Lammps_nep

This package aims to provide a simple way to install lammps python interface with NEP support. It is helpful for directly calling lammps in mdapy, which can be used to do cell optimization and phonon dispersion calculation.

Package version

• lammps version: 29 Aug 2024
• NEP_CPU version: v1.3

Prerequirement

• Make sure you have a C++ compiler and python env. We test for MSVC in windows, gcc in Ubuntu and Xcode in Mac OS.
• Use virtual python env is better. For conda user, activate the env before the installation.
• In windows, install cmake and use git bash to run the script.

Installation

• git clone https://github.com/mushroomfire/lammps_nep.git && cd lammps_nep
• bash build.sh

Validation

• After installation, check it in python cmd by typing:

import lammps
lmp = lammps.lammps()

The output should be like below:

LAMMPS (29 Aug 2024 - Development)

Example

Now one can calculate the phonon dispersion entirely in python scripts.

• pip install mdapy -U
• conda install -c conda-forge phonopy

# import packages
import mdapy as mp
from mdapy.potential import LammpsPotential
import matplotlib.pyplot as plt
mp.init()

# provide phonon path and labels, find in in seekpath website.
pair_parameter = """
pair_style nep
pair_coeff * * example/C_2024_NEP4.txt C
"""
elements_list = ['C']
path = '0.0 0.0 0.0 0.3333333333 0.3333333333 0.0 0.5 0.0 0.0 0.0 0.0 0.0'
labels = '$\Gamma$ K M $\Gamma$'
potential = LammpsPotential(pair_parameter)

# Load graphene file and do cell optimization
gra = mp.System('example/gra.xyz')
relax_gra = gra.cell_opt(pair_parameter, elements_list)

# compute and plot phonon dispersion
relax_gra.cal_phono_dispersion(path, labels, potential, elements_list)
fig, ax, _ = relax_gra.Phon.plot_dispersion()

# One can save the picture
# plt.savefig('example/phono.png', bbox_inches='tight', dpi=300)
plt.show()

If everything runs okay, the output is:

Note

• Only compile serial version for lammps.
• For reducing package size, we have removed unnecessary folder in original lammps, only keep the src, lib, python and cmake folders.
• We have modified the install.py in lammps/python folder, make it compatible with python 3.8.