depomod_toolbox

A MATLAB toolbox for reading, processing and manipulating the particle tracking models AutoDepomod and NewDepomod

Authors

Andrew Berkeley, Ted Schlicke

Dependencies

This toolbox works best with the following packages

• the rcm_toolbox MATLAB library
• the os_toolbox MATLAB library
• the UTide MATLAB library
• A working and authorised copy of Admiralty TotalTide software
• the totaltide_toolbox MATLAB library

Examples

A comprehensive suite of examples can be found in the \scripts directory

The examples below describe some basic steps for creating a new project from a template and run the model using the command line interface.

Define name and location

A reasonable default location is below, but it can be anywhere.

rootDir = 'C:\newdepomod_projects\';

Name the project, this will become the root directory name and prefix of all filenames

projectName = 'bay_of_fish';

Create project from template with desired location and name

project = NewDepomod.Project.createFromTemplate(rootDir, projectName)

% project = 
%   Project with properties:
% 
%        version: 2
%       location: [1x1 NewDepomod.PropertiesFile]
%     bathymetry: [1x1 NewDepomod.BathymetryFile]
%      flowmetry: [1x1 NewDepomod.FlowmetryFile]
%           name: 'bay_of_fish'
%           path: 'C:\newdepomod_projects\bay_of_fish'
%     solidsRuns: [1 Depomod.Run.Collection]
%       EmBZRuns: [1 Depomod.Run.Collection]
%       TFBZRuns: [1 Depomod.Run.Collection]

Notice there includes 1 solids run and 1 EmBZ run as well as objects describing the bathymetry and flow data

View the bathymetry

figure;
project.bathymetry.plot

View the flow (requires rcm_toolbox MATLAB library)

flowProfile = project.flowmetry.toRCMProfile

flowProfile.Bins{1}.scatterPlot % bed
flowProfile.Bins{3}.scatterPlot % surface

Inspect the solids run

solidsRun = project.solidsRuns.item(1)

% solidsRun = 
%   Solids with properties:
% 
%              defaultPlotLevels: [4 192 1553 10000]
%                    defaultUnit: 'g m^{-2} y^{-1}'
%                      modelFile: [1x1 NewDepomod.PropertiesFile]
%         physicalPropertiesFile: [1x1 NewDepomod.PropertiesFile]
%              configurationFile: [1x1 NewDepomod.PropertiesFile]
%                    runtimeFile: [1x1 NewDepomod.PropertiesFile]
%                     inputsFile: [1x1 NewDepomod.InputsPropertiesFile]
%            iterationInputsFile: []
%         exportedTimeSeriesFile: []
%     consolidatedTimeSeriesFile: []
%                      solidsSur: []
%                      carbonSur: []
%             iterationRunNumber: '1'
%                  modelFileName: 'bay_of_fish-1-NONE.depomodmodelproperties'
%                        project: [1x1 NewDepomod.Project]
%                    cfgFileName: []
%                      runNumber: '1'
%                          cages: [2 Depomod.Layout.Site]

Notice this references all of the input (e.g. cages, inputs, physical) files and all of the output files (sur(face), time series) which will be written when the mdoel is executed. So this object can be used to navigate all of the information related to a particular run.

Check out the biomass

solidsRun.inputsFile.FeedInputs.biomass
solidsRun.inputsFile.FeedInputs.stockingDensity

% ans =
% 1000
% ans =
% 13.0826

And some of the physical properties

solidsRun.physicalPropertiesFile.Transports.bottomRoughnessLength.smooth
solidsRun.physicalPropertiesFile.Transports.resuspension.walker.dispersionCoefficientX

% ans =
% 0.00003
% ans =
% 0.1

And some of the cage properties

solidsRun.cages.consolidatedCages.size       % count
solidsRun.cages.consolidatedCages.cageArea   % m2
solidsRun.cages.consolidatedCages.cageVolume % m3

% ans =
%      8
% ans =
%           6369.80278655024
% ans =
%           76437.6334386029

Execute model run

• Open up user interface
• Open up bay_of_fish project
• Navigate to models
• Right-click on the solids (NONE) run #1
• Select single run

Read results files

Check run ITI score (ITI contour around 80% particles)

solidsRun.log.Eqs.benthic.iti

Check DZR impact area (equivalent to 4g m-2 y-1)

solidsRun.log.Eqs.BenthicImpactedAreaEQS.area

Check mass released...

solidsRun.log.Masses.solids.released.run

...and compare with mass remaining in domain - the difference is "exported"

solidsRun.log.Masses.solids.balance.run

Measure the predicted area of a specific impact level

solidsRun.solidsSur.area(4) % 4 g m-2

Get the predicted value at a specific location

solidsRun.solidsSur.valueAt(351000,1068800) % easting, northing

Plot impact

solidsRun.plot