arrhenius_rate

About

This code calculates the Vineyard prefactor¹ and activation energy for a process generated by a climbing-image NEB² calculation in LAMMPS^{3 4 5}. Using the Arrhenius equation⁶, these two parameters define the rate of a process.

The main script is vineyard.sh, which performs various calculations in and out of LAMMPS using an input .json config file. To properly run NEB and the dynamical matrix command, LAMMPS must be built with the REPLICA and PHONON packages.

To run an example, run:

./vineyard.sh config.json

This will perform an NEB run for vacancy hopping in Si using files from the example/ directory, writing both the Vineyard prefactor and energy barrier to example/rate.txt. Details about the calculation of the prefactor calculation are in vineyard.pdf.

Acknowledgements

The work was supported by the grant DE-SC0022980 funded by the U.S. Department of Energy, Office of Science.

1: https://doi.org/10.1016/0022-3697(57)90059-8

2: https://doi.org/10.1063/1.1329672

3: https://doi.org/10.1016/j.cpc.2021.108171

4: https://lammps.org/

5: https://docs.lammps.org/neb.html

6: https://en.wikipedia.org/wiki/Arrhenius_equation