InterPhon 1.2.0

A Python Package for Ab initio Interface Phonon Calculations within a 3D Electronic Structure Framework

InterPhon

A Python Package for Ab initio Interface Phonon Calculations within a 3D Electronic Structure Framework.
If you have used InterPhon, please cite the following article (https://arxiv.org/abs/2012.04198):

"InterPhon: Ab initio Interface Phonon Calculations within a 3D Electronic Structure Framework", 
In Won Yeu, Gyuseung Han, Kun Hee Ye, Cheol Seong Hwang, and Jung-Hae Choi, arXiv:2012.04198 (2020)

The description below is a basic usage guide. If you want to learn more about InterPhon, please find the user manual at https://interphon.readthedocs.io/

Installation

Please clone this repository and install using:

$ git clone https://github.com/inwonyeu/interphon.git
$ cd interphon/
$ python setup.py install

Or install via pip:

$ pip install interphon

Basic usage in conjunction with VASP

InterPhon supports a range of options to manage phonon computations and plotting styles.
In order to see all of the available options and their default values:

$ interphon --help

1. Pre-process

In the InterPhon pre-process, a file of supercell (SUPERCELL) and files of displaced supercells (POSCAR-0*) are generated:

$ interphon -enlarge "2 2 1" -pbc "1 1 0"

-> (2×2×1) supercell and displaced supercells
-> Periodic boundary conditions (1 or True) along the a₁, a₂ lattice directions and open (0 or False) along the a₃ direction

2. Post-process

After the DFT force calculations for the displaced supercells (POSCAR-0*) are finished in each FORCE-0* folder, the evaluation of interfacial phonons can be executed by the following ways:

• Density of states (DOS):

$ interphon FORCE-0*/vasprun.xml -kdos KPOINTS_dos

• Thermal properties:

$ interphon FORCE-0*/vasprun.xml -kdos KPOINTS_dos -thermal

• Band:

$ interphon FORCE-0*/vasprun.xml -kband KPOINTS_band

• Phonon mode:

$ interphon FORCE-0*/vasprun.xml -kband KPOINTS_band -mode

Important files

1. DFT input file

InterPhon focuses on the interfacial atoms by allowing users to easily select atoms to be considered as the interface and phonon evaluation proceeds only in the selected atoms. The interfacial region is supposed to be defined through the statement of constraints on atom movements (selective dynamics). See below example of Cu(111) surface where the top three layers are selected as the surface region.

POSCAR (VASP format):

Unknown
1.00000000000000
   2.5712952614000000    0.0000000000000000    0.0000000000000000
   1.2856476307000000    2.2268070170000001    0.0000000000000000
   0.0000000000000000    0.0000000000000000   27.7901687622000004
Cu
7
Selective dynamics
Cartesian
   0.0000000000000000    0.0000000000000000    6.2983610849999998   F   F   F
   2.5712951080000002    1.4845379230000000    8.3978147799999991   F   F   F
   1.2856475540000001    0.7422689609999999   10.5098654109999998   F   F   F
   0.0000000000000000    0.0000000000000000   12.6153545979999997   F   F   F
   2.5712951080000002    1.4845379230000000   14.7267644020000006   T   T   T
   1.2856475540000001    0.7422689609999999   16.8249826169999999   T   T   T
   0.0000000000000000    0.0000000000000000   18.9121107990000006   T   T   T

2. K-points file

The abovementioned arguments of KPOINTS_dos and KPOINTS_band files, which are supported in VASP format (https://www.vasp.at/wiki/index.php/KPOINTS), are used for the mesh sampling of k-points.

KPOINTS_dos (file name is arbitrary):

kpoint
0
MP  # Monkhorst-Pack grids, use the first character ‘G’ for Gamma-centered grids.
9 9 1
0.0 0.0 0.0

KPOINTS_band (file name is arbitrary):

kpoint
41
L  # Line path
0.00 0.00 0.00  # G
0.00 0.50 0.00  # M

0.00 0.50 0.00  # M
0.333333 0.333333 0.00  # K

0.333333 0.333333 0.00  # K
0.00 0.00 0.00  # G