DEPOMOD

User manual
 ÍNDICE
What's new in DEPOMOD version 2?

1. The DEPOMOD modelling suite (summary, list of authors/steering group members,

acknowledgements and flow diagram)

2. Getting started and data specification for DEPOMOD

3. General features of the DEPOMOD modelling suite

4. Grid generation

5. Particle tracking

6. Resuspension (Including features total deposition, flux and carbon degradation)

7. Benthic module

A. GaBoM (Growth and Biomass Model)

New features in DEPOMOD version 2

The following new features have been developed in DEPOMOD:

1. Development of a second in-feed sea lice treatment chemical module which has
modelling capability for the slow release of a compound from fish over an extended
period of time

2. The release characterisitics of the compound may be modelled in one of two ways:

Either: Use of a dialog which allows the user to specify the percentage of compound
excreted from the fish for different time periods - details

Or: Use of a more powerful time series technique, where the release of compound
associated with food and faecal particles is specified every time step; feed input can also be
specified for every time step - details. A spreadsheet has been supplied to assist the user in
setting up the time series file required for modelling the compound release in this way

3. Adaption of the Westrich and Berner G-model so that the module can be used to
model degradation of the compound of the material excreted from the fish at any
time - details

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The development of this module has been undertaken to improve modelling techniques for
this specific set of characterisitcs. Modelling this compound with DEPOMOD version 1.5
requiring multiple runs and overlaying of grids was a cumbersome method. The
development of version 2 greatly improved the modelling of this compound type in terms
of accuracy and speed. In particular, capability for modelling release of the compound with
a time series file provides a high degree of flexibility, important for modelling of future
chemicals which may have varying release characteristics.

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1. The DEPOMOD modelling suite

This page contains a summary of the DEPOMOD, a list of authors/steering group members,
acknowledgements and the DEPOMOD flow diagram. Further details of the project
research and the model are given in Objectives and summary of DEPOMOD research
programme and modelling suite.

Executive summary

Increasingly regulators find themselves seeking better predictive capability for large fish
farms and improved objectivity in the decision making process. This decision frequently
adopts the precautionary approach implicit in environmental protection. Similarly, fish
farmers need methods for assessing the suitability of new sites, or the potential for
expansion at existing sites, so as to concentrate their efforts on sites which are likely to
have good husbandry characteristics and minimise the costs of future monitoring of impact
on the sea bed. The aim of this project was to provide an agreed tool which can be used by
the regulator and the industry to determine the optimum carrying capacity of a site or
proposed site.

This project takes as a starting point the model BenOss (Biological Effects and Organic
Solids Sedimentation) developed at CCMS Dunstaffnage Marine Laboratory. This was a
commission from SEPA, UK Water Industry Research Ltd. and the Environment Agency
for predicting benthic community response to varying the treatment level from long sea
sewage outfalls (Cromey, C.J., Black, K.D., Edwards, A. and Jack, I.A. 1998, Estuar.
Coast. Shelf Sci., 47, 295-308.). DEPOMOD uses similar particle tracking techniques using
models well established in scientific literature and improves on existing fish farm models
by including validated resuspension and benthic components.

DEPOMOD predicts the solids deposition on the sea bed arising from fish farms and
associated changes in the benthic community. The model has a structure made up of the
following components: grid generation, particle tracking, resuspension and benthic
response modules. The grid generation module allows the user to set up a grid containing
information on depth, cage and sampling station positions for the area of interest. Given
information on wastage rates of fish food and faeces and hydrodynamics of the area, the
initial deposition of particles on the sea bed can then be predicted with the particle tracking
module. The resuspension module then redistributes particles according to near–bed current
flow fields to predict the net solids accumulated on the sea bed within the grid area. From
quantitative relationships between benthic community descriptors and solids accumulation,
predictions of the level of benthic community impact can be undertaken, given sufficient
information on the fish farm. A sub–model GaBoM (Growth and Biomass Model) is also
available for predicting feed input throughout a growing cycle. DEPOMOD runs on a pc-
based Windows 95TM platform or later.

The project examined two sites in a detailed manner, taking hydrographic, sediment and
benthic fauna measurements. The two sites selected differed in terms of hydrodynamics,
with one site representing a dispersive site and the other representing a depositional site.
Although environmental variables (e.g. sediment type, fauna) reflected the differing

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hydrodynamics of the two sites, husbandry practices were similar between each farm
thereby assisting site comparison. Laboratory measurements were made of settling
velocities of a range of food and faecal pellets.

Validation of DEPOMOD consisted of three stages:

i. Validation of the particle tracking stage with sediment traps. To validate near–field, sea
surface to sea bed particle tracking algorithms, a 24 hour sediment trap study was
undertaken at the two sites. For the dispersive site, model predictions of flux (g m-2 d-1)
generally agreed well with field data and an accuracy of ±20% was achieved. At the
depositional site, an improved accuracy of ±13% was achieved. An extensive sensitivity
test of the model input data used was undertaken and found the most sensitive parameter in
the model to be particle starting position in the pen, which was subsequently defined in the
model as random. Some sensitivity of horizontal dispersion coefficients and current speeds
was also found.

ii. Validation of the resuspension model via a tracer study. To validate the DEPOMOD
resuspension model, a UV fluorescent particle tracer was selected with similar settling
characteristics to salmonid faeces and food. Tracer was introduced to the seabed (water
depth ~30 m) and sediment samples taken on days 0, 3, 10, 17 and 30 to measure the
horizontal and vertical distribution of tracer in sediments. The bulk of the deployed tracer
initially deposited in an area 25 m radius from the release point and was observed to
steadily decrease to zero over a period of 30 days. Redeposition of tracer in the study area
was minimal where low concentrations were measured at a distance of up to 200 m from
the release point in the direction of the residual current. The validated model generally gave
good predictions of total mass budgets (±7% of total tracer released) particularly where
tracer concentrations were high near the release point.

iii. Validation of the benthic module. Semi–empirical quantitative relationships between

predicted solids accumulation (g m-2 yr-1) and observed Infaunal Trophic Index (ITI) and
total abundance have been established using data from several fish farm sites. Envelopes of
Acceptable Precision (EAP) have also been established. These allow predictions of indices
to be obtained where the width of the EAP reflects natural variability of the benthic data
measured for duplicate samples. Data are also given for Shannon Weiner, Evenness and
number of species but no predictive relationships have been established due to the
variability with these indices in the sea loch environments studied.

Sensitivity analyses were undertaken on the main model variables and model parameters
and assessed for sensitivity on predictions of solids accumulation and ITI. The most
sensitive variables in the model were current speed, horizontal dispersion coefficients used
in the random walk model and grid cell resolution. These results demonstrated the need for
accurate and reliable current measurements in order to obtain realistic predictions from the
model. The sensitivity of the model to horizontal dispersion coefficients also demonstrates
the importance of these measurements, which are severely lacking for sea loch
environments.

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A number of fieldwork and modelling protocols were also developed which should be
taken into consideration when using DEPOMOD. The most important protocols are: sample
size of sea bed for measuring benthos for use in DEPOMOD (0.1 m2) and the limitations of
using a different sample size; sampling station location and position fixing including siting
of reference stations; current meter use and length of deployment and unsuitability of
application of the DEPOMOD benthic module (e.g. sites with steeply sloping bathymetry,
sites with coarse, hard sediments susceptible to wind–wave resuspension).

DEPOMOD may be used for assessing the potential impact of a farm throughout a growing
cycle or if biomass consent is increased. It may also be used for the site selection process
for a new farm by examining proposed positions and biomass levels. Prediction of the
dispersion of particulates during use of in–feed medicines may also be undertaken.
DEPOMOD should be used to complement, rather than replace current methods for
assessing fish farms.

The DEPOMOD project entitled ‘Economic Site Assessment Through Modelling The
Effects Of Carbon Deposition To The Benthos From Large Scale Salmon Mariculture’ was
funded by NERC MAFF LINK Aquaculture programme, Marine Harvest McConnell,
Scottish Environmental Protection Agency and Scottish Salmon Growers Association (now
Scottish Quality Salmon). Research was undertaken by CCMS Dunstaffnage Marine
Laboratory and Scottish Environment Advisory Services Limited.

List of authors

Chris J Cromey - CCMS Dunstaffnage Marine Laboratory ([email protected])

Thom D Nickell - CCMS Dunstaffnage Marine Laboratory
Kenny D Black - CCMS Dunstaffnage Marine Laboratory

List of steering group members

Andrew Grant, Douglas Runcieman - Marine Harvest McConnell

Ann Henderson, Anton Edwards - Scottish Environment Protection Agency
Julian Hunter (replaced by Jeremy Spurway) - Scottish Environment Protection Agency
Tom Pearson, John Blackstock, Amanda Coates - Scottish Environmental Advisory
Services
Gordon Rae - Scottish Salmon Growers Association (now Scottish Quality Salmon)

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Acknowledgements

The authors and Scottish Environment Advisory Services would also like to thank the
funding bodies, NERC LINK Aquaculture programme and co–ordinator Mark James,
Marine Harvest McConnell, Scottish Salmon Growers Association and Scottish
Environment Protection Agency for making this project possible. The publication of this
document was funded by the Highlands and Islands Enterprise.

Both Alan Hills and Jeremy Spurway of SEPA have contributed significantly to modelling
discussions, and the authors thank them for their patience and assistance during model
testing. For the tracer study, Paul Provost of DML is thanked for his insight and help with
the survey and the MV Seol Mara crew for their effort during the survey work. The authors
would also like to acknowledge the assistance of the MHM fish farm managers George
Nicholson and Alec Harvie for their time and effort during site surveys. Also, Kirsty
McCallum of Ardvar Salmon Ltd. for her efficiency in providing data and Nutreco Ltd. for
data contributions.

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8
The intellectual property rights of this software are owned by SEPA.

March 2000

2. Getting started and data specification for DEPOMOD

Data specification

The following data are required to set up DEPOMOD for a site. Data specifications are
given for both steady state and in-feed treatment medicines. Default data are denoted by an
asterix * and these data have been obtained either via measurements in the DEPOMOD
project or from literature values. For data marked +, recommended values are available.

When undertaking modelling studies with DEPOMOD, the authors would like to
bring to the attention of the user the importance of the protocols and sensitivity
analyses detailed in the research report. Users should ensure the model is being
applied appropriately and be aware of its limitations.

As with all models, predictions for each individual case must be critically evaluated to
assess confidence and verified with ground truthing where possible.

DEPOMOD gives model results as numerical output. No time was allocated to generating
graphical output of results as there are a wealth of software packages which already
undertake this. In particular, use of a software package which can read in x,y,z data and
contour these data to obtain contour plots is highly recommended.

Example files are given in the SITE directory for each module. The user should always
create a new sub-directory for each new site being investigated and name the sub-directory
after the site to avoid confusion. The user may use the example files in the SITE directory
as templates, but should always save the Input data configuration file with a different
name. This will preserve the example files supplied with the software and allow
continuous reference with the user manual.

Grid generation

General

1. bathymetry of the area of interest either from a site survey or from an Admiralty
chart of the area
2. number and dimensions (length, width and depth) of pens
3. position of the cage groups
4. position of sampling stations in relation to the cage groups

Particle tracking

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General

5. current velocity data for an area close to the fish farm sitea
6. some knowledge of the vertical structure of the water column; shear in the water
column can be represented in DEPOMOD by setting up different layers in the
model which can be represented by different current velocity dataa
7. horizontal and vertical dispersion coefficients for the area+

Modelling of steady state solids accumulation with DEPOMOD (g m-2 yr-1)

8. Feed input data and mean fish size (kg food d-1 for the whole farm or on a pen by
pen basis) for modelling scenariob
9. information on water content and digestibility of the food to be used at the stage of
the growing cycle for modelling scenario*
10. food and faecal settling velocity data*

The following data would be useful for assessment of site characteristics and interpretation
of model results:

11. benthic macroinvertebrates present at the site and the value of some benthic indices
(e.g. Species, Total abundance, Biomass, Infaunal Trophic Index, Shannon Weiner)
for sampling stations at the site
12. sediment type and characteristics for the site

Modelling of total deposition of in-feed sea lice treatment medicines with DEPOMOD (g
Active Ingredient m-2)

13. Total amounts of medicated feed added and over what time period on a pen by pen
basis (e.g. g Medicated feed pen-1 administered over x days)
14. Concentration of active ingredient on medicated feed (g Active ingredient kg-1
medicated feed)
15. Excretion of compound by the fish over the period modelled
16. Current velocity data for at least the length of the trial (minimum 1 spring-neap
cycle) or current velocity data which can be used to represent the time of releasea

Notes
a
depths of the instruments, mooring position, sampling frequency, time (GMT/BST) and
direction information (true or magnetic) are required for every data set used
b
Typical scenarios: Predicted benthic effects for maximum feed input for a proposed
situation; predicted benthic effects for the time period during benthic sampling

Resuspension

General

No additional data are required

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If the G-model switched on

17. Fractions of high, less and non-degradable fractions

18. Rate constants in yr-1 for high and less degradable fractions

If the wind-wave model is switched on

19. Wind speed and direction data with the same time step as the current data e.g.
hourly
20. Information on wind fetch at the position of the cages for different points of the
compass

If the primary production model is switched on

21. Estimation of sedimentation of solids from primary production for each month of
the year

When modelling in-feed treatments, if sediment concentration is required then the following
are required

22. Sediment bulk density and maximum depth in the sediment the deposited material is
mixed

Benthic

General

No additional data are required to run the model, although observed benthic fauna
observations at sampling stations are useful for comparison with model predictions.

GaBoM - Growth and Biomass Model

General

The following data are required to run GaBoM. Default values are available for all of these
data.

23. Initial fish numbers, weight and FCR

24. Fish growth and mortality functions
25. Farm starting date, consent biomass and length of operational period for farm
26. Harvesting method as a fixed tonnage or a percentage of consent biomass

3.1 Directory structure

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The directory structure of the model is shown below. Depomodv2 is the parent directory,
sub-directories Benthic, GaBoM, Gridgen, Partrack and Resus contain executable
models. Site directories contain example files and the Help directory contains the user
manual. NewSite directories should be renamed opt the same name as the site under
investigation. A new sub-directory should always be created under Benthic, Currents,
GaBoM, Gridgen, Partrack and Resus for each new site investigated.

Directory File
Depomodv2 DEPOMODv22.exe
Benthic Feed8.exe
GaBoM GaBoM8.exe
Gridgen Gridgen8.exe
Partrack Part8.exe
Resus Resus8.exe

These sub-directories contain example files for use in the model. If

the model is not installed in directory C:\depomodv2 then the example
Site
files will need some modification. See Using example files supplied
with the model below.

These sub-directories should be renamed to the same name as the site

New Site under investigation. New sub-directories should be created each time
a new site is investigated

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Help Help2_11.chm

Using Example files supplied with the model

Example files are supplied with the model in the Site directories. When loaded into the
model, these give an indication of how the model can be set up. The directories specified in
the example files are assuming that the model has been set up in the default directory
C:\Depomodv2. If this is not the case then the input data configuration files need to be
modified if example files are to be used. Undertake the following steps:

1. In the GaBoM\Site directory, open up the .cfg file in a simple text editor (e.g. Notepad).

2. Where directories are specified for locations of files, these will read
"C:\Depomodv2\GaBoM\nameoffileetc". Change the "C:\Depomodv2" text to the name of
the directory where you installed your software so that it looks like (for example)
"D:\MySoftware\Depomodv2\GaBoM\nameoffileetc". Change all the directories in this
file.

3. Close the file saving as simple text.

4. Repeat for any other .cfg or .cfh files in the GaBoM directory.

5. Repeat steps 1 to 4 for .cfg and .cfh files in the Site sub-directory of Gridgen, Partrack
and Resus directories.

6. In the Benthic directory (not Site sub-directory), undertake steps 1 to 3 for the file
"inv13.cfg".

6. Check the correct working directory is specified in the file c:\depomodv2.sys.

Example files should now load without any error messages.

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3.2 DEPOMOD file viewer

DEPOMOD has a file viewer which can be accessed at any time by either selecting the
View button in a group box as shown in the example group below or by right clicking with
the mouse.

On clicking the view button, the viewer shown below displays the file specified in the edit
box. If no file is specified or the file name is invalid, an error message is displayed.

The viewer can be used to view or print any text files using the File or Print commands. No
editing can be undertaken within the viewer. Layout of the viewer can be adjusted with the
Font command.

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3.3 Open/Save File dialogs

The DEPOMOD suite displays standard Windows 95TM file dialog for opening and saving
files. Each dialog displays directory structure, file filters relevant to the particular module
being run plus an All files (*.*) filter. The initial directory of the dialog is set to the
particular working directory of the module being run. For an open dialog, the file name
entered and directory structure must be valid. For save dialogs, the user will be prompted if
an attempt is made to overwrite an existing file. Example dialogs are shown below.

A Save dialog in the grid generation module.

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3.4 Mouse right click features

Clicking the right mouse button in DEPOMOD gives the user access to a number of options
relating to the module being used. Examples of right click mouse features are given below.

Grid generation module Particle tracking module

GaBoM - Growth and Biomass Model Resuspension module

Benthic module

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3.5 List of input/output files for each module

Note on file formats

A mixture of ASCII space delimited and comma delimited formats are used as input and
output data file formats. The following checks should be made when exporting files from
spreadsheets which are to be used as input data files for the model:

Space delimited formats - Check the columns are wide enough before exporting so that the
spreadsheet does not merge columns and always format the data to maintain the appropriate
number of decimal places. Also check that space (and not tab delimited files) are being
exported. If a space delimited file requires an end of file marker (#) this will be specified in
the appropriate section of the user manual. Occasionally, the user will need to change the
file extension to one that DEPOMOD recognises after exporting from the spreadsheet.

Comma delimited formats - Check that the spreadsheet has not exported any empty rows or
junk at the end of the file. Delete any unwanted commas at the end of the file so that the
cursor cannot move beyond the final row.

Once a file has been exported from a spreadsheet for use in the model, these checks are best
undertaken in a simple text editor such as Notepad or Wordpad.

Grid generation module

Input Output
Input data configuration Minor grid depth array containing bathymetrya, cage and
file (*.CFG) sampling station positions (.DAT)
Major grid containing
Grid generation information file (.ING)
bathymetry (.DAT)b
ASCII contour x, y, z files for major and minor grids containing
depths at the centre of each grid cell, cage and sampling station
positions (.SUR)

Notes
a
Grid with dimensions defined by the user nested within major grid
b
Grid entered by the user containing maximum area of interest for the site

Particle tracking module

Input Output
Particle tracking information file
Input data configuration file (*.CFG)
(*.INP)
Additional input data configuration files Particle tracking structured file

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(*.CFH;*.CFP) (*.FIL)a

Notes
a
The size of the structured particle tracking file (.FIL) can be quite large so delete or
overwrite any unwanted runs along with their associated information files (.INP).

Resuspension module

Input Output
x, y, z text results file for contouring
Input data configuration file (*.CFG)
(*G0.SUR)
Additional input data configuration files
Resuspension information file (*.INR)
(*.CFH)
Results file (*.OUT)

Optional - for more click here

Results files (*.ENT;*.CSV;*.PRN)
Results files for plug releases (*.PLU;*.PUT)

Benthic module

Input Output
None ITI results file (*.ITI)
Abundance results file (*.AB)
Benthic module information file (*.INB)
Statistics file (*.STS)
x,y,z text results file for contouring (*.CSV)

GaBoM - Growth and Biomass Model

Input Output
Input data configuration file (*.CFG) Results file (*.OUT)

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Grid Generation
4. Main contents page

4.1 Objectives/general description/using this A DEPOMOD minor grid generated in

module Surfer for WindowsTM showing charted
depth, cage positions (shown as squares)
4.2 Setting up procedure and 0m, 25m, 50m and 100m benthic
sampling stations (underlined).
4.3 Creating a major grid for the site

4.4 Main menu

4.5 Main input dialog

Major/minor grid specification

Major grid dimensions

4.5.1 Major grid editor

Minor grid dimensions

Contouring options

Cage position data

4.5.2 Cage
position data
dialog

Sampling station position data

4.5.3 Sampling
station data
dialog

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4.1 Objectives of the grid generation module

The objectives of this module are:

• to create a major grid with bathymetry, cages, sampling stations and additional
information on it
• to create a major grid depth array and input data files
• to generate a minor grid which is used in subsequent modules

Once the major grid is set up a minor grid can be generated in different areas if required.

General description of the grid generation module

This module requires the user to define a major grid with relevant information on it, create
a major grid depth array and create an input data file containing major and minor grid data.
The executable file GRIDGEN8.EXE is located in the GRIDGEN directory and an example
input data configuration file is located in the GRIDGEN \ SITE directory.

The module uses an input data configuration file (*.CFG) which should be located in a
SITE directory of the GRIDGEN directory.

The module creates a module output file (.DAT) used by subsequent modules which
contains minor grid dimensions and depths, cage and sampling station positions on the
minor grid. A module information file (.ING) is also created and is used by subsequent
modules. Module results files (.SUR) are also created and can be used for contouring major
and minor depth arrays. All of these module output files should be located in the SITE
directory of the GRIDGEN directory.

Using the module

Input data files and results files should be stored in a SITE directory. Subsequent modules
should be configured to find module output and information files in this directory. It is
simple to extend the major grid if a wider coverage of the area is required.

This module should take less than a minute to complete its tasks.

4.2 Module setting up procedure

The following steps are required to set up the module:

1. Examine the data specification for this module to check all relevant data are
available.
2. Collate the data required for a major grid for the site, this includes information on
depth, cage and sampling station positions.

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 3. Run the grid generation module GRIDGEN8.EXE to display the main menu dialog
and create a new input data dialog.
4. Enter the required data in the main input data dialog. An example input data file
named input.cfg located in the GRIDGEN\SITE directory can be loaded into the
module.
5. Check that all relevant files have been created using post run features, exit the grid
generation module and go on to the particle tracking stage.

4.3 Creating a major grid for the site

It is useful to create a major grid in the area of interest surrounding the fish farm and
determine depths and positions on the grid first before proceeding to enter data in the input
data dialog. The following data are required for a major grid:

• major grid dimensions (grid cell sizes and number of cells along each axis)
• bathymetry of the maximum area of interest including any land points
• all pen positions or the positions of end pens in a line or group
• sampling station positions

This is a map of cage positions (squares) and sampling stations on a major grid. This is the
example site layout and DEPOMOD grid generation module has been used to specify grid
size and grid cell resolution, cage and sampling station positions. The plot shown below for
display purposes has been generated in a contour package using the *.SUR output file from
the module.

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DEPOMOD input data for this major grid are:

• 11 columns (i) by 10 rows (j) (100m grid cell resolution) making a total size of 1100
by 1000m
• 30 cages and 7 sampling stations

These data are given in the example input configuration file (input.cfg) in the GRIDGEN \
SITE directory and can be accessed via the Grid generation main menu.

In the example file input.cfg and in the screen dumps of the main input dialog, the minor
grid is almost the same total size as the major grid but has finer grid resolution. This is
because the widest possible area on the major grid is required.

The grid generation module may also be used to zoom in on a particular area in the major
grid with a minor grid and only integrate that area into the model. The example below
shows the result of zooming in on the major grid. Input data for these are given in the input
configuration file inputzoom.cfg.

This is a map of a minor grid which has been

used to zoom in on an area in the major grid.
The minor grid has been overlaid by
DEPOMOD with its origin at major grid cell
(column 6, row 2).ie. at position (600,200).
Minor grid details can be specified in the
Minor grid dimensions group in the main
input dialog:

Minor grid details:

Number of grid cells: 16 by 16

Cell resolution: 25m by 25m

Minor grid origin on major grid i=6, j=2

The plot shown for display purposes has been

generated in a contour package using the
*.sur output file from the module.

Note the grid orientation which is true north up. The coordinate system is in metres in the
user interface but is converted into special grid coordinates by the model. This grid
coordinate system is in use throughout all modules and particle positions are tracked in
these special grid coordinates to save time in processing.

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Special Note

It is useful to make the major grid cover a large area with large cell sizes (e.g. cell size 50
or 100 metres) although local bathymetry will need to be taken into account. This
minimises the effort required by the user in estimating the depths in the grid area.

The method for creating a major grid is as follows:

1. Draw a grid of a suitable size and shape on a chart surrounding the cages. The grid
must be orientated with the vertical axis on a north-south axis and the horizontal
axis on an east-west axis. The number of grid cells, grid dimensions and shape of
the grid should be decided by the user (see major grid). This will be dependent on
the expected sphere of influence from the fish farm. The major grid can be extended
if it is found that a wider coverage is required. It is useful to have quite large grid
cell dimensions (e.g. 50m or 100m) so that the depth array can be kept to a
minimum.
2. Estimate the depth (metres below chart datum) at the centre of each grid cell. A
depth of -10.0 metres represents a land point and a drying area is also given as a
negative number. e.g. for the lowest astronomical tide (chart datum): 5.0 metres is a
cell which is 5 metres deep, -2.0 metres is a cell which has a drying height of 2.0
metres and -10.0 metres is a land point.
3. Determine positions of all pens on the grid or the positions of pens in the end of a
line

4.4 Grid generation main menu

From the Grid generation main menu:

• To create a new input data configuration file, select the New Input data
configuration file command from the File command
• To open an existing input data configuration file, select the Open Input data
configuration file command from the File command
• To exit the grid generation main menu, select the Exit command from the File
command

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24
4.5 Dialog overview

This is the main grid generation input dialog:

Major/minor grid specification

Enter the name of the major grid file using the Load button created in section 2.5. To use
the Major grid array editor, a new depth array can be created by clicking on the New depth
array button and a loaded depth array can be modified by clicking on the Edit depth array
button.

Enter the name of the minor grid file to create using the Save As button. This file should be
located in the GRIDGEN\SITE directory.

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Major grid dimensions

In the Major grid dimensions group, the number of i grid cells (columns) and j grid cells
(rows) for the major grid are shown. These variables can only be changed via the Major
grid array editor. Enter the length of i grid cells and length of j grid cells in metres for the
major grid.

Minor grid dimensions

In the Minor grid dimensions group, enter the number of i grid cells (columns) and j grid
cells (rows) for the minor grid to be generated. Enter the Length of i grid cells and Length
of j grid cells in metres and specify the position on the major grid cell for the minor grid
origin. The minor grid origin is generated at the bottom left hand corner of the specified
major grid cell.

Contouring options

In the Contouring options group, check the Output x y z files for contouring box if x, y, z
files are required for contouring minor and major grid depth arrays. If x, y, z files in ASCII
comma delimited format are required then check the Use comma separated output box. If
the positions of stations and nodes are required in the x, y, z file in addition to depths then

26
check the Write positions of stations and nodes to file box. A value of a symbol which the
contouring package will generate for the cages can be specified with the Number
representing cage symbol box. For example, a value of 5 causes the contour package Surfer
for Windows TM to generate a square at cage positions.

Cage position data

To change the cage data click on the Change button to display the Cage position data
dialog.

Sampling station position data

To change the sampling station data click on the Change button to display the Sampling
station data dialog.

27
Running the model

Click on the Run model button. The model then checks the input data and will display any
errors found with the data. On completion of error checking, a message dialog will be
displayed:

One of the following responses is required:

• Yes - The input data will overwrite existing data contained in the stored input data
configuration file (.CFG). If the input data configuration file is untitled, a Save
dialog will be displayed where the user can enter a name for the input data file. The
file should be saved in the directory GRIDGEN \ SITE with a .CFG extension.

• No - A Save dialog will be displayed so the user can save the input data file with a
new name. The file should be saved in the directory GRIDGEN \ SITE with a .CFG
extension.

• Cancel - The user will be returned to the Input data configuration file dialog and the
model run will not be executed.

On providing a response of Yes or No, the model will execute and then return to the input
data dialog. To halt model execution, click on the Cancel button next to the progress bar.

Post run features

By right clicking the mouse a number of Mouse right click features can be viewed. A list of
files created by this module are given in the page List of input/output files.

Exiting the dialog

Click on the Exit button. A message dialog will be displayed Save changes to input data
configuration file? One of the responses from the previous step Running the model is
required. On providing a response of Yes or No, control will be returned to the Grid
generati

28
Particle tracking
5. Main contents page

5.1 Objectives/general Current profiles in stratified waters are complex : Particles

description/using this settling through the layers are subject to differential settling,
module turbulence and the shear of the current, leading to spatial
sorting of particles of different settling rates.
Important decisions - which
scenario?

5.2 Setting up procedure

5.3 Preparing current

velocity data for use

5.4 Main menu

5.5 Main input dialog

Dialog overview

Minor grid file specification

Fish farm characteristics Particle tracking model validation : Observed and modelled
sediment trap deposition for traps deployed near the cages
5.5.1 Waste allocation data over a 24 hours period. The upper graph shows data for the
project dispersive site, the lower graph for the depositional
5.5.2 Cage set up site. Note the difference in the deposition scales.

Implementing current
velocity data

5.5.3 Velocity data dialog

Particle trajectory model

Turbulence model

Mean Tidal Height

Output file containing

29
particle information

Running the model

Post run features

Exiting the dialog

A sensitivity analysis for this study showed that the model

results were sensitive to the following variables (in order of
priority):

Particle starting position in cage > horizontal dispersion

coefficient increase > inaccurate current meter readings > use
of 1 settling velocity only.

Particle starting positions in DEPOMOD are therefore random

within the cage volume. Overall model sensitivity analyses
detailed in the report also highlighted the need for accurate
current meter measurements.

Users should always undertake sensitivity analyses for the site

under investigation if the user does not have complete
confidence in the input data available for the investigation.

30
5.1 Objectives of the particle tracking module

The objectives of this module are to:

• read in a minor grid generated from the grid generation module

• simulate differential settling and advection of particles and turbulence via a random
walk model
• deposit particles on the sea bed and pass information on particle distributions to the
next module

General description of the particle tracking module

This module requires the user to create a velocity data file(s) and an input data
configuration file containing fish farm waste allocation data.

The PARTRACK directory contains the executable file PART8.EXE and an example input
data configuration file is located in the PARTRACK \ SITE directory.

The module reads in an input data configuration file which should be created in a SITE
directory. The module also reads in general data files containing minor grid data and
current velocity data.

The module creates a module output file which is a structured file (.FIL) and contains data
on particle distributions on the bed. It also produces an information file associated with this
structured file (.INP). Both of these files should be created in a SITE directory and are used
by the resuspension and carbon degradation module.

Using the module

Both the input and output data files are site-specific and should be stored in a SITE
directory. Additional SITE directories can be created if necessary.

The greater the number of particles used in the model run, the better the representation of
the dispersion. The number of particles should be increased until a suitable value is where a
further increase in particle numbers will not result in any change in overall particle
distribution.

The run time for this module will depend entirely on the number of particles being used and
the computer numeric processor. It may take from 5 minutes to 24 hours to run. If the
module takes an excessive time to run try one or more of the following:

• decrease the number of particles in the simulation

• generate another minor grid decreasing the minor grid size
• generate another minor grid increasing the minor grid cell dimensions
• use hourly averages for velocity data if not already in use
• change the setting of Particle Trajectory Evaluation to the default if not already set

31
5.1.1 Important decisions - which scenario?

It is important to decide on the scenario intended for each site investigation. These
scenarios generally fall into two categories:

1. Continuous release of solids from the farm - this is the most common type of
scenario tested where solids discharges are made from a farm as a continuous
process. This is typically used to simulate the deposition and benthic effects ariging
from an operational or proposed farm. It may be used to forecast effects for a new
farm or an existing one or used to test increases in biomass or site relocations. Often
mean and maximum feed input values for the growing cycle are used in two
different scenarios for new sites (see data specification for this type of release). For
existing sites where benthic surveys have been undertaken, it is important to use
feed input for the month when benthic sampling was undertaken. It is generally not
necessary to implement this type of release as a time series.

2. Plug release of a chemical associated with the solids - this type of release is
generally used to model the release of sea lice treatment chemicals. These are
known as plug releases as the release generally has a finite time between a week to
several months. There are differerent types of sea lice tratment chemical behaviour
which can be modelled and it is important to select the correct one:

Type I - This chemical is released over a short time period specifed by the user (generally 7
days during the application of medicated feed). The chemical is excreted in large qunatities
very quickly by the fish, with the majority of the compound being released during the
application period (e.g. 7 days)

Type II - This chemical is released over a much longer period of time, with the amount of
excreted material decreasing with time. The total period over which the chemical is
excreted may be several months, where only a small amount of chemical is excreted during
the application period (e.g. 7 days)

As type II chemicals are modelled over a long period of time, it is necessary to model the
release as a time series due to the release rate changing over time. This may be undertaken
by using a dialog which specifies the percentage of chemical excreted for different time
periods (type IID release). Alternatively, the time series file method may be used which is
more complex as the chemical adhered to food and faecal particles are specified for each
time step (type IIF release). Feed input must also be specified each time step and this is an
advantage over type IID release as this assumes feed input (non-medicated) throughout the
release period is equal to medicated feed input (in terms of mass time-1). Type IIF releases
require pre-worked files to run and an example spreadsheet (Excel 95 format:
setuptsfile.xls) is included to assist the user in setting up time series files.

The information required for these types of release are specified in the data specification.
Although all this information is required for all types of release, it is implemented in

32
different ways. For example, for a type I and type IID release, all of these data are entered
directly into DEPOMOD. For type IIF releases, this information is entered into the example
spreadsheet and then the resulting time series file is implemented into DEPOMOD.

Less commonly, DEPOMOD is used for the following scenarios:

• plug release of solids without any associated chemicals

• continuous and plug releases of solids where results are given in terms of carbon
• degradation of carbon over time
• simulation of farm characteristics (biomass, feed input, etc.) over a growing cycle
with the sub-module GaBoM

5.2 Module setting up procedure

The following steps are required to set up the module:

1. Examine the data specification for this module to check all relevant data are
available.
2. Prepare the current velocity data files for the site.
3. Run the particle tracking module PART8.EXE to display the main menu dialog and
create a new input data dialog.
4. Enter the required data in the main input data dialog. An example input data file
named input.cfg located in the PARTRACK\SITE directory can be loaded into the
module.
5. Check that all relevant files have been created using post run features, exit the
particle tracking module and go on to the resuspension stage.

5.3 Preparing current velocity data for use

Example files:

CURRENTS \ SITE \ hrtop.DAT - velocity components/speed and direction data file

CURRENTS \ SITE \ hrmid.DAT - velocity components/speed and direction data file
CURRENTS \ SITE \ hrbot.DAT - velocity components/speed and direction data file

DEPOMOD offers the user some flexibility on the format of current velocity data files. The
user can use either velocity components or speed and direction data where the column
containing each must be specified as described in Implementing current velocity data. Any
other columns (e.g. time, date, yr, depth) are ignored. Invariably, some manipulation of the
data generated from instrument software will be required to obtain the standard format
required by this module. The model calculates particle trajectories using components so
speed and direction data are converted.

33
Each current velocity data file must obey the following rules:

• data must be ASCII space delimited and have a hard return at the end of each line to
allow the model to read the correct columns
• the file must have three header lines
• data must be cm s-1
• the file must have an end of file marker (denoted as #) to allow DEPOMOD to
determine the size of the file

The headings shown in the sample of a data file shown below as viewed in the DEPOMOD
viewer are time and date of measurement, easting (cm s-1), northing (cm s-1), speed (cm s-1)
and direction (degrees magnetic). The model only requires velocity data and ignores any
other data in additional columns including timing information. The format of the velocity
data must be specified in a calibration file associated with the each velocity data file in use.
Calibration details can be specified when setting up the velocity data in the particle tracking
model input data as described in Implementing current velocity data.

The end of file marker (denoted as #) is shown at the bottom of the data file.

34
5.4 Particle tracking main menu

From the Particle tracking main menu:

• To create a new input data configuration file, select the New Input data
configuration file command from the File command
• To open an existing input data configuration file, select the Open Input data
configuration file command from the File command
• To exit the particle tracking main menu, select the Exit command from the File
command

35
5.5 Main input dialog

Dialog overview

A new input data configuration file is shown below. This is the interface for the particle
tracking module data and this section describes each control shown in the dialog below.

36
Minor grid file specification

Enter the name of the minor grid file to be used for the model run by clicking on the Load
button in the Minor grid file group. The depths and positions of sampling stations are taken
from the minor grid file to generate a grid for this module. The grid can be viewed in the
DEPOMOD viewer by clicking on the View button which is disabled when no grid is
loaded. The associated minor grid information file (.ING) is read for minor grid dimensions
and relevant information required for the run. A summary of the data used in the grid can
be viewed by clicking on the Summary button. For detailed data the .ING file can be
examined in the viewer.

37
Fish farm characteristics

Waste allocation data

To change waste allocation data such as

feed wastage and particle settling velocity

data, click on the Change button to

display the Waste allocation data dialog.

Cage set up

To change pen dimensions and feed input, click

on the Change button to display the Cage set up

dialog. This button will be disabled when no minor

grid is loaded.

Implementing current velocity data

The current velocity data can be set up in the Current velocity data group. Enter the Time
step of current velocity data in seconds. Ideally, hourly data should be used as this is a
suitable time step for the model runs. Also, enter the Length of current velocity data i.e. the
length of the current velocity record. Click on the Set up button to display the Velocity data
dialog.

Particle trajectory model

In the Particle trajectory model group, specify the number of particles released for every
particle type at every cage every time step. The greater the number of particles used, the
more representative the particle tracking model (see main report). The number of particles

38
which can be released is a function of the memory of the computer being used. A suitable
value taking into account computer memory and speed will become apparent after some
initial test runs.

Specify an option for the time step for evaluation of a particle trajectory in the model. Set
the Trajectory evaluation accuracy radio button to Normal for 600 seconds, High for 60
seconds or Very high for 6 seconds. e.g. a setting of High will result in each particle
trajectory being evaluated every 60 seconds. With the generally coarse particles in fish farm
modelling with high settling velocities, the default setting of High is generally suitable.
However, with coarser particles and a layered model, it may be necessary to change this
setting to Very High (see special note).

Special Note for Particle trajectory model setting

The setting for step 9 can be determined by the following formula:

where:

vsmax = fastest settling velocity for the majority of the particles (m s-1)
teval = trajectory evaluation time step (s) (i.e.600s, 60s or 6s)
dnarrow = depth of the narrowest layer in a multi-layered model or the depth of the whole
water column in a single layered model (m)

39
For example, for the following settings in a 3 layer model with a total water column depth
of 35m

vsmax = 0.13 m s-1; teval = 600s; dnarrow = 12m;

the above formula is not satisfied and this will result in a particle trajectory being resolved
in one step of 78m through the water column. In this case, the particle trajectory will only
use the surface layer currents and will move to the sea bed in one step. By reducing teval to
60s, the particle will move in steps of 7.8m thus using different advection components as it
sinks through the water column.

The use of hourly data is recommended. However, if hourly data is not used then teval
should be a factor of the time step of the current velocity data (ðt). Furthermore, if the
Trajectory evaluation accuracy > ðt then the Trajectory evaluation accuracy is
automatically set to half of ðt.

Turbulence model

In the Turbulence model group, check the Random walk model box to initiate the random
walk model. This should always be checked as this simulates turbulence. Specify
Horizontal (x and y direction) and Vertical (z direction) dispersion coefficients for the site
in m2 s-1. Unless dispersion coefficients measurements are available for the area around the
fish farm, default values kx and ky can be used of 0.1 m2 s-1 and kz of 0.001 m2 s-1.

Mean Tidal Height

40
Mean tidal height is the mean tidal height with reference to chart datum (Admiralty 1996).
By definition, this is the average of Mean High Water Springs, Mean Low Water Springs,
Mean High Water Neaps and Mean Low Water Neaps.

Output file containing particle information

Enter the name of the Output file containing particle information by clicking on the Save
As button. These files have a .FIL extension as it is a structured file and should be created
in a PARTRACK\SITE directory. An information file with a .INP extension is created with
the same name and location which includes all information and input conditions used for
the model run.

Running the model

Click on the Run model button. The model then checks the input data and will display any
errors found with the data. On completion of error checking, a message dialog will be
displayed:

One of the following responses is required:

• Yes - The input data will overwrite existing data contained in the stored input data
configuration file (.CFG). If the input data configuration file is untitled, a Save
dialog will be displayed where the user can enter a name for the input data file. The
file should be saved in the directory PARTRACK \ SITE with a .CFG extension.

• No - A Save dialog will be displayed so the user can save the input data file with a
new name. The file should be saved in the directory PARTRACK \ SITE with a
.CFG extension.

41
 • Cancel - The user will be returned to the Input data configuration file dialog and the
model run will not be executed.

On providing a response of Yes or No, the model will execute and then return to the input
data dialog. To halt model execution, click on the Cancel button next to the progress bar.

An example input data configuration file is shown below stored in the PARTRACK \ SITE
sub-directory.

Post run features

By right clicking the mouse a number of Mouse right click features can be viewed. A list of
files created by this module are given in the page List of input/output files.

Exiting the dialog

Click on the Exit button. A message dialog will be displayed Save changes to input data
configuration file? One of the responses from the previous step Running the model is
required. On providing a response of Yes or No, control will be returned to the Particle
tracking main menu.

42
Resuspension
6. Main contents page

6.1 Objectives/general DEPOMOD deposition predictions : A plot generated in

description/using this module a contouring package showing the modelled flux of waste
solids to the sea bed using DEPOMOD arising from 3
6.2 Setting up procedure cage groups each containing 10 pens (shown as squares).
Sampling stations are underlined.
6.3 Resuspension main menu

6.4 Resuspension main input

dialog

Dialog overview

Start date and time

Models available for running in

the module

6.4.1 Resuspension model

dialog

6.4.2 G-model data dialog

6.4.3 Primary production data

dialog
Validation of the resuspension model using a tracer :
Input data specification Plots showing the change in modelled and observed mass
budgets with time for the total grid area, the inner circle
Output data file specification (25m radius centered around the release point), 'A' sectors
(in the direction of the residual current), and all other
Model output units sectors. Total tracer released was 155 kg.

Special output units for In-feed

treatments

Running the model

43
Post run features

Exiting the dialog

6.1 Objectives of the resuspension module

The objectives of this module are to:

• obtain data from the particle tracking module on the deposition of particles on the
bed from the source
• calculate total deposition (g m-2 bed) or flux (g m-2 yr-1) of waste solids, carbon or
active ingredient from an in-feed treatment

General description of the resuspension module

This module requires the user to create a module input data configuration file which
contains information on which particle tracking file to use and what output units are
required for the model run.

The RESUS directory contains the executable file RESUS8.EXE and an example input data
configuration file INPUT.CFG in the RESUS \ SITE directory.

The module creates a module output file (.OUT) which should be stored in RESUS \ SITE
directory for use in the benthic module. It also creates an information file (.INR) which
contains model data and conditions for the run.

44
Using the module

Similar to the particle tracking module, this module requires a lot of memory. If the module
runs out of memory or is very slow then a particle tracking run should be repeated to reduce
particle information to suit the computer the module is being run on (see Particle tracking-
using the module).

The run time for this module will depend on the number of particles being used and the
computer numeric processor. It may take from 5 minutes to 24 hours to run.

6.2 Module setting up procedure

The following steps are required to set up the module:

1. Examine the data specification for this module to check all relevant data are
available.
2. Decide whether additional models are to be run. DEPOMOD model runs should be
undertaken initially without the wind-wave primary production and G-models. The
wind-wave model should only be initiated if the characteristics of the site justify use
of the model. The G-model has been included with DEPOMOD as an additional
model which can be used for research purposes as this model is difficult to validate.
DEPOMOD does not give benthic predictions when the wind-wave, G-models and
primary production modules are in use. The benthic module has been validated for
predictions of solids flux (g m-2 yr-1), without wind-wave, G-model and primary
production modules in use.
3. Run the resuspension module RESUS8.EXE to display the main menu dialog and
create a new input data dialog.
4. Enter the required data in the main input data dialog. An example input data file
named input.cfg located in the RESUS \ SITE directory can be loaded into the
module.
5. The module can be run with resuspension module off, if the user wishes to
determine the effect of resuspension. In addition, the user may run the module with
resuspension off to determine the percentage of the discharge initially depositing in
the grid area.
6. Check that all relevant files have been created using post run features, exit the
resuspension module and go on to the benthic response module.

45
6.3 Resuspension main menu

From the Resuspension main menu:

• To create a new input data configuration file, select the New Input data
configuration file command from the File command
• To open an existing input data configuration file, select the Open Input data
configuration file command from the File command
• To exit the resuspension main menu, select the Exit command from the File
command

46
6.4 Resuspension main input dialog

Dialog overview

A new input data configuration file is shown below. This is the interface for the
resuspension module data and this section describes each control shown in the dialog
below.

Start date and time

If the primary production module is to be run then specify the Start time / date of model
run, otherwise there is no need to specify this. This date and time corresponds to the start of
the current meter record.

Models available for running in the module

47
The following models are available from the Models group:

Resuspension - Check the Resuspension box

Given information from the particle tracking stage on the particle distribution on the bed
direct from the outfall each time step, the resuspension model will resuspend, transport and
deposit these solids according to defined thresholds in the resuspension model. If the
resuspension model is not checked, the model will calculate the distribution of particles on
the bed without the resuspension effect. i.e. consolidation of particles occurs immediately
after deposition.

G-model - Check the G-model box and click on the Set up button to display the G-model
data dialog

The G-model (by Westrich and Berner) calculates the degradation of highly, less and non-
reactive carbon over time. In addition, degradation of total solids or kinetics of an in-feed
treatment can be modelled. The model can be run for a plug release for a certain period of
time, or for a continuous release, a steady state will be calculated.

Primary production - Check the Primary production box and click on the Set up button to
display the Primary production data dialog

It is essential to run this model if the primary production in the area under investigation is
thought to have a large effect on the carbon input in relation to the fish farm. This model
allows the user to add a time varying natural background sedimentation component to the
model domain..

Memory saver - Check the Memory saver box

If the resuspension module is causing the computer system to run out of memory or to be
very slow (greater than 24 hours for a run), then the memory saver can be used. This
summarises particle information at the resuspension stage to allow faster processing in the

48
model. However, the model is sensitive to the memory saver and will result in some
inaccuracies in rounding errors.

Specify the Number of loops to run model for. Running the model for a number of loops
allows the model to gain a steady state for continuous releases. For a current meter record
of one spring-neap cycle or more a setting of between 2 and 5 is usually necessary. For
smaller records this value should be increased. A value of 1 should not be used for
continuous releases as the model will fail to reach a steady state. The model should be run
for at least one month or 2 repeating loops of the current record, whichever is the greater.
Furthermore, this setting should be increased until no further change in results is observed.
i.e. a steady state solution is achieved. For modelling of total deposition of continuous
releases, the Number of loops to run model for can be set to any time period.

Input data specification (Particle tracking information file)

Specify the name of the particle tracking information file using the Load button in the Input
data box. This file will have the same name as the file created in section 5.5 (Output file
containing particle information) but with a .INP extension. This is an information file for
the particle tracking run and contains a link to the structured file containing the particle
distributions calculated from the particle tracking stage. It should be checked that it
contains the input conditions desired by viewing details of the information file by clicking
on Summary.

Output data file specification

In the Output data box, specify the name for the output files using the Save As button . A
default extension is added (see section 3.5).

Model Output units

In the Output units group, specify whether the units are to be in terms of Flux (mass m-2
bed yr-1) or Total deposition (mass m-2). For plug releases, the output units should be set to
Total deposition. The Mass units can also be changed and the Output units are displayed in
the adjacent panel.

49
Special output units for In-feed treatments

For in-feed treatments, to convert model output units of mass m-2 to mass kg-1 sediment,
check the Include conversions to mass deposited material per mass sediment. To undertake
this conversion, Depth of sediment in which deposited material is mixed must be specified
in cm as well as Bulk sediment density in kg m-3. The units of the mass of deposited
material are defined in the previous section. If the box For in feed treatments, write results
in terms of active ingredient is checked, results will be in terms of active ingredient and not
solids arising from the medicated feed.

For the example shown below, units will be g active ingredient kg-1 sediment.

For the example shown below, units will be g solids kg-1 sediment where solids are
medicated feed pellets or faeces arising from medicated feed.

50
Running the model

Click on the Run model button. The model then checks the input data and will display any
errors found with the data. On completion of error checking, a message dialog will be
displayed:

One of the following responses is required:

• Yes - The input data will overwrite existing data contained in the stored input data
configuration file (.CFG). If the input data configuration file is untitled, a Save
dialog will be displayed where the user can enter a name for the input data file. The
file should be saved in the directory RESUS \ SITE with a .CFG extension.

• No - A Save dialog will be displayed so the user can save the input data file with a
new name. The file should be saved in the directory RESUS \ SITE with a .CFG
extension.

• Cancel - The user will be returned to the Input data configuration file dialog and the
model run will not be executed.

On providing a response of Yes or No, the model will execute and then return to the input
data dialog. To halt model execution, click on the Cancel button next to the progress bar.

Post run features

By right clicking the mouse a number of Mouse right click features can be viewed. A list of
files created by this module are given in the page List of input/output files.

Exiting the dialog

Click on the Exit button. A message dialog will be displayed Save changes to input data
configuration file? One of the responses from the previous step Running the model is
required. On providing a response of Yes or No, control will be returned to the Particle
tracking main menu.

51
6.4.1 Resuspension model dialog

Resuspension model

The parameters of the resuspension model are:

Critical shear stress for resuspension - 0.0179 N m-2 (approximately 9.5 cm s-1 near bed
current speed)
Critical deposition speed - 0.004 N m-2 (approximately 4.5 cm s-1 near bed current speed)
Erodibility constant - 7*10-7 kg m-2 s-1
Consolidation time - 4 days (period of time a particle spends on the bed before it is
removed from the resuspension model processes)

These model parameters have been validated using a tracer study and using benthic data
from several fish farm sites (details are given in the main report).

Although the only resuspension parameter that can be varied by the user is the
consolidation time of a particle, the benthic data sets were validated using a consolidation
time of 4 days. The Resuspension model group is only shown when the resuspension model
check box has been initiated.

Output information

The dialog shown below allows the user to obtain a variety of output files. With the Write
mass balances box checked, the user can obtain mass balances for the grid cells that have
sampling stations in them. These data are written to a file with a .ENT extension. No data
will be obtain if no sampling stations have been included at the grid generation stage.

For plug releases, output can be obtained for each day or for a specified number of days
during the model run. Files with extensions .PLU, .PRN and .CSV are created which
contain DEPOMOD grids in ASCII format, grid totals and data formats for contouring
respectively.

• .PLU files give ASCII grid output at the end of each specified day
• .PRN files give total mass of material for the grid area at the end of each specified
day
• .CSV files give mass for each grid cell at the end of each specified day
• .ENT files give mass balances for sampling station positions

Typically, if results want to be analysed in this manner then .PRN and .CSV files are the
most useful.

52
Click the Accept data button to accept these data and close the dialog.

6.4.2 G-model data dialog

The G-model (Westrich and Berner, 1984. The role of sedimentary organic matter in
bacterial sulphate reduction: The G-model tested. Limnol. Oceanogr. 29(2):236-249) can
be used to degrade carbon fractions via first order decay kinetics:

where:

GT(t) = concentration of total organic carbon at time t (years)

G01 = initial concentration of the highly reactive fraction (G1-type)
G02 = initial concentration of the less reactive fraction (G2-type)
GNR = concentration of non-reactive material

53
k1 = first order decay constant of the highly reactive fraction
k2 = first order decay constant of the less reactive fraction

For each of food and faecal particles in the G-model rate constants group, enter data for
Highly and Less degradable rate constants (k1 and k2) in reciprocal year. In the G-model
percentage fractions group, enter data for the percentage of carbon fractions for Highly
degradable, Less degradable and Non-degradable carbon which must total 100% for each
particle type.

In addition to modelling carbon, the G-model can be used to degrade the solids or active
component of the particles (as in the case of an in-feed sea lice treatment- type I or II).
Where the compound does not have different degradable fractions, a single fraction may be
used represented by a single k.

For example, setting less degradable and non-degradable components to 0% and the highly
degradable component to 100% for both food and faeces, will allow the k1 value to be used
to represent degradation of the whole compound. Where a compound has a half life of 9
months, t is equal to 0.75 years so that at time t the mass of the compound is half of the
initial mass. i.e. GT(t) = G01(t)[0.5].

Thus:

exp[-k1t] = 0.5 so that k1 = -ln(0.5)/0.75 = 0.924 yr-1

Note: If undertaking any time conversions, use 365.25 days in a year not 365.

Special note

In output files, the following conventions are followed using the file name specified in
section 6.4 (Output data file specification). See also List of Input/Output files.

.SUR files (x,y,z) for contouring

total carbon without G-model - <filename>G0.sur

total carbon with G-model - <filename>G1.sur
highly + less degradable components only - <filename>G2.sur
non-degradable components only - <filename>G3.sur

.PRN files and .CSV files for grid and individual cell totals

total carbon without G-model - <filename>.prn or <filename>.csv

total carbon with G-model - <filename>G1.prn or <filename>G1.csv
highly + less degradable components only - <filename>G2.prn or <filename>G2.csv
non-degradable components only - <filename>G3.prn or <filename>G3.csv

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When examining degradation of carbon, use comparisons between <filename>.prn (without
degradation) and <filename>G1.prn (with degradation).

The G-model dialog below is set up for an in-feed treatment with a k1 value of 4.01 yr-1.

Click the Accept data button to accept these data and close the dialog.

6.4.3 Primary production module dialog

To add sedimentation from primary production into the model domain two options are
available:

1. Where a repeating loop is to be used and a steady state calculated in the resuspension
model, the Average annual sedimentation data box should be checked.

2. In the case of where a plug release or amounts on the bed are being calculated (mass
solids m-2), unchecking this box will cause the primary production sub-module to use the

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sedimentation data for the month the model is being run for. Enter a Sedimentation rate of
primary products for each month under the appropriate columns.

Click the Accept data button to accept these data and close the dialog.

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Benthic response model
7. Main contents page

7.1 Objectives/general The figure shows the DEPOMOD relationship between

description/using this module predicted solids accumulation (Savail) and the Infaunal
Trophic Index. The Envelope of Acceptable Precision
7.2 Setting up procedure (EAP) shown reflects the amount of natural background
variability expected and 88% of the observed fauna fall
7.3 Benthic main menu within this envelope. The circles show the variation in ITI
in duplicate 0.1m-2 grabs taken at the same sampling
Dialog overview station and assisted in definition of the EAP. From this
relationship, a prediction of Savail can be used to predict the
Input data file specification ITI value and EAP.

Output data file specification

Statistics

Running the model

Post run features

Exiting the dialog

7.1 Objectives of the benthic module

The objectives of this module are:

• to read in predictions of solids accumulation (Savail) from resuspension model output

files
• to generate predictions of the Infaunal Trophic Index and Total abundance for
the grid area and for sampling station positions; predictions of solids (or chemical)
accumulation/deposition are also given for sampling station positions
• to provide Envelopes of Acceptable Precision with these predictions which give an
indication of the confidence of the predictions

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Further details of the validation of this module are given in the documentation. Users
intending to use this module should read the Field work and modelling protocols in the
documentation before interpreting results. Benthic predictions are based on 0.1 m2 grab
sample size areas. Note also that benthic predictions are valid for predictions of solids
accumulation only which includes resuspension but not degradation via the G-model.
Benthic effects from the accumulation of in-feed sea lice treatment chemicals cannot be
determined from this module.

General description of the benthic module

This module requires the user to define a major grid with relevant information on it, create
a major grid depth array and create an input data file containing major and minor grid data.
The executable file FEED8.EXE is located in the BENTHIC directory.

The module should be set up to store output files in a SITE directory of the BENTHIC
directory.

The module creates a module output files containing ITI (.ITI) and abundance predictions
(.AB) for the grid and sampling station positions. Module results files (.CSV) are also
created and can be used for contouring results for the gird area. Simple statistics files can
also be created giving information on the area occupied by each contour. Standard
contouring packages often have similar features which will accept the .CSV file as input
data. A module information file (.INB) is also created for information.

Using the module

This module should take less than a minute to complete its tasks.

7.2 Module setting up procedure

The following steps are required to set up the module:

1. Examine the data specification for this module to check all relevant data are
available.
2. Run the Benthic module FEED8.EXE to display the main input data dialog.

Check that all relevant files have been created using post run features. The results files from
this module may be used to examine predictions of solids accumulation and benthic indices
at sampling stations. In addition, results may be contoured using a contouring package.

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7.3 Benthic main input dialog

Dialog overview

A new input data configuration file is shown below. This is the interface for the benthic
response module data and this section describes each control shown in the dialog below.

Input data specification

Click on the Load button to load a resuspension model results (.OUT) file, which can be
viewed by clicking on View.

Output data file specification

Select the directory for the results of the benthic module. It is recommended that a sub-
directory is created in the BENTHIC directory the same name as the site and the results
saved there. File names are automatically created depending on the file names of the
resuspension model runs.

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Statistics

Setting up the model to calculate statistics for the results from the resuspension model can
be undertaken by clicking on the Statistics button.

Running the model

Click on the Run model button to run the model.

Post run features

By right clicking the mouse a number of Mouse right click features can be viewed. A list of
files created by this module are given in the page List of input/output files.

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GaBoM
Growth and Biomass Model

A. Main contents page

A.1 Objectives/general GaBoM model validation : The figure shows a

description/using this module comparison of observed and modelled data for a fish
farm using GaBoM to model farm biomass, fish growth
A.2 Setting up procedure and mortality.

A.3 GaBoM main menu

A.4 GaBoM main input dialog

Dialog overview

Output data file specification

Farm details

Fish growth

A.4.1 Growth function dialog

Harvesting

Fish mortality

A.4.2 Mortality function dialog

Juvenile fish

Food conversion ratio (FCR)

Running the model

Post run features

Exiting the dialog

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Return to Main contents page

A1. Objective of the GaBoM model

The objective of GaBoM is to allow prediction of feed input for use in the DEPOMOD
particle tracking model.

General description of model

Where DEPOMOD is used for forecasting the deposition of solids for a given benthic
sampling month, GaBoM can be used to predict feed input for a particular month in the
growing cycle. Occasionally, husbandry data may be supplied by the farmer for a similar
size farm where this can be used for forecasting purposes. Where DEPOMOD is used for
hindcasting, actual feed input values should be used from the farm in question. The use of
feed input data for 1–3 months prior to benthic sampling should be used to model trends in
feed input prior to benthic sampling, if the monthly values are markedly different from the
average value.

GaBoM has been developed as a separate module to the particle tracking module and is run
separately. The user can then take results from GaBoM and input these into DEPOMOD.

A.2 Module setting up procedure

The following steps are required to set up the module:

1. Examine the data specification for this module to check all relevant data are
available. For GaBoM, all of the data are available as default.
2. Run the GaBoM module GaBoM8.EXE to display the main menu dialog and create
a new input data dialog.
3. Enter the required data in the main input data dialog. An example input data file
named input.cfg located in the GABOM \ SITE directory can be loaded into the
module.
4. Check that all relevant files have been created using post run features. Feed input
data from GaBoM can be adjusted from kg d-1 to kg d-1 cage-1 and used in the cage
input dialog in the particle tracking model.

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A.3 GaBoM main menu

From the GaBoM main menu:

• To create a new input data configuration file, select the New Input data
configuration file command from the File command
• To open an existing input data configuration file, select the Open Input data
configuration file command from the File command
• To exit the resuspension main menu, select the Exit command from the File
command

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A.4 GaBoM main input dialog

Dialog overview

A new input data configuration file is shown below. This is the interface for the GaBoM
module data and this section describes each control shown in the dialog below.

Output data file specification

In the Output data box, specify the name for the output files using the Save As button . A
default extension .OUT is added.

Farm details

Use the Farm details group to specify details of the farm. Specify Biomass consent
(tonnes), the date of the first day of the month on which the farm starts using Start (Month

64
beginning) and the Number of months of farming period. Check the Undertake harvesting
box if required.

Fish growth

Click on the Change button in the Fish growth function group to display the Growth
function dialog.

Harvesting

Two methods exist in the model

for harvesting:

1. Between a specified
range of farm biomass
where the range is
defined as a % above
and % below consent
biomass. This method
generally results in the
model keeping the
biomass of the farm near
the consent value.
2. Between a specified
period of time where the

65
 start of the harvest is
defined using Start
harvesting. The duration
of the harvest may be
defined for a finite
duration using the
months spin edit box, or
checking the until end of
farming period will
result in continuous
harvesting from Start
harvesting.

The amount harvested per

harvesting event can be defined

either as a % of biomass
consent(%)

or as a Fixed tonnage (tonnes)

Fish mortality

Click on the Change button in the Fish mortality function group to display the Mortality
function dialog.

Juvenile fish

Define the Starting numbers of juveniles using the spin edit box. The weight of the juvenile
fish is determined by the Growth function dialog when time = 0.

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Food conversion ratio (FCR)

The Food conversion ratio can be defined using this edit box. For example, with a FCR of
1.5, for every 1 mass unit of growth undertaken by the fish, 1.5 mass units of feed are
required.

Running the model

Click on the Run model button. The model then checks the input data and will display any
errors found with the data. On completion of error checking, a message dialog will be
displayed:

One of the following responses is required:

• Yes - The input data will overwrite existing data contained in the stored input data
configuration file (.CFG). If the input data configuration file is untitled, a Save
dialog will be displayed where the user can enter a name for the input data file. The
file should be saved in the directory GaBoM \ SITE with a .CFG extension.

• No - A Save dialog will be displayed so the user can save the input data file with a
new name. The file should be saved in the directory GaBoM \ SITE with a .CFG
extension.

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 • Cancel - The user will be returned to the Input data configuration file dialog and the
model run will not be executed.

On providing a response of Yes or No, the model will execute and then return to the input
data dialog. To halt model execution, click on the Cancel button next to the progress bar.

Post run features

By right clicking the mouse a number of Mouse right click features can be viewed. A list of
files created by this module are given in the page List of input/output files.

Exiting the dialog

Click on the Exit button. A message dialog will be displayed Save changes to input data
configuration file? One of the responses from the previous step Running the model is
required. On providing a response of Yes or No, control will be returned to the GaBoM
main menu.

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