMLINE option the input of data from file and transport computation are out of sync necessitating reading TRANS_DATA information one time step in advance For this reason when creating STREAMLINE data files the stop time should be at least one time step longer than the STREAMLINE transport is to run for Open boundary input is required if global MONOTONIC fills are used so mass flux through open boundaries can be calculated This information may be saved to file und
73. the absolute difference The relaxation constant will therefore vary spatially and temporally throughout the domain and simulation For exponential relaxation TRACERO relaxation_time_constant exponential dv tc units In this case the relaxation constant is given by rate exp dy log tc d f where d is the absolute difference in modelled tracer and that read from infile nc e g for dv 0 5 and tc 5 day dv 0 5 tc 5 days 20 T T T T T T T T T mt 4 10 4 Rate days 0 L 1 fi 1 f 1 1 M 0 1 2 3 4 5 6 7 8 9 10 Depth m A depth scaled linear relaxation may be specified using 20 08 2015 Page 35 of 185 Version 1 00 SHOC User Manual TRACERO relaxation_time_constant depth dv tc units dv tc units In this case if the depth is du then a relaxation constant of tc units is used and if the depth is dv then a relaxation constant of tc units is used with linear interpolation for other values of the depth The relaxation constant will therefore vary spatially throughout the domain and simulation Depths are truncated to the limits of dv and du Note that all depths should be negative i e dv and dv lt 0 0 An exponential depth dependent rate may be specified using TRACERO relaxation_time_constant exp_depth a tc units d tc units The relaxation rate is given by rate tc tc exp depth a tc tc where tc tc exp d a Examples for different d
74. the boundary value will assume that resulting from the solution to the continuity equation This is useful if boundaries are forced with normal and tangential components of velocity or the custom river OBC is imposed The NOTHIN boundary condition may be combined with a radiation condition e g BCOND_ELE NOTHIN GRAVTY in which case the prognostic value on the boundary is relaxed to a radiation condition using the RELAX_TIME timescale Alternatively the prognostic value may be relaxed to data NOTHIN FILEIN using the RELAX_TIME timescale 20 08 2015 Page 52 of 185 Version 1 00 SHOC User Manual 4 10 15 Sponge Layers As a simple way of damping high frequency noise in the model and sometimes to aid numerical stability it is possible to apply a region of greatly increased horizontal viscosity just inside any type of open boundary This is done by defining the parameter NSPONGE_HORZ followed by the number of cells in from the boundary that the sponge will occupy Specifies that viscosity is greatly increased for 4 cells inside this open boundary BOUNDARYO NSPONGE_HORZ 4 Within each sponge cell the horizontal viscosity is set near to the maximum numerically stable value for the particular grid and integration time step default or a multiple of the viscosity value at the boundary using e g Set the maximum value of the sponge zone equal to 5 times the boundary value B
75. therefore ensures that mixed layer depths are consistent between the tracer and density This is invoked using TRACERO data dens_scale file nc vl v2 lt code gt Where v1 is the depth at which the tracer value is equal to that in file nc at the same depth and v2 is a scaling factor for the profile if v2 lt O the profile is inverted 20 08 2015 Page 32 of 185 Version 1 00 SHOC User Manual Below depth v1 the profile in any layer k is determined by adding v2 x density gradient to the concentration in the layer k 1 This is iteratively computed down through the water column Above depth v1 the profile in any layer k is determined by subtracting v2 x density gradient to the concentration in the layer k 1 This is iteratively computed up through the water column If lt code gt c then a copy of the values in file nc is used for the profile below depth v1 and if lt code gt t then the profile values are truncated to those in file nc below the depth v1 if the profile values become greater than those in file nc This formulation is the most general for density scaling and is supported by an equivalent scaling at open boundaries see Section 4 10 18 other methods may be used that are not supported by equivalent open boundary methods TRACERO data dens_scale vl v2 Here if v2 gt 0 then v1 is the surface tracer concentration and the profile in any layer k is determined by adding v2 x density gradient to the concentr
76. this option set the create_scale attribute to a scaling map file the format of which is described below e g TRACER2 create_scale moor_temp map With the file moor_temp map with the format VAR_NAME temp name of the variable to scale VAR_UNITS Degrees_C Units of the variable OUT_NAME scale_temp_s Name of the scaling variable as it will appear in the output file 4 OUT_FILE scale_profile nc Output file name FORCING profile nc The initialisation file for the variable VAR_NAME that requires scaling May be a multifile REF_VALUE 1 Optional reference valu 20 08 2015 Page 38 of 185 Version 1 00 SHOC User Manual REF_DEPTH 100 Optional reference depth m BOT_VALUE temp_init nc Optional bottom value nfiles 2 filed moorl ts 147 34 43 05 15 0 temp filel profl ne 147 34 43 05 profile temp In the above example it is assumed that there exist files profile nc moorl ts and profil nc that contain the variable temp with units Degrees_c The file profile nc is the initialisation file for the variable temp used in the model and this file is known to contain errors which are required to be corrected by scaling to measured data contained in data files moorl ts and profl nc The geographic longitude and latitude locations and depth depth lt 0 for each mooring file are supplied e g fileo Alternatively a profile at a geographic location may b
77. to reach a solid boundary within a certain number of sub steps currently hardwired to 110 The latter case arises if a large velocity v is normal to a solid boundary which advects the particle into the boundary The model will attempt to calculate the particles position at a future time by adding the distance s the particle moves over a time interval At where s vAt If v is large then the model successively reduces At to resolve the particles position near the boundary If the position cannot be resolved after 110 reductions of At it is assumed the particle has moved through the boundary and becomes lost An example of this may be a particle settling into the sediments If settling of a particle is invoked and a particle is attempted to be advected through the bottom then the vertical diffusion is modified to counteract such effect Consequently these particles are not lost but remain close to the bottom 4 28 2 Source Colour Individual sources can be identified by the CcolourBit parameter with valid ranges between 2 and 15 the colourbit values 0 and 1 are used to flag inactive and lost particles These data are written to the output file making it possible to display particles from multiple sources and identify each individual source by colour 4 28 3 Age The age of each particle since the release time may be computed When a particle becomes lost the age is reset to zero In order to minimise output file size the age of particles are s
78. tracers use BOUNDARYO RELAX_ZON BOUNDARYO RELAX_ZON __TRAn NN _ name NN D D where n is the tracer number and name is the tracer name 4 10 13 Linear Conditions The advective and horizontal diffusive terms on the boundary may be omitted thus linearizing the boundary momentum balance This is invoked via BOUNDARYO BCOND_NOR LINEAR Linear normal boundary velocity BOUNDARYO BCOND_TAN LINEAR Linear tangential boundary velocity For normal velocities on southern or western boundaries this is not particularly successful see SHOC Science Manual Section 4 5 6 A more successful linear strategy is to shift the stagger for normal velocities one cell into the interior and linearize the normal velocity at this location This may be accomplished via BOUNDARYO BCOND_NOR NOGRAD BOUNDARYO LINEAR_ZONE_NOR 1 The linear zone make the momentum balance linear one cell into the interior of the model This can be extended to any number of cells interior to the boundary and may be applied to tangential components also BOUNDARYO LINEAR_ZONE_NOR n Linearize normal velocity n cells into the model interior Typically n 3 BOUNDARYO LINEAR_ZONE_TAN n Linearize tangential velocity n cells into the model interior 4 10 14 No Action Taken NOTHIN The boundary condition NOTHIN will not alter the value of the prognostic value on the boundary For example if BCOND_ELE NOTHIN
79. user to access this functionality The statistics available to be performed on 2D or 3D tracers are fluxel fluxe2 luxw eanfluxel eanfluxe2 eanfluxw ea variance stdev corr COV sum diff max min vmax vmin vint vmean vdiff copy sectionflux rmse 20 08 2015 Page 161 of 185 Flux of 3D tracer in the el direction usage RACER lt n gt tracerstat fluxel lt 3Dtracer gt Flux of 3D tracer in the e2 direction usage TRACER lt n gt tracerstat fluxe2 lt 3Dtracer gt Flux of 3D tracer in the vertical direction usage RACER lt n gt tracerstat fluxw lt 3Dtracer gt Mean flux of 3D tracer in the el direction usage RACER lt n gt tracerstat meanfluxel lt 3Dtracer gt optional TRACER lt n gt dt lt m gt days Mean flux of 3D tracer in the e2 direction usage RACER lt n gt tracerstat meanfluxe2 lt 3Dtracer gt optional RACER lt n gt dt lt m gt days Mean flux of 3D tracer in the vertical direction usage TRACER lt n gt tracerstat meanfluxw lt 3Dtracer gt optional RACER lt n gt dt lt m gt days Mean of 2D or 3D tracer usage RACER lt n gt tracerstat mean lt tracer gt optional RACER lt n gt dt lt m gt days Variance of 2D or 3D tracer usage RACER lt n
80. viscosity KZ0 le 5 Background diffusivity ZS D Surface length scale The Richardson number criterion in this scheme can create grid point noise when background mixing coefficients are imposed due to the flux Richardson number being greater than the critical Richardson number This can create grid point noise in the temperature solution if a heattflux is imposed A Shuman filter may be applied to the mixing coefficients to remove this noise by setting Smooth Vz and Kz using a Shuman filter SMOOTH_VzKz YES 4 21 4 Mellor Yamada 2 0 Estuarine This scheme uses an alternate mixing length parameterisation for the Mellor Yamada 2 0 mixing scheme Burchard et al 1999 Eifler and Schrimpf 1992 Demirov et al 1998 This is based on a three layer system where surface and bottom mixed layers are intersected by a stably stratified interior layer Required parameters to invoke this mixing scheme are given below Use the modified Mellor Yamada level 2 scheme IXING_SCHEME mellor_yamada_2_0_estuarine scheme type ZS 0 6 surface length offset LMIN 0 01 Minimum stratified length scale E 1 Mixed layer tuning parameter VZO 0 001 Background viscosity KZO 0 000001 Background diffusivity This type of scheme displays better results than Mellor Yamada 2 0 or k e for estuarine applications where a three layer system commonly exists A large degree of flexibility exists in tuning this mixing model where chang
81. 0 STO stime 5 days STO stype HIPR STO sp le 5 STO ss 2000 STO si 20 STO sj 20 STO se 8 STO sr 90 STO stime 10 days STO stype HIPR STO sp 7e 4 ST0 ss 3000 STO si 40 STO sj 20 STO se 0 STO sr 180 This system propagates through the domain along the E axis centered on 20 At day 0 it assumes the form of a circular anticyclone at day 5 it strengthens contracts in size and becomes elliptic with the major axis aligned in the north south direction By day 10 it has weakened and become larger again with a circular shape The wind stress field is updated according to this progression at daily intervals If a wind file is specified in conjunction with the storm system specification then the wind and storm components are added to produce the wind stress vector 20 08 2015 Page 69 of 185 Version 1 00 SHOC User Manual 4 14 Atmospheric pressure A mandatory parameter sets the background air pressure as follows Background air pressure in Pa AMBIENT_ATR_PRESSURE 101000 This value sets the air pressure throughout the model domain Because this value is uniform it is not dynamically significant unless time and space varying pressure forcing is also specified as outlined below Models covering larger domains or including phenomema such as severe storms may require such atmospheric pressure inputs These are specified by the following optional parameters A time series file containing the variable p
82. 000 01 01 00 00 00 08 t coordinate_type time double x_centre j_centre i_centre x_centre long_name Longitude at cell centre x_centre coordinate_type longitude x_centre units degrees_east x_centre projection geographic double y_centre j_centre i_centre y_centre long_name Latitude at cell centre y_centre coordinate_type latitude y_centre units degrees_north y_centre projection geographic 4 10 22 Mixing coefficient boundary conditions Open boundary conditions can be imposed on the vertical mixing coefficients Vz and Kz The same boundary conditions applicable to tracers may also be applied to Vz and Kz with the exception of FILEIN and CUSTOM If the boundary condition type for mixing coefficients is unspecified then the default condition of NOTHIN is imposed which assigns the mixing values on the open boundaries via selected mixing scheme computations Since these computations usually involve vertical velocity shear and density gradients on the open boundary all of which use values derived from other open boundary conditions it is possible that error is introduced into vertical mixing coefficients on the open boundary in this case The velocity computations interior to the open boundary use the vertical viscosity on the open boundary hence it is possible for this error to propagate into the domain Under these circumstances it is preferable to specify the mixing coeffi
83. 1 3 Model variable initialisation At the start of a model run the model variables are initialised for each grid using a netCDF input file which is either generated from the parameter file using the g option or obtained from the output of a previous run This initialisation input file for each grid is specified as follows INPUT_FILE in nc The input file may contain more than one record the record is selected based on the START_TIME parameter for this run The time in the datafile must match exactly 4 31 4 Model variable output SHOC provides two mechanisms for recording its results ASCII time series of values as computed for particular locations and as an n dimensional netCDF datafiles 4 31 5 ASCII time series ASCII time series output files contain values for significant model variables at specific locations A time series file is created for each location in the model domain and records are written at a pre determined interval Currently the output variables include time surface elevation current components 2D and 3D and tracers Non time dependent geometry information is also provided cell centre bottom depth etc in the header Time series output in SHOC are referenced to the free surface mean sea level or the bottom ASCII time series are convenient for comparisons with point observations such as tide gauges or current meters 20 08 2015 Page 119 of 185 Version 1 00 SHOC User Manual Number
84. 2 1 where C is the drag coefficient v is the bottom current speed and p is the density Given a constant eddy viscosity the Ekman depth De is given by Pond and Pickard 1983 p108 D SDV Ar 12 2 2 where V is the eddy viscosity and f is the Coriolis parameter The surface current speed Vo is then given by Pond and Pickard 1983 eqn 9 10 Je V 12 2 3 Dar where ts is the wind stress and the current speed Mu at the Ekman layer depth is Pond and Pickard 1983 p108 V V exp z 0 04V 12 2 4 Therefore using a wind stress of 0 01 Nm on and f plane with f te and V 0 0507 mie the Ekman layer depth De 100m Furthermore using 12 2 3 with p 1025 kom gives Vo 4 33x10 ms and Vp 1 87x107 ms Using the bottom velocity in 12 2 1 and a nominal drag coefficient of Ca 0 003 gives a resistance coefficient of r 0 00058 Linear friction is achieved by setting the parameter UF to a large value and z0 to a low value The value of z0 below which bottom drag is set to the parameter QBFC is given by ZO lt 0 5AZ po 12 2 5 exp x sqrt 1 QBFC 1 20 08 2015 Page 157 of 185 Version 1 00 SHOC User Manual Using the value of QBFC quoted above Z0 lt 7 7x10 Using these values with UF 1 0 provides linear bottom friction with the required resistance coefficient Using the above configuration model results should show an Ekman spiral with velocities rotating clockwise wit
85. 203 236 Orlanski 1976 A simple boundary condition for unbounded hyperbolic flows J Compt Physics 21 251 269 Palma E D and R P Matano 1998 On the implementation of passive open boundary conditions for a general circulation model The barotropic mode J Geophys Res 103 C1 1319 1341 Pielke R A W R Cotton R L Walko C J Tremback W A Lyons L D Grasso M E Nicholls M D Moran D A Wesley T J Lee and J H Copeland 1992 A comprehensive meteorological modeling system RAMS Meteorol Atmos Phys 49 69 91 Romanou A Rossow W B Chou S 2006 Decorrelation scales of high resolution turbulent fluxes at the ocean surface and a method to fill in gaps in satellite data products Journal of Climate 19 3378 Schiller A Godfrey J S 2003 Indian Ocean intraseasonal variability in an ocean general circulation model Journal of Climate 16 21 39 20 08 2015 Page 181 of 185 Version 1 00 SHOC User Manual Simons T J 1974 Verification of numerical models of lake Ontario Part circulation in spring and early summer Journal of Physical Oceanography 4 507 523 Shapiro R 1970 Smoothing filtering and boundary effects Reviews of Geophys and Space Phys 8 359 387 Sommerfeld A 1949 Partial differential equations Lect Theoret Phys vol 6 Academic San Diego Tartinville B E Deleersnijder and J Rancher 1997 The water residence time in the Mururoa atoll lagoon s
86. 5 Version 1 00 SHOC User Manual 18 References Arakawa A and Lamb V R 1977 Computational design of the basic dynamical process of the UCLA general circulation model Methods in Computational Physics 17 Academic Press pp 173 265 Blackadar A K 1962 The vertical distribution of wind and turbulent exchange in neutral atmosphere J Geophys Res 67 3095 3102 Blanc T V 1985 Variation of bulk derived surface flux stability and roughness results due to the use of different transfer coefficient schemes J Phys Oceanogr 15 650 669 Blumberg A F and J Herring 1987 Circulation modelling using orthogonal curvilinear coordinates in Three Dimensional Models of marine and Estuarine Dynamics Ed J C J Nihoul and B M Jamart Elsevier Blumberg A F and G L Mellor 1986 A description of a three dimensional coastal ocean circulation model In N Heaps Ed Three dimensional shelf models Coastal and Estuarine Sciences 5 American Geophysical Union Burchard H K O Peterson and T P Rippeth 1998 Comparing the performance of the Mellor Yamada and the k e turbulence models J Geophys Res 103 10 543 10 554 Bowden K F and P Hamilton 1975 Some experiments with a numerical model of circulation and mixing in a tidal estuary Estuarine and Coastal Marine Science 3 281 301 Bunker A F 1976 Computations of surface energy flux and annual air sea interaction cycles of the North Atlantic ocean Mon Wea Re
87. 990 01 01 00 00 00 10 20 08 2015 Page 111 of 185 Version 1 00 SHOC User Manual COLUMN1 missing_value 999 i COLUMN2 name Total mass COLUMN2 long_name Total mass COLUMN2 units kg COLUMN2 missing_value 0 000000 4 COLUMN3 name Total volume ZE COLUMN3 long_name Total volume COLUMN3 units m3 COLUMN3 missing_value 0 000000 4 COLUMN4 name Total heat ZE COLUMN4 long_name Total heat COLUMN4 units deg C m3 COLUMN4 missing_value 0 000000 4 COLUMN5 name Total salt ZE COLUMN5 long_name Total salt COLUMN5 units psu m3 COLUMN5 missing_value 0 000000 4 Additional tracer totals may be computed by appending the tracer name to the TOTALS diagnostic e g Include silt and Chla in totals diagnostic TOTALS YES silt Chla The additional tracer totals will then appear in the time series Note that temp and salt are always included If a tracer included a sediment component then the total mass is the sum of mass in the water column and the sediment If the tracer is a 2D tracer then the areal mean is reported Finally the volume flux through each open boundary in me is computed 4 30 17 De correlation length scales The de correlation length scales in the e1 and e2 directions can be computed and stored in decorr_el and decorr_e2 respectively This is computed according to Romanou et al 2006
88. ACER5 fill_value 1le 5 TRACER5 valid_range 0 1 TRACERS advect 0 TRACERS diffuse 0 TRACERS diagn I 4 21 6 ke The k e scheme is described by Burchard et al 1998 The specification for this scheme is shown below Use the k schem MIXING_SCHEME VZO KZO MIN_TKE MIN_DISS WAVE_ALPHA 20 08 2015 k e scheme type le 5 Background viscosity le 5 Background diffusivity 7 6e 6 Optional minimum TKE 5 0e 10 Optional minimum dissipation 100 Optional wave a parameter Page 81 of 185 Version 1 00 SHOC User Manual Craig amp Banner 1994 This scheme requires two additional tracers corresponding to turbulent kinetic energy tke and dissipation diss These tracers are automatically generated by SHOC when the k e scheme is chosen but may be over ridden by manually specifying the following tracers e g to change fill values or valid ranges in the parameter file tke tracer TRACER2 name tke TRACER2 long_name Turbulent Kinetic Energy TRACER2 units m2s 2 TRACER2 fill_value 7 6e 6 TRACER2 valid_range 0 1 diss tracer TRACER3 name diss TRACER3 long_name Dissipation TRACER3 units m2s 3 TRACER3 fill_value 5e 10 TRACER3 valid_range 0 1 4 21 7 ka The k scheme is similar to k e except it solves for turbulence frequency rather than dissipation Umlauf et al 2003 Use the k w schem MIXING_SCHEME k w VZO l
89. AL 43 HEI AN ZONE ELE 43 RELAX ZONE NOR 43 HEI AN ZONE AN 43 RIVER EE 112 SCALE Per EE 51 SGAWE 2S xcs et esas E 51 GMOOTH PHASE 43 STAGGER Qu cc r e raaa 37 20 08 2015 Page 183 of 185 TIDALG aii end sie dive einai 48 TIDAL inaire a 47 HDEBG A egeteeetgezeteigedeeatgen ge 47 TRCONG fs aunt iain 45 TRELUX gees Eesen 46 TRPC TRAN ioie enii 50 UPSTRM iawn aie hoe tie ete 45 BRUNT ia acest cotati 91 C CGALC FLUSE R a ae 84 94 CALC PERG Site diese ain 94 CALCDENS zaia a 12 16 CR ais air ina eit 75 84 89 AC MVE tinct anti sawed tells 89 ASIA 89 PASSIVE iii niian 89 VUN GE 89 CFL ODT neni ine ini 89 CLOUD innisis 61 101 CGODEHEADER eee eee 13 COMPATIBLE ssec 17 CORIOLIS risiini 18 90 D DEBUG LOG eegener et iarten 108 DENS MI See MIX_LAYER DEW POINT steartsdnstitttee teeta 59 DIFF SGALE ahunan antipirin 71 DRAG LA CDD 56 DRAG_LAW_COD 1 eee eee eeeeee 56 DRAG LA M A 56 DRAG LA Vi 56 DT 15 56 57 58 59 60 61 62 63 64 85 86 87 112 113 DUMP_WIN_ MAP 14 E e e UE 7 10 61 eta_relaxation file 54 ETAMAX EEN 26 27 EVAPORATION 000000 58 63 101 F FATADA tei 16 FIETERING a et Zeie Ne ea 17 FLUSHING TR 86 FROUDE we i Seinen e 91 G g option 8 11 27 29 30 53 102 120 GPRID REEINEMENT 80 GRIDTYPE GEOGRAPHIC_RECTANGULAR 25 111 GEOGRAPHIC_RECTANGULAR 25 Version 1 00 SHOC User Manual NUMERIC naaoanonnnnnnannnoennnnnnannnoennnnnn
90. CDF file hence if any changes are made to the surface initialisation then a new input netCDF file must be generated using the g option see section 8 Changes to surface initialisation have no effect when running the model using the p option The surface elevation may be explicitly overwritten at a number of arbitrary cells using the SURACE_POINTS list This option is useful for quickly initialising barotropic relaxation experiments e g tsunami modelling The format is as follows SURFACE_POINTS n n number of points in the list i j val i j location and value for point 1 iz j2 valz i j location and value for point 2 in Jn valn Similarly the surface velocity initial condition may be specified using VELOCITY velocity nc Input velocity from netCDF file The initial velocity field can be set to the geostrophic flow using VELOCITY GEOSTROPHIC 4 12 1 Elevation and velocity relaxation Surface elevation may be relaxed to a surface field supplied via a time series or netCDF file using eta_relaxation file infile nc n field to relax towards eta_relaxation_input_dt 1 hour Time interval levation is read from file eta_relaxation_time_constant elevation relaxation time constant The elevation to relax towards is read from the file infile nc at the time interval eta_relaxation_input_dt Every 2D time step the actual elevation is relaxed towards this value using a relax
91. CKES UICKES AGRANGE le Current options are 1 order upwind flux form Van Leer s scheme 2 order flux form 2 order upwind flux form stable for Courant lt 2 Ann order flux form QUICKEST flux form variable grid AD QUICKEST scheme advective form CO QUICKEST flux form constant grid formulation Semi Lagrange scheme For details of these advection schemes see section 5 Herzfeld 2002 The ULTIMATE limiter Leonard 1991 is invoked on the chosen scheme by setting the flag UTLIMATE in the parameter file This limiter eliminates non monotonic behaviour in the solutions and is generally only successful on the higher order advection schemes i e 2 4 order and QUICKEST The ULTIMATE limiter is not invoked by default e g ULTIMATE YES invoke the ultimate limiter ULTIMATE NO no ultimate limiting A choice of advection scheme is also available for momentum This is set via the flag MOM_SCHEM E in the parameter file and the current options are ORDER1 ORDER2 VANLEER ANGULAR ANGULAR3D LAGRANGE Se 20 08 2015 1 order upwind scheme 2 order scheme Van Leer s scheme 2 order flux form angular scheme for momentum As for ANGULAR but applied to 3D momentum only Semi Lagrange scheme Page 63 of 185 Version 1 00 SHOC U
92. CODEHEADER SHOC default version A single line description of the model run This string is written into all output files PARAMETERHEADER NWS 20km rectangular grid Run 1 4 2 Windows SHOC is designed to operate in a distributed processing environment where domain decomposition is performed on the grid to divide it into a number of partitions or windows which are solved on different processors The number of windows used is set via Indicates the number of windows in the model domain WINDOWS 2 Generally the number of windows is equal to the number of processors available If SHOC is to operate on a single processor the WINDOWS 1 The domain decomposition be a striping or blocking method or may be any arbitrary congregation of grid points This allows total flexibility when decomposing geographically complex domains The distributed processing procedure requires common information to be transferred between windows hence by minimising the size of boundaries between windows e g by utilizing the geography and placing window boundaries across narrow regions the amount of data transferred is minimised and execution speed increases The window partitioning method is specified using the WINDOW_TYPE where WINDOW_TYPE STRIPE_E1 Stripe in the el direction default WINDOW_TYPE STRIPE E2 Stripe in the e2 direction WINDOW
93. DT value of SEASONAL or MONTHLY is also supported for seasonal or monthly means respectively These quantities may be written to file using the SEASONAL or MONTHLY netCDF file output time increments see Section 4 32 6 here the mean dumped at the start of the season corresponds to the mean computed over the previous season ditto for months e g output on 1 March corresponds to a mean computed over the previous summer for SEASONAL means and means computed over February for MONTHLY means Additionally if SEASONAL Of MONTHLY means are written to netCDF file at the same interval as MEAN_DT e g fileO tinc SEASONAL with MEAN_DT SEASONAL then the mean will be cumulative over the season for successive years e g for a multi year run the mean dumped to file on 1 March will be that of all previous summers for SEASONAL means and that of all previous Februaries for MONTHLY means If the mean is not desired to be cumulative in this fashion then the mean for each season of each year should be saved using MONTHLY dumps for SEASONAL means The means computed are running means where the value present in the output file is the mean from the start of the computation period to that point in time When the MEAN_DT time is reached the mean values are reset to zero and the running mean begins again If a restart is performed the running mean values are correctly populated from the restart file but the time counter for the
94. EATION and then Create New Boxes to draw required boxes over the bathymetry Note that instructions are provided in the matlab window 5 Click on Edit Boxes to optimize the regions Click on Partition SHOC to partition all of the water cells into the 2D regions 7 Clickon Assign Box Layers as many times as there are regions that are required to be a function of depth e g enter a vector suchas 4 0 20 40 100 to create 3 layers in Box 4 with layer faces at 0 20 40 and 100m A maximum of 5 layers can only be assigned to any box The depth slider can be used to scan layers and observe the different 3D regions 8 The output is saved to a bnc file This can be read back via Read netcdf File ata later date to make more changes by repeating the above procedure D Any bnc file that SHOC attempts to read must contain the variable boxnos and have the dimensions i_centre j_centre and k_centre to specify the grid size in x y and z directions respectively Note be sure that bnc files are created for the input file you wish to use lf the variable regionid in the output file shows values of 9999 as region numbers then this is probably not the case and region exchanges may be incorrect A warning is only issued if the grid dimensions in the bnc and input file differ wet cells are not compared To invoke the budgets over the regions use REGION path name bnce Path and file
95. ED_VARS are included in the list of hardwired names and if so then will automatically include that tracer in the tracer list Additionally a 3D diagnostic tracer named tss is automatically generated and 2D tracers named ustrcw_skin and depth_sed Again these additional tracers are hardwired into sediments sediments c and can be expanded as desired The sediment tracer attributes associated with these tracer classes are defined using SED_VARS_ATTS lt specification_name gt Where lt specification_name gt is the name of a default set of attributes the tracers will be assigned to These default attributes are hardwired to the tracers in sediments sediments c and can be expanded as desired Currently the default sets available are standard Standard set of attributes estuary Attributes applicable to an estuarine environment 20 08 2015 Page 174 of 185 Version 1 00 SHOC User Manual If any of the tracer classes are explicitly defined in the tracer list then any attributes associated with that tracer takes precedence over the defaults defined by SED_VARS_ATTS Furthermore and tracer attribute can be defined in the parameter file using TRACER lt m gt attname or lt name gt attname Where lt m gt is the tracer number in the list attname is the tracer attribute name see the MecoSed Users Guide for a list of attribute names and lt name gt is the name of the tracer e g Mud svel 0 0001 Redefine the
96. FI BLEND1 45 47 260 298 NE2_BLEND 1 E2_BLENDO 18 22 100 110 20 08 2015 Page 97 of 185 Version 1 00 SHOC User Manual 4 30 Tracer diagnostics There exist several options for SHOC to generate diagnostics of interest which are subsequently saved to 2D or 3D tracers These tracers then appear in any specified netCDF output files or timeseries files Currently these diagnostic tracers include mixed layer depth heat flux described in section 4 17 steric height vorticity mixing length scale flushing time CFL time steps tracer fluxes mean velocity or mean tracer flux and tendencies in the momentum balance Specification of these diagnostics is described below 4 30 1 Tracer Fluxes The advective and vertical diffusive flux of a specified tracer may be calculated The flux calculation of a tracer is invoked by specifying a tracer name e g CALC_FLUXES salt Name of tracer for flux calculation To disable the flux diagnostic set the flux diagnostic to NONE This diagnostic requires the specification of tracers representing the advective fluxes in e1 e2 and z directions and a diffusive flux in the z direction These tracers are automatically generated by SHOC when the CALC_FLUXES flag is invoked but may be over ridden by manually specifying any of the following tracers in the parameter file RACER name flux_el1 RACH Long name Advective flux el RACER units kgs 1 RACER
97. Figure 14 3 6 Bathymetry interpolated onto the South Australian Gulfs 6 Create a SHOC auto file Click on Save AUTO file to create an auto file Section 5 suitable for generating a full parameter file and netCDF input file The auto file will be saved to shoc auto This file should be edited before invoking the a option to modify the START_TIME and STOP_TIME to the start and end times desired INPUT_FILE changed to a unique name and BATHYMIN and MIN_C should be ELL THICKNESS should be set to desired values The original shoc auto is shown in Figure 14 3 7 a and the modified file in 14 3 7 b now renamed to gulfs auto Additionally any optional parameterisations outlined in Section 5 may be added at this stage e g if the model forcing initial conditions or boundary data are known they may be included and will be propagated into the parameter file generated by the a option Alternatively this generated parameter file may be edited to include forcing and initial conditions The parameter file gulfs prm and input file gulfs nc may then be generated shoc ag gulfs auto using Gnds Tools Optio 22s S222 clk Dep SHOC parameter file PROJECTION geographic TIMEUNIT seconds since 1990 01 01 00 00 00 9 5 QUTPUT_TIMBUNIT days since 1990 01 01 00 00 00 9 5 START_TIME 5265 days STOP_TIME 5265 05 days 1st Jun 2004 INPUT_FILE shoc QUTPUTFILES 0 id GRIDTYPE NUMERICA
98. HEME constant Vertical eddy diffusivity VZO 0 001 Vertical diffusivity for tracers KZO 0 001 4 21 2 Csanady The vertical momentum diffusion coefficient V and vertical tracer diffusion coefficient K are calculated using a formulation along the lines described in Csanady 1982 equation 6 22b with modification due to stratification as described by Bowden and Hamilton 1975 1 V V o Qy MH 1 10R 2 3 K z K o t OH 1 3 33R ES where A is the maximum of the surface and bottom friction velocities to account for both tidal and wind mixing H is the depth of water V o K o and Oe are constants and R is a Richardson number dependent on the vertical stratification and vertical velocity shear The constants MN and K specify small background mixing values This scheme is specified as follows Use the Csanady mixing scheme MIXING_SCHEME csanady VZO 0 00001 Background viscosity ms VZ_ALPHA 0 0625 Viscosity coefficient KZ0 0 00001 Background diffusivity ms KZ_ALPHA 0 03 Diffusivity coefficient Csanady 1982 suggests a value of 1 16 0 0625 for 4 21 3 Mellor Yamada 2 0 The Mellor Yamada level 2 scheme is described Mellor and Yamada 1982 This is specified as follows 20 08 2015 Page 79 of 185 Version 1 00 SHOC User Manual Use th llor Yamada level 2 scheme MIXING_SCHEME mellor_yamada_2_0 VZO le 5 Background
99. L N 50 NCE2 40 BATHYMIN MI CELL ease 0 Surface Sieg Fer 20 Ss Ol ele e Sizigizie gulfs auto wWarnings S SEI SHOC parameter file PROJECTION geographic TIMEUNIT seconds since 1990 01 01 00 00 00 9 5 QUTPUT_TIMBUNIT days since 1990 01 01 00 00 00 9 5 START_TIME 7670 days ist Jan 2011 STOP_TIME 7701 days Ist Feb 2011 INPUT_PILE gulfs OUTPUTFILES 0 Grid CRIDTYPE NUMERICAL 50 NCE2 40 BATHYMIN 1 MIN CELL THICKNESS 15 Surface Elevation CO SURFACE SURFACE 2000 D D Bathymetry Bathymetry BATHY 2000 BATHY 2000 171 333 SUIS 294 861 294 861 488 528 488 528 666 194 666 194 902 028 902 028 1059 361 1059 361 1258 278 1258 278 1461 750 1461 750 T62 n 1562 750 1682 556 1682 556 1807 639 j 1807 639 UTF8 L22 C15 Top shoe auto Fundamental Il upps 11 en Top gulfs auto Fundamental a Original file from PLUM b Modified file Figure 14 3 6 Parameter files for the South Australian Gulfs 20 08 2015 Page 171 of 185 Version 1 00 SHOC User Manual 7 Edit the parameter file gulfs prm This generally includes initial condition data for temperature salinity and surface elevation surface fluxes wind pressure heatflux and saltflux and specification of open boundary conditions For example if BLUElink data were available where the file j an2011_ets nc contained the variables temp salt and eta the file jan2011_uv nc co
100. LH Using forcing with velocity can lead to discontinuities in elevation and tracers on corners where there is boundary overlap and elevation is solely determined by the forcing velocity data with no option for self adjustment via interior velocities In some cases this can lead to a constant drift in sea level ultimately causing instability Hard relaxation is imposed at these locations to attempt to mitigate this however if this fails then elevation and tracers may be over ridden with a corner mean value using 20 08 2015 Page 49 of 185 Version 1 00 SHOC User Manual BOUNDARYO OPTIONS CORNER_MEANS 4 10 8 Tracer Equation OBCs The standard custom routine use_eqn may be used to create an open boundary value for a particular tracer from an equation that has valid tracers as arguments e g BOUNDARYO BCOND_NO3 CUSTOM BOUNDARYO CUSTOM NO3 use_eqn 14 01 neg 127 8562 0 8621 temp 4 0403 salt Where neg is the unary negative operator and temp and salt are valid model tracers There is no binary operator precedence so parentheses must be used to enforce this otherwise the equation is evaluated left to right The current list of operators is ii ultiply Addition Subtraction Power exp Exponential unary neg Negative unary The unary operators must be enclosed by parenthesis as in the above example and spaces are allowed anywhere in the equation Division is not supported as y
101. OUNDARYO SPONGE_FACT 5 The alternate sponge formulation of Israeli and Orszag 1981 may be implemented where the coefficient of bottom friction is increased linearly to 4 times the interior value over a region NN cells wide This sponge condition acts on 2D and 3D normal and tangential velocity components and is invoked by setting the following keyword for boundaries requiring a sponge BOUNDARYO NSPONGE_VERT NN Where NN is the width of the sponge zone typically NN 10 The sponges are applied to only the normal component of velocity To generate sponge zones for normal and tangential components use BOUNDARYO options ISO_SPONGE 4 10 16 Atmospheric Pressure If atmospheric pressure is specified as a model forcing input see section 4 14 then by default elevation boundary conditions include an additional increment for the eta variable which is proportional to the difference between the specified pressure and a background ambient atmospheric pressure the inverse barometer effect This behaviour can be turned off for a particular boundary as follows Turn of the inverse barometer boundary calculation This is necessary where the specified eta values on the boundary already incorporate the effects of atmospheric pressure differences nested grids can be an example of this BOUNDARYO INVERSE_BAROMETER FALSE or BOUNDARYO INV_BAR FALSE 4 10 17 Advecti
102. RACER2 units gm 3 TRACER2 fill_value 0 0 20 08 2015 Page 39 of 185 Version 1 00 SHOC User Manual RACER2 valid_range 0 100 RACER2 advect 1 RACER2 diffuse 1 RACER2 diagn 0 RACER2 tag surf_flux flux This implies a 2D tracer flux must exist which may vary in space and time using the reset function The tracer may also be scaled to achieve the correct units RACER3 name flux RACER3 long_name Surface flux RACER3 units kgs 1 RACER3 type WC2D RACER3 fill_value 0 0 RACER3 valid_range 0 100 RACER3 advect 0 RACER3 diffuse 0 RACER3 diagn 0 RACER3 tag scale_p 0 001 RACER3 data flux_data nc RACER3 reset_file flux_data nc RACER3 reset_dt 1 day Note that a positive flux implies a flux out of the surface layer 4 9 7 Tracer types The following flags are currently supported by the TRACER type flag WATER The tracer is a 3D water column tracer SEDI The tracer is a 3D sediment tracer INTER The tracer is a 2D tracer HYDRO The tracer is a hydrodynamic tracer SEDIMEN The tracer is a sediment transport tracer ECOLOGY The tracer is a biogeochemical tracer WAVE The tracer is a wave tracer TRACERSTAT The tracer is a tracer statistic tracer PROGNOSTIC The tracer is prognostic DIAGNOSTIC The tracer is diagnostic PARAMETER The tracer represents a parameter FORCING The tracer contains forcing data
103. SHOC User Manual SHOC Sparse Hydrodynamic Ocean Code V5199 User Manual d CSIRO MARINE RESEARCH M Herzfeld and J R Waring CSIRO Marine Research GPO Box 1538 Hobart 7001 17 August 2015 20 08 2015 Page 1 of 185 Version 1 00 SHOC User Manual 1 Introduction 6 2 Installation and operation 7 2 1 Getting the model source code 7 2 2 Building and installing the model executable file 7 2 3 Running the model 8 3 Model setup 11 3 1 Setting up a model application 11 4 The parameter file 12 4 1 Parameter header 12 4 2 Windows 13 4 3 Time 15 4 4 Computational settings and flags 16 4 5 Horizontal coordinate system 19 4 5 1 Defining a Cartesian coordinate system 20 4 5 2 Defining a latitude longitude coordinate system 20 4 5 3 Defining a map projected coordinate system 20 4 6 Horizontal grid geometry 24 4 6 1 Rectangular grid 24 4 6 2 Polar grid 25 4 6 3 Numerical grid 25 4 6 4 Geographic rectangular grid 26 4 7 Vertical grid geometry 27 4 8 Bathymetry 28 4 9 Tracers salinity temperature and others 31 4 9 1 Tracer initialisation 34 4 9 2 Relaxation 34 4 9 3 Resetting 37 4 9 4 Tracer Increments for State Variables 37 4 9 5 Scaling 37 4 9 6 Surface fluxes 39 4 9 7 Tracer types 40 4 9 8 Tracer filling and filtering 40 4 10 Open boundaries 42 4 10 1 Boundary condition types 43 4 10 2 Boundary Implementation stagger 44 4 10 3 For
104. TA eta ts salt ts temp ts SHOC selects the first file that contains the requested variable and for which the current model time is within it s range While overlap between files in time are permitted care must be taken to ensure that there are no time gaps between files The resulting extrapolation would be ill defined A path for all files included in the boundary specification e g including custom velocity forcing files for all boundaries may be specified using BDRY_PATH lt file_path gt e g lt file_path gt home disk project model 4 10 4 Flather Radiation The Flather condition is most successful when using an inner stagger STAGGER INFACE A uniform bathymetry gradient across the boundary assists stability BATHY_CON 1 This radiation condition requires data input for both normal depth averaged velocity and elevation If depth averaged velocity and elevation are input as zero then the condition behaves in a passive manner This scheme is invoked via BOUNDARYO BCOND_NOR2D FLATHR lt datain gt BOUNDARYO BCOND_ELE FLATHR lt datain gt lt radiation gt Where lt datain gt is FILEIN if 2D velocity or elevation data is read from file or CUSTOM if 2D velocity or elevation data is supplied by custom routines lt datain gt TIDALH or TIDALC may be used for elevation For elevation lt datain gt is the condition used to specify eta for the Flather OBC and lt radiation gt may be any radiation c
105. TH MARS 16 17 SMOOTH Vakz 67 SMOOTHING eeeeeceseseerseses 28 75 SECH lees E E E AA 92 el O le EE 18 SPEED E EE 93 SPEED SD defteg eisereen 93 SLAB ITY EE datedtace tere 75 NONE i setts chute beleet 75 SUB STE Eet ge E Lt 75 SUB STEP NOSURPF ossnnnnaasnnnennnaana 75 SUB STEP TRACER osen 75 GIART TIME 15 102 111 122 STERIC HEIGHT 87 STOP TIME 15 111 122 SUWREAGC GE 53 GE 89 GW ATTENUATION 60 61 SWR_BOT_ABSORB cccccceeeeeeeees 61 SWR_TRANSMISSION oa 60 61 T TENDENC See MEAN VORTICITY TIMEUNIT cs eececeeeeeee aeons 14 113 122 TIRE Mix See MIX_LAYER See MIX_LAYER RR on ARTE 96 TRACER nfe et 29 75 101 Ee WEE 30 Ca EE 112 COCA EE A aia 30 el EE 30 TU VANS ege fen te tected 30 Ipcrement 32 Jong name 29 IN LE 29 relaxation ccccceeeeseseeeeeeeeeeanees 31 114 TEE eebe bech 32 51 EM eeh 30 YPO enger g aiaa 20 DS eege eege ee 29 20 08 2015 Page 185 of 185 Valid TANGE autara aea 30 TRANS_OUTPUT seee 122 TRL Eegen a enie aaaea e 53 U UA aV uniin 90 UA ue TEE 90 OT lt eine die dee e 90 U1_OMMIT oseese 90 UTAV OMMIT 90 HMR eiert nterne 71 113 UTY e EE 71 113 Y2 OMM Eeselen 90 U2AV OMMI Tai ee enii iaer 90 E EE 71 114 UAV Aircon kink teeta 71 113 Eeer aint neti bine 64 UPGTRM METHOD 45 NN BI MR EE 52 V WAN EE ee ees dete eeebek Ee 52 V DIF Fastin ddr ae te eel aie 90 VELMAX oirmi ieee 16 95 VELMAX OD 16 NORTICITN iann 88 ABSOLUT E ais
106. TION 341707 BOUNDARY0 T_AMPLITUDE 0 2 BOUNDARYO T_PERIOD 12 0 BOUNDARYO T_MOD_AMP 0 0 BOUNDARYO T_DIR_AMP 0 0 BOUNDARYO T_MOD_PSE 0 0 BOUNDARYO T_DIR_PSE 0 0 BOUNDARYO T_NAME S1 BOUNDARY0 T_XLOCATION 652000 BOUNDARY0 T_YLOCATION 341500 BOUNDARY0 T_AMPLITUDE O 1 BOUNDARYO T_PERIOD 24 0 BOUNDARYO T_MOD_AMP DECHE BOUNDARYO T_DIR_AMP 350 0 BOUNDARYO T_MOD_PSE 0 17 20 08 2015 Page 56 of 185 Version 1 00 SHOC User Manual BOUNDARYO T_DIR_PSE 5920 4 10 20 Global Tidal Model The global tide model of Cartwright and Ray 1990 may be applied to the open boundaries using BOUNDARYO BCOND_ELE TIDALH This condition is described in Section 4 11 of the Science Manual The tide may be directly imposed on the boundary as above or may be superimposed on some low frequency sea level signal using BOUNDARYO BCOND_ELE FILEIN TIDALH BOUNDARYO DATA low_frequency nc netCDF file containing low frequency sea level data The global tide model requires paths to the orthotide functions and nodal corrections to be present e g IDE_CSR_CON_DIR tide nodal Path to nodal correction directory IDE_CSR_ORTHOWEIGHTS tide ortho_csr_4 0 Orthotide functions 4 10 21 Custom Tidal Constituents Tidal constituents amplitude and phase may be specified via file input This allows the model to be boundary forced with spatially variable tidal phases and amplitud
107. This will always occupy the same cell providing the cell is wet For the surface and bottom cases the sign of the depth may be positive or negative If the vars field is absent then all tracers are included in the time series file Time series files are ASCII files with a header containing information about the data in the files and data in columns Their format is described in section 11 1 4 31 6 NetCDF dump files More than one netCDF output dump file maybe specified in the SHOC parameter file Each output file contains the grid geometry times and selected model variables The number of output files are specified by the parameter OutputFiles The parameters for each output are specified with the prefix i1e lt N gt where lt N gt is the output file number Four netCDF output conventions are supported by SHOC the standard dumpfile output as used when hot starting a run a simple format a point array output or a sparse array output 1 The standard output contains up to four staggered grid geometries based on a Arakawa C Grid 2 The simple format contains only one grid geometry with all data variables interpolated on to the cell centre Velocity components are therefore represented as eastward and northward components rather than components relative to the grid 20 08 2015 Page 120 of 185 Version 1 00 d d i i SHOC User Manual used i e e4 and e directions which may be spatially variable for curvilinear gri
108. Turn on grid refinement Use a zoom factor of 3 so that 3 x 3 9 fine grids comprise 1 coarse grid ZOOM_POINTS 28 List the i j locations of the cell 17 9 centers of the coarse grid There are 28 i j locations in the list K Ww N On OW VO WO VO US T2 20 12 2 3 42 26 12 29 A 20 08 2015 Page 94 of 185 Version 1 00 32 35 17 20 23 26 1 29 1 32 35 17 20 23 26 1 29 1 32 35 OO o oO oo OO oo o Om Om Om Om WH WON NH SHOC User Manual The resulting grid for a closed basin test domain is illustrated in Figure 4 29 1 Figure 4 29 1 Grid refinement example A section of the grid can be retained at high resolution or a coarse resolution section can be created using ZOOM_HR_ZONE or ZOOM_CR_ZONE 17 9 35 18 17 9 35 18 Set a high resolution zone Set a coarse resolution zone Grid refinement may be turned off using GRID_REFINEMENT NO The default is for no grid refinement Note that the bathymetry is averaged over the coarse grid cells hence a new netcdf input file must be created when grid refinement is invoked Anisotropic grid ref
109. Type of grid GRIDTYPE POLAR Number of cells in the el i or azimuthal direction NCE1 5 Number of cells in the e2 j or radial direction NCE2 10 F Coordinates of polar origin X00 250000 YOO 5770000 Radial distance from origin to edge of first grid cell metres RO 40 Angle in degrees between e1 0 radial i 0 direction and the real world X axis which is East in most reasonable projections his represents a mathematical rotation ue anticlockwise ROTATION 20 Angular extent of grid degrees running clockwise from the el 0 i 0 radial ARC 120 The above describes a polar grid with 5 by 10 cells with a minimum radius of 40m and covering an angular range of 120 from 110 to 230 with respect to true north The grid polar origin is located at Easting 250000 Northing 5770000 The polar grids generated for the model have square cells in the sense that the size of any given cell is approximately equal in the azimuthal and radial directions A brief analysis shows that this causes the cell size to increase exponentially in the radial direction as j increases so that the grid has higher resolution near the origin and lower resolution further away The origin itself cannot be part of the grid ie RO must be greater than zero as the grid becomes singular at that point Like the rectangular grid Polar grids are generally suitable
110. VARS_INPUT_DT 2 hours How often to read the wave data Alternatively the wave variables may be created by SHOC and provided with values via the wave library see below using WAVE_VARS YES Ifa WAVE_VARS YES ora file is specified then SHOC will automatically create 2D tracers for the wave variables This is done even if the input file does not contain data for the wave variables e g an empty file The wave variables created by SHOC are see Section 4 31 15 20 08 2015 Page 76 of 185 Version 1 00 SHOC User Manual Tracer name Variable name in input file Description wave_amp amplitude wave amplitude m wave_period period wave period s wave_dir direction wave direction deg T wave_ub ub bottom orbital velocity ms ustrcw wave current friction wave_Fx force_x force_el x Radiation stress Mm Wave Eu force_y force_e2 y Radiation stress Nm wave_stel stokes_x stokes_el x Stokes drift velocity ms wave_ste2 stokes_y stokes_e2 y Stokes drift velocity me The influence of wave action on the hydrodynamics is controlled by the parameter WAVES Currently feedback of wave enhanced bottom friction to the hydrodynamics and the influence of waves on currents due to radiation stresses is supported The wave options are invoked by listing the following WAVES BOT_STRESS Allow feedback of wave bottom frietion TAN_RADIATION Include tangen
111. YO BCOND_ELE FLATHR CLAMPD In this case elevation will use a zero value in the Flather computation for normal velocity and a zero value for the elevation condition Generally radiation conditions may be used to approximate the elevation and velocity data lt datain gt e g BOUNDARYO BCOND_NOR2D FLATHR NOGRAD BOUNDARYO BCOND_ELE FLATHR MILLER 4 10 5 Custom Routines Another mechanism for associating data with an open boundary is the CUSTOM parameter A CUSTOM parameter may be defined for any variable by appending the variable name to the keyword with a fullstop see below Following the parameter on the same line are a sequence of space separated arguments If the first argument is a numeric value or the string default then the variable will be set to that fixed value on the boundary default corresponding to the fill value for a tracer or zero for u1 or u2 If the first argument is the name of a standard or custom function supported by the SHOC code then the responsibility for evaluating the variable boundary value will be passed on to that function along with the remaining arguments These parameters are optional and additional to the DATA parameter described above If present they override the DATA parameter for the variable concerned For example Set salinity to a constant value of 35 5 on this boundary BOUNDARYO CUSTOM salt 35 5 Set the tracer called contam to its default value BOUNDARYO CUSTOM
112. _TYPE BLOCK_E1 n Blocking n is an optional integer when present the block is made rectangular in the el direction by n cells WINDOW_TYPE BLOCK_E2 n Same as BLOCK EI but rectangles are in the E2 direction WINDOW_TYPE EXPLICIT The user supplies the partitioning see below The striping methods divides the wet domain into the number of specified windows hence all 2D partitions contain the same number of cells the last window may not if the total number of wet cells is not divisible by the number of windows The blocking methods divide the total grid size into blocks of size sqrt ncel x nce2 A block must contain at least 1 wet cell for it to be valid i e blocks that contain all dry cells are ignored This results in blocks containing quite different numbers of cells depending on how many wet cells are encountered in each block Consequently load balance may be poor However for large numbers of windows it may be preferable since the amount of information exchanged between windows decreases as windows increase with blocking and the model load balance will be determined by blocks containing all wet cells which will be more numerous as the number of windows increases For STRIPE_E1 and STRIPE_E2 The window sizes may be set using the command 20 08 2015 Page 13 of 185 Version 1 00 SHOC User Manual Sets the window sizes for n windows WINDOW_SIZE SC D EN NS Ce ches E or WINDOW_SIZE default
113. _temp UPSTR BOUNDARY1 ADJUST_FLUX 200 second BOUNDARY1 DATA jan2011l_ets nc BOUNDARY1 RANGE 50 0 50 23 20 08 2015 Page 172 of 185 Version 1 00 SHOC User Manual BOUNDARY2 NAME Offshore BOUNDARY2 TYPE u2 BOUNDARY2 BCOND_NOR CUSTOM BOUNDARY2 CUSTOM u1 uv_to_ul jan2011_uv nc BOUNDARY2 BCOND_TAN CUSTO BOUNDARY2 CUSTOM u2 uv_to_u2 jan2011l_uv nc BOUNDARY2 BCOND_ELE NOTHIN FILEIN BOUNDARY2 BCOND_salt UPSTRM BOUNDARY2 BCOND_temp UPSTR BOUNDARY2 ADJUST_FLUX 200 seconds BOUNDARY2 DATA jan2011_ets nc BOUNDARY2 RANGE 0 0 49 0 If a tide is required to be included using the CSR tide model then set TIDE_CSR_CON_DIR to the nodal correction directory and TIDE_CSR_ORTHOWEIGHTS to the orthoweight database see Section 4 10 20 and use the elevation boundary condition BOUNDARYO0 BCOND ELE NOTHIN FILEIN TIDALH Numerous other parameters may be edited in the file gulfs prm to suit the application e g PARAMETERHEADER DESCRIPTION NAME netCDF output files Section 4 31 6 time series output Section 4 31 5 WINDOWS Section 4 2 horizontal friction Section 4 22 turbulence closure Section 4 21 HEATFLUX Section 4 17 or diagnostics Section 4 30 The example here is the minimum required to set up a simulation and many alternative parameterisations or options may be invoked as described in this manual Note that the
114. a few tracers out of many need a specific boundary condition 4 10 2 Boundary Implementation stagger The stencil for the open boundary stagger may use the outer face for normal velocity the default Fig 4 1 Science Manual or an inner stagger for normal velocity Fig 4 2 Science Manual The outer stagger is generally more stable and may use direct forcing with or without relaxation to radiation conditions for elevation forcing The inner stagger must use a Flather condition if the model is to be forced with elevation The stagger is imposed via BOUNDARY1 STAGGER OUTFACE Outer stagger default or BOUNDARY1 STAGGER INFACE Inner stagger If the STAGGER keyword is absent an outer stagger is assumed 4 10 3 Forcing Data The open boundary condition example given above describes a u1 boundary spanning 3 grid cells i 4 j 7 8 9 where surface elevation values and tracer concentration values if any are found in the time series file of fshore nc The surface elevation variable must be called eta and the tracer variables must match the tracer names specified in the model parameter file see section 4 9 Unique among the input data forcing the boundary DATA parameter supports the specification of multiple time series data files The files must all be defined on the same parameter line and separated by white space spaces or tabs 20 08 2015 Page 44 of 185 Version 1 00 SHOC User Manual BOUNDARY1 DA
115. a longer time step than momentum which is achieved by setting the flag TRATIO n where n is the multiple of the 3D time step the tracers are to operate on e g if n 4 and dt 50 seconds then the tracers are updated every fourth 3D time step every 200 seconds Note that the Semi Lagrangian scheme has conservation and numerical diffusion characteristics inferior to some of the other schemes available semi Lagrange characteristics improve with increasing Courant number but if many tracers exist and speed is a priority then this scheme may be attractive Note that the effective upper limit of TRATIO may be determined by other events in the time scheduler s control i e the routine cgrid_step may be called with a stop time less than the tracer time step For this reason ideally the TRATIO time step must be less than any other time IO interval used for output dumps output timeseries or forcing data input In transport mode TRATIO may be 0 lt TRATIO lt 1 This effectively reduces the time step used with the transport model and may be useful using the FFSL scheme if the DT time step violates the stability criterion Lipschitz stability i e streamlines cannot cross In this case a constant flux and linear elevation change is assumed over the interval DT and at each substep TRATIO x DT the velocity profile is reconstructed according to these assumptions Due to the undesirable characteristics of the LAGRANGE scheme it is possible to a
116. abase gradient and the gradient in the grid cell where the gradient is defined above stored in bathy_grad_max 4 9 Tracers salinity temperature and others The model may include salinity and temperature as dynamic tracers which affect the density field via an equation of state As well some of the more complex vertical mixing schemes may use variables like turbulent kinetic energy which also essentially act as tracers as far as most of the model code is concerned Finally the model can include an arbitrary number of passive tracers which are advected and diffused in the model grid but which play no dynamic role The set of tracers included and their physical behaviour are defined as shown in the example below The number of tracers included is specified using the parameter NTRACERS and attributes for each tracer are prefixed by TRACER lt M gt where lt M gt corresponds to the tracer number starting at zero Tracers can be defined to exist in the water column 3D tracers the benthos 2D tracers these tracers may also represent vertically integrated 3D tracers or values at the air water or water sediment interfaces or in the sediment 3D sediment tracers The following example shows the specification of three tracers salinity temperature and a passive dissolved contaminant Detailed comments are provided for the salinity tracer NTRACERS 3 Three tracers in this grid The following tracer attributes are manda
117. aling tracer e g tracer2 must be set up and initialised e g RACER2 name scale RACER2 long_name Scaling tracer RACER2 units degrees C RACER2 scale_s temp Add tracer2 values to tracer temp RACER2 fill_value 20 0 RACER2 valid_range 0 40 RACER2 advect 0 RACER2 diffuse 0 RACER2 diagn 0 RACER2 data scale_profile nc Initialisation for tracer2 In this case the tracer named temp is scaled additively by the data contained in the file scale_profile nc If the tracer were to be scaled multiplicatively then use TRACER2 scale_p temp Multiply tracer temp by tracer2 values Alternatively within the tracer attributes for the tracer desired to be scaled e g temp in this case the following attributes may be set RACER1 name temp Additively scale tracer temp by the values in tracer scale RACER1 tag scale_s scale Multiplicatively scale tracer temp by the values of scale RACER1 tag scale_p scale Additively scale tracer temp by a constant 2 in this case RACER1 tag scale_s 2 0 Multiplicatively scale tracer temp by a constant 0 01 RACERI1 tag scale_p 0 01 Tracer scaling is invoked upon initialisation and if any tracers are reset Section 4 9 3 A tracer scaling file may be generated from time series files of moored instrument data or from profile measurements To invoke
118. ameter file as a constant value kg m 3 AIRDENS L225 Specific heat of water Again the model could calculate this based on salinity temperature etc For now however this is specified as a constant J C 1 kg 1 FIX CHECK THIS SPECHEAT 3990 The Coriolis parameter value for the area of interest This is an NCE1 NCE2 floating point array so that it is possible to set a different value in every grid cell However for most applications where the grid geographical extent is not large a uniform value can be used as shown here for a hypothetical 40 50 The CORIOLIS parameter will be automatically computed if not supplied but the PROJECTION parameter is CORIOLIS 2000 0 000019 4 5 Horizontal coordinate system SHOC uses a sparse or compressed array configuration Herzfeld 2006 which represents a three dimensional region as a one dimensional vector in computer memory One of the advantages of this approach is that all non wet land cells may be omitted from the grid in memory This means that when constructing a grid there is no computational penalty when large amounts of land are included in the grid This approach requires however that at least one land cell must be adjacent to wet cells at coastal boundaries i e a solid boundary is not allowed to be adjacent to a cell containing water land cells only must be adjacent to wet cells
119. ameter file make sure the abovementioned parameters are set to zero a very large value and zero respectively Note also that the SMOOTHING option will also have this effect Heat flux increasing with time Using the HEATFLUX NET_HEAT with a HEATFLUX_FILE_INPUT_DT gt DT 3D time step in conjunction with a RADIATION file SWR_ATTENUATION gt 0 SWR_TRANSMISSION gt 0 will result in the heatflux increased by the surface short wave contribution during the period WHEATFLUX_FILE_INPUT_DT Set HEATFLUX_FILE_INPUT_DT DT to overcome this effect Model crashes Check that momsc ORDER2 SHOC is a second order model in time and space and 17 order momentum schemes have proved consistently unsuccessful Negative variable values inexplicably appear in output Set bytespervalue in the output file to 4 Using short representation of output may make very large or small values wrap bits and become negative Use double representation to avoid this Open boundaries appear as OUTSIDE cells Each u1 or u2 open boundary should be associated with a FRONT BACK LEFT or RIGHT edge If an open boundary cell location list contains both FRONT and BACK or LEFT and RIGHT edge cells then they will be masked as OUTSIDE Output file does not record further dumps Check that the 2 0 Gb limit for output files has not been exceeded Reading parameter file difficulties Check that no white space tabs or M exists after entries in the parameter file River open
120. and is therefore not sensible to output to a 2 D or 3 D tracer The syntax for the specification of sectionfluxes is therefore different An example is given below where the prefix RTSTAT refers to run time statistic NRTSTAT 1 RTSTAT name sectionflux salt ul type of run time statistic RTSTAT data bay_mouth sect file containing i j list RTSTAT dt 6 hours time interval to write output RSTAT startt 3182 days optional start time for the section integration Default is the model start time RTSTAT tscale 6 hours optional time interval to write output RTSTAT tunit minutes time interval to write output RTSTAT outscale 1000 optional scaling factor for output flux RTSTAT outunit kg optional output flux units The user may submit any number of individual sections A step attribute may be specified to compute tracerstats at a particular point in the sequence of computations within a time step This is invoked by prescribing TRACER step n Where the computational sequence is n 1 After computation of mixed layer depth vorticity balance flushing times tracer percentiles steric height and numbers n 2 After tracer decay relaxation increments and computation of totals 6 After the wave library is called 3 After the sediment library is called 4 After the biogeochemistry library is called 5 After the tracerstats library is called i e statistics
121. and u2 0 above the free surface for horizontal fluxes V4201 Run with 32 bit netCDF output default is 64 bit Exclude certain points in the model domain from wave tracer statistic sediment transport or biogeochemical computations EXCLUDE_PROCESS_POINTS lt n gt Number of points to exclude ia J CODE ia j are i j locations of i2 j2 CODE the cell to exclude CODE is a list of keywords s EX_WAVE to exclude waves dn Jn CODE EX_TRST for tracer statistics EX_SED for sediment transport EX_BGC for biogeochemistry EXCLUDE_BGCSED EX_SED amp EX_BCG using blocks e g EXCLUDE_BGCSED 3 Set a series of rectangular regions to 0 3 82 69 exclude BGC and sediments 184 3 248 69 248 131 MOM_CONVERT momgrid Convert the input file to a MOM4 compatible grid_spec nc Output file is momgrid_spec nc ROMS_CONVERT romsgrid Convert the input file to a ROMS compatible file Output file is romsgrid_roms nc 20 08 2015 Page 18 of 185 Version 1 00 SHOC User Manual Physical constants Values must be provided for a number of physical constants Most are rarely changed far from the values shown below An exception is the Coriolis parameter which is latitude dependent t Acceleration due to gravity m s 2 G RER Air density note that it might be better to calculate this internally in the model code based on the air temperature For the moment however it is specified in the par
122. ange le 10 1e10 TRACER advect 0 TRACER diffuse 0 TRACER diagn 0 If the attribute TRACER dt is absent the mean for the whole simulation is calculated For statistics involving multiple tracers the tracer names are separated by a colon in the tracerstat attribute For example to calculate the covariance of tracers passivel and passive2 use TRACER name covariance TRACER long_name Covariance of passivel and passive2 TRACER tracerstat cov passivel passive2 TRACER fill_value_we 0 TRACER valid_rang le 10 1e10 TRACER advect 0 TRACER diffuse 0 TRACER diagn 0 The variance standard deviation and covariance statistics for any tracers also require that that tracer s mean be specified The correlation coefficient of two tracers requires that those tracers means and standard deviations are specified The vertical integral mean or 20 08 2015 Page 162 of 185 Version 1 00 SHOC User Manual difference of a 3D tracer is placed in a 2D tracer e g to specify the vertical integral of a tracer chl_a use RACER name vint_chla RACER long_name Vertical integral of chl_a RACER type WC2D RACER tracerstat vint chl_a RACER fill_value_we 0 RACER valid_rang le 10 1e10 RACER advect 0 RACER diffuse 0 RACER diagn 0 The vertical difference tracer statistic calculates the difference between the sums of various layers e g vdiff 3 topran
123. any pressure levels and 6 is the anomaly of specific volume where a S T p a 35 0 p with a 1 p the specific volume S salinity T temperature and p pressure For the steric height diagnostic the pressure p is taken as the pressure at the level of no motion nm where it is assumed velocity 0 and pz is taken as the sea surface The geostrophic current relative to the level of no motion in the e direction is then given by 20 08 2015 Page 102 of 185 Version 1 00 SHOC User Manual de u SE f de where zu is the steric height m and f is the Coriolis parameter The gradient of steric height in the e2 direction gives geostrophic velocity in the e2 direction If 1nm 0 then the steric height diagnostic is not calculated 4 30 7 Vorticity The vorticity may be calculated and stored in 2 D tracer diagnostic variables by invoking the flag VORTICITY lt string gt Where lt string gt is a string containing ABSOLUTE RELATIVE POTENTIAL TENDENCY or NONE with ABSOLUTE absolute vorticity saved to tracer abs_vor e RELATIVE relative vorticity saved to tracer rel_vor s POTENTIAL potential vorticity saved to tracer pot_vor ms TENDENCY barotropic tendency terms saved to tracers see below NONE no vorticity calculations performed Relative vorticity is defined as and absolute vorticity Cf where f is the Coriolis parame
124. ard input file for initialization from which model initial conditions grid layer structure and bathymetry are defined A forcing file containing the variables eta ul u2 w Kz must also be supplied If the grid definition is incompatible with the forcing file the model will terminate with an error The variables temp salt may optionally be included in the forcing file if the advect and diffuse attributes are false for these variables in the tracer list A transport mode is also defined to specify the format of the offline file which has consequences for the speed at which I O is performed To define input and offline data a transport parameter file is created which defines INPUT_FILI Gl jn pc Initialisation file TRANS_DATA offline nc File containing eta ul u2 w and Kz This may be a multifile using variable substitution TRANS_MOD a SP_EXACT The TRANS_DATA file is expected to be in sparse format with time records corresponding exactly to the input intervals required by the model t T determined by the start time and ime step DANZ DATA is in sparse format contains information on exactly the same grid as the transport model but el DO IO SP_INT 20 08 2015 XYZ_INTERP NONI may be at diff nput interval s performed w RANS_DATA is ifferent to t n space and t nput most disk spac erent times to interpolat
125. are compromised when resolution is increased laterally in a river section of the grid A grid section where variables are linearly blended can be useful to overcome this In the case of a river if variables are blended laterally across the entire width of the river then there will be no transverse flow since the lateral boundary conditions prohibit flow through the solid boundaries This makes flow along river only and the cross river direction is irrelevant in terms of determining the time steps for stability The river effectively consists of a number of independent channels stacked side by side Tracer exchange between the channels may exist via horizontal mixing Such a configuration has the benefit of allowing increased resolution of the bathymetric cross section of the river and aids in constructing river branches Blending is invoked using NEI BLEND 1 Number of blend areas in the el direction Kl BLENDO 1s ls 2s e2 Start amp end el coordinates els and ele and start amp end e2 coordinates e2s and e2e for blend area 0 Or NE2_ BLEND ab Number of blend areas in the e2 direction E2 BLENDO 2s 2 Is el Start amp end ei coordinates e2s and e2e and start amp end el coordinates els and ele for blend area 0 Examples may be NE1_BLEND 2 KI _ BLENDO 45 47 241 255 20 08 2015 Page 96 of 185 Version 1 00 SHOC User Manual
126. arious aspects of the simulation using the REGULATE_FILE command By defining a valid filename with this command the user can enter commands in real time to stop pause resume and re configure various aspects of the run This functionality is invoked via a scheduled function that reads the nominated file at a user defined interval The run regulation is invoked via REGULATE_FILE filename txt Name of the file that contains run regulation commands REGULATE_DT 1 hour Time interval that the file is read Note that the REGULATE_FILE may be the parameter file Any run regulation commands may begin with the keyword REGULATE Valid commands are REGULATE STOP Stop the simulation Output is dumped prior to quitting REGULATE PAUSE The run is suspended REGULATE RESUME A paused run is resumed REGULATE DUMP_REINIT A new dump file specification is invoked Any existing files are appended Dump specification should be listed in the input parameter file REGULATE TS_REINIT A new ascii time series file specification is invoked Any existing files are appended REGULATE WIN_REINI A new window partitioning is invoked Window information should be listed in the input parameter file REGULATE OBC_REINIT lt obc_name gt lt obc_type gt A the boundary condit
127. ast Location 147 31 43 06 10 5 Source between 10 and 5m The X Y Z locations may be entered as a time series file and be allowed to vary with time In this case pss0 location contains the name of the time series file and the file must contain the variables X or x Y or y z_low and z_high e g Gesi Location input_location ts Time dependent input The time series file has variables COLUMNS 5 COLUMN1 name time COLUMN1 long_name Time COLUMN1 units days since 1990 01 01 00 00 00 10 COLUMN1 missing_value 99999999 COLUMN2 name X COLUMN2 long_name Longitude COLUMN2 units Degrees COLUMN3 name Y COLUMN3 long_name Latitude COLUMN3 units Degrees COLUMN4 name z_low COLUMN4 long_name Lower depth range COLUMN4 units m COLUMN5 name z_high COLUMN5 long_name Upper depth range COLUMN5 units m 4382 147 31 43 06 10 5 4392 147 31 43 06 20 15 The source sink may be distributed over multiple cells horizontally and a depth range using pss0 location 200 100 Depth range pss ncells 3 Number of entries 12 25 1 1 3 location 2 5 10 11 2 i j range 24 27 3 1 3 location If a range is given SHOC will determine only those cells within the range that are wet Therefore for example if a flux were to be input in the bottom layer over the whole domain approximating a groundwater flux then assuming the grid size is 100x100 one would use pss reference botto
128. ation in the layer k 1 This is iteratively computed down through the water column If v2 lt 0 then v1 is the bottom tracer concentration and the profile in any layer k is determined by subtracting v2 x density gradient to the concentration in the layer k 1 This is iteratively computed up through the water column A file netCDF or ascii time series may be used as the surface or bottom value in preference to v1 in this case use TRACERO data dens_scale file nc v2 The tracer profile may be the inverse of the density profile if the following is specified TRACERO data dens_scale v1 v2 n TRACERO data dens_scale file nc v2 n or TRACERO data dens_scale vl v2 inverse TRACERO data dens_scale file nc v2 inverse An alternative density scaling is possible where the normalized density profile is stretched between a surface value of v1 and bottom value of v2 This is invoked using TRACERO data dens_profile vl v2 Tracer values may be specified in regions using TRACERO data region region bne rl ivl r2 v2 rnivn Where region bnc is a region file see Section 4 29 16 The vales in specified regions rl r2 rn are then assigned the values vl v2 vn respectively Tracer specification examples are T re TRACI TRACI TRACI TRAC TRACI Pa 20 08 2015 mperature tracer only mandatory attributes given here Th st will assume their default values ER1 name temp ER1 long_name Temperatu
129. ation time constant of eta_relaxation_time_constant The relaxation time constant is the time it takes for the elevation to converge to the elevation field 20 08 2015 Page 65 of 185 Version 1 00 SHOC User Manual in infile nc i e if the time constant is equivalent to the 2D time step then elevation is reset to that found in infile nc every 2D step If the eta_relaxation_time_constant is the name of a file netCDF or ascii then the units for the time constant in the file must be a date unit e g Ascii relaxation file where relaxation is 48 hours at day 0 and 2 hours at day 10 Note Time is converted to the model units specified by TIMEUNIT COLUMNS 2 COLUMN1 name Time COLUMN2 long_name Time COLUMN1 units days since 1990 01 01 00 00 00 8 COLUMN1 missing_value 999 COLUMN1 fill_value 0 0 COLUMN1 name eta_relaxation_time_constant COLUMN2 long_name Eta relaxation time constant COLUMN1 units hours COLUMN1 missing_value 999 COLUMN1 fill_value 0 0 0 48 10 2 Adaptive relaxation can be invoked by specifying eta_relaxation_time_constant linear dv tc units dv tc units eta_relaxation_time_constant exponential dv tc units In the linear case if the absolute difference between modelled eta and that read from infile nc is dv then a relaxation constant of tc units is used and if the absolute difference is dv then a relaxation constant of tc units is used with linear
130. atlab package Once the normal and tangential u v components are saved to file from the coarse scale grid they may be re read and rotated onto the fine scale boundaries using the custom routines e g for a ul boundary BOUNDARYO NAME Offshore BOUNDARYO TYPE ul BOUNDARYO BCOND_NOR CUSTOM BOUNDARYO CUSTOM ul uv_to_ul bdry_uv_nor nce BOUNDARYO BCOND_TAN CUSTOM BOUNDARYO CUSTOM u2 uv_to_u2 bdry_uv_tan nec BOUNDARYO ETA NOTHIN Forcing with velocity is often prone to boundary over specification issues which may lead to instability These are harder to control than when forcing with elevation where partially passive conditions may be used see Section 4 11 8 Also when using velocities interpolated from a coarse grid to a fine grid there is no guarantee that the flux through the open boundary in the coarse and fine grid are identical e g due to differences in bathymetry resolution hence cross sectional area of the open boundary This may lead to a gradual filling or emptying of the domain over time To avoid this the flux prescribed at the normal boundary face that is required to achieve a target elevation via the flux divergence may be inversely computed and added to the normal boundary velocity In practice normal velocities are relaxed to this value over a timescale This flux adjustment is invoked by specifying an elevation value in the DATA boundary specification e g derived from a coarse scale model
131. aw The bottom stress T is calculated as follows T pC U max j u where p is the water density U is the bottom velocity and U is a small background friction velocity below which the friction law changes from quadratic to linear with an effective drag coefficient of C U The bottom drag coefficient C is calculated using a bottom roughness length z which may vary spatially as follows C max zs C K gt d min Xo Here is the von Karman constant 0 4 and z is the height of the nearest velocity point above the sea bed C is a parameter typically between 0 002 and 0 003 which places a d min lower limit on the value of C when the velocity point is a long way from the bottom The model parameters associated with the formulations described above are specified as follows Minimum bottom drag coefficient If QBFC lt 0 then this value is used directly for the bottom drag QBFC 0 0025 Background friction velocity ms 1 UF 0 01 Bottom roughness values in metres ZO 0 001 4 20 Waves Waves are primarily used in SHOC in conjunction with sediment transport libraries so that bottom friction may be enhanced by wave action to result in increased resuspension This requires that wave period wave amplitude wave direction and orbital velocity are supplied or computed These quantities may be supplied via file input using WAVE_VARS wave nc Wave time series fil WAVE_
132. ayer 4 27 Thin layers In order to maintain stability when layers become very thin an option exists whereby if a layer becomes thinner than the parameter HMIN then that layer is merged with the layer below prior to the calculation of the advective terms The velocity of the merged layer is set to the layer weighted mean of the two layers merged It is assumed that the velocity is uniform throughout the merged layer and subsequent to the calculation of the advective terms the merged layer is split back to the original thin layer and associated layer beneath and the thin layer is assigned the updated velocity This option is initiated via the flag Invoke thin layer merging MERGE_THIN YES HMIN 0 05 The default is MERGE_THIN NO The implementation of the thin layer code effectively decreases the k coordinate of the surface and resets the velocity of the layer to the mean when thin layers are encountered The optimum value of HMIN generally needs to be derived on a trial and error basis but generally 2 3 of the surface layer thickness is a good initial estimation 20 08 2015 Page 89 of 185 Version 1 00 SHOC User Manual 4 28 Particle tracking Particle tracking is currently supported in SHOC If an input particle file is specified then the domain will be seeded with an initial distribution of particles Particles will be advected and diffused according to parameters defined below Particles maybe reset to t
133. boundaries aren t advecting tracers Make sure there are at least 3 wet cells in the normal direction to the open boundary or change the boundary condition for tracers from UPSTRM to FILEIN The UPSTRM condition uses a velocity one cell into the interior of the domain to reflect dynamics occurring in the interior rather than the prescribed boundary dynamics when solving the 1 dimensional advection equation that constitutes the UPSTRM condition If this interior cell falls on a solid boundary i e only 2 wet cells exist normal to the boundary then the velocity will be zero and tracer concentration will not change due to the UPSTRM condition Segmentation fault using g option a Open boundaries in the inside of the domain i e open boundaries not on the edges of the grid must be adjacent to outside cells Check that interior open boundaries are adjacent to outside cells using jvismeco b Solid boundaries on the edge of the grid SHOC requires a land cell to surround all wet cells even along the edges of the grid This is so that there exists a ghost cell location adjacent to each wet cell for setting lateral boundary conditions When to re make an input file using the g option The input netCDF file must be re generated if changes are made to the bathymetry list the number of layers or layer spacings used data used for tracer initialisation BATHYMIN BATHYMAX MIN_CELL_THICKNESS SMOOTHING 20 08 2015 Page 179 of 18
134. bours which are nowhere near the cells geographic position This explicit mapping method can be useful for example for connecting two ends of a channel if the channel cannot be resolved by the models discretization Furthermore a range of vertical cells may be specified which are subjected to this explicit mapping This makes it possible to simulate flow beneath solid structures floating on the surface Explicit maps can be specified in either the e1 or e2 directions The i j cell locations listed for the maps must correspond to the cell centers For the e1 direction one of the cells must be adjacent to a solid boundary on the left edge and the other a solid boundary on the right edge The cell with the right edge will then map through the solid boundary to access water properties in the cell with the solid left edge and vice versa For the e2 direction one of the cells must be adjacent to a solid boundary on the back edge and the other a solid boundary on the front edge Explicit maps through the whole water column are specified using the following MAP_POINTS_EFl 2 Maps cell 2 4 to cell 4 4 and cell 24 44 2 5 to 4 5 in the el direction The 2 Ss 8 reverse maps are also implied MAP_POINTS_E2 2 Maps cell 9 12 to cell 9 14 and cell 9 12 9 14 10 12 to 10 14 in the ei direction The 10 12 10 14 reverse maps are also implied If the source and destination cells have different depths the mapping is perfor
135. bution in the interior The input netCDF file for sigma coordinates is the same as that used for z coordinates SHOC linearly interpolates the initial condition for tracers onto the sigma grid then also applies a smoothing filter in the vertical The bathymetry is checked to ensure no extreme gradients are encountered if the bottom slope becomes greater than 0 07 then the bathymetry is smoothed up to a maximum of 5 passes until the gradient becomes less than 0 07 The bathymetry may be optionally smoothed n times by setting the flag SMOOTHING n The sigma layers converge at the coast and this can lead to small vertical grid spacing which in turn may lead to vertical velocity stability violations To avoid program termination due to this violation the sigma system should always be used with STABILITY SUB STEP or 20 08 2015 Page 88 of 185 Version 1 00 SHOC User Manual STABILITY SUB STEP TRACER Note also that the minimum depth at the coast may need to be increased to maintain stability when using sigma coordinates It is reccomended to use Smagorinsky diffusivity when using the sigma system so that mixing along sigma surfaces over steep bathymetry does not lead to cross isobaric exchange in the absence of any motion 4 26 Stability sub stepping SHOC can invoke several methods to ensure the model remains stable if there exist local violations of the advection scheme stability criteria which may occur fo
136. cients on the boundary via an open boundary condition 4 10 23 Split conditions for tracers A NOGRAD boundary condition may be applied above a certain depth for tracers and a FILEIN or CUSTOM condition below this depth This is invoked by setting BOUNDARYO BCOND_TRA lt n gt FILEIN NOGRAD or CUSTOM NOGRAD BOUNDARYO TRPC_TRA lt n gt 50 Where lt n gt is the tracer number and in this case the depth above which the NOGRAD condition is applied is 50m The depths should always be entered as a negative number 4 10 24 Constant boundary bathymetry Bathymetry may be specified as constant adjacent to an open boundary via BOUNDARYO BATHY_CON n Specify bathymetry constant for n cells into the model interior This is performed by finding the bathymetry n cells into the interior and setting the bathymetry at all cells between the boundary and this n cell equal to this nf cell bathymetry value Note that the input file must be re created when the bathymetry is altered using this option Additionally the boundary zone may be smoothed using 20 08 2015 Page 59 of 185 Version 1 00 SHOC User Manual BOUNDARYO BATHY_SMOOTH n Specify bathymetry smoothing for n cells into the model interior 4 10 25 Scaling The values of the tracer values computed on the boundaries may be scaled by adding a constant or multiplying by a constant Elevation values on the boundary may be scaled by adding a constant This is use
137. cing Data 44 4 10 4 Flather Radiation 45 4 10 5 Custom Routines 46 4 10 6 River Flow Custom Routines 46 4 10 7 Forcing with Velocity 48 4 10 8 Tracer Equation OBCs 50 4 10 9 Relaxation to Forced Data 50 4 10 10 Boundary Relaxation 51 4 10 11 Phase Speed Smoothing 51 4 10 12 Flow Relaxation Scheme 51 4 10 13 Linear Conditions 52 4 10 14 No Action Taken NOTHIN 52 20 08 2015 Page 2 of 185 Version 1 00 SHOC User Manual 4 10 15 Sponge Layers 53 4 10 16 Atmospheric Pressure 53 4 10 17 Advection flux conditions for tracers 53 4 10 18 Profile Methods for Tracers 55 4 10 19 Tidal Synthesis for Elevation 56 4 10 20 Global Tidal Model 57 4 10 21 Custom Tidal Constituents 57 4 10 22 Mixing coefficient boundary conditions 59 4 10 23 Split conditions for tracers 59 4 10 24 Constant boundary bathymetry 59 4 10 25 Scaling 60 4 10 26 Boundary geographic location 61 4 10 27 Standard boundary conditions 61 4 11 Advection Schemes 63 4 12 Surface elevation and velocity 64 4 12 1 Elevation and velocity relaxation 65 4 13 Wind 67 4 13 1 Generic Storm Systems 68 4 14 Atmospheric pressure OH 4 15 Rainfall 70 4 16 Evaporation 70 4 17 Surface heat flux ssa 4 18 Surface salt flux 75 4 19 Bottom friction 75 4 20 Waves 76 4 21 Vertical mixing 78 4 21 1 Constant 79 4 21 2 Csanady 79 4 21 3 Mellor Yamada 2 0 79 4 21 4 Mellor Yamada 2 0 Estuarine 80 4 21 5 M
138. ckness ZO 0 002 Bottom roughness optional required for sediment transport only NAME Comments optional A tracer list Section 4 10 and the definition of the open boundaries Section 4 11 is also required The latter is required so that the open boundary conditions for any additional tracers may be defined Open boundary conditions for temp and salt are best created offline and 20 08 2015 Page 143 of 185 Version 1 00 SHOC User Manual stored in a point array file in conjunction with the FILEIN open boundary condition The UPSTRM open boundary condition is reconfigured for the transport mode to use the characteristic for outward flowing velocity Additionally any diagnostics e g source sink particle tracking mixed layer diagnostic numbers flushing times steric height conservation diagnostics tracer statistics and any surface forcing e g HEATLUX for temp SALTFLUX for salt these may require additional atmospheric input may be specified in the transport parameter file Additional tracers may exist in the forcing file and these may be reset in the transport mode by listing the names of these variables using the TRANS_ VARS attribute e g TRANS_VARS NO3 Chl_a sand silt A transport parameter file may be generated from a full parameter file when using the g or p option by including TRANS_DATA in the parameter file In this case the transport file will adopt the name specified by the INPUT_FILE appended wit
139. coefficients Here they are as used by Large and Pond 1981 VO and V1 have units of m s DRAG_LAW_V0O 10 0 DRAG_LAW_V1 26 0 DRAG_LAW_CDO 0 00114 DRAG_LAW_CD1 0 00218 The wind speed components in the north and east directions must bear the names u and v in the wind input file see Section 4 29 These wind components are then rotated onto the grid to conform to the grid e1 and e2 directions If the wind components already conform to the grid orientation they may be directly applied without rotation by specifying the names wind_e1 and wind_e2 in the wind input file Wind stress may be directly applied to the grid by using the WIND_TYPE flag eg Wind input file contains wind speed ms used by default WIND_TYPE SPEED Wind input file contains wind stress Nm WIND_TYPE STRESS If the WIND_TYPE flag is absent the wind input file is assumed to contain wind speeds 4 13 1 Generic Storm Systems Wind stress may be applied to the domain corresponding to the passage of generic cyclonic or anticyclonic synoptic weather systems This is useful for performing idealized experiments or prescribing a realistic time and space dependent wind field in the absence of measured data These systems are defined by their i j location in the grid relative to the grid origin maximum pressure gradient rotation to a latitude circle and eccentricity Any number of these systems may be defined cor
140. contam default Set surface elevation by calling the etabdry routine and passing it the argument string data ts 280000 5700000 BOUNDARYO CUSTOM eta etabdry data ts 280000 5700000 For a given open boundary it is not necessary to specify a DATA parameter if a CUSTOM parameter has been specified for every tracer and the appropriate dynamic variable ul or u2 The CUSTOM mechanism allows a high degree of flexibility in boundary specification particularly when combined with custom subroutines 4 10 6 River Flow Custom Routines There exist several standard custom routines that allow a parabolic velocity profile to be imposed as the normal open boundary condition This type of boundary forcing is designed to emulate a river inflow Velocities decrease in a parabolic fashion from a maximum value at the surface to zero at a pre defined depth such that the flow rate over the entire open boundary corresponds to a user specified rate given in cumecs mell The syntax for this type of open boundary for a u1 boundary is as follows BOUNDARYO BCOND_NOR CUSTOM BOUNDARYO CUSTOM ul ulflowbdry BOUNDARYO U1_HC 5 0 BOUNDARY0 U1_FLOW lt flowfile ts gt or flow_value 20 08 2015 Page 46 of 185 Version 1 00 SHOC User Manual In this case a river flow boundary is set as the normal velocity condition on boundaryO and the parabolic profile exists from the surface to 5m depth The flow rate can either be imposed in a time varying manner b
141. d region it is not incremented To specify the region using a list of points use AGE_TR 3 Number of points in the list 18 5 Points list 19 5 20 6 Blocks can also be used to specify the region e g AGE_TR 3 Number of points in the list T2 25 1 i j location 2 5 10 11 2 i j range 24 27 3 i j location To specify the region using a region file see Section 4 29 16 AGE_TR region bnce 3 4 n Region file and numbers In the above case the age region will comprise regions 3 4 n ofthe region file region bne A depth range for the age region may be specified using AGE_RANGE top_depth bot_depth If this is absent the region encompasses the whole water column The age tracer is named age in output files and is generated automatically Alternatively the age tracer may be manually specified in the tracer list 4 30 6 Steric Height The steric height within a domain can be calculated by specifying the flag STERIC_HEIGHT lnm Level of no motion Where Inm is a number corresponding to the level of no motion used in the steric height calculation If this flag is set a 2D tracer is automatically created to store the steric height output with units of metres Steric height is defined as the geopotential anomaly divided by the acceleration due to gravity e g Godfrey and Ridgeway 1985 Geopotential anomaly is defined as p2 A dap pl where p gt Da are
142. d using shoc v 14 2 Run a test case Test cases are located in ems src model tests hd A useful first test case is test 7 where a wind with positive curl is blown over a closed basin with sloping bathymetry Section 12 7 To run this test Make an input file Section 2 3 and 8 shoc g test7 prm in7 nc Make sure no output files exist rm out7_z nc Run the model shoc p test7 prm View the output 14 3 Generate a custom grid The generation of custom grids requires the matlab based package PLUM john andrewartha csiro au for details with the executables gridgen and gridbathy installed The executable gridbathy is located in ems utilities grid however gridgen is currently not a member of ems Refer to the README documentation supplied with PLUM for installation Note that dedicated bathymetry and coastline databases may be required for custom grid generation of certain areas Default databases are supplied with PLUM 1 Invoke matlab and PLUM for unix linux matlab nodesktop nosplash nojvm gt gt plum 2 Generate a grid in this case a geographic rectangular grid This is a spherical grid where the spheroid is rotated so that the equator passes through the centre of the grid Section 4 6 4 On the main PLUM menu click on GRID GENERATION and the following is displayed 20 08 2015 Page 167 of 185 Version 1 00 SHOC User Manual Zoom icon M a Ppn View lt tracy gt
143. d wind stress forces balance resulting in no flow Boundary effects and numerical error may make one of these forces dominate leading to non zero flow in the east west direction in the northern southern hemisphere if the sea level pressure gradient dominates and vice versa if wind stress dominates Assuming a linear model with linear bottom friction the analytical solution for sea level profile is given by Chapman 1985 eqn 4 13a 2 A TAn 12 5 1 dy pgD dy Using a domain with two cyclic cross shelf open boundaries and one offshore boundary with elevation clamped to zero and the linear depth profile used by Chapman 1985 eqn 4 1 then the sea level profile is given by Chapman 1985 eqn 4 14 and shown in Figure 12 5 1 and Table 12 5 1 The boundary conditions of eqn 12 5 1 for this domain are Da aty 0 On ts and7 0 aty L 12 5 2 dy dy pgD oO where L is the distance to the offshore boundary Figure 12 5 1 Sea level profile for onshore wind stress E 0 035 r r T T ation o 2 o a CG T 0 02 0 015 0 017 0 005 20 30 40 50 60 70 80 90 100 Offshore distance km Sea surface elevatio CH CH or 20 08 2015 Page 159 of 185 Version 1 00 SHOC User Manual Offshore distance km Surface elevation m 5 0 0301 15 0 0189 25 0 0137 35 0 0103 45 0 0077 55 0 0057 65 0 0039 75 0 0025 85 0 0012 95 0 0001 Table 12 5 1 Sea level profile for onshore wind s
144. data Path for output SEQUENCE setup txt Sequence set from file OutputFiles i Output files file0 name out nc fileO filetype standard fileO tinc 1 hour fileO bytespervalu 4 fileO vars ALL Then to run mkdir home data run lt n gt lt n gt is the current run shoc p test prm nrt 6 4 Crash recovery cr option Often when a model fails the strategy to maintain stability is to reduce the time step modify time dependent parameterisations e g horizontal mixing coefficients and restart the model before the failure occurred This process can be automated using the cr option e g shoc p test prm cr A restart file Section 6 2 must be specified for this option to operate If the model fails when this option is invoked e g due to sea level rising above ETAMAX then the time step is progressively reduced currently by a factor of 5 horizontal mixing is adjusted and the prognostic fields are re initialised from the last restart file dump The model then progresses using the smaller time step to the next restart dump event whereupon the time step and mixing are reset to original values If the model fails during the restart the time step is further reduced and the process repeated Output to netCDF and timeseries files are over written during the period the time step is reduced If the time step is reduced more than 5 times then the model will exit on the assumption that it cannot recover by simply reducing the time step I
145. de gt t then the profile values are truncated to those in input_file nc below the depth v1 if the profile values become greater than those in input_file nce 4 10 19 Tidal Synthesis for Elevation The boundary condition TIDEBC will calculate the elevation on open boundaries from tidal constituent data supplied by the user Data required are T_CONSTITUENTS Number of tidal constituents to include T_NAME Name of the tidal constituent T_XLOCATION i the x location of the supplied tidal amplitude and period m T_YLOCATION jo the y location of the supplied tidal amplitude and period m T_AMP A the tidal amplitude at location isje m T_PERIOD P the tidal period at location isje hours T_MOD_AMP a the rate of modulation of tidal amplitude cm km T_DIR_AMP the direction towards which the tidal amplitude is progressing i e direction of increasing ol degrees T B the rate of modulation of tidal phase degrees km A the direction towards which the tidal phase is progressing i e direction of increasing B degrees T T_MOD_PS T_DIR_PSI EI pR These data must be included for each tidal constituent on each boundary with the TIDEBC specification An example of the domain forced with an M2 tide of amplitude 0 2m and an S1 tide of amplitude 0 1m is given below BOUNDARY0 T_CONSTITUENTS 2 BOUNDARYO0 T_NAME 2 BOUNDARY0 T_XLOCATION 641300 BOUNDARY0 T_YLOCA
146. diagn RACER name flux_e2 RACER long_name Advective flux e2 RACER units kgs 1 RACER diagn RACER name flux_w RACER long_name Vertical advective flux RACER units kgs 1 RACER diagn RACER name Flux_kz RACER long_name Vertical diffusive flux RACER units kgs 1 RACER diagn Fluxes are calculated at each grid cell via flux _el u TAh Az flux _e2 u TAh Az flux __w wTAh Ah flux _kz K oA A where u and up are the velocities in the e and e directions respectively T is the tracer concentration at the cell face Ah and Ah are the grid metrics at the cell faces and Az is the layer thickness 20 08 2015 Page 98 of 185 Version 1 00 SHOC User Manual 4 30 2 Means The mean of certain variables may be calculated via the flag MEAN Options are EAN NONE No mean velocity calculation EAN VEL3D ean 3D velocity calculation EAN VEL2D ean 2D velocity calculation EAN ETA ean sea level calculation EAN TS an temperature and salt EAN KZ ean vertical diffusivity calculation EAN WIND ean wind calculation EAN VOLF LUX ean volume flux calculation EAN TENDENCY ean momentum tendencies EAN FLUX ean tracer flux calculation EAN TIDAL eans calculated over a tidal cycle EAN TRANSPORT Tracers advected with mean velocities EAN_DT 1 day Averaging period A MEAN_
147. diffusion Use th llor Yamada 2 5 scheme MIXING_SCHEME mellor_yamada_2_5 20 08 2015 Page 80 of 185 Version 1 00 VZO KZO ZS MIN_TKE MIN_DISS LMIN SHOC User Manual le 5 Background viscosity le 5 Background diffusivity 0 3 Surface length scale le 8 Optional minimum TKE le 12 Optional minimum dissipation 0 17 Optional minimum length scale This scheme requires four additional tracers corresponding to turbulent kinetic intensity tki turbulent kinetic intensity length scale tki_l turbulence length scale Iscale and turbulence diffusion Kq These tracers are automatically generated by SHOC when the mellor_yamada_2_5 scheme is chosen but may be over ridden by manually specifying the following tracers in the parameter file Q2 tracer TRACER2 name tki TRACER2 long_name Turbulent Kinetic Intensity TRACER2 units m2s 2 TRACER2 fill_value 2 0e 8 TRACER2 valid_range 0 1 Q2L tracer TRACER3 name tki_l TRACER3 long_name Turbulent Kinetic Intensity Length Scale TRACER3 units m2s 1 TRACER3 fill_value 3 4e 9 TRACER3 valid_range 0 1 Length scale tracer TRACER4 name lscale TRACER4 long_name Turbulence length scale TRACER4 units m TRACER4 fill_value 0 17 TRACER4 valid_range 0 Lei TRACER4 advect 0 TRACER4 diffuse 0 TRACER4 diagn 1 Turbulence mixing tracer TRACERS name Kq TRACERS long_name Turbulence Mixing TRACER5 units m2s 1 TR
148. dition for relaxing surface elevation to observed data may appear as BOUNDARYO TYPE ul BOUNDARYO NAME Offshore BOUNDARYO BCOND_NOR NOGRAD BOUNDARYO BCOND_TAN GRAVTY BOUNDARYO BCOND_ELE ORLANS FILEIN BOUNDARYO RELAX_TIME 1 hour BOUNDARYO BCOND_TRAO UPSTRM BOUNDARYO BCOND_TRA1 CLAMPD BOUNDARYO DATA offshore nc BOUNDARYO RANGE 4 7 4 9 4 10 10 Boundary Relaxation Elevation bay be relaxed throughout a user defined zone with differing relaxation times on the inner and outer limits of the zone Elevation relaxation is invoked via BOUNDARYO0 RELAX ELE r_width ts_b ts_i where r_width is the number of cells into the interior the relaxation zone extends ts_b is the relaxation time scale on the boundary and ts_i is the relaxation time scale at the interior limit of the zone It is permissible for ts_b ts_i The values of ts_b and ts_i are relative to the 2D time step i e the actual time scale used for relaxation is ts_b x Atz and ts_i x Atp where At is the 2D time step For example if the 2D time step is 60 seconds and the relaxation zone is defined as BOUNDARYO RELAX_ELE 8 1 100 then a relaxation zone for elevation is created 8 cells into the interior with a relaxation time scale of 60 seconds on the boundary and 6000 seconds at the inner limit of the zone Note that this option also requires an accompanying relaxation file to be specifi
149. ds Vector variables can be stored as vector components or speed and direction The point array parray is essentially a standard output on user defined cells therefore generally using significantly less disk space than other file formats This is useful for outputting open boundaries for nesting purposes Velocities are represented as eastward and northward components The sparse output contains a dump of the sparse format used internally in SHOC i e a one dimensional vector of only the wet cells in the grid If a large amount of the model grid contains land the sparse format can therefore use significantly less disk space than standard formats and is an extremely useful format to use in conjunction with the transport t mode Note that the sparse format cannot be sub sectioned i e the whole array must be dumped for 3D or 2D variables The exception to this is that the surface only may be dumped if the filename is appended with _surf n b The sparse netCDF format does contain geographic information in the file and mappings from sparse position to Cartesian i j k locations This information may be used to visualize a sparse format file directly If a sparse format is to be read back into the model then it must be un packed using the routine unpack_sparse to scatter the file data to wet cell locations Specifying two output files for a grid OutputFiles 2 Specify the path for output files Time series files are als
150. dvect tracers temp and sal with a higher order scheme VANLEER and all remaining tracers with LAGRANGE using TRA_SCHEME LAGRANGE VANLEER T S VANLEER other tracers LAGRANGE The TRATIO facility may be used in conjunction with these split schemes 4 12 Surface elevation and velocity 20 08 2015 Page 64 of 185 Version 1 00 SHOC User Manual The initial condition for the surface elevation may be specified by input from file netCDF or timeseries or by direct input in the parameter file The latter consists of specifying an NCE1 NCE2 floating point array so that it is possible to set a different value in every grid cell However for most applications where the grid geographical extent is not large a uniform value can be used Examples of surface initialisation are given below SURFACE surface nc Input eta from netCDF or timeseries file SURFACE 2000 Elevation set uniformly to 1m fora LH hypothetical domain of size 40 50 SURFACE 4 Elevation set at each cell for a domain of 0 1 0 2 size 2 2 0 2 0 3 If file input is used for surface initialisation and this file doesn t contain an elevation dump at the time corresponding to the model start time then linear interpolation of elevation to the start time is performed Surface elevation initialisation using the above methods generates a surface field that is written to the input net
151. e 0 30 TRACER5 valid_range 0 1 TRACERS diagn 0 TRACERS advect 1 TRACERS diffuse 1 The flushing tracer concentration is automatically initialised to 1 0 within the flushing region and zero elsewhere during startup The flushing region is defined by listing a series of i j locations whose total number is FLUSHING_PTS The i j locations of any sub region of the domain may be retrieved using the marked facility in jvismeco The total mass in the flushing region is printed to the time series file flushing ts at the time interval FLUSHING_DT This time series file contains the total mass in the flushing region the normalised mass i e the ratio of total mass total initial mass and the flushing time The flushing e folding time can be calculated from this output i e the time when the normalised mass falls below 1 e When this occurs the flushing time variable in the time series file will assume this time value Subsequent to this flushing time being reached the initial concentration is re set after a further two flushing times 4 30 5 Age tracer An age tracer may be specified where the value of the age tracer is indicative of the time the tracer has spent in a defined region The region may be defined using a list of points blocks or a region If the tracer lies within the specified region it is incremented at a rate of 1 day 20 08 2015 Page 101 of 185 Version 1 00 SHOC User Manual and outside the specifie
152. e 5 Background viscosity KZO le 5 Background diffusivity ZS 0 8 Surface length scale MIN_TKE 7 6e 6 Optional minimum TKE MIN_DISS 7 27e 19 Optional minimum dissipation This scheme requires two additional tracers corresponding to turbulent kinetic energy tke and turbulence frequency omega These tracers are automatically generated by SHOC when the k w scheme is chosen but may be over ridden by manually specifying the following tracers in the parameter file tke tracer TRACER2 name tke TRACER2 long_name Turbulent Kinetic Energy TRACER2 units m2s 2 TRACER2 fill_value 7 6e 6 TRACER2 valid_range 0 1 diss tracer TRACER3 name omega TRACER3 long_name Turbulence frequency TRACER3 units s l TRACER3 fill_value 1 0e 12 TRACER3 valid_range 0 1 4 21 8 W88 The W88 model of Wilcox 1988 is the same as the k o model but using f feo 1 0 20 08 2015 Page 82 of 185 Version 1 00 SHOC User Manual Use the k w schem MIXING_SCHEME w88 Additional parameters required for the W88 scheme are identical to the k w scheme 4 21 9 Stability functions The stability function used in the turbulence closure schemes for k e k o and MY2 5 may be specified using STABILITY_FUNC The stability functions available are STABILITY FUNC CANUTO_A Canuto et al 2001 model A STABILITY _FUNC CANUTO_B Canuto et al 2001 model B STABILITY
153. e base time unit that will be used for all timeseries and netCDF output files OUTPUT_TIMEUNIT days since 1990 01 01 00 00 00 08 A single line description of the model run This string is written into all output files PARAME TERHEADER NWS 20km rectangular grid Run 1 The internal 3 d time step and the number of times the external 2 d code will be run per 3 d time step The external 2_d time step is thus DT divided by IRATIO DT 120 seconds TRATIO 5 Vertical geometry z coordinates of the model layer interfaces LAYERFACES 5 10 0 8 0 4 0 2 0 0 0 Bathymetry limits All cells will be at least 20m deep BATHYMIN 20 No cell will be more than 2000m deep BATHYMAX 2000 Invoke thin layer merging HMIN 0 05 Bottom roughness values in metres 20 0 001 Mixing scheme mellor_yamada_2_0 ZS 0 2 Horizontal viscosity in ul equation U1VH 1 0 Horizontal viscosity in u2 equation U2VH 1 0 Horizontal diffusivity in the x direction mie ii U1KH 100 20 08 2015 Page 133 of 185 Version 1 00 SHOC User Manual t Horizontal diffusivity in the y direction mis U2KH 100 Sigma SIGMA YES Tracer relaxation RACERO relaxation_file saltprof nc How often to perform relaxation calculation RACERO relaxation_input_dt 1 hour Relaxation time constant RACERO relaxation_time_constant 20 days
154. e heat flux mechanism is implemented by relaxation of the surface layer temperature to some prescribed possibly time varying field using the SURF_RELAX option as follows Time series file specifying surface temperatures containing the variable heatflux_temp with units Degrees C HEATE LUX_TEMP temp nc HEATFE LUX_TEMP_DT 1 day Relaxation time constant HEATFLUX_TC 20 days This mechanism is similar to the more general tracer relaxation mechanism described in section 4 9 except that it only operates on the surface layer of the model rather than throughout the model The BULK heat flux formulation uses a more complex bulk formulation and long wave parameterisation in addition to calculating the short wave component rather than supplying a time series file see Herzfeld et al 2002 section 9 2 A number of input data sets are required all of which are optional as described below Sensible heat flux requires the specification of the air temperature as well as wind inputs see section 0 Air temperatures are specified as follows Time series file containing the variable air_temp with units Degrees C AIRTEMP airtemp nc How often to read the air temperature fil AIRTEMP_INPUT_DT 10 minutes The sensible heat flux is proportional to the product of the wind speed and the difference between the model surface layer temperature and the air temperature T
155. e producing better results Also RAMS may 20 08 2015 Page 74 of 185 Version 1 00 SHOC User Manual produce latent heat gt 0 when it is raining hence the latent heat imposed using this option has a maximum of zero This option is invoked for example via Impose RAMS heat flux components HEATF LUX COMP_HEAT HEATFLUX_FILE RAMS nc HEATFLUX_DT 30 minutes In this case the file RAMS nc must contain variables with names swr short wave radiation lwr_in downward long wave radiation lwr outward long wave radiation sensible sensible heat flux and latent latent heat flux See Section 7 for more detail on COMP_HEAT Heatflux components used in the global ocean model MOM4 may also be assembled in a similar manner In this case the short wave radiation is provided as a mean over some fraction of a day defined by HEATFLUX_DT The daily profile is reconstructed from these means using the methodology of Schiller and Godfrey 2003 Also latent heat is provided as an evaporation rate in units of kom e which is converted to Wm by multiplication by the latent heat of evaporation Lv 2 5x10 This option is invoked for example via Impose MOM4 heat flux components HEATF LUX COMP_HEAT_MOM HEATFPLUX_FILE MOM nc HEATFLUX_DT 30 minutes In this case the file MoM nc must contain variables with names swr short wave radiation lwr outward long wave radiation sensible sensible
156. e splitting to separate the two dimensional 2D mode from the three dimensional 3D mode This allows fast moving gravity waves to be solved independently from the slower moving internal waves allowing the 2D and 3D modes to operate on different time steps resulting in a considerable contribution to computational efficiency The model uses explicit time stepping throughout except for the vertical diffusion scheme which is implicit The implicit scheme guarantees unconditional stability in regions of high vertical resolution A Laplacian diffusion scheme is employed in the horizontal on geopotential surfaces SHOC can invoke several turbulence closure schemes including k e k Mellor Yamada 2 5 Mellor Yamada 2 0 and Csanady type parameterisations Input and output is handled through netCDF data formatted files with the option of submitting ascii text files for simple time series forcing The netCDF format allows input of spatially and temporally varying forcing and initialization data in a grid and time step independent manner SHOC is capable of performing particle tracking and may be coupled to ecological and sediment transport models SHOC uses a Sparse coordinate system which maps all cells in the grid into a 1 dimensional vector This process effectively eliminates all land from the domain representation in computer memory Arbitrary domain composition can be efficiently performed allowing SHOC to operate in a true distributed processing envir
157. e used in this case use profile instead of a numeric depth value e g filel The variable name used in the each mooring or profile file must also be supplied Mooring files generally contain the variable as a function of time ts files and profile files contain the variable at a specific time as a function of depth at a fixed geographic location nc files The scaling routine will compute the difference between the measured data and the FORCING data and store this as a spatially and temporally varying netCDF file OUT_FILE i e the sum of OUT_FILE and FORCING will equal the measured data The scaling function is spatially interpolated over the model grid Only an additive scaling function is available i e product scaling is not supported Additionally an ascii file OUT_NAME ts containing the raw data TIME file observed data FORCING data is produced This is useful for creating scatter plots of the observed vs FORCING data Additionally the bottom value may be explicitly set to a particular value temperature in this example using the optional BOT_VALUE This may be a number or a filename whose value s are used in preference to those contained in the measured data files moor1 ts and profi nc at the sea bottom For example if the BOT_VALUE were the same data as used for the FORCING i e profile nc then this would ensure that the scaling function would equal zero at the bottom The scaling code actually adopts this
158. e variables will then appear in any specified output netCDF and time series files These diagnostics are invoked by invoking the flag MOM_TEND Y ti S This diagnostic automatically generates the following tracers with units ms representing the momentum tendencies when the MOM_TEND flag is invoked ul_adv ul advective tendency ul_hdif ul horizontal diffusion tendency ul_vdif ul vertical diffusion tendency ul_btp ul barotropic pressure gradient tendency ul_bcp ul baroclinic pressure gradient tendency ul_cor ul Coriolis tendency ul_sto ul Stokes Coriolis and vortex forces u2_adv u2 advective tendency u2_hdif u2 horizontal diffusion tendency u2_vdif u2 vertical diffusion tendency u2_btp u2 barotropic pressure gradient tendency u2_bcp u2 baroclinic pressure gradient tendency u2_cor u2 Coriolis tendency ui sto ul Stokes Coriolis and vortex forces The Stokes tendencies are only generated for waves STOKES see Section 4 20 mom_balance A code representing the maximum term in the momentum balance where the cod 1 advection 2 horizontal diffusion 4 vertical diffusion 8 Coriolis 16 barotropic pressure 32 baroclinic pressure 20 08 2015 Page 105 of 185 Version 1 00 SHOC User Manual The sum of the momentum diagnostic tracers for u1 or u2 velocity is equal to the total change in velocity over the time step If the MOM_TEND flag is set to No but any of the above tracers
159. each tracer to achieve mass conservation and the corresponding multiplicative fill factor is created This also contains the total domain volume error and open boundary scaling factor 9 4 Flux form semi Lagrange The flux form semi Lagrange FFSL advection scheme developed by Leonard et al 1996 and Lin and Rood 1996 is a conservative advection scheme that can be used with the transport model While not unconditionally stable the scheme is constrained by the less 20 08 2015 Page 147 of 185 Version 1 00 SHOC User Manual restrictive Lipschitz condition that basically ensures that streamlines cannot cross The advantage of the FFSL scheme lies in that it is locally conservative It is based on the 3 order scheme of Van Leer hence is more accurate than the 17 order semi Lagrangian scheme The FFSL scheme may be used in fully coupled mode or in transport mode For the latter the average volume fluxes through cell faces must be additionally saved to the transport files To invoke this when running shoc using the p option use TRANS_MODE SP_FFSL Save volume fluxes to transport files When running the transport model with the FFSL scheme use TRANS_MODE SP_FFSL Use FFSL transport mode FILL METHOD NONE No fill method TRA_SCHEME FFSL FFSL advection STABILITY SUB STEP NOSURF Enable sub stepping MERGE_THIN YES erge thin layers CONSERVATION ETA W Conservation
160. ed e g eta_relaxation_file bdry_eta nc eta_relaxation_input_dt 20 minutes 4 10 11 Phase Speed Smoothing The phase speed computed by the radiation schemes for elevation may be temporally smoothed using em Fe 1 F c A typical value of F 0 7 This smoothing assists in reducing numerical noise e g MOM Users Guide This smoothing is invoked using BOUNDARYO SMOOTH_PHASE O 4 10 12 Flow Relaxation Scheme The flow relaxation scheme of Martinsen and Engedahl 1987 has been included to relax boundary data to interior data This is accomplished over a region NN cells wide The value of the prognostic values on the boundary n u1 u2 or tracers are given by any of the conditions outlined in Table 3 2 9 1 whatever is specified on the boundary is relaxed to the model 20 08 2015 Page 51 of 185 Version 1 00 SHOC User Manual integrated values over NN cells If the prognostic variable at the boundary is equal to zero then this flow relaxation scheme acts as a sponge type condition This condition is invoked by adding the following flags for normal velocities tangential velocities and elevation respectively where NN is the number of cells the relaxation method is to act over typically NN 10 BOUNDARYO RELAX_ZONE_NOR NN BOUNDARYO RELAX_ZONE_TAN NN BOUNDARYO RELAX_ZONE_ELE NN For all tracers to have the same relaxation zone include BOUNDARYO RELAX_ZONE_ALL NN For individual
161. ed in Section 4 4 e g if HMIN 0 07 m then cells dry when the sea level gets within 3 5 mm of the bottom UNIT A passive tracer with an initial value of 1 Good for testing the constancy condition in ransport models DUMMIES Three generic 3D dummy variables dum1 dum2 and dum3 are created for hardwiring debugging diagnostics internally in the code ALL_NUMBERS Invokes all the diagnostic numbers 4 30 14 Tracer percentiles The tracer percentile diagnostic calculates the spatial distributions of percentiles of a snapshot of a given tracer distribution i e it shows the spatial position of the percentile values of a given tracer at a particular time This diagnostic is useful for determining the position in a domain where e g a median 95 ile or 5 ile tracer concentration may be found This diagnostic is time dependent but if a mean is created using the tracerstats library then the position in the domain where the average of a particular percentile e g average median over a simulation may be determined The percentile calculation of tracer is invoked by specifying a tracer name e g CALC_PERCS salt Name of tracer for percentile calculation A 3D tracer containing the specified tracer percentiles is automatically created with the tracer name appended to percentile_ e g in this case percentile_salt 20 08 2015 Page 109 of 185 Version 1 00 SHOC User Manual 4 30 15 Alerts The alert d
162. ed using any data specified or if this is absent then the f i111_value Additionally a netCDF file may be specified using Specify a netCDF file to initialise any new tracers RACER_DATA lt data_file gt In this case if the data attribute is absent for any new tracers SHOC will search the file lt data_file gt for the new tracer and if found interpolate the initial tracer distribution from that in the file This is done for 3D 2D and sediment tracers 4 9 2 Relaxation Tracer values throughout the model domain can be relaxed towards some specified values which may themselves vary in space and time To enable relaxation for a particular tracer three parameters are required the relaxation data file an ASCII or netCDF time series file see section 10 how often to perform the relaxation and the relaxation time constant Data file containing prescribed tracer values RACERO relaxation_file saltprof ne How often to perform relaxation calculation RACERO relaxation_input_dt 1 hour Relaxation time constant RACERO relaxation_time_constant 20 days Tracer relaxation may also be specified via a streamlined notation relax_trname infile nc dt ts in units where t rname is the name of tracer infile nc is the file containing values to relax to and in units is the input_dt e g to relax salt to saltprof nc with file input of 1 hour and rela
163. edge and adjusting boundary ghost cells using an upstream advection algorithm accordingly BOUNDARYO OPTIONS DYNAMIC_HC NO_HDIFF GEOSTR UPSTRM Note that the dynamic halocline depth is referenced to the free surface and the absolute value will therefore change with the tide Additional tracers are generated to report the depth the flow is distributed over 1low_depth and the salinity of the flow flow_salt If the salinity boundary condition is TRCONC CUSTOM or TRCONF CUSTOM then amass balance is performed to alter the salinity in the ghost cell where salinity river salt mass landward mass flux river flow landward flow If zero salinity is input to the river then river salt mass is zero This salt balance approximates mixing in a salt wedge estuary where the up estuary salt flux is entrained into the surface layer along the length of the salt wedge and mixed with the river outflow For a tidally mixed estuary an effective river length can be specified and the standing salt mass in the volume occupied by this river length is mixed with river inflow and landward salt wedge flow A river length can be specified using BOUNDARYO U1_LENGTH 10000 0 or BOUNDARYO U2_LENGTH 10000 0 20 08 2015 Page 47 of 185 Version 1 00 SHOC User Manual Additional options are as follows NO_SALT Do not adjust input ghost cell salinity using the salt mass balance FULL_DEPTH Use water
164. eeeeeeeeeeeeneeeeees 91 O ORBITAL VEL aii asena aiaa 64 101 ORDER Terie eaaa a e ttan tad 52 ORDER 2a ane ean i e eseu 52 ORDER4 sachin Ree a e es 52 O tputF EE 103 OutputPath E 104 OufpuiTransport eneee eeens 104 OUTSIDE Srei a n a 35 112 OUTSIDE elle n eta 27 P P Option 00 0 eee 27 29 114 120 PARAMETERHEADER 12 13 113 Particle tracking seeen 76 POTEN IAL aaaeeeaa See VORTICITY PRECIPITATION osasin 58 63 101 PRESS BG wise aha cael 90 PRESS BY sisal iain 90 PRESSURE iniit ini 58 Eege ege T 64 QUICK GE RETTEN 52 R RADIA ION oosooannnnneansennnnnnaeano 59 60 101 RAMPEN D a hirri tiee tode ronnen roa ius 15 55 RAMPSTART itii naten 15 55 RAMPVARS vle a ege Dees 15 HEAD WIN MAD 14 REGIONessscectesveteiceseadeeavtvleetnededeetivien eet 97 HEI ATIWE eert itiinnt See VORTICITY RELAX ZONE s seiccvescecsvietteteeedeicives chert 43 e Le EE 115 restart Elise n a 115 FESTA _NAMEC ccceeeecccsssssceeeeeeeeeeeeeees 115 REYNOLDS eirean aeea the le Bet 91 RICHARDSON FL 91 RICHARDSON_ GP 91 ROSSBY EE 92 ROSSBY IN gege 91 er 16 FV beta EE 88 VE 88 DN aY eege geen ee 88 IV e terete EE Eege 88 DN DEET eegen gees ei 88 IVESUCI WEE 88 DI WSO EE a anato NEES 88 Version 1 00 SHOC User Manual S SALT FEUX ara nia tines ieee 63 SGALE VARS ia iaai 17 SE ee EAE EEN 89 SHOW WINDOWG ooeec 14 le OW 75 114 legt a 16 SMAGORINSKY eeeseeereeerreesesess 71 GMOOTH MAk 28 GMOO
165. efaults c This dynamical specification is invoked if auto is specified for lt processes gt The ecological parameters are specified using biofname lt parameters gt name of ecology parameters The name lt parameters gt may be one of the following lt filename gt standard estuary auto If lt filename gt is specified then the BGC parameters are defined in a file bearing that name If default is specified then the processes are hardwired into the module parameter_defaults c in the ecology library Additional parameter lists may be included in this module with associated modifications to the calling routine get_eco_params in parameter_info c Additionally there is scope to define processes dynamically using the currently empty routine eco_params_auto iN parameter_info c This dynamical specification is invoked if auto is specified for lt parameters gt Note that the default parameters include hardwiring of the phytoplankton growth rates that have traditionally been specified as netcdf files It is no longer necessary to supply this netcdf file just specifying the name 10pp1kINP or 10benINP is sufficient 20 08 2015 Page 176 of 185 Version 1 00 SHOC User Manual If a tracer list of the tracers required for the ecology processes is not explicitly specified then these tracers will be automatically generated based on the defined processes The attributes for these tracers are defined using ECO_VARS_ATTS
166. efined above Relative tim specifications here and elsewhere in the parameter file can be specified in seconds minutes hours or days Here the start time corresponds to 1995 02 10 00 00 00 8 and the end time to 1995 03 13 00 00 00 8 START_TIME 1866 days STOP_TIME 1897 days Defines the period during which external forcing variables wind open boundary elevations and or velocities are smoothly ramped from 0 to their normally prescribed values This mechanism allows the suppression of start up transients and shocks in the simulation Prior to RAMPSTART forcing is set to zero After RAMPEND i i forcing is applied normally In between forcing values are scaled by a raised cosine ramp RAMP START 1866 days RAMPEND 1866 5 days Defines which variables are ramped in Suppression of wind and boundary forcing global tide file or custom specification are invoked by listing the processes subject to the ramp All processes are suppressed by default E g all processes are suppressed via 20 08 2015 Page 15 of 185 Version 1 00 4 4 SHOC User Manual RAMPVARS WIND Ramp the wind i TIDALH Tidal OBC N computed using TIDALH TIDALC Tidal OBC n using custom constituents IDEBC Tidal OBC n using tidal synthesis FILEIN OBC n using FILEIN input CUSTO OBC velocity using CUSTOM INV_BARO OBC inve
167. efined as the time for the total mass in the sub region to decrease by a factor of 1 e 38 i e the e folding time This representation of the 20 08 2015 Page 100 of 185 Version 1 00 SHOC User Manual flushing time assumes that tracer is well mixed in the sub region and the total mass is assumed to decrease exponentially according to Miz Me where Mb is the initial mass and 7 is the flushing time scale Tartinville et al 1997 When M M e then t qt hence the flushing time can be recovered This diagnostic is invoked by specifying the tracer number of a flushing tracer e g FLUSHING_TR YES Invoke flushing diagnostic FLUSHING_DT 30 minutes Output interval FLUSHING_PTS 3 Grid cells defining the 15 5 flushing region 16 5 17 6 The flushing region may also be distributed over multiple cells horizontally using blocks FLUSHING_BLOCKS 3 Number of entries 12 25 1 i j location 2 5 10 11 2 i j range 24 27 3 1 3 location If a range is given SHOC will determine only those cells within the range that are wet A region file see Section 4 29 16 may also be used to specify the flushing region FLUSHING_REGION region bnc 3 4 n Region file and numbers Invoking the flushing tracer diagnostic will automatically create a tracer named flush with the following attributes TRACER5 name flush TRACERS long_name Flushing tracer TRACER5 units mot TRACER5 fill_valu
168. ellor Yamada 2 5 80 4 21 6 k e 81 4 21 7 k 82 4 21 8 W88 82 4 21 9 Stability functions 83 4 21 10 Waves 83 4 22 Horizontal mixing 83 4 23 Point sources sinks 85 4 23 1 Steady State Approximation 87 4 24 2D Mode 88 4 25 Sigma vertical coordinates 88 4 26 Stability sub stepping 89 4 27 Thin layers 89 4 28 Particle tracking 90 4 28 1 Particle Status 91 4 28 2 Source Colour 91 4 28 3 Age 91 4 28 4 Size 92 4 28 5 Settling 92 20 08 2015 Page 3 of 185 Version 1 00 SHOC User Manual 4 28 6 Swimming 94 4 28 7 Mortality 94 4 29 Grid Refinement 94 4 30 Tracer diagnostics 98 4 30 1 Tracer Fluxes 98 4 30 2 Means 99 4 30 3 Mixed Layer Depth 100 4 30 4 Flushing Time 100 4 30 5 Age tracer 101 4 30 6 Steric Height 102 4 30 7 Vorticity 103 4 30 8 Mixing Length Scale 104 4 30 9 CFL Time steps 104 4 30 10 Momentum Balance Tendencies 105 4 30 11 Tracer Tendencies 106 4 30 12 Selective Momentum Calculations 106 4 30 13 Diagnostic numbers 106 4 30 14 Tracer percentiles 109 4 30 15 Alerts 110 4 30 16 Total mass volume heat and salt 111 4 30 17 De correlation length scales 112 4 30 18 Mass Budgets 113 4 30 19 Diagnostic tracer names 116 4 31 Data variables and input time series files 118 4 31 1 Variable substitution 118 4 31 2 Multiple datafiles 119 4 31 3 Model variable initialisation 119 4 31 4 Model variable output 119 4 31 5 ASCII time seri
169. ensitivity analysis of a three dimensional model Coral Reefs 16 193 203 Wilcox D C 1988 Reassessment of the scale determining equation for BULK turbulence models A AA Journal 26 11 1299 1310 20 08 2015 Page 182 of 185 Version 1 00 SHOC User Manual 19 Index 2 Z2D MODE wavsietcaxatcacevoncsdastestvAastucvsasecast 74 A A OPIO Minura 111 113 114 ABSOLUTE 000008 See VORTICITY ADV EGS arrouina ain 61 90 ARDEN S eis Set ea iu nee 18 AIRTEMP gusuistee is egen Geist gu egee 59 101 ALBEDO arni dicted gefillte 60 ALERT eessen Sieden a 94 ALERT DP eneon aaa 94 ALLE NUMBERS cccccccsesesesesesereres 93 AMBIENT_AIR_PRESSURE 57 58 ANGULAR traten aatan 52 B ST eh aa 12 27 28 111 BATHY GON iene e aa 50 BATHY_ MASK orinar 28 BATHYMAX irie 28 113 BATHYMIN ainai 28 113 BOUNDARY ADJUST_FLUX eeen 40 148 149 BCOND ELE miia d a 37 BCOND_NOR ensen 37 38 BCOND_NOR2D eenn 37 BCOND_TAN eessen 37 38 BCOND_TAN2D ccccccceeeeeeeeeeees 37 BCOND TRA ALL 37 BCOND_ bR n rann a 37 GUS TOM sescisssessisaceasssaiscarsnaacacaasdacacies 39 UITOWDOPY EE 39 U2ZFIOWDATY esre aa 40 ATARDI EA 40 148 149 UV tO U2 ionun i nR 40 148 149 DATA etit a a tae 37 38 INVERGE BAROMETER 44 NSPONGE_HORZ oaen 44 NGPONGE VERT 44 OUTSIDE ZONE 36 POINTS ETE A RT 36 RIIN eegene 36 REALX_ZONE_TRAD eeen 43 RELAX ELE reena Ta AA 42 RELAX MMEA tennara a 42 HEI AN ZONE
170. epths d are shown below a 500 d 4000 tc1 100 tc2 7 100 T T T T T 80 60 Vi 4 40 J 20 Rate days 0 P L 0 500 1000 1500 2000 2500 3000 3500 4000 Depth m a 40 d 200 tc1 100 tc2 7 100 T T T T T T T T T mr 4 60 4 40 4 Rate days 20 4 0 i i J i i 0 20 40 60 80 100 120 140 160 180 200 Depth m An cosine depth dependent rate may be specified using TRACERO relaxation_time_constant cos_depth d tc units d tc units The relaxation rate is given by rate 0 5 tc tc cos depth PI d d d PI d d tc tc This formulation assumes d gt d An example is shown below 20 08 2015 Page 36 of 185 Version 1 00 SHOC User Manual d 30 tc 100 d 1500 tc 10 T T T T T T T T T dieses 4 EI ss 4 60 4 a is amp aot D Ze S 20 4 0 L li L 0 200 400 600 800 1000 1200 1400 1600 1800 2000 Depth m Relaxation rate linear in time may be specified using TRACERO relaxation_time_constant temporal dv tc units dv2 Los units In this case the relaxation rate is tc units at dv days relative to the TIMEUNIT changing linearly to tc units at dv days then thereafter capped at tc units 4 9 3 Resetting Tracer values throughout the model domain can be reset to some specified distribution which may vary in space and time To
171. er above below a threshold usage Tracer lt n gt tracerstat exposure lt 3Dtracer gt lt threshold gt lt expose_time gt optional RACER lt n gt dt lt m gt days optional RACER lt n gt start lt m gt days optional RACER lt n gt scale_factor lt m gt days where lt 3Dtracer gt is a 3 dimentional tracer lt tracer gt is a 3 dimensional or 2 dimensional tracer To initiate a tracerstat operation an additional attribute TRACER tracerstat in the tracer list must be specified The form of this attribute is of the type operation tracer_name where operation is the statistic from the list above and tracer_name is the name of the tracer to operate on For example to specify the flux in the e1 direction of a tracer named temp and output to a tracer called 1ux_temp the following tracer is specified TRACER name flux_temp TRACER long_name Temp flux in el direction TRACER tracerstat fluxel temp TRACER fi11_value_we 0 TRACER valid_range le 10 1e10 TRACER advect 0 TRACER diffuse 0 TRACER diagn 0 Note that these tracers are diagnostic and are not to be advected or diffused Also the diagn flag is turned off so that these tracers are not re initialized to zero at every dump step If a mean of tracer temp is required at 12 hourly intervals use TRACER name mean_temp TRACER long_name Average temp TRACER tracerstat mean temp TRACER dt 12 hours TRACER fill_value_we 0 TRACER valid_r
172. er aks 88 POTENTIAL ci ceeded 88 RELATIVE tege els 88 TENDENCY meriiri aan 88 WwW WATER TYPE fates tiniest enaa 60 UN 64 70 WET BUERG canines 59 101 WIMPUIEGIaeuebeserggesugesgeestage ege deeg 52 WIND T 56 101 112 WINDOW_RESET aaaiesseeeeen 13 14 WINDOW _ SIZE 1 00 eecceceecteeeeeteeeeeeees 13 WINDOW mn PONTS aeee 13 WINDOWS sssessseeseeeseeseesreserrsrrnsernees 13 WIMAX cet ce sthfeeciuirt EEN 95 WRITE_BDRY An 51 Z Z064 65 67 113 ZOOM FACTOR iiome ta en 80 ZOOM FACTOR EI 81 ZOOM FACTOR A 81 ZOOM DOINT 80 Version 1 00
173. er normal operation of the transport mode and re read using the open boundary specification Alternatively complete u1 and u2 velocity fields may be saved to the STREAMLINE data files which may be used in the global filling This approach will be automatically invoked if BCOND_NOR NOTHIN for all open boundaries Note that when files are read into SHOC interpolation is always performed even if the input file geometry and model grid are exactly the same this can lead to slightly different numerical values entering the code compared to the values in the file SPARSE formats do not suffer this problem since no interpolation in space occurs when they are read into SHOC The STREAMLINE mode is invoked via TRANS_MODE STREAMLINE 9 3 Conservation The transport model is non conservative for two reasons 1 The semi Lagrange scheme is cast in advective form and is non conservative Continuity is not achieved when using snapshots or temporal averages of velocity and surface elevation fields For a snapshot this is obvious continuity is only achieved if the velocity is constant over the transport time step For temporal means the elevation change over a time step An is not equal to the horizontal divergence of depth averaged mean velocity multiplied by mean total depth i e t2 t2 t2 An ndt V Dat iat tl tl tl hence continuity is also not achieved The global filling attempts to compensate
174. er product RACER2 units fraction RACER2 fill_value 0 0 RACER2 valid_range 0 10 RACER2 advect 0 RACER diffuse 0 RACER2 diagn 0 RACER2 reset_file scale nc RACER2 reset_dt 1 hour The values of this tracer will assume spatially interpolated values from the file scale nc at 1 hour intervals The reset_file may be a netCDF or time series file Next define different tracers to be scaled on each boundary by referencing to this tracer Add the boundary values in tracer scale_p to the boundary value of eta BOUNDARYO SCALE_ETA scale_p Add the boundary values in tracer scale_p to the boundary value of tracer with name lt trname gt BOUNDARYO SCALE_S lt trname gt scale_p 20 08 2015 Page 60 of 185 Version 1 00 SHOC User Manual Multiply the boundary value of tracer with name lt trname gt by the boundary values in tracer scale_p BOUNDARYO SCALE_P lt trname gt scale_p For example to add the boundary values in scale_p to the temperature boundary value use BOUNDARYO SCALE_S temp scale_p 4 10 26 Boundary geographic location The latitude and longitude of the cell and face centres may be output to file using WRITE_BDRY lt bdry_file gt where lt bdry_file gt is the name of the file the information is written to This file will contain the latitude and longitude of cell centres for tracer elevation normal velocity face centres and tangen
175. es to the original locations PT_KH Horizontal diffusion coeff PT KZ MULT Vertical diffusion coeff F multiplier PT Mass 1 Particle mass kg PT Restart yes Interpolate particle positions from the InputFile onto the grid If true then the particles are not lost when they move outside the model domain instead they stick to the boundary and are released when the current changes direction PT_StickyBoundary TRUE A continuous source of particles along a line is specified by a rate of release and the start end positions of the line These parameters are not mandatory and multiple sources are permitted PT _NSource 1 PT_Source0 Rate 20 Number of particles second PT_Source0 ColourBit 2 The bit to set in the flag array when the particle is seeded Valid range 2 15 PT _Source0O StartLocation 280000 7000000 15 XYZ of start position PT_Source0 EndLocation 280000 7020000 25 XYZ of start position 20 08 2015 Page 90 of 185 Version 1 00 SHOC User Manual 4 28 1 Particle Status The status of a particle may be active inactive and unlost lost Active unlost particles are the particles that appear in the domain If a particle exits through an non sticky boundary then it becomes lost and returns to the inactive pool of particles available to be released at each source A particle may become lost by moving through an open boundary or by failing
176. es 119 4 31 6 NetCDF dump files 120 4 31 7 Multi dumpfiles 123 4 31 8 Customised parameters 124 4 31 9 Coastlines 124 4 31 10 Bathymetric data 124 4 32 Diagnostic files 125 4 32 1 Run regulation 127 4 33 Explicit mapping 128 5 Automatic setup a option 131 6 Restarts 135 6 1 Basic restarts 135 6 2 Restarts using restart file restart option 135 6 3 Near real time restarts nrt option 135 6 4 Crash recovery cr option 136 7 ROAM r option 137 8 Input file generation g option 141 9 Transport mode t option 142 9 1 Multiple grids 145 9 2 STREAMLINE mode 146 9 3 Conservation 146 20 08 2015 Page 4 of 185 Version 1 00 SHOC User Manual 9 4 Flux form semi Lagrange 147 10 Percentile computations ps option 150 11 File formats 151 11 1 ASCII time series 151 11 1 1 Units Kei 11 1 2 Utilities 152 11 2 NetCDF time series 152 11 2 1 Units 152 12 Tests 157 12 1 No forcing 157 12 2 Ekman Spiral 157 12 3 Constant wind stress closed basin 158 12 4 Constant wind stress alongshore open channel 158 12 5 Constant wind stress cross shore open domain 159 12 6 Propagation of a bore 160 12 7 Wind stress curl closed basin 160 13 Tracer Statistics 161 14 Getting Started 167 14 1 Compile SHOC 167 14 2 Run a test case 167 14 3 Generate a custom grid 167 15 Sediment Transport 174 16 Ecology 176 17 Troubleshooting 179 18 References 180 19 Index 183 The latest SHOC User Manual may be downloaded from
177. es of the user s choice File formats may be netCDF for spatially variable or ascii time series for non spatially variable constituents The custom tidal constituent prescription is specified using BOUNDARYO BCOND_ELE TIDALC BOUNDARYO T_CONSTITUENTS M2 S2 K1 O1 List of constituents The tide may be directly imposed on the boundary as above or may be superimposed on some low frequency sea level signal using BOUNDARYO BCOND_ELE FILEIN TIDALC BOUNDARYO T_CONSTITUENTS M2 S2 K1 O1 List of constituents BOUNDARYO DATA low_frequency nc netCDF file containing low frequency sea level data The global tide model requires paths to the file specifying constituent phases and amplitudes and the nodal correction directory to be present e g IDE_CSR_CON_DIR tide nodal Path to nodal correction directory IDE_CONSTITUENTS tide nc Constituent file If any of the constituents listed in the BOUNDARYO T_CONSTITUENTS list cannot be found in the TIDE_CONSTITUENTS file SHOC will terminate with an error The list of constituents 20 08 2015 Page 57 of 185 Version 1 00 SHOC User Manual should be a subset of the following if a constituent is not found in this subset it will be omitted from the forcing with an accompanying error
178. es to ZS LMIN E VZ0 KZO and density gradient threshold hardwired as variable thr in routine mld in My2 0 c may affect the solution The bottom roughness z0 also influences the mixing length scale in the bottom mixed layer ZS is analogous to ZO for the surface layer Solutions may be particularly sensitive to the background viscosity and diffusivity If the mixed layer interfaces are required to be identified using turbulent kinetic energy rather than the density gradient then the routine mld must be changed to mldk in MY2_VzKz_mod in mixing MY2 0 c The threshold is given by the variable thr in mldk in the same module Finally the mixing length scale may be modified by the local turbulent kinetic energy in the mixed layers Blackadar 1962 via the flag lof in the routine get_Lscale in mixing MY2 0 c This option is switch off by default lof 0 and can be included by hardwiring lof 1 Accounting for local turbulent kinetic energy in the mixed layers generally decreases the mixing length scale in those regions These hardwire options can generally be left unaltered unless complex tuning of the mixing scheme is required 4 21 5 Mellor Yamada 2 5 Finally the Mellor Yamada 2 5 or kkl scheme Mellor and Yamada 1982 includes the transport of turbulence kinetic intensity and turbulence length and requires four additional tracers Note length scale and turbulence mixing are diagnostic tracers and do not undergo advection and
179. et use multiplication of the reciprocal Any keywords in the equation that are not valid unary operators will be considered as a model tracer An error will occur if any specified tracers are not found in the model 4 10 9 Relaxation to Forced Data Boundary data specified from a file may be combined with a radiation condition so that the transient response of the domain is transmitted through the boundary while allowing the boundary to respond to the prescribed forcing This is accomplished by or ing an active data forcing condition FILEIN or CUSTOM with a passive boundary condition The time scale of relaxation is input via the keyword RELAX_TIME and must be supplied for the following boundary conditions ORLANS FILEIN CAMOBR FILEIN MILLER FILEIN GRAVTY FILEIN NOGRAD FILEIN CLAMPD FILEIN LINEXT FILEIN POLEXT FILEIN Specifying RELAX_TIME assumes that incoming and outgoing waves are relaxed equally Alternatively relaxation may differ for incoming and outgoing waves by specifying BOUNDARYO RELAX_IN 1 hour BOUNDARYO RELAX_OUT 30 days Long relaxation times are typically associated with outgoing waves so that the OBC behaves like a radiation condition and short relaxation times are associated with incoming waves so that the OBC converges to the forcing data 20 08 2015 Page 50 of 185 Version 1 00 SHOC User Manual A boundary con
180. f the area To do this you need an ASCII file containing bathymetric data in 3 columns x y and depth free format An example file is as follows This is an optional comment line This is another comment line The 3 columns are x y and depth 1000 1000 20 2020 2 1354 10 1520 7322 15 You can even have comments in the middle of the data 7261 6123 8 8761 7991 5 20 08 2015 Page 124 of 185 Version 1 00 SHOC User Manual The data does not need to be on any sort of regular grid they may be randomly scattered in x and y This data can be read with jvismeco and the the interpolated model bathymetry saved as a text file suitable for inclusion in a SHOC parameter file 4 32 Diagnostic files A summary of the simulation is always printed to the file setup txt upon execution of SHOC This file is written to the path specified by OuputPath and the directory SHOC is run from Typically this summary contains the following information SHOC Simulation Summary Version v1 0 Input file open prm Open channel test domain Grid description Coarse open channel 120 1 Simulation start time Mon Jul 31 16 02 58 2006 Operating in 3D mode 3D time step 40 000 2D time step 5 000 Tracer time step 40 000 Sub stepping stability compensation Thin layer adjustment implemented Exit on fatal eta instabilities when Exit when above variables NaN excluding surface layer leta gt 10 00
181. facilitates the implementation of higher order advection schemes These open boundaries are generally called velocity boundaries below More specifically they are called u1 boundaries if the left or right hand edge of the cell is open or u2 boundaries if the back or front edge of the cell is open The orientation of the ul or u2 velocity boundaries must be known so that the normal and tangential velocity components may be identified in the SHOC code Flagging a boundary as ul or u2 requires the user to make this decision Alternatively a boundary may be classified as a velocity boundary in which case SHOC will decompose the boundary cell into u1 and u2 boundaries on left right front or back faces The cell location provided in the POINTS list for u1 and u2 boundaries corresponds to the cell face This means that the cell locations of ul boundaries on right faces and u2 boundaries on front faces are incremented by one in the x and y directions respectively from the interior cell center adjacent to the boundary If the boundary is specified as a velocity boundary then the boundary cell location corresponds to the cell center When specifying open boundaries in the parameter file it is first necessary to indicate how many open boundaries the model grid has This grid has 3 open boundaries NBOUNDARIES 3 Then each boundary is described by a number of parameters of the form BOUNDARY lt M gt XXXX where lt M gt is the boundary index The
182. file All tracer diagnostics including sediment transport biogeochemistry tracer statistics source sinks and particle tracking will function in the transport mode The advection scheme used in this mode is the unconditionally stable semi Lagrangian scheme allowing increased time steps e g 1 hour to be used which dramatically increases run time ratios This scheme is however quite diffusive and does not possess as good conservation characteristics as other schemes available in SHOC hence some accuracy is forfeited at the expense of speed The semi Lagrangian scheme is unconditionally stable because it traces streamlines back in space from the point of origin e g cell centres using velocity information then interpolates tracers using the origin location The concept of using offline velocities to drive a transport model is not new however in practice it is rarely used due to the enormous amounts of disk space required to run for extended periods This problem is circumvented by generating the offline velocity diffusivity files with a sparse file format Section 4 31 6 which eliminates land from the dumpfile and can lead to large saving in disk space savings up to 90 are possible I O overhead can be reduced if the sparse format file is read into SHOC without interpolation i e the dumpfile contains information on exactly the same grid as the transport model is using for exactly the times required The transport option requires a stand
183. filled data These keywords can be combined sequentially e g TRACER_FILTER FILL2D FILL3D SMOOTH SHUMAN MEDIAN 20 08 2015 Page 41 of 185 Version 1 00 SHOC User Manual 4 10 Open boundaries Each open boundary if there are any is specified as a list of horizontal grid cell locations together with parameters which define the nature and behaviour of the boundary The cells in a single open boundary do not necessarily need to be adjacent to one another but it is usually desirable to group boundary cells that are physically or logically related For each open boundary it is usually necessary to define data files from which the boundary values surface elevations velocities or tracer concentrations may be read Constant values or custom routines returning boundary values may also optionally be specified Open boundaries may be defined anywhere in the grid however if a boundary is defined in the domain interior as opposed to the limits of the domain then the boundary must lie adjacent to an OUTSIDE cell Open boundaries require that velocities normal and tangential to the open boundary elevation and tracer concentrations are specified Velocities are specified at the outer edge s of open boundary cells while elevation and tracers are specified at the cell centers This formulation allows for a suite of BULK open boundary conditions to be implemented radiation extrapolation relaxation conditions and
184. for local areas only unless a Latitude Longiutude PROJECTION is used 4 6 3 Numerical grid The numeric grid allows the specification of a general orthogonal curvilinear grid using the XCOORDS and YCOORDS parameters The grid must include not only the cell corners but also the position of the cell centre and the u1 and u2 positions In effect the parameters define a grid twice the resolution of that being modelled At this time there is no simple toolkit available for generating such grids and grid generation is left to the reader 20 08 2015 Page 25 of 185 Version 1 00 SHOC User Manual 4 6 4 Geographic rectangular grid A Geographic rectangular differs from a normal rectangular grid as it defines a grid that is orthogonal on a spheroid A geographic rectangular grid can only be specified if the PROJECTION parameter is set to geographic SHOC supports three different ways of defining a geographic rectangular grid Auxiliary pole The first method computes the grid metrics using an auxiliary coordinate system defined by a false pole PROJECTION geographic GRIDTYPE GEOGRAPHIC_RECTANGULAR NCE1 10 NCE2 20 DLAMBDA 0 01 Long cell interval in aux coords degrees DPHI 0 01 Lat cell interval in aux coords degrees X00 144 3856 Longitude of origin degrees YOO 38 2030 Latitude of origin degrees POLE_LONGITUDE 0 Longitude of false pole degrees POLE_LATITUDE 90 Lat
185. ful for easily manipulating input data without creating a new input forcing file for example when scaling is required to convert to the correct units for tracer input The scaling may be either a constant specified value or may be scaled by the value of a tracer existing in the tracer list In the latter case the scaling may be temporally and spatially variable To scale by a constant use Add the value of one to the boundary value of eta BOUNDARYO SCALE_ETA d Multiplicative scaling on eta can be invoked using e g multiply by 1 5 BOUNDARYO SCALE_ETA WEE Add the value of one to the boundary value of tracer with name lt trname gt BOUNDARYO SCALE_S lt trname gt 1 Multiply the boundary value of tracer with name lt trname gt by 0 9 BOUNDARYO SCALE_P lt trname gt 0 9 For example to add 1 C to the temperature boundary value use BOUNDARYO SCALE_S temp 1 A tracer may be set up where its value is updated using the reset function Section 4 10 2 The tracer should not be advected diffused and should not be a diagnostic This tracers value will therefore be updated with data from a specified file at a specified time interval The values of this tracer on the open boundary can then be used to scale elevation or a different tracer s boundary values First define the scaling tracer in the tracer list e g RACER2 name scale_p RACER2 long_name Scaling trac
186. ge 3 botrange where toprange and botrange are a list of individual layer numbers or layer ranges in the format lt from gt _ lt to gt separated by commas e g TRACER tracerstat vdiff salt 2 6 9_12 15_17 20 will result in the sum of salinity concentration in layers 15 16 17 and 20 subtracted from the sum of salinity concentration of layers 2 6 9 10 11 and 12 The variable strict is given as 0 or 1 with O used as the default If strict 1 then the difference is given as zero if any of the layers in the toprange or bot range are not present e g if one or more layers happens to lie below the sea bed The tracer statistics are computed in the order of the operation list provided above hence it is possible to compute a statistic of a statistic if the order permits this For example a vertical integral of a mean may be computed but a mean of a vertical integral will result in operations performed at different time levels In addition to the tracers in the tracer list it is possible to compute tracers on the following 2D and 3D hydrodynamic variables eta sea level 2D Kz Verical diffusivity 3D Vz Vertical viscosity 3D ulvh Horizontal viscosity in the el direction u2vh Horizontal viscosity in the el direction ulkh Horizontal diffusion in the el direction u2kh Horizontal diffusion in the el direction For example the mean sea level may be calculated using
187. gt BOUNDARYO BCOND_TRA lt n gt UPSTRM FILEIN DEPROF Density profile for tracer lt n gt BOUNDARYO DATA input_file nc netCDF input file containing measured data for tracer lt n gt Tracers may also be scaled to a normalized density profile that exists through the water column i e at the deepest point in the domain This ensures that the gradient of the tracer profile is some constant multiple of the density gradient and therefore ensures that mixed layer depths are consistent between the tracer and density This is invoked using 20 08 2015 Page 55 of 185 Version 1 00 SHOC User Manual BOUNDARYO BCOND_ lt trname gt FILEIN DESCAL BOUNDARYO SCALE_D lt trname gt vl v2 lt code gt Where lt trname gt is the name of the tracer v1 is the depth at which the tracer value is equal to that in input_file nc at the same depth and v2 is a scaling factor for the profile if v2 lt O0 the profile is inverted Below depth v1 the profile in any layer k is determined by adding v2 x density gradient to the concentration in the layer k 1 This is iteratively computed down through the water column Above depth vi the profile in any layer k is determined by subtracting v2 x density gradient to the concentration in the layer k 1 This is iteratively computed up through the water column If lt code gt c then a copy of the values in input_file nc is used for the profile below depth v1 and if lt co
188. h t ran e g TRANS_DATA dummy txt If the time step does not violate stability criteria alternative advection schemes may be used The ULTIMATE and STABILITY options may be used in conjunction with this Often the velocity fields read into the transport model snapshots or means are not conservative in the sense that the divergence of the depth averaged velocity does not always equal the change in elevation over the time step This can lead to conservation errors using advection schemes solved using the flux method Conservation may be forced locally in time by computing the change in elevation over the time step and vertical velocity from the specified velocity distributions This maintains conservation for tracers using non semi Lagrangian advection schemes and is invoked using CONSERVATION YES Force volume conservation The sea level may be re initialized to that in the transport file or left to evolve over time by using CONSERVATION RE_INITIALIZE Force volume conservation with eta re initialization CONSERVATION NO_INITIALIZE Force volume conservation with no eta re initialization Additionally only vertical velocity or sea level may be forced to conserve by adding W or ETA to the CONSERVATION specification e g CONSERVATION NO_INITIALIZE ETA CONSERVATION RE_INITIALIZE W The default is CONSERVATION RE_INITIALIZE W ETA For the FFSL scheme
189. h depth surface current speed 0 0043 me and bottom current speed 0 00019 ms Surface elevation should be equal to zero 12 3 Constant wind stress closed basin This test examines the set up due to a steady wind applied to a 1 layer depth averaged model domain If a constant wind is applied to a homogeneous closed basin of constant depth then depth averaged velocities are equal to zero in the steady state For a linear model and constant wind stress in the x direction the surface slope should balance the applied wind stress and the equations of motion reduce to an expression for the sea level gradient in the x direction EE 12 3 1 ox pgD where D is the water depth If a wind stress of 1Nm is applied to a homogeneous ocean of temperature 20 C and salinity 35 psu so p 1024 76 kgm then the slope in a 10m deep basin is equal to 9 958x1 0 and the depth averaged velocities should be near zero 12 4 Consiant wind stress alongshore open channel An analytical solution exists for a linear model of constant wind stress applied in a longshore direction along an infinitely long coast Assuming cross shelf transport and alongshore sea level gradient are small then along shelf transport U is given by Chapman 1985 eqn 4 5 Dt U 1 exp tr D 12 4 1 pr with a steady state velocity t given by U A 12 4 2 Note U is the transport hence velocity u U D The sea surface slope is given by Chap
190. han number of cells x0 X coordinate origin yO Y coordinate origin dx Width of cell in X direction dy Height of cell in Y direction rot Mathematically defined angle of rotation of grid To define an analytic attribute for a polar grid use the following syntax var analytic polar ioff joff ni nj x0 y0 rmin arc ioff I offset within the grid 0 is grid edge 0 5 is centre joff J offset within the grid 0 is grid edge 0 5 is centre ni number of grid points along i dimension one more than number of cells nj number of grid points along j dimension one more than number of cells 20 08 2015 Page 153 of 185 Version 1 00 SHOC User Manual x0 X coordinate origin yO Y coordinate origin rmin Minimum radius arc Angular width of cell This example netCDF CDL snippet defines a geographic grid If a PROJECTION parameter was specified as the default coordinate system then SHOC will automatically convert from geographic coordinates to the map projection if necessary when reading the data file netcdf file dimensions nrecord UNLIMITI ni 10 nj 20 nk 5 Fi ei ER variables Time coordinate variable double t nrecords t units seconds since 1990 01 01 00 00 00 10 t coordinate_type TIME Latitude coordinate variable of a 2d rectangular grid double lat nj ni lat units degrees_east lat coordinate_type latitude
191. he major steps Installation of the model software This is described in section 2 Definition of the horizontal and vertical geometry of the model grid This may require the use of an interactive grid generation program with the ability to plot coastlines etc or may be a simple specification of a test area such as a swimming pool Construction of the model parameter file This step incorporates the grid geometry obtained above along with information about bathymetry and the location and types of boundary points As well forcing data sets are specified and the physical parameters mixing friction etc are chosen With the auto config mode this file is automatically generated Creation of the model variable initialisation netCDF file either from the parameter file by using the g option described in section 8 or by using output from a previous model run Running the model Commands needed to do this are described in section 4 Examination of the results This is done either by using an interactive viewer jvismeco olive or by producing plots with various scripts or tools such as gnuplot To set up the model for a particular area or application it is necessary to gather together a diverse set of parameter specifications and input data These are all defined in the model parameter file an easily edited ASCII file which completely defines the model for a particular application and run Amongst other things the parameter file describe
192. he latent heat flux requires data to calculate specific humidity Time series file containing the variable wet_bulb with units Degrees C 20 08 2015 Page 71 of 185 Version 1 00 SHOC User Manual WET _BULB wetbulb nc WE BULB _INPUT_DT 10 minutes In the absence of wet bulb measurements the dew point temperature may be substituted Time series file containing the variable dew_point with units degrees C WET_BULB dewpoint ne WET_BULB_INPUT_DT 10 minutes If available a file containing short wave radiation may be supplied directly as below t Time series file containing the variable swr with units W m 2 RADIATION Swr nc How often to read the solar radiation data RADIATION _INPUT_DT 10 minutes Albedo of the surface ALBEDO 0 2 If 1 lt ALBEDO lt 0 then the albedo is computed as a function of cloud amount and hour angle sect 9 1 1 Science Manual In the absence of a CLOUD file clear skies are assumed There are five bulk schemes available to specify latent and sensible heat fluxes These are specified via Specify the bulk method BULK_SCHEME L amp P Large and Pond 1982 scheme Ko Kondo 1975 scheme B Bunker 1976 scheme K W Kitaigorodskii et al 1973 scheme M Masagutov 1981 scheme These schemes are compared in Blanc 1985 The default is the scheme of Kondo 1975 A
193. he value of the constant above typically c 0 1 and any combination of U1VH U2VH U1KH U2KH is negative For example if the y compoment of horizontal diffusivity is to be calculated using Smagorinsky diffusion then set SMAGORINSKY 0 1 U2KH 100 0 If DIFF_SCALE SMAG then Smagorinsky diffusion is set for all horizontal mixing coefficients using a constant smagorinsky 0 1 This constant may be over ridden if the SMAGORINSKY constant is explicitly defined If Smagorinsky diffusion is to be used then an extra tracer is required which stores the value of the diffusion coefficient This tracers is automatically generated by SHOC when the smagorinsky diffusion is invoked but may be over ridden by manually specifying the following in the parameter file RACERn name smag RACERn long_name Smagorinsky RACERn units m2s 1 RACERn diagn 1 RACERn advect 0 RACERn diffuse 0 RACERn decay 0 0 RACERn svel 0 0 RACERn fill_value 0 0 RACERn valid_range D 10000 The Smagorinsky distribution can be smoothed prior to use any number of times n using SMAG_SMOOTH n 20 08 2015 Page 84 of 185 Version 1 00 SHOC User Manual Note that the horizontal mixing of momentum in SHOC follows the full formulation Herzfeld et al 2002 section 2 4 A simple formulation exists e g Apel 1987 p99 Eqn 3 61 where metric terms are omitted and incompressibility assumptions are made these can
194. heat flux and latent latent heat flux These variables usually require the use of variable substitution since they typically have the following MOM names swr sw_flux lwr lw_flux sensible t_flux latent q_flux 4 18 Surface salt flux A surface salt or freshwater flux may be included to account for the effect of water fluxes on salinity This can be specified via the flag SALTFLUX NONE No salt flux included SALTF LUX BULK BULK salt flux SALTFLUX BULK Salt flux partially determined using bulk schemes The BULK method requires PRECIPITATION and EVAPORATION time series files to be defined sections 4 15 and 4 16 from which the surface salt flux is calculated and applied as a surface boundary condition for the vertical diffusion of salinity see Herzfeld et al 2002 section 9 4 Evaporation is difficult to measure over water and the latent heat of evaporation may be used to estimate this parameter Herzfeld et al 2002 section 9 4 when the BULK method is invoked Since this bulk flux is used the BULK method will only function if the HEATFLUX flag is set to BULK so that latent heat of evaporation is calculated If a PRECIPITATION time series file is present then the effect of rain is added to the calculated evaporation 4 19 Bottom friction 20 08 2015 Page 75 of 185 Version 1 00 SHOC User Manual Bottom friction in the model is implemented as a combination of a linear and quadratic drag l
195. heir initial locations periodically if requested If desired particles can also display a specific vertical movement prescribed on a time series The time series file should contain the vertical velocity as a function of time and space This allows implementing particle swimming behaviour Mortality or the loss of a percentage of the remaining particles at every time step can be prescribed with a time series file Output files will contain the variable ptconc if particle tracking is invoked this variable indicates the concentration of particles kom for each cell over time For ptconc to be computed the particle mass has to be given as non zero Particle tracking will only occur if an input file is specified Following is an example particle tracking specification t Defines the input particle input file This is a netCDF time series containing the variables t x y and z for a specified number of particles n PT_InputFile pt pt50000 nc 50000 particle file PT_InputRecord 0 Dump number to use for initial particle distribution The output file where the position of all active particles will be written PT_OutputFile pt ne PT_StartTime 1580 days Start time for PT PT_StopTime 1612 days Stop time PT_OutputStep 1 hours Output interval PT_TimeStep 10 minutes Update period for recalc particle positions PT_ResetStep 100 days How often to reset particl
196. hould be run with the help option Following is an example output shoc help SHOC Sparse Hydrodynamic Ocean Code Version v0 00 beta rev000 Run start Thu Jun 24 14 31 51 2004 Usage shoc p prmfile lt options gt Run SHOC using standard parameter file prmfile Standard parameter file shoc g prmfile dumpfile lt options gt Generate initial dump using standard parameter file prmfile Standard parameter file dumpfile Initialisation dump file shoc a prmfile lt options gt Run SHOC using autostart parameter file prmfile Autostart parameter file shoc ag prmfile lt options gt Generate initial dump using autostart parameter file prmfile Autostart parameter file shoc t tranfile lt options gt Run SHOC in transport mode tranfile Transport input file shoc ps prmfile Compute percentile statistics prmfile Parameter file shoc v Print shoc version information 20 08 2015 Page 9 of 185 Version 1 00 options diag_log lt file gt off setup_log lt file gt off window_log on loff l Pag agin debug tag tag Examples main info warn debug trace metric all conversions time dump particles init_m init_w ecology sediments SHOC User Manual Enable disable diagnostic log default diag txt Enable disable setup log default setup txt Enable disable window log default off A text file listing all master slave mappings is
197. hout having to manually alter the parameter file this mode is invoked using shoc p test prm nrt In this case the START_TIME for the simulation is read from the netCDF file specified as the INPUT_FILE the stop time for the simulation is this START_TIME STOP_TIME specified in the parameter file i e the STOP_TIME is an increment rather than an absolute value both the RAMSTART and RAMPEND are set equal to the START_TIME i e no ramping is performed and the output file tstart and tstop are set to the start and stop simulation times This means that the START_TIME RAMSTART RAMPEND tstart and tstop are not required to be set in the parameter file Furthermore if a restart file is overwritten to the same location then this may be used as the INPUT_FILE Additionally the SEQUENCE option may be used 20 08 2015 Page 135 of 185 Version 1 00 SHOC User Manual to store model output in a unique directory requiring that the only manual tasks to initiate repetitive simulations are the creation of the directory and commencement of the simulation both of which are easily scripted A near real time parameter file for daily simulations may therefore appear as STOP_TIME 1 day Run length INPUT_FILE home data restart nc Input file restart_dt 1 day Restart interval restart_name home data restart nce Restart file name OutputPath home
198. iagnostic attempts to detect early signs of instability by monitoring maximum absolute velocities divergences and if invoked maximum absolute momentum tendencies These maximums are written to an alert diagnostic file every time step along with the maximums encountered during the whole simulation A time series file containing the history of the maximum values is also created To invoke alert tracking in passive mode ALER PASSIVE lt alert_file gt ALERT_DT 1 hour Where lt alert_file gt is an optional filename to write the maximum value information to This file name is appended with t xt If lt alert_file gt is absent then output is written to the file alert txt by default If ALERT_DT is present then a time series file is created with the alert filename appended with ts and maximum values are output at the specified time interval The maximum values printed to file are absolute maximum values Note that maximum tendencies are only printed if the MOM_TEND flag is invoked The mechanical energy excess mass mean sea level and boundary energy flux are defined according to Palma and Matano 1998 and are useful for diagnosing the stability of a domain Mechanical Energy ogn dA 0 spDU U dA Um A A Excess Mass fina m A A 1 OBC Energy Flux T DU en 0 5U Ay mie WwW Where A domain area W OBC width the energy flux is for a u1 boundary in this case see Sect
199. ially dependent velocities interpolate the settling velocity onto cell centres of the grid and all particles within a particular cell will adopt that corresponding settling velocity NOTE The differences between invoking PT_Source0 Svel settling velocity type and the PT_w_file are that the former is used for particles released from sources in which case a continuous source of particles along a line is specified by a rate of release and the start end positions of the line Each source must have their own time series file The second from is used for a release of particles determined with the particle input file in which case the domain is seeded with an initial distribution of particles In this case the settling velocity can vary asa function of time t and space 20 08 2015 Page 93 of 185 Version 1 00 SHOC User Manual 4 28 6 Swimming Similar to the settling for particles released from an initial distribution particles may be assigned horizontal swimming velocities applicable to an initial release This swimming is read from netCDF file as a function of time and space and is specified via PT_uv_file vel nc File containing settling variable upt for swimming in the x east west direction and vpt for swimming in the y north south direction Note that upt and vpt are velocities are relative to the east west north south axis rather than the numerical grid and must generally undergo rotation within the particle t
200. ides a frame work for reading and writing blocks of data but it does not provide any implicit mechanism by which coordinate information is associated with data variables This association needs to be explicitly made by the software reading the netCDF file To assist in automating this association SHOC has adopted it s own coordinate convention for binding data variables and coordinate variables The convention requires the specification of special attributes for both data and coordinate variables Data variables contain a coordinates attribute which defines a list of coordinate variables associated with it The coordinate variables contain an attribute coordinate_type that describes the spatial coordinate this dimension corresponds to Following is an example NetCDF CDL snippet netcdf file dimensions nrecord UNLIMITED ni 10 nj 20 nk 5 variables Time coordinate variable double t nrecords t units seconds since 1990 01 01 00 00 00 10 t coordinate_type TIME 20 08 2015 Page 152 of 185 Version 1 00 SHOC User Manual X coordinate variable of a 2d rectangular grid double x nj ni xX units m x coordinate_type X x analytic rectangular 0 0 10 20 0 0 1000 1000 0 Y coordinate variable of a 2d rectangular grid double y nj ni yrunits m y coordinate_type Y y analytic rectangular 0 0 10 20 0 0 1000 1000 0 2 coordinate variable double z nj ni Zrunits
201. ied in the hydrodynamic simulation with volume fluxes i e hydrodynamic point source files contain flow and copied to the point source volume flux variables when re read in the transport mode This only occurs if the point sources are also specified in the transport simulation with volume fluxes i e transport point source files contain flow To override this transfer of vertical velocity to volume fluxes in transport mode use CONSERVATION NO_PSS_FLOW No volume flux transfer A no gradient condition can be enforced for each tracer before entering the FFSL advection scheme by using CONSERVATION NOGRAD Enforce no gradient conditions This can assist in ensuring the transverse terms do not contain spurious data however should only be used if severe non conservation is observed as this option has been known to degrade the solution in some applications 20 08 2015 Page 148 of 185 Version 1 00 SHOC User Manual If the transport files contain unreasonable data due to the hydrodynamic model tending toward instability then this may be mitigated in the surface layer by merging volume fluxes and velocities using CONSERVATION MERGED Merge surface layer volume fluxes This should be a last resort option when trying to ensure conservation in the FFSL model To ensure that consistency and hence conservation occurs between hydrodynamic transport files and transport simulations ALWAYS USE THE SAME POINT SOURCE
202. ile per day it depends on the file increment The option merely enforces at most one days months or years worth in each file For MONTHLY only the year and month suffix is added and for YEARLY only the year This applies to standard simple simple_cf parray and sparse output netcdf formats A sparse or standard formatted files may have the additional modulo attribute which may take the value year month week day hour minute Or second g filedO modulo year yearly modulo When these sparse formatted files are input via tracer resets or in the transport mode then the model time is converted relative to the defined modulo For example if a year modulo is specified then all model times are converted to times within the range 0 to 365 and an input file of length 1 year may be used to cycle through a simulation of many years length When dumping the modulo is relative to the tst art time specified for the output file e g for year modulo set tstart to be 1 Jan for a particular year A filling algorithm may be applied to the output variables prior to dumping which re assigns values over land e g fileO fill_rule default eta 0 and 3D tracers NaN at land cells fileO fill_rule no_fill No filling applied fileO fill_rule zero_fill eta 0 and 2D amp 3D tracers 0 at land cells 20 08 2015 Page 122 of 185 Version 1 00 SHOC User Manual fileO fill_rule cascade_search Land cells filled with the
203. ime series file then the rate of momentum input is P p Qv pV me where p density of the inflow kg m if temperature and salinity are associated with the source in the time series file then the inflow density is computed using the equation of state If no temperature and salinity are specified the inflow density is assumed to be equal to the receiving water Q is the flow rate me and v is the velocity associated with the inflow u1 or u2 velocity in ms both specified in the time series file p is the density of the receiving water and V is the cell volume where the vertical depth distribution of the source is used to compute this volume if specified see below Point source sinks are specified as follows Number of point source sinks npointss 2 Parameters for each point source sink pss0 name Nasty stuff Point source sink name pss0 location 447174 5442668 0 Location X Y Z2 pss reference surface reference level pss0 data nasty ts Time series fil pssl name Nice stuff pssl location 450477 5446628 10 pssl data nice ts The z location i e depth of the source sink input may encompass a depth range with the deepest limit entered first and depths below the surface entered as negative The tracer input 20 08 2015 Page 85 of 185 Version 1 00 SHOC User Manual values are equally distributed over the depth range e g for tracers to be distributed between 5m and 10m G
204. in Section 4 14 OBC_PHASE Open boundary phase speed for elevation as given by radiation conditions in Science Manual Section 4 6 The phase speed is bounded by the CFL condition 20 08 2015 Page 108 of 185 Version 1 00 SHOC User Manual 0 lt phase lt 1 if waves are incoming then the phase is negative hence bounded to zero Out going waves have the phase gt 0 SIGMA_T o7 kgm is output as dens_0 1000 ENERGY Mechanical energy Um given by Kowalik and Murty 1993 eqn 1 24 E E E 1 pu u w pen KINETIC Kinetic energy Um given by Kowalik and Murty 1993 eqn 1 24 2 2 2 E 4p uf u w SLOPE Computes the surface slope in the e1 and e2 directions stored in surf_slope_x and surf_slope_y respectively SURF_LAYER The k index of the surface layer is stored in the 2d array surf_layer BOTSTRESS Bottom stress in e and e2 directions and bottom stress magnitude WET_CELLS Adiagnostic to show wet and dry cells Water columns are assigned the percentage of water they contain relative to being dry i e a dry water columns is assigned 100 cell with sea level at msl is assigned 0 and when sea level rises the percent dry is negative If sea level falls to half the water depth the cell is 50 dry Note that a cell is considered dry when the water falls below DRY_FRAC HMIN where DRY_FRAC is currently hardwired to 0 05 and HMIN is defin
205. indow and similarly for cells in the y direction Right click the mouse to exit and define the grid or click RECT sphere Grid again for further definition of the grid An example of the final grid is shown in Figure 14 3 3 in this case focussed on the South Australian Gulfs Note the x and icons in the Plan View pane can be used to zoom in centre and zoom out around the image while creating the grid right click to exit from x 3 Create a land mask Click on the Create Mask button see Figure 14 3 1 The land in the domain is coloured green Land water or outside cells Section 4 8 can be manually reset using the Edit Mask button The resulting masked image is shown in Figure 14 3 4 The number of 2D wet cells is displayed in the matlab window 4 Load the bathymetry from a database Bathymetry can be loaded from pre existing ascii or netCDF databases or can be loaded from a SHOC output file In this case bathymetry is loaded from the AGSO 2002 database by clicking Get Ncdf Bty Data and choosing the appropriate database Bathymetry is loaded onto the image as depicted in Figure 14 3 5 a Return to the GRID CREATION menu and click on Get Ncdf Div Data again A decimation value for the bathymetry dataset may be then entered enter O for default and the bathymetry is truncated to the grid domain size Figure 14 3 5 b 5 Interpolate the bathymetry onto the grid Click on
206. inement may be invoked using ZOOM_FACTOR_E1 or ZOOM_FACTOR_E2 3 Use a zoom factor of 3 in the el direction only Use a zoom factor of 5 in the e2 direction only It is possible to construct a grid which has refinement in one direction e g Figure 4 29 2 has a refinement of factor 3 in the e1 direction This grid may be reverted to a uniform grid using the PRI 20 08 2 ECONDITIONED grid refinement option GRID_REF INEM ENT ZOOM_FACTOR_ 015 El Y 3 ES PRECONDITIONED Page 95 of 185 Version 1 00 SHOC User Manual This option is useful for reverting a portion of the grid to a uniform grid while increasing the resolution of another part of the grid e g an upstream river section In the example below the river section that is three cells wide may be retained at this resolution while the remainder reverted to uniform Note that the ZOOM_POINTS of the cell centres required to be reverted must also be supplied 153 3 4 E 153 3 6 E 153 3 8 E 153 4 E 26 34 4 S STEE L Se oe ES 4 aes i N 26 34 6 26 34 8 S 26 34 8 26 35 S 4 26 35 8 200528 26 35 2 153 3 4 E 153 3 6 E 153 3 8 E 153 4 E Figure 4 29 2 Grid example with refinement of factor 3 through the river section in the e1 direction Usually time steps
207. ion in standard for he grid hich slows I O the in time mat and Interpolation ime is performed on i J Al may be spatially and temporally d a i ER The slowest method using the No reading of forcing data and no advection is performed Useful for format conversion using tracer reset Page 142 of 185 Version 1 00 SHOC User Manual F capability in conjunction with different forms of file output SP_CHECK Used to check transport data files for NaN values or values greater than specified limits etamax amp velmax Set TRANS_DATA to the file required to be checked when using this mode TR_CHECK Checks the input data for NaN and values greater than specified limits and checks valid source cells amp interpolation weights gt 0 and lt 1 are computed R a t GLOBAL eads BRAN or OceanMAPS global data nd reads eta_t T S u and v into he model variables Velocities are rotated onto the grid Monthly transport files in sparse format can be automatically generated using TRANS_OUTPUT YES TRANS_DT 1 hour optional dump increment In this case the transport files will be created for each month with the name prmname_trans_mmmyyyy nc where prmname is the name of the parameter file mmm is the month e g jan and yyyy is the year An alternative to prmname can be generated using OutputTransport Section 4 31 6 Files
208. ion lt obc_type gt is applied to open boundary lt obc_name gt Valid types are NEST1IWAY 1 way nesting Section 4 10 7 20 08 2015 Page 127 of 185 Version 1 00 SHOC User Manual NEST2WAY 2 way nesting RIVER River OBCs Section 4 10 6 NOTHIN No OBCs Section 4 10 14 SOLID The OBC emulates a solid boundary REGULATE DT_REINIT Re initialises the time step to that specified in the input parameter file Horizontal mixing is also adjusted REGULATE HVISC_REINIT Re initialises the horizontal viscosity to a constant value i e non Smagorinsky REGULATE PSS_REINIT Re initialises the point source sink specification The run regulation may be invoked at a specific time by using n days where n is a valid day number relative to the timestamp e g REGULATE OBC_REINIT West NESTIWAY 10 days or REGULATE PAUSE 0 5 days 4 33 Explicit mapping SHOC operates on a sparse coordinate system internally where all cell locations are aggregated in a one dimensional vector and each cell s position in space is determined by the location in the vector of its neighbours Ordinarily every cell is mapped to its immediate neighbour in three dimensional space but with the sparse system this does not need be the case Cells can be made to have neigh
209. ion 3 11 Note that p OBC Energy Flux has units Wm Alert tracking may be made active using the following ALERT ACTIVE lt alert_file gt Using the ACTIVE alert mode when a maximum value exceeds defined thresholds then specific action is taken This action falls into three categories LEVEL1 2D or 3D velocities exceed the VELMAX parameter Horizontal diffusion is increased to the value Ax 4At which most effectively damps the shortest waves possible in the grid Kowalik and Murty 1993 eqn 3 141 Velocity thresholds may be defined using the following parameters VELMAX 2 Maximum horizontal velocity ms WMAX le 3 Maximum vertical velocity ms EVEL2 2D divergence 07 0f or 3D divergence dw dzexceed a hardwired threshold The Shapiro 1970 smoothing filter is applied to the relevant velocity field Kowalik and Murty 1993 eqn 3 136 EVEL3 momentum tendencies exceed hardwired thresholds The relevant process is omitted during the next time step Individual alert actions can be turned on or off by prescribing 0 or 1 for each individual action eta vel2d vel3d w tend 2d_div 3d_div cfl ts shear hdiff ALERT_CODE 1 1 T 0 0 0 0 0 D 1 k 20 08 2015 Page 110 of 185 Version 1 00 SHOC User Manual Alert information written to file has the following format note indexes in brackets are in Cartesian coordinates outside the brackets are sparse coordi
210. ired for a specific location and netCDF files for input output of time varying grid or multi point data 11 1 ASCII time series An ASCII time series file contains data formatted into columns and a header describing the number of columns their names units missing values etc Typically the first column contains the time which must monotonically increase and the remaining columns the data and coordinate variables Following is a schematic represenation of a time series file Comments COLUMNS n COLUMN1 name time COLUMN1 long_name Time COLUMN1 units days since 1990 01 01 00 00 00 10 COLUMN1 missing_value 99999999 COLUMN2 name XXXX COLUMN2 long_name XXXX COLUMN2 units XXXX COLUMN2 missing_value XXXX b v v v v v v v v v v v v 11 1 1 Units The units for each variables should follow the standard udunits conventions however at this stage other than time no interpretation of the units is made by SHOC Since SHOC uses SI units internally it is suggested that these units be adopted for all input variables An ISO date time format has been adopted in for time units it has the following syntax units since yyyy MM dd hh mm ss sss hh ss l I l l 2 l l 3 l IM 1 The scaling units e g days hours seconds ms us etc 2 Date year month day_of_month 3 Time of day hours minutes seconds milliseconds 4 Time zone
211. is case the default flux adjustment is used and the boundary condition for temperature and salinity is TRCONC Section 4 10 17 Any other tracers must be individually specified 2 2 way nesting BOUNDARYO BCONDO NESTIWAY data_1l mpk data_2 mpk data_n mpk bdry_uv_nor mpk bdry_uv_tan mpk where the format is the same as for 1 way nesting except forcing files are memory packets 20 08 2015 Page 61 of 185 Version 1 00 SHOC User Manual 3 Clamped nesting BOUNDARYO BCONDO NEST_CPD data_ets mpk data_uv_nor mpk data_uv_tan mpk 3D velocities are clamped gravity wave radiation on sea level 4 River boundaries Section 4 10 6 BOUNDARYO BCONDO RIVER flowfile ts data_1l ts data_2 ts data_n ts Where data_ lt n gt ts file containing temperature at the cell centre Other tracer data is also required if the tracer OBC is active There must be at least one of these files listed flowfile ts file containing river flow In this case the depth over which the flow profile is distributed is the mean depth of the boundary and salinity is input with a value of zero 5 No action taken BOUNDARYO BCONDO NOTHIN Velocity tracer and sea level open boundaries are set to NOTHIN Section 4 10 14 6 Emulate a solid wall BOUNDARYO BCONDO SOLID This OBC is the same as No action taken except normal velocities are clamped to zero such that a zero flux condition exists 7 Flather radiation This OBC sets up a Flather
212. itude of false pole degrees Equally spaced grid in degrees This is almost identical to the auxiliary pole definition except that a rotation is used instead on a false pole The resulting cells are unequally spaced on the sphere but equally spaced in degree space PROJECTION geographic GRIDTYPE GEOGRAPHIC_RECTANGULAR NCE1 10 NCE2 20 DLAMBDA 0 01 Long cell interval in aux coords degrees DPHI 0 01 Lat cell interval in aux coords degrees X00 144 3856 Longitude of origin degrees YOO 38 2030 Latitude of origin degrees ROTATION 315 Grid orientation Equally spaced grid over sphere The third method requires that the grid cells preserve their distances over the sphere The lat long s of the grid are computed by projecting the interval or multiple there of along given a direction This method does not always produce perfectly orthogonal grids but the error is minimal PROJECTION geographic GRIDTYPE GEOGRAPHIC_RECTANGULAR NCE1 10 NCE2 20 DX 1000 1000m along i axis DY 1000 1000m along j axis ROTATION 315 Grid orientation degrees This rotation is on the sphere X00 144 3856 Longitude of origin degrees YOO 38 2030 Latitude of origin degrees FALSE POLE YES Optional if YES then a grid is constructed using a false pole where th quator lies 20 08 2015 Page 26 of 185 Version 1 00 SHOC User Manual
213. lt nrecords nk nj ni salt units practical salinity units salt long_name Salinity salt coordinates t x y z D I Finally if the data is not stored on a grid but as a series of discrete points then an evalatuion at an arbitary point will use an inverse weighted interpolation scheme 1 r Of course this assumes the coordinates and coordinate_type attributes have been specified netcdf file dimensions nrecord UNLIMITI np 1000 ea ei ER variables Time coordinate variable double t nrecords t units seconds since 1990 01 01 00 00 00 10 t coordinate_type TIME X coordinate variable of a 2d rectangular grid double x np x units m x coordinate_type X Y coordinate variable of a 2d rectangular grid double y np y units m y coordinate_type Y 2 coordinate variable double z np Zrunits m zZ coordinate_type Z2 Bach record and point has a unique T X Y and Z coordinate associated with it double salt nrecords np 20 08 2015 Page 155 of 185 Version 1 00 SHOC User Manual salt units practical salinity units salt long_name Salinity salt coordinates t x y z D I 11 2 1 2 Utilities The simplest way to view the contents of a netCDF file is to use the standard netCDF utility ncdump To view the file header use ncdump h filename or to view the entire file use ncdump filename This get
214. lt attributes gt name of tracer attribute set The name lt attributes gt may be one of the following standard estuary If standard is specified then the attributes for all possible ecology tracers are hardwired into the routine eco_defaults_standard in hd ecology ecology c and can be expanded as desired by creating additional attribute routines and adding them to the calling function eco_set_tracer_defaults in the same module Note that a list of all possible ecology tracer names and long names water column sediment and benthic must be maintained in the structures ECONAME3D and ECONAME2D in ecology c in order for tracer automation to operate correctly If any of the tracer classes are explicitly defined in the tracer list then any attributes associated with that tracer takes precedence over the defaults defined by ECO_VARS_ATTS Furthermore any tracer attribute can be defined in the parameter file using TRACER lt m gt attname or lt name gt attname Where lt m gt is the tracer number in the list attname is the tracer attribute name and lt name gt is the name of the tracer e g PhyL_N svel 4e 6 Redefine the settling velocity for large phytoplankton nitrogen The ecology specification is written in full in the diagnostic file setup txt see Section 4 31 If a transport parameter file is generated from a full parameter file using TRANS_DATA see Section 9 then the ec
215. lt in identical solutions using 1 and multiple windows It is known that if the model is subjected to SUB STEP Section 4 27 then at window boundaries values from different time levels are used resulting in solutions that differ To avoid sub stepping the time step should be reduced When invoking extended functionality with multiple windows it is prudent to check results against a single window 4 3 Time Internally the model represents time in seconds since some epoch date time These parameters allow the specification of that epoch the period of the simulation the ramp up period for external forcing and the model s internal 8 d and external 2 d time steps for integration Defines the epoch for all time related parameters as well as for all output files generated by the model Currently the units must be seconds since but this may change in future versions The epoch is specified in standard ISO date time format including a possible timezone specification The timezone here is 8 hours ahead of UTC IMEUNIT seconds since 1990 01 01 00 00 00 08 se sth zt H Defines the base time unit that will be used for all timeseries and netCDF output files OUTPUT_TIMEUNIT days since 1990 01 01 00 00 00 08 Define length units this parameter is redundant and must always be metre sENUNIT metre Defines the start and stop time of the model simulation period relative to the epoch d
216. m pss0O location 1 0 pss ncells 1 0 0 100 100 The source sink may also be distributed over multiple cells horizontally and a depth range using a region file see Section 4 29 16 where the flux can be specified over one or multiple regions Gast Location 200 100 Depth range 20 08 2015 Page 86 of 185 Version 1 00 SHOC User Manual pss region region bne 3 4 n Region file and numbers The flux may be scaled according to pss0O flag AREA _ WEIGHTED Input flux scaled by cell area pss0O flag VOL_WEIGHTED Input flux scaled by volume of the cell mass is delivered into The reference level is determined by the following ms1 by default pssO reference surface referenced to the free surface pssO reference msl referenced to mean sea level pssO reference bottom referenced to the bottom Major inflows or outflows of water which carry significant momentum should not be specified in this way as the point source sink code ignores momentum input considerations Such inputs can be specified at open boundaries see section 4 9 6 Sometimes the mapping of the point source location from geographic space lat long to index space i j is unsuccessful for the slaves This is because sometimes custom curvilinear grids have land or outside cells that are not associated with valid coordinate values in the parameter file and cannot be assigned geographic locations Also the preci
217. man 1985 eqn 4 6 Sha E t expr 12 4 3 with steady state sea level given by n y dl 12 4 4 where L is the width of the channel and it is assumed 77 0 aty L 2 Cyclic open boundaries are used to represent an infinite coastline Using a wind stress of 0 1 Mm in a channel 500km wide the dimensions of this domain are the same as the test 20 08 2015 Page 158 of 185 Version 1 00 SHOC User Manual domain used by Palma and Matano 1998 except the Southern hemisphere is considered with linear resistance coefficient r 0 0005 Coriolis 1 028e and p 1024 76 kom the along shore depth averaged velocity is 0 195 ms the cross shore depth averaged velocity is zero and elevation at the coast is 0 49 m slope of 2 05x10 Note the first elevation cell center is found at y 10km This result assumes a linear depth averaged model is used and a non linear 3 D model with quadratic bottom friction is expected to give different results 12 5 Constant wind stress cross shore open domain A wind applied perpendicular to an infinitely long coastline on the southern boundary in this case will result in an elevation setup against the coast with zero depth averaged currents everywhere The on shore wind stress drives depth averaged flow to the west east in the northern southern hemisphere and the sea level gradient resulting from setup at the coast drives this flow to the east west In a perfect situation the sea level gradient an
218. mber of points in the list 1 2 or BATHY_MASK_VAL 5 0 Value to set bathymetry to BATHY_MASK 1 Number of blocksin the list 1 1 2 1 The points list may be obtained using the Marked facility in jvismeco A linear gradient of bathymetry may also be applied to the masked sub region in either the e1 or e2 direction i or j direction e g to apply a linear bottom slope in the e1 direction from 5m to 10m Set a linear bottom slope from 2m to 10m in the el direction from i l to i 4 Any points in the list with i coordinates between the start and end coordinates are set to a linear interpolation of the start and end depths BATHY_MASK_IS 1 Start i coordinate for gradient BATHY_MASK_IE 4 End i coordinate for gradient BATHY_MASK_DS 2 0 Depth at start i coordinate BATHY_MASK_DE 10 0 Depth at end i coordinate BATHY_MASK 40 Number of points in the list Similarly this applies to BATHY_MASK_JS and BATHY_MASK_JE for the e2 direction Multiple blocks may be specified where a single bathymetry value only may be altered i e no gradients of bathymetry using BATHY_NBLOCKS 2 Number of blocks BATHY_MASK_VALO 5 0 Block 0 bathymetry value BATHY_MASKO 1 Block 0 blocks Lyd 2 2 BATHY_MASK_VAL1 2 0 Block 1 bathymetry value BATHY_MASK1 2 Block 1 blocks 10 1 20 10 50 1 50 20 NOTE The bathymetric parameters described above are not used by the model when a run is initiated usi
219. me steps at x days ACTIVE3D 3D time step is set to CFL step whenever CFL_DT lt x gt days the CFL step becomes less than the 3D step and the simulation time is less than x days By or ing WVEL to the above flags the vertical advection stability constraint i e Courant number lt 1 is included in the stability calculation i WV An example of the CFL stability diagnostic is CFL AVTIVE3D WVEL CFL_DT 20 days Tracer names in output files for these stability limits are cfl2a 2D CFL stability time step cfl3d 2D CFL stability time step courant Courant stability time step lipschitz Lipschitz stability time step diffstab Horizontal diffusion stability time step 20 08 2015 Page 104 of 185 Version 1 00 SHOC User Manual 4 30 9 1 Heat Flux Diagnostics If the heat flux is calculated see section 4 17 then the components of the heat flux are automatically written to 2D diagnostic tracers The attributes of these tracers are listed below Heat Flux Diagnostic Attributes 2D Tracer Name Description Units swr Short wave radiation Wm lwr Long wave radiation Wm shf Sensible heat flux Wm Ihf Latent heat flux Wm nhf Net heat flux Wm 4 30 10 Momentum Balance Tendencies The contribution to each of the terms in the 3D momentum balance may be saved to 3D diagnostic tracers Thes
220. med through the water column until the bottom of shallower of the cells is reached A vertical range of the map can be specified by appending the upper and lower k level the maps are operate within after the number of mapping points e g Map the first cells in the list between layer 22 and layer 10 The upper most layer closest to the surface is always listed first The second cells in the list are mapped through the whole water column MAP_POINTS_El 2 E E He He 20 08 2015 Page 128 of 185 Version 1 00 SHOC User Manual 2 4 44 22 10 AS 4 5 The explicit mapping list may contain any combination of cells mapped only between certain layers and cells mapped through the whole water column i e any combination of the formats is ie js je is ie js je kt kb Using the auxiliary program jvismeco is generally helpful when determining the map lists An example of a domain using 2 explicit maps in the e1 and e2 directions is illustrated in Figure 4 31 1 The domain is divided into 9 sub sections separated by land but the explicit maps make the domain behave as if it were one connected region The explicit mapping function only works with z coordinates 20 08 2015 Page 129 of 185 Version 1 00 SHOC User Manual Figure 4 31 1 a Un partitioned closed basin solution A7 N LD A A Y A 3 3 pt 4 N ZEN bak oar wae nar ca ar N N a a ae ecco 2 N DEE EE ES o Current 0 2 ms7 0000 11 Jan 2000 08
221. metry smoothing may be performed over a discrete number of cells with n smoothing passes using SMOOTH_MASK m m is the number of cells to smooth 1 1 List of i j cell locations 2 1 Note that depth values need not correspond to layer interface positions In each cell the model implements a bottom layer which has a thickness which may be less than the full layer thickness so that bathymetry is well resolved even in vertically coarse or single layer depth averaged grids However very thin bottom layers can cause numerical problems so one final parameter prevents the creation of very thin layers as follows If the difference between a layer boundary and the bathymetry for a cell is too small numerically instabilities can arise in the model Specifying a minimum cell thickness ensures that no cell can get too thin The value may be specified as a minimum thickness in metres or aS a minimum percentage of the grid layer thickness as shown below MIN_CELL_THICKNESS 15 A sub section of the bathymetry may be masked to a user defined value using the BATHY_MASkX attribute This consists of a list of i j values whose bathymetry value in the grid is set to the value of BATHY_MASK_VAL e g Set the bathymetry at points 1 1 and 2 1 equal to 5 0m 20 08 2015 Page 29 of 185 Version 1 00 SHOC User Manual BATHY_MASK_VAL 5 50 Value to set bathymetry to BATHY_MASK 2 Nu
222. n this case the instability may have to be diagnosed and rectified by other means e g alternative OBCs better forcing etc 20 08 2015 Page 136 of 185 Version 1 00 SHOC User Manual 7 ROAM r option SHOC may be configured to operate in the ROAM Relocatable Ocean and Atmospheric Model environment The ROAM configuration is essentially the same as the a option configuration with a number of alternative parameterisations The ROAM configuration is invoked using the r option The same mandatory information as used in the a option is requited start stop time grid information bathymetry The ROAM option is designed to nest SHOC within a global ocean model and use information from this larger scale model for initial and boundary conditions It is assumed that global model output exists covering the region of interest containing output dumps at approximately 1 day intervals Temperature salinity and sea level are required to be present in this output Currently the global model is a derivative of the GFDL MOM3 Modular Ocean Model model termed OFAM Ocean Forecasting Australia Model Using the r option these global model data are specified using OFAM_ DATA EAC_200401 nc OFAM input filename These data will then be used for T S and initial and boundary conditions Whenever an open boundary is located the information found in the global model file is used to prescribe T S and n OBC s The sea level contained in
223. na 24 POLAR EE 24 RECTANGULAR cccccccecsesssseceeees 23 H HDF Res tsk eee cielo ae 90 HEATFEWUX deisde ite 59 61 62 63 ADVANGED wisest geed ess 59 COMP HEA Tir egene ege Ae 62 COMP_HEAT_ MOM aasaoannnaannnannnaaa 63 NET HEAT niia tk 62 SURF RELAX eia 59 HEATELUN TEMP 59 61 62 HMIN niert ete geess 16 75 76 113 I ID NUMDBER 17 INT WAVE cmenn eye aeaii 91 RATIO EE 15 113 L LAGRANGE oeii neasa et 52 LAYERFACEG 0 5 26 75 113 120 LENUNIT opentuinen nae nita 14 122 Inf 89 l g ET 16 Ee TE 68 88 89 UE 89 M MAP POINTG EI 109 EIS RE 28 MEAN Elte eebe Oia 85 NONE casks el tees ene es 85 TENDENC Weeder 85 TIDAL peirin e Wain ea ea ae uian 85 TRANSPORT T ethe ie ee oirra tausti 85 VEL2D aeree iar eat 85 VEL 3 I D E A AE 85 WIND oeei eere eetika ee ia 85 MERGE THIN iertarea ias 76 MIN_CELL_THICKNESS 008 28 MIX_LAYER DENS MIX renr eaa 86 NONE E A EEE 86 TK MIX oreren eiaa 86 MIXING_SCHEME CONSTANT E PE N TEET 66 E e EE 66 KG EEE E dened tteestesvcdess EAEE PIEN 69 KAN a ee eae a eea a acetone 69 70 mellor vamada 20 67 mellor_yamada_2_0_estuarine 67 mellor_yamada_2_ bi 68 MOM END 90 N NBOUNDARIES onniinnininnonnnnnnaeanene 35 112 NEI BLEND dee Reo es 82 20 08 2015 Page 184 of 185 NEZ BLEND ireid ierti 83 WU 89 NONLINEAR ossein 12 15 ABOISSO 72 a a T 115 NSTORM forrinnen 56 57 NTRACERS senais danian 29 114 NUMBERS 0 00 cccceeeeeseee
224. name of the bnc region file REGION_DT 10 days The time interval over which the budgets are computed REGION_VARS passive Tracers for which the budgets ar computed The variables salt and temp are always computed by default i e these variables do not need to be specified in REGION_VARS A volume budget is also created by default The keywords MONTHLY SEASONAL and YEARLY may be input as REGION_DT and ALL TRACERS_WC and TRACERS_DIAGN_WC may be used for REGION_VARS Output is created for each region in the ascii file region ts where is the region number If OutputPath is present the files will be written to this directory These files contain the mass at the start of the interval REGION_DT for each variable mass at the end of the interval the mean mass and standard deviation over the interval the mass fluxes through segments connecting regions or through open boundaries i e mass transfers from region to region or across open boundaries and the mass budget of the region where mass budget start mass mass fluxes end mass 20 08 2015 Page 113 of 185 Version 1 00 SHOC User Manual Note that the mass fluxes are positive if mass is imported into the region and negative if mass exits the region If the budget is not approximately zero then this means that there has been net import of mass into positive budget or export from negative budget the region This may be due to a poin
225. nates Simulation time 10 000000 days aximum absolute sea level elevation 0 248644 at 26 25 1 22 aximum absolute velocity ul 3D 0 203112 at 1226 1 25 22 ul 2D 0 093261 at 1066 45 21 22 u2 3D 0 093234 at 1225 0 25 22 u2 2D 0 001336 at 1023 2 21 22 w 0 000044 at 12290 49 25 14 Div 3D 0 000004 at 1249 24 25 22 Div 2D 0 000000 at 767 1 16 22 Maximum absolute tendencies ul velocity u2 velocity Area averaged energy echanical energy 231 513328 J m2 Excess mass 0 003424 m Energy flux W m2 Boundary 0 West 2 276448 Boundary 1 East 2 272259 Simulation maximum absolutes eta 0 248644 ul 3D 0 203115 ul 2D 0 093282 u2 3D E ak u2 2D 0 006932 wW 5 72e 05 div 3D 5 20e 06 div 2D 3 60e 06 4 30 16 Total mass volume heat and salt The total mass volume heat and salt in the domain useful for diagnosing conservation properties may be output in time series format The totals are output to the time series file totals ts If OutputPath is set then the totals file will reside in this directory To invoke the totals diagnostic use OTALS YES Invoke totals diagnostic OTALS_DT 1 hour Interval to print totals The default is 1 hour The default is for no totals to be calculated The output timeseries file consists of the following COLUMNS 5 COLUMN1 name Time COLUMN1 long_name Time COLUMN1 units days since 1
226. nction of position when an initial particle distribution is prescribed i e no sources For the former different types of settling behaviour for particles released from each source may be prescribed using PT_Source0 Stype NONE No settling imposed CONSTANT Particles from this source settle with a constant settling velocity STOKES The stokes settling formula is used Co compute the settling velocity This is a function of particle size density and water density DIURNAL A periodic settling velocity is used where the amplitude and period are prescribed FILEIN Velocity is read from file For all particles a negative settling velocity means the particle will sink and a positive velocity will result in a buoyant particle The CONSTANT settling velocity for particles released from each source may is prescribed using 1 PT_Source0 Svel 1e 3 velocity in ms The STOKES settling velocity may be computes using Stokes settling formula 20 08 2015 Page 92 of 185 Version 1 00 SHOC User Manual y 8 Pw p d 18u 3 27 1 where g 9 81 mell is the acceleration due to gravity pw kgm is the density of surrounding water Pp kom is the density of the particle d m is the particle diameter size in this case and m 1 4e 3 kom e is the viscosity of water at 20 C This settling velocity is calculated and applied to each particle if the particle size is set see Section 4 28 4 and the particle de
227. nd field respectively These averages are stored in 2D tracer arrays which are automatically created by SHOC when these flags are invoked If the TIDAL flag is present then the mean values are calculated over a tidal period To do this SHOC attempts to find the maximum sea level in a 24 hour period at each point in the grid then proceeds to average until the next maximum sea level is encountered at that point Note that this may result in the exact averaging period differing throughout the grid e g if a modulation of tidal phase exists across the grid After each output dump event the mean arrays are reset When invoking this option the file output interval should be set to around 3 times the dominant tidal period i e 3 days for diurnal tides since SHOC may require up to 1 tidal period to locate the start of the averaging period 1 tidal period to calculate the mean and 1 tidal period for safety to avoid any overlap of the tidal averaging into the next cycle The TRANSPORT flag allows tracers to be advected using the mean 3D velocity field If the averaging period is set so as to filter out higher frequency oscillation e g the tide then these velocities represent the residual current field which may be much smaller than the instantaneous current In these cases the time step for tracers may be dramatically increased resulting in an improvement in execution speed The mean fields appear in the output file and time series files a
228. new variable name to the default expected variable name Multiple assignments are separated by commas The assignments are enclosed within parentheses No whitespace is permitted For example for a standard file assignment such as WIND_TS windfile ts SHOC would search for the variables u and v within windfile ts If these variables were not present then SHOC would quit with an error If however there were two variables called wu and wv then the following substitution could be used WIND_TS windfile ts wind_u wu wind_v wv 20 08 2015 Page 118 of 185 Version 1 00 SHOC User Manual 4 31 2 Multiple datafiles At this time the specification of multiple datafiles is only permitted when defining boundary inputs wind files relation and resetting Following is an example of how to substitute variable names and specify multiple time series files for a boundary parameter BOUNDARY1 DATA tl nc salt salinity t2 nc temp tmp A list of files may be included in a separate text file to which the boundary or wind etc specification may define e g a multi file netcdf text file boundary mnc may be generated having the following format multi netcdf version 1 0 nfiles 2 filedO filename tli nce filel filename t2 nc Boundary data may then be defined via with variable substitution included BOUNDARY1 DATA boundary mnc salt salinity temp tmp This is a convenient method of specifying a long list of files as input 4 3
229. ng i j locations from a domain The last window is created to consist of all cells not included in a list The window partitioning can be written to the output file using SHOW_WINDOWS YES Creates a tracer window_partitions containing window configuration This facility is switched off by default The window map may be written to netCDF file using DUMP_WIN_MAP lt mapfile nc gt Where lt mapfile nc gt is the name of the file the map is written to This may then be subsequently read at runtime rather than computed using READ_WIN_MAP lt mapfile nc gt Note that computing the sparse map for many windows on very large grids can take several hours reading the window map from file provides a means of rapidly starting a simulation DUMP_WIN_MAP will operate in the p and g modes and READ_WIN_MAP operates in the p mode When using multiple windows the message passing library must also be specified e g DP_MODE openmp Use the openMP libraries pthreads Use the pthreads library 20 08 2015 Page 14 of 185 Version 1 00 SHOC User Manual Comparisons using 1 or multiple windows have shown identical results in simple test domains and a complicated real case study However not all functionality advection schemes mixing schemes open boundaries etc or combinations of bathymetry geography and window partitions have been tested hence it is possible that some combinations of the above do not resu
230. ng the p option They are used when the g option is invoked see section 8 to generate the model input netCDF file which contains model initial values and geometric information Any alteration to model bathymetry must be accompanied by the creation of a new model input netCDF file using the g option Cells can be changed to OUTSIDE or LAND status at runtime as a series of rectangular blocks e g NOUTSIDE 3 Set a series of rectangular regions to 0 3 82 69 OUTSIDE 184 3 248 69 O10 248 T31 Or NLAND 4 Set a list of points to LAND 01 QO Wes A wN 20 08 2015 Page 30 of 185 Version 1 00 SHOC User Manual Bathymetry statistics can be generated using BATHY_STATS lt infile gt eli e2i Here lt infile gt is a path and filename of a bathymetry database and eli and e2i are decimations in the e1 and e2 directions respectively Bathymetry statistics are generated by comparing the database bathymetry at its native resolution with the decimation applied with the interpolated bathymetry in a model grid Statistics generated are e Maximum depth between the shallowest database depth in a grid cell and the model grid cell depth stored in bathy_range_min e Maximum depth between the deepest database depth in a grid cell and the model grid cell depth stored in bathy_range_max e The gradient of the model grid cell Bir Ei stored in bathy_grad e The maximum gradient difference between the dat
231. ns respectively 4 6 1 Rectangular grid Following is an example file fragment that describes all of the parameters required to define a rectangular grid Type of grid GRIDTYPE RECTANGULAR Number of grid cells in the el i and e2 j directions NCE1 57 NCE2 T2 Real world coordinates of the lower left hand corner of the lower left hand grid cell i 0 j 0 x00 257300 YOO 5770180 Grid cell size in el i and e2 j directions DX 1000 DY 1000 Angle in degrees between el i direction and the real world X axis which is East in most reasonable projections This represents a mathematical rotation so that the value of 315 degrees would probably make the grid i axis run ina south easterly direction ROTATION S15 The rectangular grid is defined as being 57 by 72 cells with a 1000m resolution along both axes rotated at 315 degrees and an origin the bottom left corner of cell i 0 j 0 at Easting 257300 Northing 5770180 If no PROJECTION parameter is specified then it should the grid should only be used to model local areas where the Earth s curvature is not 20 08 2015 Page 24 of 185 Version 1 00 SHOC User Manual considered significant This also true if a map projection is specified but it s appropriateness depend on the region and projection 4 6 2 Polar grid Polar grids are specified is a similar way to rectangular grids as shown below
232. nservative 20 08 2015 Page 164 of 185 Version 1 00 SHOC User Manual The file containing a list of lt i j gt locations or optionally lt i j topk botk gt defining the section is specified using the data attribute Again if the direction is ul then this list should contain constant i coordinates etc The section is integrated in time over a timescale defined by the dt attribute and subsequently output to an ascii file specified by the output attribute Note that the integrating timescale may not be exactly the specified dt since if dt is not an integral number of model time steps output will be written to file at the next larger time step The output file contains the time and value of integrated flux over the section and interval dt A start time may be optionally defined by the startt attribute The default is the model start time The default time unit in the output file is that defined by OUTPUT_TIMEUNIT in the parameter file This may be scaled by supplying optional attributes tscale and tunit where output time format is OUTPUT_TIMEUNIT tscale tunit Similarly the units of the calculated flux may be optionally scaled using the attributes outscale and outunit where integrated fluxes are written to the output file in units of 3D tracer unit outscale outunit This form of tracer statistic computes one number for each section which is written to a time series file i e the result of the calculation is not a 2 D or 3 D field
233. nsity is prescribed PT_Source0 Dens 1030 Density in kom Hence if a growth rate is also prescribed then as the particle grows its diameter increases and therefore settles faster The DIURNAL settling velocity is computed using the formula v svel cos 2I1 t sper floor t sper 3 27 2 where zuel is the maximum vertical velocity ms at which the particle will move t is time and sper is the periodicity of the cosine function e g PT_SourceO0 Svel le 3 Velocity in ms PT_Source0 Sper 1 day Periodicity The FILEIN settling velocity is prescribed using an ASCII or netCDF time series file PT_SourceO0 File svel ts Time series file containing variable and wpt mei The settling velocity variable in the file must be named wpt The settling velocity in the file may be a function of time or space or both The spatial coordinates of the source i e StartLocation and EndLocation are used to interpolate from the file onto the source location if spatial information is contained in the file Additionally particles released from an initial distribution i e without sources specified may undergo settling as a function of their position in time and space as read from file This is specified using PT_w_file Suel ne File containing settling variable wpt The settling velocity variable in the file must be named wpt and the velocity may be a function of time space or both Spat
234. ntained 3D velocities u and and ACCESS A data jan2011_met nc were available containing variables pressure u and v then gulfs prm may be modified thus In the tracer list add see Section 4 9 TRACERO data jan2011_ets nc and TRACER1 data jan2011_ets nc Surface initial condition see Section 4 12 SURFACI Gl jan2011_ets nc Wind and pressure forcing see Section 4 13 amp 4 14 WIND_TS jan2011_met nc WIND_INPUT_DT 10 minutes WIND_SPEED_ SCALE 1 0 DRAG_LAW_V0O 10 0 DRAG LAW V1 26 0 DRAG _LAW_CDO 0 00114 DRAG _LAW_CD1 0 00218 PRESSURE jan2011_met nc PRESSURE_INPUT_DT 10 minutes Open boundary forcing see Section 4 10 7 amp 4 10 17 NBOUNDARIES 3 BOUNDARYO NAME West BOUNDARYO TYPE ul BOUNDARYO BCOND_NOR CUSTOM BOUNDARYO CUSTOM ul uv_to_ul jan2011_uv nc BOUNDARYO BCOND_TAN CUSTO BOUNDARYO CUSTOM u2 uv_to_u2 jan2011_uv nce BOUNDARYO BCOND_ELE NOTHIN FILEIN BOUNDARYO BCOND_salt UPSTR BOUNDARYO BCOND_temp UPSTRM BOUNDARYO ADJUST_FLUX 200 seconds 0 2 x DT BOUNDARYO DATA jan2011_ets nc BOUNDARYO RANGE 0 0 0 14 BOUNDARY1 NAME East BOUNDARY1 TYPE ul BOUNDARY1 BCOND_NOR CUSTO BOUNDARY1 CUSTOM ul uv_to_ul jan2011_uv nc BOUNDARY1 BCOND_TAN CUSTOM BOUNDARY1 CUSTOM u2 uv_to_u2 jan2011_uv nce BOUNDARY1 BCOND_ELE NOTHIN FILEIN BOUNDARY1 BCOND_salt UPSTRM BOUNDARY1 BCOND
235. nual 4 30 8 Mixing Length Scale The mixing length scale is saved to the diagnostic tracer 1scal1e if this tracer is defined e g if RACER name lscale RACER long_name ixing length scale RACER units m RACER fill_value 0 0 RACER valid_range D 100 RACER diagn HE RACER advect 0 RACER diffuse 0 is defined then this tracer will be populated with the mixing length scale calculated in the Mellor Yamada 2 0 k e or k w mixing schemes 4 30 9 CFL Time steps The Courant Friedrichs Levy stability time step see section 2 7 Herzfeld et al 2002 for barotropic and baroclinic modes the Courant and Lipschitz stability criterion and horizontal diffusion stability limit may be calculated at every grid point and time step The CFL time steps are saved to 2D diagnostic tracers in units of seconds This is useful to precisely set the time steps used by the model An option exists to include the vertical advection Courant constraint i e wAt Az lt 1 The minimum time step for the simulation is printed to the diagnostic file diag txt Section 4 32 Options exist to adaptively alter the time step used by the model to the CFL condition This process is performed for a user defined time period The CFL diagnostics are invoked via CFL PASSIVE CFL calculated and output to tracers ACTIVE 2D and 3D time steps are set to the minimum CFL_DT lt x gt days CFL ti
236. o F Output to this path If the SEQUENCE flag is invoked Section 4 4 then run lt n gt is appended to the path where lt n gt is the run sequence number OutputPath home data output OutputTransport lt tag gt i i d fi fi fi fi 20 08 20 Output transport files Files are created for each month with the name tag_trans_mmmyyyy nc where tag is the tag specified F above mmm is the month e g jan and yyyy is the year Files are output in sparse format Variables output are eta ulmean u2mean wmean temp salt Kzmean Output file 0 The tag ALL for the vars parameter means the following variables are save to the output dump file eta ul u2 w ulav u2av topz wtop windl wind2 patm dens dens_0O Kz Vz Cd ulbot u2bot ulvh u2vh flag all the tracers and ptconc if particle tracking is enabled This is in addition to the coordinate variables The following fields are manadatory Jet name out nec Output prefix leO type standard Standard dumpfile leO tstart 0 days Output start time leOQ tinc 1 day Output interval leO tstop 44 days Output stop time leO bytespervalu 4 2 shorts 4 floats 8 doubles fileO vars ALL ALL variables Output file 1 A spatial subset of the grid possible for use in nesting Notice only a subset of the variables are being output lel name nested_smp nc leO type simple simple
237. o mechanism is provided to specify the ellipsoid parameters instead it is hard coded as a sphere with a radius of 6370997 0m It is hoped this restriction will be relaxed in a later version of SHOC 4 5 3 Defining a map projected coordinate system Of the three coordinate systems supported defining the map projection is by far the most complicated with a variety of map projections each with their own arguments The basic syntax is as follows PROJECTION proj lt projection name gt lt proj param0 gt lt arg gt Standard projections SHOC supports six standard projections A description of each projection and their arguments are described below Transverse Mercator Transverse Central Cylindrical The Transverse Mercator is a conformal cylindrical projection where the cylinder is rotated horizontally transverse across the ellipsoid proj tcc lon_0 lt long gt k_O lt number gt lon_O Central meridian k_0 Scale factor 20 08 2015 Page 20 of 185 Version 1 00 SHOC User Manual Universal Transverse Mercator UTM The Universal Transverse Mercator UTM projection is based on the Transverse Mercator projection described above However the scale factor is fixed to 0 9996 and the central merdian is parameterised by zone Each zone defines a 6 degree window in longitude around the Earth making a total of 60 zones Zone 1 is located at a 180W with the zone number increasing in
238. of field measured SST from which the sensible heat is computed In this case a HEATFLUX_TEMP file see above containing sea surface temperature must be supplied Correcting air temperature and humidity for advection effects see section 9 3 Herzfeld et al 2002 is invoked via Include the correction to air temperature and humidity due to advective effects HEATFLUX_ADVECT YES Note that the advection correction uses a calculation of fetch from 8 compass points if all these directions are not required then the array mask in init_fetch in the module forcings heatflux c may be modified zero values omit the corresponding wind directions in the advection calculation The NET_HEAT option imposes a net heat flux directly from time series input as the surface boundary condition for temperature and requires the following Time series file containing the variable heatflux with units W m 2 HEATFLUX_FILE heatflux nc HEATFLUX_DT 1 day Note that a positive flux indicates heat input into the ocean Short wave radiation may be input separately and distributed with depth as per the BULK option above In this case the net heat flux corresponds to the sum of long wave radiation sensible and latent heat fluxes Finally the INVERSE option calculates a heat flux inversely based on a time series of surface water temperatures see Herzfeld et al 2002 section 9 4 for detail
239. of statistics can be computed using step 5 P YP YD vi Alternatively these steps may be invoked via keywords where PRE_DECAY or POST_DIAG corresponds to n 1 PRE_WAVE or POST_DECAY corresponds to n 2 PRE_SED or POST_WAVE corresponds to n 6 20 08 2015 Page 165 of 185 Version 1 00 SHOC User Manual PRE_ECO or POST_SED corresponds to n 3 PRE_RTSTAT or POST_ECO corresponds to n 4 POST_RTSTAT corresponds to n 5 For example if tracerstats were to be invoked before the ecology library is called then set TRACER step PRE_ECO or TRACER step POST_SED If no step is specified the standard tracerstats library call is between step 4 and 5 The tracerstats library may be easily expanded to provide functionality suited to a users specific needs 20 08 2015 Page 166 of 185 Version 1 00 SHOC User Manual 14 Getting Started The steps required to compile SHOC run on a simple test case and generate a custom application are detailed below Note that visualisation and grid generation requires the matlab based software package PLUM 14 1 Compile SHOC Install the source code depicted by the directory structure Figure 2 1 Configure the code making sure any netCDF library paths are correctly specified Section 2 2 conf configure Make the executable make The SHOC executable now resides in ems src model hd The version number is retrieve
240. ology specification is also written to this file Outputting these ecology specifications may be invoked without running the full sediment transport by using DO_ECOLOGY WRITE Ecology requites a LIGHT variables which historically was a daily mean but with newer versions of the ecology processes can be a copy of short wave radiation i e diurnally variable This can be input via file LIGHT light ne LIGHT_INPUT_DT 1 hour ALBEDO_LIGHT 0 0 LIGHT can point to a tracer which reads LIGHT via the reset function e g LIGHT inlight LIGHT_INPUT_DT 1 hour ALBEDO_LIGHT 0 0 with RACER name inlight RACER name Light input from swr 20 08 2015 Page 177 of 185 Version 1 00 SHOC User Manual RACER units W m 2 RACER type WC2D RACER fill_value 0 0 RACER valid_range 0 0 2000 0 RACER reset_file swr nc RACER reset_dt 1 hour If swr is included in the transport files then LIGHT can be read from this variable along with all other transport variables using LIGHT file 20 08 2015 Page 178 of 185 Version 1 00 SHOC User Manual 17 Troubleshooting Bathymetry altered on successive input file generations The bathymetry written to the input file using the g option is modified from that read in from the parameter file by the BATHYMIN BATHYMAX and MIN_CELL_THICKNESS parameters If the input file bathymetry is to be modified using jvismeco and used in a successive par
241. ominated tracer must be greater than by default if this threshold is prefixed with then the tracer must also be greater this threshold if prefixed with the tracer must be less than the threshold for the exposure to be incremented For example if an exposure is to be set up for salinity where the model salinity is integrated below values of 10 psu starting in summer 1990 1 Dec 1990 using the tracer salt_ex_time as the exposure time then use RACER name salt_exposure RACER long_name Salinity exposure RACER units psu days RACER tracerstat exposure salt 10 salt_ex_time RACER dt 1 day RACER start 334 days RACER fill_value_we 0 RACER valid_range le 10 1e10 RACER advect 0 RACER diffuse 0 RACER diagn 0 RACER name salt_ex_time RACER long_name Salinity exposure time RACER units days RACER fill_value_we 0 RACER valid_rang le 10 1e10 RACER advect 0 RACER diffuse 0 RACER diagn 0 In this case the salinity must be greater than 10 psu for 1 day at a location before the salinity exposure is reset to zero at that location Note that salt_exposure may be integrated for periods greater than 1 day the dt used only sets a time period for when salt_exposure Is reset to zero The salinity exposure time salt_ex_time contains the accumulated time days within the period dt that the salinity is actually below 10 psu
242. on flux conditions for tracers A simple boundary condition for tracers is the upstream advection condition UPSTRM This condition is a 1 dimensional implementation of the upwind scheme discretized in advective form and suffers the errors associated with this type of implementation i e it is diffusive and non conservative Since the advective form only computes concentrations as opposed to fluxes it is uncertain as to what the actual flux of tracer entering the domain is when this 20 08 2015 Page 53 of 185 Version 1 00 SHOC User Manual condition is used It is however easily implemented The UPSTRM condition must be used in conjunction with another viable condition e g UPSTRM CLAMPD UPSTRM NOGRAD UPSTRM LINEXT UPSTRM POLEXT UPSTRM CYCLIC UPSTRM FILEIN UPSTRM CUSTOM In this case the value derived from the additional boundary condition is used in the upstream equation as the boundary value when flow is into the domain The UPSTRM FILEIN condition is used as the default if no additional boundary condition is specified e g BCOND_TRA_ALL UPSTRM and this requires the user to supply a data file containing boundary values Note that the UPSTRM CLAMPD condition sets the boundary value to the water column fill value specified for that tracer when flow is into the domain The UPSTRM method effectively solves a one dimensional advection equation Eqn 4 8 1 Science Manual and the location in the grid of
243. on that one may typically use for a case study While this configuration may have higher accuracy than standard ROAM configurations it is also more prone to instability This option is recommended only for more experienced modellers The configuration is as follows e The model starts from rest The k mixing scheme is used Smagorinsky horizontal diffusion is used with a constant of 0 1 with 2 smoothing passes The ULTIMATE QUICKEST tracer advection is used Boundary sponges of 8 cells ramp to 5 times the interior value No active alerts Flux adjusted open boundaries using the default timescale Using ROAMv RECOMv2 sets the ROBUST parameterisation as 20 08 2015 Page 139 of 185 Version 1 00 SHOC User Manual ROBUST 1 Same as ROBUST 0 above Smagorinsky no alerts ROBUST 2 Same as ROBUST 0 above constant viscosity no alerts ROBUST 3 Same as ROBUST 1 active alerts ROBUST 4 Same as ROBUST 2 active alerts ROBUST 5 Standard ROAM parameteristion Smag 0 1 rest start ROBUST 6 Standard ROAM parameteristion Smag 0 1 OFAM start ROBUST 7 Rest hard T S ramp relaxation Smagorinsky 0 1 ROBUST 8 Rest hard T S ramp relaxation Smagorinsky O 1 ROBUST 9 OFAM currents constant horizontal viscosity ROBUST 10 Start from rest constant horizontal viscosity As mentioned the time step parameterisation using the r option is very conservative Speed may be increased using the SPEED
244. ondition used to set the elevation OBC A common specification is BOUNDARYO BCOND_NOR2D FLATHR CUSTOM BOUNDARYO CUSTOM ulav uv_to_ulav 3D_velocity_data nc BOUNDARYO BCOND_ELE FLATHR FILEIN GRAVTY BOUNDARYO DATA eta_data nc With additional conditions typically as BCOND_NOR NOGRAD BCOND_TAN GRAVTY or NOGRAD If normal depth averaged velocity and elevation data are unavailable then a local solution e g Palma and Matano 1998 p1340 may be used for velocity and elevation BOUNDARYO BCOND_NOR2D FLATHR LOCALN BOUNDARYO BCOND_ELE FLATHR LOCALE BOUNDARYO BCOND_TAN LOCALT This condition may be improved by using a radiation condition on elevation rather than the solution to the 1 dimensional continuity equation e g BOUNDARYO BCOND_NOR2D FLATHR LOCALN BOUNDARYO BCOND_ELE FLATHR GRAVTY BOUNDARYO BCOND_TAN LOCALT If elevation data only is available a linearized local solution may be used retaining the elevation forcing e g BOUNDARYO BCOND_NOR LINEAR BOUNDARYO BCOND_NOR2D FLATHR LINEAR BOUNDARYO BCOND_ELE FLATHR FILEIN BOUNDARYO DATA eta_data nc 20 08 2015 Page 45 of 185 Version 1 00 SHOC User Manual If the velocity and elevation data are required to be zero then this may be accomplished by creating a file with zero values and using the FILEIN specification above or using the CLAMPD condition BOUNDARYO BCOND_NOR2D FLATHR CLAMPD BOUNDAR
245. onment The sparse representation leads to increases in speed and simplified housekeeping allowing techniques such as distributed process 2 way nesting and hybrid physics to be performed with no overhead SHOC is written in C and evolved during 2002 from the MECO model with subsequent improvements post 2002 This document is designed to assist the user in operating SHOC For a description of the theory the model is based on refer to Herzfeld et al 2002 20 08 2015 Page 6 of 185 Version 1 00 SHOC User Manual 2 Installation and operation This section describes how to acquire compile and install SHOC At present SHOC is designed to run under the UNIX operating system It has successfully been installed on SUN workstations Silicon Graphics workstations and Intel Linux which is the current development platform 2 1 Getting the model source code The source code to SHOC and associated libraries and utilities is available from CSIRO Marine Research subject to approval and acceptance of a license agreement If you wish obtain the source code or require further information please contact John Parslow csiro au 2 2 Building and installing the model executable file This section provides a brief description of how to compile and install SHOC and the supporting libraries ecology sediments and tracerstats as provided with the SHOC source distribution Additional compilation and installation instructions are provided with each package
246. or the constant b1 to be altered via WAVE_B1 default is 0 0014 MIX_BVM The wave induced mixing coefficient Bv method for monochromatic waves Qiao F Yuan Y Ezer T Xia C Yang Y Lu X Song Z 2010 A three dimensional surface wave ocean circulation coupled model and its initial testing Ocean Dynamics 60 1339 1355 This method allows for the constant a to be altered via WAVE_ALPHA default is 100 as per the MIX_JONES method and should be changed to 1 or 4 T Version 1 00 20 08 2015 Page 77 of 185 SHOC User Manual The radiation stresses are applied to the 2D mode following the implementation of Bye 1977a If the MOM_TEND flag is true then tangential radiation stress tendencies me are added to the tracer list Alternatively if radiation stresses may be read from file as provided by a wave model These variables may be aligned with the grid or east north and have units of Nm In this case the depth averaged velocity is augmented to reflect the forcing due to these radiation stresses To invoke this forcing the WAVE_FORCING keyword should be specified The stokes drift velocity may be aligned with the grid or east north and have units of ms In this case the drift velocity is added to the 3D and 2D Coriolis terms To invoke this forcing the STOKES keyword should be specified The Stokes Coriolis and vortex forces are applied according to Moon 2005 Eq 14 A wave librar
247. osalt respectively read in on a daily time interval e RAMPVARS WIND TIDALH is used e Active alerts are implemented on 2D amp 3D velocity and eta ALERT ACTIVE The eta relaxation file is taken to be the global model data i e SHOC sea level is relaxed back to the low frequency sea level if the difference between the mean ROAM sea level tidally averaged and OFAM sea level exceeds the prescribed threshold e Thresholds for ACTIVE ALERTS are o VELMAX 3 51 ms o VELMAX_2D 2 40 ms o ETA_DIFF 0 26 m e Mean sea level is computed for the active eta alerts MEAN ETA 20 08 2015 Page 138 of 185 Version 1 00 SHOC User Manual The robustness of ROAM may be altered using the parameter ROBUST which is assigned from 1 least robust to 10 most robust The ROBUST levels 1 to 5 linearly increase the Smagorinsky coefficient from 0 1 to 0 5 For ROBUST gt 2 the horizontal diffusion distribution is smoothed using a 9 point convolution filter and mixing coefficients have an upper limit corresponding to the computed constant mixing coefficients For ROBUST gt 5 constant mixing coefficients are used and the time step is linearly decreased from its computed value using ROBUST 6 to half its computed value with ROBUST 10 The model starts from an initial velocity distribution at rest for ROBUST gt 6 The default value is ROBUST 6 Note that more robust parameterisations are generally le
248. oundary forcing The ROAM configuration may be restarted from a previous run using the rs option In this case a restart file must be supplied RESTART_FILE runl_all nc Restart filename The restart may be configured to commence using the temperature and salinity initial conditions from OFAM using the rso option The rq option will terminate after the input and parameter files have been created i e the setup is complete but the simulation does not commence 20 08 2015 Page 137 of 185 Version 1 00 SHOC User Manual Bathymetry may be specified in the ROAM configuration using a bathymetric database rather than supplying the bathymetry list via BATHY e g by specifying BATHYFILE home bathy ga2002_tiled bth the bathymetry will be interpolated onto the grid using the information contained in the bathymetric database ga2002_tiled bth This file has a unique format and lists all the tiled netCDF bathymetry files that comprise the database ROAM is designed to use surface fluxes from a relocatable atmospheric model currently RAMS Relocatable Atmospheric Model The wind and pressure inputs may be the same as for the a option Alternatively if wind and pressure are present in the same file then use RAMS_DATA home atmos EAC_rams nc Atmospheric forcing file If the RAMS_DATA file contains heatflux data e g incident flux of shortwave radiation W m 2 incident flux of longwave radia
249. p years in their simulation to account for this specify NO_LEAP_YEARS YES Always use 365 days per year A transport file can be created from a standard prm file by specifying TRANS_DATA in the prm file The name of the transport file in this case is lt INPUT_FILE gt tran e g if the input file in the prm file is infile nc then the transport filename will be infile tran When the transport mode is invoked using semi Lagrangian advection a tracer vi with long name Volume error is created which contains the volume conservation error in m for each cell resulting from the use of the semi Lagrange scheme 9 1 Multiple grids It is possible to perform transport on a subset of the grid used to save the transport files In this case the streamline origin is computed on the source grid which is defined as the grid on which the TRANS_DATA were Created and the values of tracer variables are interpolated on a different target grid All output is performed on the target grid The target grid must lie completely within the source grid and will conform to one of the following 1 The target grid may be an exact duplicate of the source grid This may be for a smaller subset of the source grid In this case the target grid is defined as having an EXACT relationship to the source grid and resolution of source and target grids are the same 2 The target grid may be a decimation of the source grid i e 4 9
250. parameter which is assigned from 1 to 10 The speed is controlled by altering the safety factor applied to the CFL condition The ROAM safety factor is assigned a value 0 4 note 0 8 is used for a option and further decreases depending on the maximum depth If SPEED 1 then the safety factor is unchanged For SPEED gt 1 the safety factor linearly scales to 0 9 for SPEED 10 Using SPEED 10 will generally double the time step used and still satisfy the CFL condition Es T 20 08 2015 Page 140 of 185 Version 1 00 SHOC User Manual 8 Input file generation g option The input netCDF file containing initial values for the model variables over the model grid and the model geometry bathymetry required to run SHOC using the p option may be generated from any parameter file using the g option i e shoc g prmname infile nc where prmname is the name of the model parameter file and infile nc is the name for the generated input netCDF file Note that whenever initialization data is changed e g TRACER data model geometry is changed e g number of LAYERFACES or the bathymetry is changed a new input netCDF file must be generated 20 08 2015 Page 141 of 185 Version 1 00 SHOC User Manual 9 Transport mode t option The transport option invokes the tracer transport only in SHOC using offline velocities and vertical diffusivities read from
251. parameterisation demonstrated here does not guarantee model stability and parameters or schemes may require alteration to achieve a stable model run Describing the process of stability analysis is beyond the scope of this manual Once a satisfactory parameter file is created the input file must be re created so that the specified initial conditions are included rm gulfs nc shoc g gulfs prm gulfs nc It is good practice to view gulfs nc graphically to ensure initial conditions and bathymetry are satisfactory The resolution of this example is 9 5 x 12 2 km with maximum depth of 5400 m resolved by 52 layers 8 Run the simulation shoc p gulfs prm Any warnings encountered during setup are written to the file runlog model progress is written to diag txt and the model parameterisation as used internally by the model is listed in setup txt see Section 4 32 It is good practice to view the setup txt file to ensure the model configuration is as expected Output may be vied using PLUM or a similar java based application DIVE see http www emg cmar csiro au www en emg software Visualization htm The process of stability analysis sensitivity analysis and calibration may now commence 20 08 2015 Page 173 of 185 Version 1 00 SHOC User Manual 15 Sediment Transport The sediment transport routines may be fully coupled to SHOC by invoking DO_SEDIMENTS YES or DO_SEDIMENTS DO
252. parameters specify the boundary type name boundary condition type used cell indices and forcing data Specification of a u1 boundary is shown below BOUNDARYO TYPE ul BOUNDARYO NAME Offshore boundary BOUNDARYO DATA offshore nc BOUNDARYO BCOND_NOR NOGRAD BOUNDARYO BCOND_TAN CLAMPD BOUNDARYO BCOND_ELE FILEIN BOUNDARYO BCOND_TRA_ALL UPSTRM BOUNDARYO POINTS 3 4 7 4 8 4 9 20 08 2015 Page 42 of 185 Version 1 00 SHOC User Manual Alternatively if the BOUNDARY POINTS are contiguous e g not interrupted by land then the BOUNDARY RANGE specification may be used e g BOUNDARYO RANGE 4 7 4 9 Generally this specification takes the form BOUNDARY 0 RANGE is js ie je where is and js are the start i j coordinates and ie and je are the end i j coordinates Note that is ie for u1 boundaries and js je for u2 boundaries No white space is to be inserted in the syntax for this specification A specified zone of wet cells may be changed to OUTSIDE cells by specifying BOUNDARYO OUTSIDE_ZONE n Set n wet cells into the interior as OUTSIDE This must be performed using the both the g and p option New boundary ranges are listed in the runlog file 4 10 1 Boundary condition types The boundary conditions available are based on a variety of approaches and are listed in Table 3 2 9 1 The name and keyword used as input to SHOC are lis
253. pecified as follows Maximum allowable z coordinate for water surface elevation If the water surface ever exceeds this value the model run stops and produces an error message This value is also used by the grid generation program to decide whether the top layer is land or not land if bathymetry above ETAMAX ETAMAX 10 0 The o coordinate system scales the layer interfaces to the total water depth This allows the bottom to be well resolved at any depth If the sigma option is invoked see section 4 25 then the o levels are generated by SHOC such that a logarithmic distribution exists at the surface and bottom and a linear distribution in the interior The user need only specify the number of layers to be used in this case 20 08 2015 Page 27 of 185 Version 1 00 SHOC User Manual The number of coordinates for the model layer interfaces LAYERFACES 6 NOTE The vertical grid geometry described above is not used by the model when a run is initiated using the p option Layers are defined when the g option is invoked see section 8 to generate the model input netCDF file which contains model initial values and geometric information Any alteration to model vertical grid geometry must be accompanied by the creation of a new model input netCDF file using the g option 4 8 Bathymetry When a run is initiated using and existing parameter file and input netCDF file i e using the
254. r ER1 units degrees C ER1 fill_value 20 0 ER1 valid_range 0 40 ssive dissolved contaminant tracer specifying an Page 33 of 185 Version 1 00 SHOC User Manual initial distribution from a netCDF time series file called profile nc Note that the fill_value attribute must still be present but isn t used RACER2 name contam RACER2 long_name Contaminant RACER2 units kg m 3 RACER2 fill_value 0 0 RACER2 valid_range 0 2 RACER2 data profile nc Note that the valid range attribute is a recommendation only and SHOC takes no action other than supplying a warning if these bounds are violated The exception is however if the minimum range is zero and the model begins to produce negative results In this case the tracer value is clipped to zero in SHOC to ensure positive definiteness 4 9 1 Tracer initialisation When a run is initiated the initial distribution for each tracer are read from the INPUT_FILE This file may be generated using the g option or be an output file from a previous run If the g option was used then the INPUT_FILE will contain tracer distributions that reflect either the f i11_value or data specified for that tracer see above However if a run is initiated which has tracers in the tracer list that do not have corresponding distributions in the INPUT_FILE i e new tracers are added then the initial distributions for those tracers will be specifi
255. r sparse format including multiple datafiles Section 4 32 2 sparse files P_OFILE Output file If OutputPath is specified the file is placed in this directory P_VARS Variable names to compute percentiles P_STIME Start time of the computations relative to TIMEUNIT P_ETIME End time of the computations relative to TIMEUNIT P_DT Processing interval subsamples the input file An example is as follows TIMEUNIT seconds since 2000 01 01 00 00 00 08 OutputPath home work P_IFILE inut txt P_OFILE perc nc P_VARS temp salt P_STIME 10 days P_ETIME 20 days P_DT 12 hours With input txt containing multi netcdf version 1 0 nfiles 2 filedO filename ti ne fileO filename t2 nc the files t1 nc and t2 nc may be sparse formatted files Every record in the input file is read and included in the computations unless P_DT is specified when every n record is included where n P_DT in seconds output interval of P_IF ILE in seconds 20 08 2015 Page 150 of 185 Version 1 00 SHOC User Manual 11 File formats SHOC uses two file formats for input and output data exchange An ASCII time series column format and a multi dimensional netCDF format Both of these files support multiple variables an unlimited number of time records and the association of geometry with variables Typically ASCII time series files are used when a time series of multiple variables is requ
256. r example if the forcing becomes locally large for a short period of time The advective terms for 2D 3D momentum and tracers are calculated using a sub timestep based on the maximum Courant number in the grid and the remaining terms in the model equations are calculated using the original time step Note that the original time step must still obey the CFL condition so as fast moving gravity and internal waves are adequately resolved To invoke the sub time stepping the parameter STABILITY is set in the parameter file as follows STABILITY SUB STEP Sub stepping stability adjustment STABILITY SUB STEP NOSURF As for SUB STEP but excluding the surface layer STABILITY SUB STEP TRACER Only sub step for tracers STABILITY NONE No stability compensation The default option is NONE If STABILITY SUB STEP NOSURE then the vertical velocity in the surface layer is not included in the maximum sub step calculation This is consistent with the original MECO formulation This option avoids sub stepping when the surface elevation is only slightly greater than a layer level the surface layer is thin and moderately large vertical velocities exist This condition may occur often and increase the run time ratio due to frequent sub stepping However the model may go unstable in the surface layer in this case and HMIN may need to be increased to maintain stability in the surface l
257. racking code to be transformed onto the grid 4 28 7 Mortality Mortality or the loss of particles expressed as a percentage of active unlost particles at every time step can be prescribed with a time series file note this input is not spatially dependent e g PT_mortality_file mp ts mortality percentage fil The mortality percentage variable in the file must be named mpt 4 29 Grid Refinement Grid refinement or two way nesting allows a fine resolution grid FRG to be embedded within a coarse resolution grid CRG so that increased resolution is achievable in a sub region of the whole domain Although the time step for the simulation is determined by the smallest grid savings in computer time is generally achieved by not highly resolving the whole domain The method used for grid refinement is detailed in Section 14 of the Science Manual There must exist at least 2 windows for grid refinement to operate A grid must be constructed where the number of fine grid cells that comprise one coarse grid cell i e the zoom factor zf is an odd number so that cell faces and centers in the coarse grid are coincident with fine grid locations at the coarse fine boundary The user must therefore choose a zoom factor and provide a list of the l j locations of the centers of the coarse grid An example of invoking grid refinement is given below N WINDOWS GRID_REFINEMENT ZOOM_FACTOR At least 2 windows are necessary ES
258. rcury 1960 mod_ever a 6377304 063 b 6356103 039 Modified Everest mod_merc a 6378150 0 b 6356768 337303 Modified Merc 1968 new_intl a 6378157 5 b 6356772 2 New International 1967 Seasia a 6378155 0 b 6356773 3205 Southeast Asia walbeck a 6376896 0 b 6355834 8467 Walbeck wgs66 a 6378145 0 b 6356759 769356 WGS 66 wgs72 a 6378135 0 b 6356750 519915 WGS 72 wgs84 a 6378137 0 rf 298 257223563 WGS 84 20 08 2015 Page 23 of 185 Version 1 00 SHOC User Manual Ellipsoid Parameters Description agd66 a 6378160 0 rf 298 25 Same as aust_nil agd84 a 6378160 0 rf 298 25 Same as aust_nil gda94 a 6378137 0 rf 298 25722101 New Aust ellip sphere a 6370997 0 es 0 0 Sphere of 6370997 m An example definition of an AMG projection for Port Phillip Bay in Eastern Australia follows Port Phillip Bay is located at Zone 55 of the UTM projection PROJECTION proj amg zone 55 4 6 Horizontal grid geometry SHOC supports five orthogonal horizontal grid geometries rectangular polar geographic_rectangular elliptic and numeric All internal grid metrics are stored in units of metres although the coordinates maybe specified in either x y or latitude longitude units depending on how the PROJECTION parameter was specified All grid definitions share the following two parameters NCE1 and NCE2 NEC1 and NEC2 define the number of cells in the e1 or i or x and e2 j or y directio
259. responding to certain times and SHOC piecewise interpolates the defined systems to produce a wind pattern at any particular time during the simulation The i j location need not be defined within the dimensions of the domain but may assume any value lt i lt 00 00 lt j lt oo For this reason the locations must be supplied in 20 08 2015 Page 68 of 185 Version 1 00 SHOC User Manual terms of i j rather than geographic coordinates since there only exists a map between geographic coordinates and i j locations within the confines of the domain Generally the user must perform some type of extrapolation if the storm center is to be defined beyond the confines of the domain this may not be trivial for curvilinear grids and some trial and error may be necessary The storm systems are defined via NSTORM n Number of storm systems to define STORM_INPUT_DT day Interval wind stress is updated STO stime days Time this system is defined at STO stype HIPR or LOPR High pressure or low pressure systems STO sp aximum pressure gradient HPa km STO ss Radius km STO si i i location of system center STO sj J j location of system center STO se Eccentricity 0 lt e lt 1 STO sr 2 Rotation 0 lt lt 360 An example of a propagating storm system is given below NSTORM 3 STORM_INPUT_DT 1 day STO stime 0 days STO stype HIPR STO sp 7e 4 ST0 ss 3000 STO si 20 STO sj 20 STO se 0 STO sr
260. ressure with units of Pa PRESSURE cyc_bobby95 nc How often to read the file and update the pressur field in the model PRESSURE_INPUT_DT 10 minutes Update every 10 minutes In this case horizontal gradients in atmospheric pressure are dynamically included in the model and any difference between the pressure specified in the PRESSURE data file and the AMBIENT_AIR_PRESSURE value may cause an inverse barometer effect at elevation open boundaries see section 4 10 16 4 15 Rainfall Rainfall can be included as a model forcing input by using the following optional parameters A time series file containing the variable precipitation with units mm day 1 the SI unit would be m s 1 but this results in ridiculously small values PRECIPITATION rain nc How often to read the precipitation data PRECIPITATION_INPUT_DT 10 minutes Rainfall is assumed to be fresh zero salinity at ambient air temperature see section 4 17 and have zero concentration of all other tracers Rainfall increases the volume of water in the model and so may directly affect the model surface elevation 4 16 Evaporation Evaporation can be included as a model forcing input by using the following optional parameters A time series file containing the variable evaporation with units mm day l EVAPORATION evap nc How often to read the
261. river will be located at the nearest coastal location in the model grid to lt lon gt lt lat gt A ul or u2 custom river open boundary is created for each river specified If lt lon gt lt lat gt lies outside the footprint of minimum amp maximum longitude and latitude for the grid it is ignored An example is RIVERO riverl 137 9 33 4 flowl ts RIVER river2 137 8 33 5 flow2 ts Alternatively a full boundary specification may be included giving the user exclusive control over the open boundaries Often this is best performed using a two step approach where a grid is first created with all boundaries closed i e by specifying Set all boundaries closed NBOUNDARIES 0 Then boundaries are defined in jvismeco and pasted back into the parameter file 20 08 2015 Page 132 of 185 Version 1 00 SHOC User Manual Various parameters automatically generated by SHOC using the a option may be over ridden by specifying that parameter in the input parameter file Parameters which fall into this category are Open boundaries s above The epoch for all time related parameters as well as for all output files generated by the model Currently the units must be seconds since but this may change in future versions The epoch is specified in standard ISO date time format including a possible timezone specification The timezone here is 8 hours ahead of UTC TIMEUNIT seconds since 1990 01 01 00 00 00 08 Th
262. rod SPEED_2D 2D Current Speed ms current_speed_2d 20 08 2015 Page 116 of 185 Version 1 00 SHOC User Manual ENERGY Mechanical energy Jm energy KINETIC Kinetic energy Jm kenergy SPEED_3D 3D Current Speed ms current_speed_3d SPEED_SQ 3D Current Squared me speed_sq WIND_CD Momentum drag coefficient wind_Cd UNIT Unit passive tracer unit OBC_PHASE OBC phase speed ms obc_phase CALC_PERCS Tracer percentiles percentile_ lt tr name gt ALERTS Alert information alerts_actual alerts_cumulative SHOW_WINDOWS Window partitions windows WET_CELLS Wet cell diagnostic wet_cells SHOW_LAYERS Layer thickness m layer_thick BOTSTRESS Bottom stress tau_bel tau_be2 tau_bm SURF_LAYER k index of surface layer surf_layer SLOPE Surface slope mm surf_slope_x surf_slope_y REGION Region budgets regionid AGE Age tracer age DECORR_LENGTH De correlation length scale decorr_el decorr_e2 Particle tracking invoked Particle concentration ptconc 20 08 2015 Page 117 of 185 Version 1 00 4 31 There are a variety of parameters in SHOC for specifying input time series datafiles e g SHOC User Manual Data variables and input time series files WIND_TS john hunter utas edu au BOUNDARY DATA It is expected that e The datafile specified be either a Ne
263. rofile is made by matching two exponential profiles at an inflection corresponding to the mixed layer depth The PROFIL method therefore requires MIX_LAYER DENS_MIX to be set so that a mixed layer depth is available These methods are useful for forcing the model with surface and bottom data collected using moored instruments Both these methods require a netCDF file to be provided to SHOC containing the measured data The data must be input at the exact geographic coordinates of the cell centers of the open boundaries The surface measurements which may vary spatially across the boundary must be input at the surface i e Om and the bottom measurement must be input at the layer in which the bottom is located for each cell comprising the boundary i e the layer in which the bottom lies must be found for each cell and the same bottom measurement must be written to the netCDF file for that layer and geographic coordinates corresponding to that cell This arrangement of the netCDF input file is necessary so that the profile method knows where to find surface and bottom measurements for each boundary cell This means that netCDF files used for the profile methods are layer configuration and boundary location dependent i e if the layer configuration or location of the boundary changes a new file must be created Profile methods are specified using BOUNDARYO BCOND_TRA lt n gt UPSTRM FILEIN PROFIL Synthetic profile for tracer lt n
264. rse barometer contribution ETA RELAX Relaxation to eta FLUX_ADJUST OBC local flux adjustment STOKES Stokes Coriolis and vortex forces Specifies the internal 3 d time step and the number of times the external 2 d code will be run per 3 d time step The external 2_d time step is thus DT divided by IRATIO DT 120 seconds IRATIO 5 Computational settings and flags A number of parameters change the way in which calculations are performed as follows or A flag which includes or excludes the non linear terms in both the momentum equations and the surface elevation NONLINEAR YES A flag which enables the calculation of density at each time step from the salinity and temperature of the water If this flag is turned on then the model must include tracers called salt and temp If it is turned off the density field used by the model is as read from the input netCDF file and doesn t change over time regardless of the behaviour of any tracers in the model If a valid tracer name is input for CALCDENS then the density used in the model is the distribution represented by that tracer CALCDENS YES CALCDENS density_tracer The minimum layer thickness m value to be used when dividing by the layer thickness in any of the momentum equations This prevents numerical problems particularly in areas which are drying
265. s In the absence of any heat flux information this constitutes a helpful first estimate of heat input This option requires a timeseries of SST observation input in the same manner as relaxation to the surface i e t Time series file specifying surface temperatures containing the variable heatflux_temp with units Degrees C HEATF LUX_TEMP temp nc Time constant HEATFLUX_TC 20 days In this case the time constant determines the time scale over which the SST will change due to the applied heatflux i e the shorter the time constant the larger the estimated fluxes Generally the time constant should be of the order of the frequency of observations The heat flux generated with the BULK and INVERSE methods and heat flux components are saved as tracers which may be viewed in the model output If the BULK option is invoked the heat flux components are written to the time series files The atmospheric model RAMS Pielke et al 1992 can output heatflux components that may be assembled to generate a net heat flux comprising of sensible latent and longwave fluxes and a short wave component that is depth distributed as above Note that this formulation the longwave radiation is replaced with analytical blackbody outgoing radiation and clear sky longwave input since this seems to generate heatfluxes that balance i e do not excessively heat or cool the ocean in the long term henc
266. s an additional tracer Note that if tracers are set as diagnostic tracers TRACER diagn 1 then SHOC initializes the tracer to zero every time the tracer is dumped to file Since mean tracers sum contributions over the averaging period always set TRACER diagn 0 when manually defining mean tracers 4 30 3 Mixed Layer Depth The mixed layer depth may be computed using a threshold on the vertical density profile currently hardwired to 0 01 kgm in the routine mld or threshold on the turbulent kinetic energy hardwired to 10 Wkg in the routine mldk see Burchard et al 1999 p26 Obviously the latter will only function if the mixing scheme calculates TKE e g Mellor Yamada 2 5 k e k w Finally the mixed layer may be computed as the level where water temperature attains a value of 0 1 x SST The mixed layer option is invoked by setting the flag MIX_LAYER NONE Default no mixed layer calculation MIX_LAYER DENS_MIX Density gradient computation MIX_LAYER KE MIX KE threshold computation MIX_LAYER EMP_MIX Temperature 0 1 x SST computation The default is no mixed layer calculation If this flag is invoked then a 2D tracer is automatically created to store the mixed layer depth in units of metres 4 30 4 Flushing Time The time required to flush a sub region of the model domain may be calculated using the flushing diagnostic The flushing time is d
267. s impractical for large output files and doesn t produce graphical output this is particularly true for model dumpfile Another way to view the netCDF dumpfiles is to use jvismeco which can read these files and display the values of most variable This technique is useful for examining the model in detail to find the cause of an instability for example However it still doesn t allow you to save any sort of graphical output yet Modules to read and write netCDF files have been added to the commercial application Matlab commonly used in the scientific community Matlab is a good tool for analysing the model dumpfiles A number of supplementary Matlab scripts mecoread2d mecoread3d and ncinfo have been installed in the Matlab software repository directory home software matlab for reading SHOC netCDF dumpfiles e mecoread2d reads a two dimensional variable and associated geometry from a SHOC file Following is an example of how to use mecoread2d xl yl ulav mecoread2d out nc ulav 10 e mecoread3d reads a three dimensional variable and associated geometry from a SHOC file The data is returned as a 3d volume unless a specific layer is specified Following is an example of how to use mecoread3d xc yc eta mecoread3d out nc salt 44 or xl yl ulav mecoread3d out nc ul 10 151 e ncinfo provides summary information bout all variables within a netCDF file and their dimensions ncinfo out nc 20 08 2015 Page
268. s not use the fetch If all the wave variables are included in the WAVE_VARS file then waves are assumed to be swell waves and the values retrieved from file are used for wave amplitude period and direction A Grant Madsen style bottom boundary layer see Grant and Madsen 1986 or Madsen 1994 is used to compute wave enhanced bottom friction In this case the bottom roughness Z0 is replaced by a time and space varying apparent bottom roughness calculated according to specified wave input data The bottom friction model parameters are still required with z0 becoming the bottom roughness value in the absence of waves 4 21 Vertical mixing SHOC currently supports seven vertical mixing schemes one of which must be specified for any model run For more details on these mixing scheme formulations see section 6 Herzfeld et al 2002 Mixing schemes can be specified by one of the following Mixing scheme types MIXING_SCHEME constant MIXING_SCHEME csanady 20 08 2015 Page 78 of 185 Version 1 00 SHOC User Manual MIXING_SCHEME mellor_yamada_2_0 MIXING_SCHEME mellor_yamada_2_0_estuarine MIXING_SCHEME mellor_yamada_2_5 MIXING_SCHEME k e MIXING_SCHEME k w MIXING_SCHEME w88 4 21 1 Constant The first scheme simply specifies constant values for the vertical diffusivities for momentum and mass as follows Use the constant mixing scheme MIXING_SC
269. s the model geometry forcing data run period and where and how to write results This section describes the various datasets that are needed to create a model parameter file and the elements of the parameter file itself 20 08 2015 Page 11 of 185 Version 1 00 SHOC User Manual 4 The parameter file The parameter file is an ASCII text file containing comments keywords and values Its contents completely describe a particular model implementation and run parameters apart possibly from initial values for model variables All lines starting with a character are considered as comment lines Comment lines are valuable for documenting certain choices of parameter values or for reminders of the significance of certain infrequently used parameters Comment lines and blank lines are generally ignored by the model itself but may not appear in certain positions described below Other lines typically contain a keyword the parameter name and a value Parameter values may be strings integers floating point values arrays of floating point values or more complex lists Such as boundary point lists or time series point lists The order in which parameters appear in the file is largely unimportant Examples of string parameters are PARAMETERHEADER River model fileO name out Examples of boolean parameters and comment lines are All boolean parameters may be set with either TRUE FALSE YES NO
270. scientific manual CSIRO Marine Research Herzfeld M and M Tomczak 1999 Bottom driven upwelling generated by eastern intensification in closed and semi closed basins with a sloping bottom Mar Freshwater Res 50 7 613 627 Israeli M and S A Orszag 1981 Approzimation of radiation boundary conditions J Compt Physics 41 115 135 Jones N L Monosmith S G 2008 Modelling the influence of wave enhanced turbulence in a shallow tide and wind driven water column J Geophys Res 113 C03009 doi 10 1029 2007JC004246 Kitaigorodskii S A O A Kuznetsov and G N Panin 1973 Coefficients of drag sensible heat and evaporation in the atmosphere over the surface of the sea Izv Acad Sci USSR Atmos Ocean Phys 9 644 647 Kondo J 1975 Air sea bulk transfer coefficients in diabatic conditions Boundary Layer Meteorology 9 91 112 Kowalik Z and T S Murty 1993 Numerical modelling of ocean dynamics BULK series on ocean engineering Volume 5 World Scientific Singapore 481 pp Large W G and S Pond 1981 Open ocean momentum flux measurements in moderate to strong winds J Phys Oceanogr 11 324 336 Large W G and S Pond 1982 Sensible and latent heat flux measurements over the ocean J Phys Oceanogr 12 464 482 Leonard B P 1991 The ULTIMATE conservative difference scheme applied to unsteady one dimensional advection Comp Methods in Appl Mech and Eng 19 17 74 Leonard B P
271. ser Manual Several additional options may be appended to the MOM_SCHEME definition WIMPLICIT Implicit vertical advection ADVECT_FORM Horizontal advection solved in the advection form WTOP_O2 2 order approximation for surface vertical velocity WTOP_0O4 4 order approximation for surface vertical velocity ZERO_DRYK Velocity 0 for horizontal terms above free surface SHAPIRO Use 1 order Shapiro filter on advection tendencies The default approximation for surface vertical velocity is A order Velocities used in the horizontal fluxes are set to zero above the free surface using ZERO_DRYK then set to a no gradient for the vertical fluxes The default is a no gradient condition for horizontal and vertical fluxes An example using these options may be MOM_SCHEME ORDER2 ADVECT_FORM ZERO_DRYK The semi Lagrangian scheme can be used with 1 to 4 order interpolations using ORDER_SL n Order of scheme n 1 2 3 or 4 The default is first order using a tri linear interpolation The scheme is also unconditionally stable and can therefore be used with any time step However this scheme is only suitable to use with multiple windows if the CFL condition is satisfied in practice the stencil of the higher order schemes n gt 1 mean that insufficient partition transfers are available to provide an accurate solution This allows the possibility to operate the tracers on
272. settling velocity for Mud Various sediment parameters may be spatially varying e g settling velocity If the settling velocity attribute is the name of a 2D tracer in the tracer list then the values of that tracer will be used as the settling velocity In automated mode if a 2D tracer is found in the tracer list with the name of a sediment tracer class appended with _svel e g Mud_svel Sand_svel then that 2D tracers values will be used as the settling velocity for that sediment tracer class e g Mud may be spatially variable if a 2D tracer exists with the name Mud_svel or for example if a 2D tracer exists with the name settling_mud and the settling velocity attribute for Mud is redefined as Mud svel settling_mud The global sediment transport attributes are defined in automated mode using SEDFILE lt param_filename gt Where lt param_filename gt may be 1 The name of a file containing the global parameters 2 A default name for hardwired parameters Currently the names standard and estuary are accepted The initialisation of these parameters exists in model lib sediments sed_init c and may be expanded as desired 3 auto where the parameters may be dynamically prescribed in the routine sed_params_auto in model lib sediments sed_init c Currently this routine is empty 4 If none of the above are specified the parameters are assumed to be listed in the main parameter file The sediment specification is wri
273. simulations and satellite data assimilation on parallel computers Technical report EUR 18129EN European Commission 76pp Dyer K R 1997 Estuaries a physical introduction J Wiley amp Sons Chichester Eifler W and W Schrimpf 1992 ISPRAMIX a hydrodynamic program for computing regional sea circulation patterns and transfer processes CEC Report EUR 14856 EN Eringen A C 1962 Nonlinear theory of continuous media McGraw Hill New York Evenden G I 1995 Cartographic Projection Procedures for the UNIX Environment A User s Manual United States Department of the Interior Geological Survey Open File Report 90 284 Galperin B L H Kantha S Hassid and A Rosati 1988 A quasi equilibrium turbulent energy model for geophysical flows J Atoms Sci 45 55 62 Gill A E 1982 Atmosphere Ocean Dynamics Academic Press Inc Grant W D and O S Madsen 1986 The continental shelf bottom boundary layer Ann Rev Fluid Mech 18 265 305 Herzfeld M 2006 An alternative coordinate system for solving finite difference ocean models Ocean Modelling 14 174 196 Herzfeld M Andrewartha J 2011 A simple stable and accurate Dirichlet open boundary condition for ocean model downscaling Ocean Modelling In press 20 08 2015 Page 180 of 185 Version 1 00 SHOC User Manual Herzfeld M J Waring J Parslow N Margvelashvili P Sakov and J Andrewartha 2002 SHOC Model for estuaries and coastal oceans
274. sion of the inverse tetragonal bilinear texture map that performs this mapping is sometimes not sufficient to discriminate cell indices for point sources close to cell faces If the code exits with the warming Mismatch between point sourcesinks on master and slave then refer to the runlog to identify the point source that could not be successfully mapped and redefine its geographic location Placing point source locations at the cell centre and avoiding open boundary locations will rectify this problem 4 23 1 Steady State Approximation The steady state concentration resulting from a point source input into a grid cell is dependent on the grid size and can be approximated via the following Assume a flux Fin gs 1 is input into a cell with dimensions Ax Ay Az in the e1 2 z directions The e direction only is considered it is assumed that a constant e velocity of u ms exists and the horizontal diffusion is Ay m s The concentration of tracer c kgm at time t 1 can be written in terms of mass as EFI Vce t Vc source input mass advected out mass advected in mass diffused out where V AxAyAz Over a time step At this is equivalent to t 1 t l cV c V F At c AyAzuAt 0 AyAzuAt AyAzA A It is assumed that the concentration of tracer advected in c _ is zero and that a zero gradient of tracer exists down current from the source c c This is simplified to cl ae dc A
275. sity DEPROF T Idealised profile PROFIL s T Density gradient scaled DESCA s T 20 08 2015 Page 43 of 185 Version 1 00 SHOC User Manual No condition imposed NOTHIN un ut n Implementation of the open boundaries requires that a boundary condition type is assigned to normal and tangential velocity components elevation and tracers for each open boundary via the use of the following keywords BCOND_NOR for normal velocity components BCOND_TAN for tangential velocity components BCOND_ELE for elevation BCOND_TRAn for tracers where 0 lt n lt number of tracers or BCOND_ lt tr_name gt where lt tr_name gt is the name of the tracer e g BCOND_temp or BCOND_salt Different boundary conditions may be optionally set for the 2D components of velocity by defining the keywords BCOND_NOR2D for 2D normal velocity components BCOND_TAN2D for 2D tangential velocity components If these flags are absent then the 2D velocity components use the same open boundary condition as the 3D components specified by BCOND_NOR and BCOND_TAN The tracer boundary condition allows different conditions to be specified for each tracer If all tracers are required to have the same boundary condition the tracer flag used is BCOND_TRA_ALL If this condition precedes a condition for individual tracers then all the tracers are set to BCOND_TRA_ALL except the individually specified tracers This is useful if only
276. ss accurate These configurations are applicable for the default ROAM version 4 ROAMv 4 An additional set of configurations can be invoked using ROAMv flag ROAMV CPD Standard ROAM clamped open boundaries ROAMv RMD Standard ROAM RAYMND radiation OBCs ROAMV FLA Standard ROAM FLATHR OBCs ROAMv ROAMv1 Standard ROAM velocity forced OBCs ROAMv ROAMv2 ROAMv1 with alternative ROBUST parameterisation ROAMv RECOMv1 Standard RECOM no ROBUST ROAMv RECOMv2 RECOM with ROBUST parameterisations ROAMv T Same as CPD ROAMv 2 Same as RMD ROAMv 3 Same as FLA ROAMv 4 Same as ROAMv1 ROAMv 5 Same as ROAMv2 ROAMv 6 Same as RECOMv1 ROAMv 7 Same as RECOMv2 The default ROAM should use ROAMv ROAMv2 which sets robustness according to ROBUST 1 OFAM currents Smagorinsky 0 1 ROBUST 2 OFAM currents Smagorinsky 0 2 ROBUST 3 Geostrophic currents Smagorinsky 0 1 ROBUST 4 Start from rest hard T S relaxation Smagorinsky 0 1 ROBUST 5 Start from rest Smagorinsky 0 1 ROBUST 6 Start from rest Smagorinsky 0 2 ROBUST 7 OFAM currents constant horizontal viscosity ROBUST 8 Geostrophic currents constant horizontal viscosity ROBUST 9 Start from rest constant horizontal viscosity ROBUST 10 As for ROBUST 9 with reduced time step A ROBUST 0 flag has been implemented that will use a more optimized configurati
277. t source sink delivering mass into the region over the interval fluxes through the surface or sediment or non conservative processes associated with the tracer The mean concentration in the region can be computed using mean mass divided by mean volume The mass fluxes in the hydrodynamic model are computed using the same fluxes as are used to update tracer advection which are basically the tracer concentration at a cell face x velocity through the face x area of the face x model time step The transport model computes fluxes by multiplying any interpolation weights that lie outside the region by the mass of the destination cell Both these methods are inaccurate near open boundaries the hydrodynamic model because conservation is not respected in the boundary cell and the transport model because a source cell for outflow may be a destination cell beyond the domain grid These issues can be overcome by effectively migrating the open boundary location into the domain or creating extra boundary regions for which it is acknowledged that the mass budget will be inaccurate To migrate a boundary into the interior use D EGION_MODE OBC_BDRY Migrate OBC into the interior REGION_OBC_ZONE al Number of cells to migrate the OBC For the hydrodynamic model it is sufficient to migrate the boundary only 1 cell and this is recommended a warning is displayed if this is not the case To create new regions adjacent to open bo
278. tCDF file A warning is issued if this is not the case 6 2 Restarts using restart file restart option Alternatively a restart facility exits to allow the model to be seamlessly hot started Firstly when initially running the model a restart_dt must be specified which defines an output interval that a special restart file named restart nc is dumped at in standard format containing ALL variables e g restart_dt 2 days Create a restart nc file every 2 days This restart file is overwritten at the interval restart_dt A path and restart filename may be specified using restart_name lt path gt lt name gt Restart path and name e g lt path gt home data lt name gt restart_l nc Once this file is written the model may be terminated or may crash and can be restarted using the restart nc file e g shoc p test prm restart Using this restart method the model will read the appropriate START_TIME from the restart nc file and will append subsequent data generated to existing netCDF and time series output files defined in the prm parameter file in the above example test prm Note that restarts generally do not produce bit exact solutions if output dumps are saved in floating point precision bytespervalue 4 6 3 Near real time restarts nrt option A near real time operation mode may be invoked capitalising on restarts This allows simulations to be repetitively started daily wit
279. tCDF or ASCII time series datafiles e The files conform to the coordinate conventions described in section 10 e The files contain the necessary variables name s for the parameter Following is a list of the parameters names and the variables that each parameter expects to find in the datafile Parameter name Expected variable Substitution names names in datafile AIRTEMP air_temp air_temp BOUNDARY DATA elevation eta eta BOUNDARY DATA u1 ul oruandv ul or u and v BOUNDARY DATA u2 u2 or u and v u2 or u and v BOUNDARY DATA tracers tracer name tracer name CLOUD cloud cloud ETA_RELAXATION_FIL eta eta EVAPORATION evaporation evaporation HUMIDITY humidity humidity ORBITAL_VEL ub ub WAVE AMPLITUDE amplitude amplitude WAVE PERIOD period period WAVE DIRECTION direction direction PRESSURE pressure pressure PRECIPITATION precipitation precipitation WET_BULB wet_bulb wet_bulb RADIATION swr swr RACER RELAXATION_FILE tracer name tracer name RACER DATA tracer name tracer name WIND_TS u V wind_u wind v 4 31 1 Variable substitution Since it is not always possible to supply datafiles with exactly the required variables names SHOC permits the expected variable name to be substituted for an alternate name This is done by assigning the
280. ted along with a reference to the original study if this exists The variables the condition may be applied to are also included where un normal velocity Un depth averaged normal velocity ut tangential velocity n surface elevation and T tracers Table 3 2 9 1 SHOC Open Boundary Conditions Condition name Keyword Reference Variable Clamped CLAMPD un ut n T Data prescription from file FILEIN S un ut n T Custom data prescription CUSTO un ut n T Tidal synthesis TIDEBC Bye 1977 n Global tide model TIDALH Cartwright and Ray 1990 n Custom tide constituents TIDALC n 3D vertical integral for 2D VERTIN S un ut No gradient OGRAD un ut n T Linear least squares INEX un ut n T 2 order polynomial POLEX un ut n T Cyclic CYCLIC un ut n T Linear calculation INEAR un ut Gravity wave radiation GRAVTY Sommerfeld 1949 un ut n Orlanski ORLANS Orlanski 1976 un ut 7 Camerlengo and O Brien CAMOBR Camerlengo amp O Brien 1980 un ut n Miller and Thorpe MILLER Miller and Thorpe 1981 un ut n Raymond and Kuo RAYMND Raymond and Kuo 1984 un ut n Flather FLATHR Flather 1976 un Upstream advection UPSTR T Tracer advection TRCONC T Tracer flux TRF LUX T Tracer flux using concentration TRCONF T Statistical prescription STATIS T Profile scaled to den
281. ted to grid Figure 14 3 5 Bathymetry loaded onto the South Australian Gulfs 20 08 2015 Page 170 of 185 Version 1 00 SHOC User Manual Enter 1 for averaging for non Sibsonian natural neighbours for Sibson natural neighbours 4 for linear interpolation 5 for inverse distance 6 for inverse distance fill in 7 for weighted area pk Warning 1 bathy cells still not eg rk Enter 1 for averaging 2 for non Sibsonian natural neighbours 3 for Sibson natural neighbours 4 for linear interpolation 5 for inverse distance 6 for inverse distance fill in for weighted area kk All cells filled B a MENU e ix Grid Creation Clear Read ASCII Files Read PRM File Read NETCDF File RECT sphere Grid RECT fiat Grid POLAR sphere Grid CURVILINEAR Grid DrawiErase Points Draw Erase Grid Edit Grid Draw Erase Mask Create Mask Edit Mask Get Ascii Bty Data Get Nedf Bty Data Get Shoo Bty Data Draw Erase Bathy Clear Bathy Create Bathy Edit Bathy Decimate Grid Create Clear Patch Draw Partitions Edit Partitions Draw Erase Var Edit Variable Save AUTO File Run SHOC auto Main Menu Quit Add MSL ls Depth m 32 S 1 3611 2689 2 5377 1 9295 SCH 345 34s 36 S 36 S ES 38 S 134 E 136 E 138 E 140 E 142 E
282. ter equivalent to planetary vorticity Potential vorticity is then defined as Gill 1982 p232 LEG H cons tan t i e potential vorticity is equal to absolute vorticity divided by water depth and is conserved following the flow Relative vorticity is calculated using the depth averaged velocity to provide a 2 dimensional vorticity diagnostics which are saved to the 2D tracers abs_vor rel_vor and pot_vor The 2D relative vorticity equation is described in the SHOC Science Manual The contributing terms to this balance are automatically generated and saved as 2D tracers if TENDENCY is specified These tracers have the following attributes rv_drvdt Temporal rate of change of relative vorticity production of relative vorticity s5 rv_nonlin Nonlinear contribution to relative vorticity Includes advection metric terms and diffusion s rv_beta Transport across contours of constant planetary vorticity SH rv_strch Vortex stretching i e transport across f H contours Ciel rv_jebar Joint Effect of Baroclinicity And Relief the contribution of the mass field to vorticity production S rv_WSC Production of vorticity due to wind stress curl and the interaction of the wind stress with the gradient of topography s rv_bsc Dissipation of vorticity due to bottom stress curl and the interaction of the bottom stress with the gradient of topography s 20 08 2015 Page 103 of 185 Version 1 00 SHOC User Ma
283. thal equidistant alsk Alaska Mod Stereographic apian Apian Globular bipc Bipolar Conic bonne Bonne cass Cassini cc Central Cylindrical cea Cylindrical Equal Area collg Collignon eck1 Eckert eck2 Eckert Il eck3 Eckert Ill eck4 Eckert IV eck5 Eckert V eck6 Eckert VI eqc Equidistant Cylindrical eqdc Equidistant Conic gall Gall Stereographic gnom Gnomonic gs50 50 State U S Mod Stereographic gs48 48 State U S Mod Stereographic hataea Hatano Asymmetrical Equal Area labrd Laborde laea Lambert Azimuthal Equal Area leac Lambert Equal Area Conic Projection Description lee_os Lee Oblate Stereographics Pacific loxim Loximuthal Isat LANDSAT Space Oblique Mercator mbtfpp McBryde Thomas Flat Polar Parabolic mbtfps McBryde Thomas Flat Polar Sinusoidal mbtfpq McBryde Thomas Flat Polar Quartic mill Miller mill_os Miller Oblate Stereographics Euro Africa moll Mollweides nicol Nicolosi Globular nsper General Vertical Persepective nzmg New Zealand Map Grid ocea Oblique Cylindrical Equal Area 20 08 2015 Page 22 of 185 Version 1 00 SHOC User Manual omerc Oblique Mercator ortho Orthographic parab Caster Parabolic poly Polyconic American puip2 Putnins P2 putp5 Putnins P5 quau Quartic Authalic robin Robinson sinu Sinusoidal stere Stereographic tcea Transverse Cylindrical Equal Area tpers Tilted perspective ups Universal Polar Stereographic
284. the OFAM data represents the low frequency component only and the ROAM configuration will prescribe these values on the open boundary with a tide superimposed using the global tide model of Cartwright and Ray 1990 see Section 4 11 Science Manual This model requires paths to the orthotide functions and nodal corrections to be present e g IDE_CSR_CON_DIR home tide nodal Path to nodal correction directory IDE_CSR_ORTHOWEIGHTS home tide ortho_csr_4 0 Orthotide functions Temperature and salinity are prescribed on the open boundary using an upstream advection open boundary condition Normal velocity uses a no gradient condition and tangential velocity is clamped to zero A horizontal sponge zone 8 cells wide is also imposed on the open boundaries It is possible to prescribe initial conditions for T S and n which are different to the open boundary data defined in OF AM_DATA by using INIT_DATA EBAC_2004_init nc T S Initialisation data file Furthermore each stream of T S and h may be defined independently using TEMP_DATA EAC _temp nc Input temperature filenam SALT_DATA EAC_salt nc Input salinity filename ETA_DATA EAC_eta nc Input sea level filenam If only these specifications are present then the data contained in these files is also used for open boundary forcing However if OF AM_DATA is present then the data contained in this file is used for T S and n b
285. the velocity used in this equation may influence the results depending on the type of forcing in effect For example if low river flow is used as a boundary condition in conjunction with large tides in the model interior then using a velocity located at one cell into the interior to the boundary in the UP STRM condition will drag tracer into the domain whenever the tide flows in an outward direction from the boundary The result is that too much tracer enters the model domain If the velocity at the boundary cell is used then river velocity is always directed into the domain and the tracer in the boundary cell will converge to the data forced value thus will not be influenced by flow into the cell from the model interior due to the tide Again too much tracer enters the domain Clearly neither of these scenarios are optimum and ideally a combination adaptive method of the two would yield the best result The user has the ability to choose which velocity location is used in the equation to best suit the forcing conditions via UPSTRM_METHOD FACE Use the face centered velocity at the boundary location INTERIOR Use the velocity one cell into the interior of the boundary CENTER Use the mean of the boundary and interior velocities ADAPTIVE Use the FACE velocity if the CENTER velocity is away outward from the boundary and the INTERIOR velocity if the CENTER velocity is toward the boundary
286. tial radiation stresses WAVE_FORCING Include 2D wave forcing using radiation stresses read from file STOKES Include Stokes drift velocity VERT_MIX Wave amplitude used for surface length scale in vertical mixing NONE No wave options invoked The default is NONE Note that multiple options may be invoked in the list e g Allow wave enhanced bottom friction and radiation stresses WAVES BOT_STRESS TAN RADIATION SHOC will automatically create the following 2D tracers if these conditions are invoked Wave enhanced bottom drag for BOT_STRESS Tangential radiation stresses mie for TAN_RADIATION wave_Fy Radiation stresses Nm wave_ste2 Stokes drift velocity wave_Cd wave_Sxy wave_Syx Wave BS wave_stel for WAVE_FORCING ms ii for STOKES If wave enhanced mixing is invoked several methods are available for the k e and k mixing schemes only MIX_JONES The method outlined in Jones N L and Monismith S G 2008 Modelling the influence of wave enhanced turbulence in a shallow tide and wind driven water column JGR 113 C03009 This method allows for the constant to be altered via WAVE_ALPHA default is 100 MIX_WOM The wave orbital method Babanin and Haus 2009 On the existence of water turbulence induced by non breaking surface waves JPO Notes and Correspondence 39 2675 2679 This method allows f
287. tial velocity face centres for every boundary present The information is written in the point array output file format Section 4 32 6 and may be directly pasted into a parameter file when outputting point array data for nested grids The WRITE_BDRY option will only function when running the model under the p or g options 4 10 27 Standard boundary conditions A simplified format may be used to specify certain open boundary conditions A list of these standard boundaries may be specified currently the list size is 2 where boundaries may be re configured to any in the list using run regulation Section 4 31 1 The standard boundaries are specified using BCOND lt n gt type lt data_1l gt lt data_n gt Where n is the list number 0 to 1 type is the type of the condition and lt data gt is a list of data required for the type The type may be 1 1 way nesting Section 4 10 7 BOUNDARYO BCONDO NEST2WAY data_l nc data_2 nc data_n nc bdry_uv_nor nc bdry_uv_tan nc where data_ lt n gt nc file containing elevation temperature and salinity data at the cell centre Other tracer data is also required if the tracer OBC is active There must be at least one of these files listed bdry_uv_nor nc file containing east and northward velocity components u v at the normal velocity boundary face bdry_uv_tan nc file containing east and northward velocity components u v at the tangential velocity boundary face In th
288. time 0 day s 00 08 22 Total time ratio 68844 621514 Time to completion 0 day s 00 00 00 Percent complete 100 0 Running Information useful for debugging model crashes may be generated using 20 08 2015 Page 126 of 185 Version 1 00 SHOC User Manual DEBUG_LOC i jk where i j and k are integers specifying the i j k location in the grid information is desired to be generated at Note the k index for the surface layer is given by LAYERFACES 2 At present the debug information relates mostly to the 2D mode providing velocity values at the debug location after each term in the equations is computed for each step of the 2D mode Maximum velocities in the window containing the debug location are listed Elevation flux divergence details and elevation at the forward time step are also provided The debugging information is written to the file debug txt at the current time step If a history of debugging information is required use DEBUG_LOC i j k append Note that these files can then become quite large The debugging information may be written after n days or hours minutes seconds etc of simulation using DEBUG_LOC i j k append after 2 days The debugging can print the position in the computational flow of control i e what numerical algorithm the code is currently computing using DEBUG_LOC i j k step 4 32 1 Run regulation The user may interactively control v
289. tion W m 2 upward flux of longwave radiation W m 2 surface sensible heat flux W m 2 surface latent heat flux W m 2 then a heat flux may be imposed using HEATF LUX COMP_HEAT Create net heatflux from components This formulation of the heatflux will create a net heat flux from the longwave sensible and latent fluxes truncating the latent heat flux to zero to omit contributions from condensation The shortwave flux is depth distributed according to the SWR_TRANSMISSION and SWR_ATTENUATION parameters note defaults are 0 42 and 0 2 respectively All atmospheric data are read in with a time interval of 10 minutes Wind and pressure may have an alternative input time specified The ROAM configuration was designed for robust simulation at the expense of accuracy and therefore various defaults differ in comparison to the a configuration vis e The Mellor Yamada 2 0 mixing scheme is used e Smagorinsky horizontal diffusion is used with a constant of 0 1 e One bathymetry smoothing pass is performed SMOOTHING 1 and a maximum bathymetry gradient of 0 05 is specified MAXGRAD 0 05 e Minimum bathymetry is 1m If maximum bathymetry is gt 200m and minimum bathymetry lt 4m then minimum bathymetry 4m e The time step is far more conservative by at least one half e Relaxation of T and S to OFAM data is performed using a 20 day relaxation time e OFAM temperature and salinity are present as tracers otemp and
290. tive semi Lagrangian advection scheme and an underlying flow field that is non conservative see Section 9 3 These errors are rectified globally using the global 20 08 2015 Page 114 of 185 Version 1 00 SHOC User Manual fill i e mass is conserved over the whole domain but this manifests as an input or removal of mass within a region which is represented by global f1i11 If global filling is not invoked then this error is zero lf ALL_TRANSFERS is included in REGION_MODE when using the transport model then mass or volume transfers from all defined regions are reported as opposed to only those that share common boundaries The residence time for each region is output in each time series file and as a tracer in netCDF output having the name residence This time is computed over the interval REGION_DT The residence time in this case is the time it takes for the volume in each region to be turned over i e replaced with water from other regions due to volume fluxes through the region perimeters or open boundaries Note that this must be considered in the context of the time and space scales of dynamics in play and the size and location of the region For example a small region in an area of large tidal flow will have a small residence time which may not be informative for e g the time it takes fresh water deposited in the region to become saline again since the tidal current may have a large instantaneous flux but a small
291. tored as unsigned bytes with values ranging from 0 to 255 The actual age in floating point precision is scaled to this output range via the parameter AgeLimit e g PT_AgeLimit 20 days If the AgeLimit parameter is present then the age is calculated and scaled age is included in the output file Scaling is performed linearly such that an age of O is scaled to zero and an age of AgeLimit is scaled to 255 Typically AgeLimit is the flushing time of the water body Particles older than AgeLimit remain scaled to 255 These scaled ages may be plotted as a colour spectrum for all sources A histogram of the distribution of ages in bin sizes of 1 day can be produced This is in the form of a time series file named part_hist ts with the histogram output at a specified interval e g PT_Histogram_DT 1 hour Output the histogram at 1 hour intervals to the file part_hist ts A region file see Section 4 29 16 may be used to specify a subsection of the domain within which the mean age of partices is reported PT_age_region region bne 3 In the above case the mean age region will comprise regions 3 of the region file region bne 20 08 2015 Page 91 of 185 Version 1 00 SHOC User Manual 4 28 4 Size A size of particles released from each source may be prescribed using PT_Source0 Size le 4 Size inm A growth or decay rate may also be specified for the source and the particle will decay to zero or double in size on this timescale
292. tory and must be present for each tracer Tracer name must be salt for dynamic salinity variable RACERO name salt A more descriptive name RACERO long_name Salinity Units string RACERO units PSU Standard units Fill value for use with the g option if no data is present see below RACERO fill_value 35 0 20 08 2015 Page 31 of 185 Version 1 00 SHOC User Manual Range minimum and maximum of valid values RACERO valid_range 0 40 The following tracer attributes are optional he type of tracer Options are WATER WC3D or WC for 3D water column tracers BENTHIC INTER or WC2D for 2D tracers and SEDIMENT or SED for sediment tracers Tracers are assumed to be 3D water column tracers by default RACERO type WATER se Oth zt H CJ Allow the tracer to be advected default is 1 or TRU RACERO advect 1 e lt Allow the tracer to be diffused default is 1 or TRU RACERO diffuse 1 e Decay constant in seconds default is 0 0 meaning no decay This may also be the name of a tracer in this case the values of that tracer with units of that tracer seconds minutes hours days will be used as the decay rate This allows for spatially and temporally varying decay rates Negative decay is equivalent to growth RACERO decay 0 0 E Settling veloci
293. tress Again a non linear 3 D model with quadratic bottom friction is expected to give different results and bottom friction is generally required to be increased for solutions to match theory Specifically adequate solutions were obtained using the CONSTANT mixing scheme with background vertical viscosity vzo 0 0507 see Test2 and minimum bottom drag coefficient of QBFC 0 003 UF 20 1e 8 Horizontal viscosity of U1VH U2VH 800 is also required for stability 12 6 Propagation of a bore This test simulates a wetting bore propagating along an initially dry channel The model domain represents a channel 2km wide and 100km long with uniform flat bathymetry A constant velocity of 1 ms is applied at one end of the initially dry channel A bore propagates along the channel with a parabolic shape surface elevation profile determined by a balance between the quadratic bottom friction and surface slope The length of the bore is related to the depth at the inflow via gD L ery 12 6 1 2C U 12 7 Wind stress curl closed basin Wind stress possessing curl applied to a closed basin with a gradient of f D results in the formation of a gyre due to conservation of potential vorticity which is biased to the east if f D lt 0 and biased to the west if f D gt O e g Herzfeld and Tomczak 1999 The gradient of f D may result from a gradient of f B effect or a change in topography This test consists of a closed basin in the so
294. tten in full in the diagnostic file setup txt see Section 4 31 If a transport parameter file is generated from a full parameter file using TRANS_DATA see Section 9 then the sediment specification is also written to this file Outputting these sediment specifications may be invoked without running the full sediment transport by using DO_SEDIMENTS WRITE 20 08 2015 Page 175 of 185 Version 1 00 SHOC User Manual 16 Ecology The ecology routines may be fully coupled to SHOC by invoking DO_ECOLOGY YES or DO_ECOLOGY DO Additionally a sediment layer structure must be defined for ecology to operate see Section 15 Ecology also requires a process definition and a parameter specification These are defined via processfname lt processes gt name of ecology processes The name lt process gt may be one of the following lt filename gt standard estuary auto If lt filename gt is specified then the BGC processes are defined in a file bearing that name If defaults is specified then the processes are hardwired into the module process_defaults c in the ecology library Additional process lists may be included in this module with associated modifications to the calling routines get_eco_processes in process_defaults c and read_process_group_from_defaults in ecology c Additionally there is scope to define processes dynamically using the currently empty routine eco_process_auto in process_d
295. ty components u v at the tangential velocity boundary face In this case the default flux adjustment is used and the boundary condition for temperature and salinity is TRCONC Section 4 10 17 Any other tracers must be individually specified Versions prior to v1670 input the elevation via the eta relaxation file This input method is backwards compatible using eta_relaxation_file bdry_eta nc eta_relaxation_input_dt 20 minutes COMPATIBLE V1670 Note that the time scaling applied to the velocity increment is dt2d dtr where dt2d is the 2D time step and dtr is the relaxation time scale above Therefore if it is required that the flux be adjusted so that at every 3D time step the boundary elevation becomes that in the eta_relaxation_file thenset dtr dt where here dt is the 3D time step note that the adjustment is done on the 2D time step and dt IRATIO x dt2d If FLUX_ADJUST is specified in RAMPVARS then the time scaling decreases from 1 year at the start of the ramp to the ADJUST_FLUX value at the end of the ramp If SCALE_ETA is specified for the boundary Section 4 11 24 then the relaxation value is adjusted by the scale value before the inverse calculation Note that if FILEIN is included in RAMPVARS and the initial condition for sea level is non zero then the sea level for flux adjustment will start from zero over the ramp which may cause instability The RAMPVARS for this forcing is generally RAMPVARS WIND CUSTOM TIDA
296. ty if required m s ve down default is 0 0 RACERO svel 0 0 Y The data attribute allows the specification of initial values for each tracer This is of use when the initial values vary in space or are obtained from observations Data to initialize the tracer TRACERO data lt data_field gt The tracer data field lt data_field gt may be one of the following e The size of the grid nce1 Xx nce2 xX nz followed by an array of values of size ncel x nce2 X nz listed in that order a netCDF file on a regular grid in which case the values will be bilinearly interpolated a netCDF file on an irregular grid in which case interpolation is performed using an inverse distance weighting scheme e an ascii file in column format with spatial information only e no time field Lon and lat must be present In this case the tracer values are interpolated linearly by default or as specified in the interp_type field This is useful for interpolating sparsely collected measurements onto the grid Interpolation method for ascii data input TRACERO interp_type cubic valid options are cubic linear average nn_sibson or nn_non_sibson where nn refers to Natural Neighbours e Tracers may be scaled to a normalized density profile that exists through the water column i e at the deepest point in the domain This ensures that the gradient of the tracer profile is some constant multiple of the density gradient and
297. undaries use D EGION_MODE OBC_AREA Migrate OBC into the interior REGION_OBC_ZONE 5 Cell width of the OBC regions Regions may be used with multiple windows for the hydrodynamic model but must be used with one window with the transport model When REGION is used the region partitions are written to the variable regionid which is written to the output files For the transport model the update rule for tracer concentration ci in destination cell is c K a eo rE St 3 S d S A R where ci is the tracer concentration in source cell j at time t 1 The mass at time tin a ea 7 destination cell jis c V therefore a c VI can be regarded as a mass transfer from cell j to cell i This is the basis of our mass conservation analysis It follows that a c VI is also a mass transfer from region rto r If the total mass fluxes between regions is to be computed then all these mass transfers are required to be cumulated For the transport model the mass budget is represented as start mass mass fluxes mass error global fill end mass and as above denoting the budget as mass budget start mass mass fluxes end mass then mass budget mass error global fill 0 Here mass error is the mass conservation error for source cells in a region and global fill is the mass change in the region due to the global filling algorithm The former errors arise from using the non conserva
298. uted at every time step These are invoked via the NUMBERS diagnostic as follows NUMBERS lt string gt Where lt string gt is a string containing BRUNT INT_WAVE RICHARDSON_GR RICHARDSON_FL REYNOLDS FROUDE ROSSBY_IN ROSSBY_EX SOUND SHEAR_V BUOY_PROD SHEAR_PROD SPEED_2D SPEED_3D SPEED_SQ SIGMA_T UNIT or ALL_NUMBERS These diagnostics are computed as follows BRUNT Brunt Vaisala buoyancy frequency s N where d nN Po Gill 1982 eqn 6 4 9 P d INT_WAVE Internal wave speed ms For constant N the n mode long wave phase speed is approximated by _ NH nn C n Gill 1982 eqn 6 11 1 20 08 2015 Page 106 of 185 Version 1 00 SHOC User Manual where H is the water depth Mode 1 internal waves are produced as this diagnostic RICHARDSON_GR Gradient Richardson number dimensionless where N Ri Guia Dyer 1997 eqn 4 2 uUloz lf Ri gt 0 flow is stable Ri 0 flow is neutral Ri lt 0 flow is unstable RICHARDSON_FL Flux Richardson number dimensionless where KE Rf f V Dyer 1997 p54 REYNOLDS Reynolds number dimensionless where _ uD D The diagnostic produced uses layer thickness for D and vertical eddy viscosity Vz for the kinematic viscosity v Re Dyer 1997 eqn 4 1 FROUDE Interfacial Froude number dimensionless where 2 u Fr Dyer
299. uthern hemisphere with constant depth in the east west direction 50m depth at the southern coast and 100m depth at the northern coast Wind stress in the e1 direction is applied with 0 1 Nm at the southern boundary and 0 at the northern boundary hence this stress possesses negative curl The gradient of f D is positive in this case thus an anticyclonic gyre biased to the west is expected generated by topographically induced conservation of potential vorticity Theory predicts that e A negative gradient of f D i e CORIOLIS 1 0e 4 results in an eastward biased gyre e Aflat bottom BATHYMAX 50 results in an unbiased gyre e Wind stress with positive curl WIND_SPEED SCALE 1 results in a cyclonic gyre with unaltered bias 20 08 2015 Page 160 of 185 Version 1 00 13 Tracer Statistics SHOC User Manual A library named tracerstats exists in the directory ems model lib See Figure 2 1 which allows various operations to be performed on existing tracers in the model This includes sediment transport and ecological tracers if they exist The tracerstats library offers a convenient way to perform processing on the fly rather than post processing an output file The advantage of using processing while the model is running is that statistics are computed at every time step rather than at the times data is dumped in an output file Note that the tracerstats library must be present when the code is configured for the
300. v 104 1122 1140 Burchard H K Bolding and M R Villarreal 1999 GOTM a general ocean turbulence model Theory implementation and test cases Technical Report EUR 18745EN European Commission 103pp Burchard H K O Peterson and T P Rippeth 1998 Comparing the performance of the Mellor Yamada and the k e turbulence models J Geophys Res 103 10 543 10 554 Bye J A T 1977 The flow series of Thallasso models Selected topics in atmospheric and marine sciences No 6 Flinders University of South Australia 59pp Bye J A T 1977a The flow series of Thallasso models The FLOWM model supplement to the FLOWC model Selected topics in atmospheric and marine sciences No 6 Flinders University of South Australia Camerlengo A L and J J O Brien 1980 Open boundary condition in rotating fluids J Compt Physics 35 12 35 Cartwright DE and R D Ray 1990 Oceanic tides from Geosat altimetry J Geophys Res 95 C3 3069 3090 Chapman D G 1985 Numerical treatment of cross shelf open boundaries in a barotropic coastal ocean model J Phys Oceanogr 15 1060 1075 Craig P D Banner M L 1994 Modelling wave enhanced turbulence in the ocean surface layer J Geophys Res 24 2546 2559 Csanady G T 1982 Circulation in the coastal ocean D Reidel Publishing company Demirov E E Eiter M Ouberdous and N Hibma 1998 ISPRAMIX a three dimensional free surface model for coastal ocean
301. vertical velocity may be only recomputed in the water columb if the new vertical velocity does not violate the Lipschitz condition using WSTAB instead of w Note that the semi Lagrangian scheme is not compatible with multi processing hence the transport model will only operate on one window unless an alternate advection scheme is specified The order of the semi Lagrange advection scheme may be specified using ORDER_SL 0 Original tri linear formulation 1 1 order tri linear same as ORDER_SL 1 2 2 order tri quadratic 3 3 order tri cubic 20 08 2015 Page 144 of 185 Version 1 00 SHOC User Manual 4 4 order tri quartic The default is ORDER_SL 0 The higher order schemes are non monotonic and require a monotonicity constraint to be applied The higher the order the slower the scheme Speed is reduced if IO is excessive hence any variables read into the model from file should have an INPUT_DT at least as much as the timestep used e g don t input a variable at INPUT_DT 10 minute intervals or output data with tinc 10 minutes if the timestep DT 1 hour Additionally if file input or output is less than the time step then the model will effectively run using the smaller time step this may cause the semi Lagrangian scheme to become stuck in an infinite loop The transport model may be used with input fields derived from other models e g MOM Sometimes these models do not account for lea
302. xation constant set in dt ts then specify 20 08 2015 Page 34 of 185 Version 1 00 SHOC User Manual relax_salt saltprof ne dt ts 1 hour This specification is particularly useful with the automated a or r options but will only operate if the relaxation time constant is input via file The relaxation_time_constant may be time dependent by specifying a netCDF or ascii filename In this case the units for the time constant in the file must be a time unit e g Ascii relaxation file where relaxation is 48 hours at day 0 and 2 hours at day 10 Note Time is converted to the model units specified by TIMEUNIT COLUMNS 2 s COLUMN1 name Time COLUMN1 long_name Time COLUMN1 units days since 1990 01 01 00 00 00 8 COLUMN1 missing_value 999 COLUMN1 fill_value 0 0 COLUMN2 name relaxation_time_constant ZE COLUMN2 long_name Relaxation time constant COLUMN2 units hours COLUMN2 missing_value 999 COLUMN2 fill_value 0 0 s D 48 10 2 Adaptive relaxation can be invoked by specifying TRACERO relaxation_time_constant linear dv tc units dv tcz units In this case if the absolute difference between modelled tracer and that read from infile nc is dv then a relaxation constant of tc units is used and if the absolute difference is dv then a relaxation constant of tc units is used with linear interpolation for other values of
303. y exists which is responsible for the calculation of wave variables period amplitude direction orbital velocity bottom stress enhanced bottom drag and tangential radiation stresses If this library is to be invoked then the following parameters are set DO_WAVES YES Invoke the waves library WAVES_DT 1 hour Time interval which waves are invoked The wave variables are computed according to the amount of information supplied in the WAVE_VARS file If WAVE_VARS YES or the WAVE_VARS file doesn t contain any of the wave variables then the waves are assumed to be wind waves and are estimated using Eqns 10 9 10 11 and 10 14 in the Science Manual Wave direction is assumed to be the same as the wind direction Alternatively Eqns 10 12 and 10 13 may be used to estimate wave amplitude and period This choice is controlled by the flag WIND_WAVE TOBA Use eqns 10 9 and 10 11 USAC Use eqns 10 12 and 10 13 The fetch is required when estimating wind waves using these methods This is automatically created by SHOC when using DO_WAVES The fetch at the limits of the model domain open boundaries may be specified via spatially variable netCDF of spatially constant ts file input FETCH fetch_OBC nc Boundary values for fetch If the wave period only is supplied in the WAVE_VARs file then wind wave amplitudes are estimated using the simpler formulation of Eqn 10 8 Science Manual which doe
304. y specifying a time series file lt flowfile ts gt or can be set to a constant value by specifying the constant flow_value The flow rate should always be positive regardless of the orientation of the open boundary Similarly a river flow for a u2 boundary is specified via BOUNDARYO BCOND_NOR CUSTOM BOUNDARYO CUSTOM u2 u2flowbdry BOUNDARYO U2_HC 5 0 BOUNDARYO U2_FLOW lt flowfile ts gt or flow_value A simplified specification for rivers is input as follows BOUNDARYO NAME Riverl BOUNDARYO TYPE ul BOUNDARYO BCONDO RIVER flowfile ts data_l ts data_2 ts data_n ts where data_ lt n gt ts file containing temperature at the cell centre Other tracer data is also required if the tracer OBC is active There must be at least one of these files listed flowfile ts file containing river flow In this case the depth over which the flow profile is distributed is the mean depth of the boundary and salinity is input with a value of zero If this is used a diagnostic tracer flow is generated which records the flow used in that river The halocline depth generally has to be set a priori and is typically used as a tuneable parameter This may not be desirable if many rivers exist A dynamic pycnocline depth may be dynamically prescribed using BOUNDARYO bcond_salt TRCONC CUSTOM BOUNDARYO CUSTOM salt 0 0 BOUNDARYO OPTIONS DYNAMIC_HC NO_HDIFF This can be further enhanced by computing the baroclinic landward flow in the salt w
305. yA Voy E ee AyAzu Ae At dr Ax At steady state dc dt 0 thus steady state concentration Cg is 20 08 2015 Page 87 of 185 Version 1 00 SHOC User Manual F c AyAzu DA Aur H or F in C e AyAzu AyAzA Ax For uniform grid size Ax Ay this reduces to F in c m Az Ayu Ap Therefore as the horizontal grid size decreases then the steady state concentration will increase to a limit where horizontal diffusive process dominate 4 24 2D Mode SHOC can be operated in the capacity of a 2D depth integrated model This is achieved by setting 2D MODE YES The default is 2D MODE NO The 3D currents are not calculated in this case resulting in large increases in execution time The initial tracer distribution is vertically averaged and tracers are subsequently advected using the 2D current i e the water column is assumed to be well mixed 4 25 Sigma vertical coordinates SHOC can be configured to use sigma coordinates in the vertical The formulation follows that of Blumberg and Herring 1987 for curvilinear coordinates Sigma coordinates are invoked by setting the flag SIGMA YES The default value is SIGMA NO In the sigma case the value of LAYERFACES is equal to the number of sigma levels the model uses and the distribution of these layers is generated by SHOC such that a logarithmic distribution exists at the surface and bottom and a linear distri

Sparse Hydrodynamic Ocean Code V5199 User Manual

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