README.md

This repository contains all the scripts and data to compute the results and figures presented in "Quantifying the environmental impact of a major coal mine project on the adjacent Great Barrier Reef ecosystems" by A. Saint-Amand, A. Grech, S. Choukroun, E. Hanert (doi: [https://doi.org/10.1016/j.marpolbul.2022.113656](https://doi.org/10.1016/j.marpolbul.2022.113656)).

Most of the scripts require the open-source [SLIM model](https://www.slim-ocean.be), freely downloadable [here](https://git.immc.ucl.ac.be/slim/slim).

Contact : antoine.saint-amand@uclouvain.be

## Creation of the mesh
1. Generate a first mesh with `mesh.py` (requires [seamsh](https://pypi.org/project/seamsh/))
2. Add rivers open boundaries with `mesh_add_rivers.py`
3. Partition the mesh with `mesh_manual_partitionning.py`

## Preprocessing steps
1. Download required forcing data with `download_forcings.py`, `get_streamflow.py` and `download_ereefs_wind.py`.
2. Run the data preprocessing with `prepro2D.py'.

## Hydro model
The hydro simulation can be launched (on a HPC) with `run2D.py`

## Particle dispersal simulations
The simulation of particle dispersal (Lagrangian Particle Tracker) can be launched with `LPT_quasi3D_sediments.py`

## Compute final results
- `LPT_analyze_stats.py` computes several metrics from the results of the particle tracker results (figures 4 and 5 in the article)
- `LPT_seagrass_risk.py` computes a risk map for the seagrass (figure 6 in the article)
- `plot_sediments_footprint.py` computes figure representing the dispersal extent of sediments (figure 3 in the article)
- `plot_subplots_abin_hydro.py` computes a figure representing the currents as simulated by the model at different time steps (figure 2 in the article)

The other scripts available in this repository contain functions and parameters used by previously mentionned scripts.