dyson-code

Julia codebase and scripts to accompany the paper Restoring thermodynamic structure in stochastic dynamics.

How to use

In src/ the main functionality is written. The scripts/ folder contains script that use this functionality to generate the figures as shown in the manuscript. Run run_all.sh as a bash script to initialise the Julia project and run all scripts. The resulting figures can be found under results/figures. To test other set-ups, the default_initialisation() function in src/dyson.jl can be edited. Read dyson.pdf for a general overview of the functionality, and use in-code docstrings for a detailed API guide.

Figure index:

• Figure 1: scripts/entropy_figures.jl
• Figure 2: scripts/H_figure.jl
• Figure 3: scripts/statistics.jl
• Figure 4: scripts/transition.jl
• Figure 5: scripts/steady_state.jl
• Figure 6: scripts/convergence.jl

Reproducibility

Each figure is generated with a seed started at 1234 as defined in dyson-setup. The results in the manuscript are generated with julia v1.11.7 aand the package versions as defined in the [compat] section of Project.toml.