ase-unwrap

A simple tool for unwrapping ASE-readable atomic structures.

Installation

The following installation procedure was tested:

conda create -n ase-unwrap python=3.9
conda activate ase-unwrap
python -m pip install -e .

Usage

Command-line usage:

ase-unwrap <ASE_readable_file>

The code relies on ASE neighborlists to determine the interatomic connectivity. Bonds are found automatically using natural_cutoffs (covalent radii). The default radii are usually a reasonable estimation, but a multiplier for all cutoffs may be introduced as follows:

ase-unwrap <ASE_readable_file> <cutoff_multiplier>
ase-unwrap <ASE_readable_file> 0.9
ase-unwrap <ASE_readable_file> 1.1

The output file is automatically generated. If you wish to use a non-default output name:

ase-unwrap <ASE_readable_file> <cutoff_multiplier> <output_filename>
ase-unwrap <ASE_readable_file> 1.0 my_filename.cif

The src/ase_unwrap/unwrap.py module may also be run as a Python script:

python unwrap.py <ASE_readable_file> <cutoff_multiplier> <output_filename>

or used as a library:

import ase.io
from ase_unwrap.unwrap import unwrap

atoms = read('wrapped_structure.traj')

unwrap(atoms)