Workflows

Standalone terminal scripts for computing Bond-Network Entropy and Disorder Linewidth for IRG T9 irradiated graphite. All shared configuration — file paths, phonon mesh, fitting hyperparameters, and BNE settings — lives in config.py — Shared Workflow Configuration; every workflow script imports from it.

The structure of irradiated graphite used in the workflow can be found at the following link: https://doi.org/10.24435/materialscloud:jm-cg. If you use this structure in your research, you should cite both Iwanowski et al. [W1] and Farbos et al. [W2].

Configuration

File

Purpose

config.py — Shared Workflow Configuration

All paths, phonon mesh, band-structure path, L-BFGS fitting parameters, and BNE settings

1-series — Bond-Network Entropy

Step

Script

Topic

1a

1a_BNE_workflow.py — Compute Bond-Network Entropy

Compute BNE for IRG T9 across all configured LAE sizes; save one HDF5 per size

1b

1b_BNE_plot.py — Plot BNE Growth Rate

Read HDF5 results from 1a; plot BNE vs LAE size and growth-rate analysis

2-series — Disorder Linewidth

Step

Script

Topic

2a

2a_DL_workflow_precompute.py — Precompute Phonon Quantities

Phonon mesh, crystal VDOS + group speed, disordered VDOS, density-shifted VDOS (mirrors Notebooks 1-4)

2b

2b_DL_fit_params.py — Fit L and R Parameters

Fit L and R with L-BFGS via PyTorch autodiff; saves model_parameters.hdf5 (mirrors Notebook 6)

2c

2c_DL_diffusivity_decomposition.py — Diffusivity Decomposition

Disorder linewidth, propagation velocity, mean free path (mirrors Notebook 5)

Note

Run scripts in order: 1a → 1b (BNE series) and 2a → 2b → 2c (DL series). All scripts must be executed from the workflows/ directory. The 2-series requires the BNE + DL installation (see setup_dl.sh).

[W1]

Kamil Iwanowski, Gábor Csányi, and Michele Simoncelli. Bond-Network Entropy Governs Heat Transport in Coordination-Disordered Solids. Physical Review X, 15(4):041041, December 2025. URL: https://link.aps.org/doi/10.1103/w4p6-b9mp (visited on 2025-12-12), doi:10.1103/w4p6-b9mp.

[W2]

Baptiste Farbos, Helen Freeman, Trevor Hardcastle, Jean-Pierre Da Costa, Rik Brydson, Andrew J. Scott, Patrick Weisbecker, Christian Germain, Gérard L. Vignoles, and Jean-Marc Leyssale. A time-dependent atomistic reconstruction of severe irradiation damage and associated property changes in nuclear graphite. Carbon, 120:111–120, August 2017. URL: https://www.sciencedirect.com/science/article/pii/S0008622317304542 (visited on 2023-05-24), doi:10.1016/j.carbon.2017.05.009.