Empirical Potentials

These examples demonstrate kALDo workflows using empirical interatomic potentials. Classical potentials like Tersoff and Stillinger-Weber provide computationally efficient force evaluations, enabling thermal transport calculations for large systems and complex structures. The workflows shown here use LAMMPS and ASE for force constant calculations.

Setup Instructions

These examples use the Tersoff potential for interatomic interactions.

Requirements

Download and install LAMMPS before running these examples.

Compiling LAMMPS with Python/ASE support

To calculate 2nd and 3rd order force constants with LAMMPS and ASE, compile LAMMPS with shared library support using cmake:

cd path/to/lammps/src
mkdir build
cd build
cmake ../cmake -DLAMMPS_EXCEPTIONS=yes \
               -DBUILD_SHARED_LIBS=yes \
               -DMLIAP_ENABLE_PYTHON=yes \
               -DPKG_PYTHON=yes \
               -DPKG_MANYBODY=yes \
               -DPKG_KSPACE=yes \
               -DPKG_PHONON=yes \
               -DPYTHON_EXECUTABLE:FILEPATH=`which python`
make -j 16
make install-python

GPU/CPU Configuration

For TensorFlow-based calculations, you can specify GPU or CPU usage following these instructions.

List and content of examples folder

For each example, more detailed information is provided by the README.md file contained in the corresponding directory.

  • amorphous_silicon_Tersoff_LAMMPS: This example illustrates how to perform thermal transport simulation for an amorphous silicon system (512 atoms per cell) with LAMMPS PHONON package as force calculator.

  • carbon_diamond_Tersoff_ASE_LAMMPS: This example illustrates how to perform thermal transport simulation for a carbon diamond (2 atoms per cell) system using ASE and LAMMPS as force calculator.

  • carbon_nanotube_Tersoff_LAMMPS: This example illustrates how to perform thermal transport simulation for a 10,0 carbon nanotube (40 atoms per cell) system using LAMMPS PHONON package as force calculator.

  • silicon_clathrate_Tersoff_LAMMPS: This example illustrates how to perform thermal transport simulation for a type I clathrate (46 atoms per cell) system using LAMMPS PHONON package as force calculator.

Git Large File Storage (LFS)

This repository uses Git LFS to handle large files. Ensure Git LFS is installed on your system by following the instructions on the Git LFS website.

Once installed, clone the repository as usual with git clone — large files will be downloaded automatically. If you’ve already cloned without Git LFS, retrieve the large files with:

git lfs pull