Initialisation

Introduction

Initialisation is a fundamental part of any OSMOSE simulation. Because OSMOSE is a stochastic, school-based, multispecies model, the initial condition is not just a total biomass by species. It must define, directly or indirectly, the demographic and ecological structure from which the simulation begins. In practice, this means specifying or reconstructing enough information to determine total biomass, age or size structure, the number of schools used to represent the population, trophic level, and, depending on the method, spatial distribution. Initialisation therefore conditions the early demographic and trophic dynamics of the model and can influence not only the length of the transient adjustment, but also the long-term regime eventually reached by the simulation.

This point is closely related to, but distinct from, spin-up. Initialisation is the construction of the starting state at simulation time zero. Spin-up is the subsequent adjustment phase during which the model evolves from that imposed state towards a regime more consistent with its equations, parameterisation, and forcing. In some applications, especially steady-state ones, spin-up is a central part of the workflow. In interannual simulations, however, the early transient dynamics are often part of the target of the analysis, so a satisfactory initial condition is one that already captures the relevant demographic and ecological structure at the beginning of the run.

OSMOSE 4.4 currently supports three main conceptual routes for initialisation:

• Egg seeding initialisation (default)
• Reconstructed population-level initialisation (recommended)
• Direct school-based initialisation (used to restart a simulation)

Conceptual background on initialization methods in general and in Osmose in particular are provided here.

The detailed description of the parameterizations are provided here (to complete)

---

Suggested reading path

If you are new to the initialisation module, start here:

1. Conceptual background
2. Overview of initialisation methods in OSMOSE 4.4
3. Reconstructed population-level initialisation

If you want practical setup guidance:

1. Reconstructed population-level initialisation
2. User guidance and parameter documentation
3. Appendix C. Example data-layer configuration for reconstructed population-level initialisation
4. Appendix D. Example generated population.initialization block
5. Appendix F. Troubleshooting checklist

If you need alternative workflows:

• Other implemented initialisation methods
• Appendix A. Example configuration for egg seeding
• Appendix B. Example configuration and file structure for direct school-based initialisation

---

Complete Overview

• Introduction
• Conceptual background
• Overview of initialisation methods in OSMOSE 4.4
• Reconstructed population-level initialisation
• Other implemented initialisation methods
• User guidance and parameter documentation
• Limitations and outlook
• Conclusion

---

Legacy pages

The following pages correspond to older initialisation workflows and naming conventions. Their content has been incorporated into the current documentation, especially under:

• Reconstructed population-level initialisation
• Other implemented initialisation methods
• Appendix B. Example configuration and file structure for direct school-based initialisation

They are retained here for reference and backward compatibility:

• Initialisation NetCDF Restart
• Initialisation Seeding
• Initialisation Relative-biomass

---

Appendices

• Appendix A. Example configuration for egg seeding
• Appendix B. Example configuration and file structure for direct school-based initialisation
• Appendix C. Example data-layer configuration for reconstructed population-level initialisation
• Appendix D. Example generated population.initialization block
• Appendix E. Workflow diagram from data layer to school creation
• Appendix F. Troubleshooting checklist