Scottish Shelf Model. Part 6: Wider Domain and Sub-Domains Integration

Appendix A

Particle Tracking and Connectivity Methodology

Contents

1 Introduction
1.1 Calculation of Connectivity Indices among Aquaculture Management Areas in Scotland
1.2 Background
1.3 Sea Lice
1.4 Infectious Salmon Anaemia
1.5 Infectious Pancreatic Necrosis
1.6 Scottish Aquaculture Management
1.6.1 Farm Management Areas ( FMAs)
1.6.2 Disease Management Areas (DMAs)

2 Particle Tracking in FVCOM
2.1 Method
2.2 Offline particle tracking code
2.3 Fixing the code
2.4 Input output files
2.5 Output files
2.6 Compiling and running particle tracking

3 Methodology for Scottish Waters Model
3.1 Model output preparation
3.2 Particle tracking
3.3 Post-processing of particle tracking output
3.4 Connectivity Indices

4 Results
4.1 FMA separation and connectivity matrices
4.2 Sea Lice Connectivity
4.3 Virus Connectivity
4.3.1 ISA Virus
4.3.2 IPN Virus

5 Summary

6 Recommendations for future work

References

Appendix: Particle Tracking code