findtde 1.3.0

Set of scripts to facilitate easy calculations of threshold displacement energies for materials in VASP/LAMMPS using ab initio/classical molecular dynamics.

findTDE

findTDE comprises a set of scripts to facilitate easy, high-throughput calculations of threshold displacement energies (TDEs) for materials using ab initio/classical molecular dynamics in VASP/LAMMPS. The threshold displacement energy is the minimum kinetic energy transfer from incident radiation to a lattice atom that produces a permanent defect. This property is useful for understanding the radiation hardness of a material, and it is a required parameter for binary collision approximation calculations (e.g., SRIM/TRIM).

Installation

Automatic installation is available with pip install findtde. The files may also be either downloaded manually or using git clone.

We recommend creating a virtual environment through Conda first, then installing findTDE. If you plan to use LAMMPS to perform calculations, you can install LAMMPS in the same environment with Conda.

Usage

The find_tde script may be called directly from the command line with several options. The usage may be displayed using the help (-h) option. The convergence mode (-c) determines how subsequent kinetic energy values are chosen for the displacement event, either "standard" (adjust by 5 eV until opposite defect generation is found, then adjust by 1 eV until the TDE is found) or "midpoint" (adjust by 8 eV until opposite defect generation is found, then adjust by half the distance from the current energy to the nearest energy of opposite defect generation). The program selection (-p) chooses whether VASP or LAMMPS is used for the calculations. If LAMMPS is used, the force field file may be chosen (-f).

Two options exist to use LAMMPS as the calculation program: lammps and lammpsish. lammps uses exclusively LAMMPS for all input files and simulations, while lammpsish uses the POSCAR/POTCAR files from VASP to convert to LAMMPS input files and performs just the calculations in VASP.

find_tde [-h] [-c <standard|midpoint>] [-p <vasp|lammpsish|lammps>] [-f <lmp_ff.type>]

The script is currently written to execute via Slurm workload manager. This can be adjusted temporarily to execute the appropriate program.

The script relies on a directory structure. Only the base directory (e.g., "project," can be named anything), main input file ("latt_dirs_to_calc.csv"), inputs directory ("inp"), and perfect supercell directory ("perfect") are required to be made and named as described. findTDE should be executed in the "project" directory. Each "displacement" directory, associated "energy" directories, and relevant .csv/.txt files are created by the program.

project
│   latt_dirs_to_calc.csv   
│
└───displacement1
│   │   displacement1_data.csv
│   │   displacement1_out.txt
│   │   KE_calcs_list.txt
│   │
│   └───energyA
│   |   │   program_inputs
│   |   │   program_outputs
│   |   │   ...
│   │
│   └───energyB
│   |   │   program_inputs
│   |   │   program_outputs
│   |   │   ...
│   │
│   └───...
│
└───...
│   
└───inp
│   │   INCAR_cgm
│   │   INCAR_md
│   │   KPOINTS
│   │   POSCAR
│   │   POTCAR
│   │   lmp_ff.type
│   │   ...
│   
└───perfect
|   │   OUTCAR

The input file "latt_dirs_to_calc.csv" is required to specify the displacement event. This can either be created manually, or by using the multi_tde.py accessory script. The heading of this file may be used to describe the file format. The bottom row of the file is read when findTDE is executed, and that info is used for that TDE calculation. The first value is a "pseudo" to correspond to the displacement direction, given as an integer number (changes with each unique direction) and either "L" or "S" (describes whether the direction is given as a lattice direction [u v w] or spherical direction (rho, phi, theta)). The "atom_type" and "atom_number" detail which atom in the supercell is given the velocity vector to simulate the displacement event (e.g., atom_type: ga and atom_number: 34 corresponds to the 34th Ga atom, as listed in the POSCAR file, being displaced). The initial kinetic energy "ke_i" and cutoff kinetic energy "ke_cut" (stops the program if a defect is not found below this kinetic energy) are then defined. The direction is then defined, either using lattice direction integer notation or spherical coordinate notation (may be floats).

########################################
# format of text file
# nL    atom_type    atom_number    ke_i    ke_cut    u    v    w
# n+1S    atom_type    atom_number    ke_i    ke_cut    r    p    t
########################################

Citations

If you use findTDE in your research, please cite:

• A. S. Hauck, M. Jin, and B. R. Tuttle, “Atomic displacement threshold energies and defect generation in GaN, AlN, and AlGaN: A high-throughput molecular dynamics investigation,” Applied Physics Letters, vol. 124, no. 15, p. 152107, Apr. 2024, doi: 10.1063/5.0190371.

Acknowledgements

The findTDE code was developed by Alexander Hauck, Dr. Mia Jin, and Dr. Blair Tuttle at The Pennsylvania State University.