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