DOI: 10.5281/zenodo.10225315
title: Data for "Thermal transport of glasses via machine learning driven simulations"

description: This repository contains input and analysis scripts supporting the findings of *Thermal transport of glasses via machine learning driven simulations*, by P. Pegolo and F. Grasselli.
Content:

README.md: this file, information about the repository
SiO2: vitreous silica parent folder

NEP: folder with datasets and input scripts for NEP training

train.xyz: training dataset
test.xyz: validation dataset
nep.in: NEP input script
nep.txt: NEP model
nep.restart: NEP restart file 
DP: folder with datasets and input scripts for DP training

input.json: DeePMD training input
dataset: DeePMD training dataset
validation: DeePMD validation dataset
frozen_model.pb: DP model 
GKMD: scripts for the GKMD simulations
Tersoff: Tersoff reference simulation

model.xyz: initial configuration
run.in: GPUMD script
SiO2.gpumd.tersoff88: Tersoff model parameters
convert_movie_to_dump.py: script to convert GPUMD XYZ trajectory to LAMMPS format for re-running the trajectory with the MLPs
DP: DP simulation

init.data: LAMMPS initial configuration
in.lmp: LAMMPS input to re-run the Tersoff trajectory with the DP
NEP: NEP simulation

init.data: LAMMPS initial configuration
in.lmp: LAMMPS input to re-run the Tersoff trajectory with the NEP. Note that this needs the NEP-CPU user package installed in LAMMPS. At the moment it is not possible to re-run a trajectory with GPUMD. 
QHGK: scripts for the QHGK simulations

DP: DP data

second.npy: second-order interatomic force constants
third.npy: third-order interatomic force constants
replicated_atoms.xyz: configuration
dynmat: scripts to compute interatomic force constants with the DP model. Analogous scripts were used also to compute IFCs with the other potentials.

initial.data: non optimized configuration
in.dynmat.lmp: LAMMPS script to minimize the structure and compute second-order interatomic force constants
in.third.lmp: LAMMPS script to compute third-order interatomic force constants
Tersoff: Tersoff data

second.npy: second-order interatomic force constants
third.npy: third-order interatomic force constants
replicated_atoms.xyz: configuration
NEP: NEP data

second.npy: second-order interatomic force constants
third.npy: third-order interatomic force constants
replicated_atoms.xyz: configuration
qhgk.py: script to compute QHGK lifetimes and thermal conductivity
Si: vitreous silicon parent folder

QHGK: scripts for the QHGK simulations

qhgk.py: script to compute QHGK lifetimes 
[N]: folder with the calculations on a N-atoms system 

second.npy: second-order interatomic force constants
third.npy: third-order interatomic force constants
replicated_atoms.xyz: configuration
LiSi: vitreous litihum-intercalated silicon parent folder

NEP: folder with datasets and input scripts for NEP training 

train.xyz: training dataset
test.xyz: validation dataset
nep.in: NEP input script
nep.txt: NEP model
nep.restart: NEP restart file 
EMD: folder with data on the equilibrium molecular dynamics simulations

70k: data of the simulations with ~70k atoms

1-45: folder with input scripts for the simulations at different Li concentration

fraction.dat: Li fraction, y, as in Li_{y}Si
quench: scripts for the melt-quench-anneal sample preparation

model.xyz: initial configuration
restart.xyz: final configuration
run.in: GPUMD input
gk: scripts for the GKMD simulation

model.xyz: initial configuration
restart.xyz: final configuration
run.in: GPUMD input 
cepstral: folder for cepstral analysis

analyze.py: python script for cepstral analysis of the fluxes' time-series generated by the GKMD runs