Data for "Thermal transport of glasses via machine learning driven simulations"

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