BLOSSOM - BioLOgical Simulation in SOil Model

A soil biota agent based model (ABM) based on Repast4Py

The ./blossom folder contains the model itself, notebook to create trophic networks, input files, and output files. The ./blossom_viz folder contains notebooks for model run visualizations. The ./experiments folder contains notebooks for analysis. The ./figures folder contains notebooks used to create the thesis figures, including result and discussion visualizations.

Install/Run instructions

Tested for Windows with WSL2 Ubuntu 22.04, and Python 3.10.7.

1. Install MPI (in this case mpich, but openMPI should also work fine (not tested)): sudo apt install mpich
2. Install Python libraries to run the BLOSSOM model (consider making a venv) env CC=mpicxx pip3 install repast4py scikit-learn
   • If you encounter issues with Repast4Py, try following the Repast4Py install instructions
3. Install Python libraries to run the Jupyter Notebooks (consider making a venv) pip3 install jupyter pandas matplotlib seaborn statsmodels
4. Run the model from the ./blossom folder with the command mpirun -n 4 python3 blossom_2d.py ./inputs/run_2d.yaml, where -n <#_processes> sets the number of processes that are used. NOTE: -n 1 is not supported!