FormatTransformer

The package FormatTransformer move molecular structure (single frame or trajectory) within the periodic box and convert XYZ trajectories to VASP (POSCAR) or Quantum Espresso (QE) Input files.

Installation

Clone repository and install package:

git clone git@github.com:rahulumrao/FormatTransformer.git
cd FormatTransformer
pip install .

Usage

xyzcenter - shift molecule at the center of box

❯ xyzcenter -h

usage: xyzcenter [-h] [-i INPUT] [-o OUTPUT] [-b BOX_SIZE]

Center molecular structure within PBC

options:
  -h, --help            Show this help message and exit
  -i INPUT, --input INPUT
                        Input XYZ trajectory file
  -o OUTPUT, --output OUTPUT
                        Output XYZ trajectory file
  -b BOX_SIZE, --box_size BOX_SIZE
                        Box size in Å (default: 15.0)

xyzconverter - Convert XYZ (cartesian) to VASP (POSCAR) or Quantum Espresso input files

❯ xyzconverter -h

usage: xyzconverter [-h] [-i INPUT] [-b BOX_SIZE [BOX_SIZE ...]] -o {VASP,QE} [-pp PSEUDO]

Convert XYZ to VASP POSCAR or Quantum Espresso input files

options:
  -h, --help            Show this help message and exit
  -i INPUT, --input INPUT
                        Input XYZ file containing multiple frames
  -b BOX_SIZE [BOX_SIZE ...], --box_size BOX_SIZE [BOX_SIZE ...]
                        Box size in Å (default: Cubic box of 12.0)
  -o {VASP,QE}, --output_type {VASP,QE}
                        Specify the output format: VASP or QE
  -pp PSEUDO, --pseudo PSEUDO
                        PseudoPotentials directory (required for Quantum Espresso)

Examples

❯ xyzcenter -i trajec.xyz -o centered_trajec.xyz -b 12.0

==============================
Reading... trajec.xyz
==============================
Centered structure saved in centered_trajec.xyz wihtin periodic box 12.0

❯ xyzconverter -i centered_trajec.xyz -o VASP -b 12.0

Converting to VASP POSCAR format...
=============================================================
 Reading file : centered_trajec.xyz
 Box dimensions : A = 12.0, B = 12.0, C = 12.0
=============================================================
100%|███████████████████████████████████████████████████████████████████████| 99/99 [00:00<00:00, 4407.79it/s]
POSCAR files written in directory, poscar_files.

❯ xyzconverter -i centered_trajec.xyz -o VASP -b 12 13 11

Converting to VASP POSCAR format...
=============================================================
 Reading file : centered_trajec.xyz
 Box dimensions : A = 12.0, B = 13.0, C = 11.0
=============================================================
100%|███████████████████████████████████████████████████████████████████████| 99/99 [00:00<00:00, 5886.62it/s]
POSCAR files written in directory, poscar_files.

Author:

RAHUL VERMA
Department of Chemical and Biomolecular Engineering
NC State University, Raleigh, USA
Email: rverma7@ncsu.edu