This repository is a curated research package for molecular-dynamics and lattice-vibration calculations on monolayer GaS, GaSe, and InSe. It collects the project files needed to inspect the main thermal-transport results without reproducing the much larger working Google Drive archive.
The study combines:
- non-equilibrium molecular dynamics (NEMD) thermal transport;
- finite-length thermal-conductivity analysis;
- armchair/zigzag tensile-strain studies;
- metal, chalcogen, and bonded metal-chalcogen vacancy studies;
- MD-derived mass-weighted VDOS/PDOS;
- harmonic phonon dispersion and projected DOS calculations using LAMMPS + phonoLAMMPS/phonopy;
- validation against published GaS/GaSe/InSe literature.
The summary tables are in results/. The present finite-size analysis gives approximately:
| Material | Extrapolated kappa_inf (W m^-1 K^-1) | Effective characteristic length (nm) |
|---|---|---|
| GaS | 14.05 | 34.19 |
| GaSe | 10.19 | 35.55 |
| InSe | 3.30 | 23.57 |
These values come from the shorter-length finite-size dataset and should be read together with docs/REPRODUCIBILITY_NOTES.md.
At 6% tensile strain, the fixed-length armchair conductivities increase to about 12.95, 8.67, and 3.18 W m^-1 K^-1 for GaS, GaSe, and InSe, while the zigzag response is substantially weaker. Vacancy creation strongly suppresses thermal conductivity for all three materials.
scripts/- vacancy generation, VDOS/PDOS processing, NEMD post-processing, and harmonic phonon scripts.inputs/- representative LAMMPS NEMD, VDOS, and phonon inputs.potentials/- Tersoff EIAP files used in the archived workflows. Two variants are retained because the working project used differently formatted files in MD/VDOS and harmonic-phonon branches.structures/- pristine cells and representative strain/vacancy/phonon structures.results/strain/- Excel summaries, CSV table, and strain figures.results/vacancy/- Excel summaries, CSV table, and vacancy figures.results/vdos/- pristine GaS/GaSe/InSe VDOS and representative GaS defect spectra, including raw/smoothed spectral tables and metadata.results/phonon/- harmonic phonon dispersion/PDOS data and figures.results/validation/- finite-size workbooks, derived CSV, figures, and a literature benchmark table.validation/representative_nemd/- compact raw NEMD examples containing the LAMMPS input, cumulative thermostat energy, and processed figures.docs/- file guide, exclusions, and important reproducibility notes.references/REFERENCES.md- bibliography/DOIs instead of redistributed publisher PDFs.
The conductivity post-processing follows effective thicknesses of 8.712 A (GaS), 8.875 A (GaSe), and 8.775 A (InSe). These are the same thicknesses used by Wang et al., J. Appl. Phys. 125, 245104 (2019), DOI: 10.1063/1.5094663. For 2D materials, reported W m^-1 K^-1 values depend directly on the adopted thickness convention.
The scripts require Python plus common scientific packages. See requirements.txt. Harmonic phonon scripts additionally require a working LAMMPS installation with its Python module, plus phonoLAMMPS and phonopy.
A typical Python environment can be prepared with:
python -m venv .venv
source .venv/bin/activate
pip install -r requirements.txtLAMMPS itself should be installed separately with the pair styles/packages required by the provided input files.
This is a curated GitHub package, not a byte-for-byte mirror of the full simulation workspace. Very large raw trajectories (profile.langevin, pdos.lammpstrj), repeated LAMMPS logs, duplicate potential/script copies, and publisher PDFs are intentionally excluded. Representative NEMD raw energy files and processed VDOS/phonon tables are retained.
Known methodological/statistical limitations are documented openly in docs/REPRODUCIBILITY_NOTES.md. In particular, the archived NEMD equilibration scripts include a 3D fix npt ... iso stage that should be re-evaluated for a vacuum-separated monolayer before treating the current package as the final publication archive.
GitHub can read CITATION.cff. Update the citation metadata with the associated manuscript DOI and final author/contributor list when available.
No open-source or open-data license has been assigned automatically. See LICENSE_NOTICE.md before granting reuse rights, especially for interatomic-potential files or any third-party-derived assets.