DWBuilder - Bug Fix: Handle periodic boundary conditions in remove_close_atoms function

The remove_close_atoms function did not consider periodic boundary conditions, which led to non-stoichiometric domains due to incorrect atom removal.

This fix updates the function to correctly account for periodic boundary conditions using the minimum image convention (mic). The NeighborList and distance calculation now work properly with periodic systems.

Issue resolved and functionality improved.

Scientific Software - Peer-reviewed - Python
Published by mzkhalid039 over 1 year ago

DWBuilder - DWBuilder2.0.0

What's Changed

• set numpy dependency <2.0 by @mailhexu in https://github.com/mzkhalid039/DWBuilder/pull/1
• main.py script was added.
• Updated dwbuilder to develop P6_3cm domain walls, addressing the issue of missing atoms in both neutral (ndw.py) and charged domain walls (cdw.py).
• Introduced a new feature to define a cutoff limit for removing closely positioned atoms.
• Introduced slab.py,supercell.py and vasp2cif.py to develop vacuum slabs, supercell and convert files from vasp to cif, .xyz or .in formats, respectively.
• Introduced bondanalysis.py to make bonding analysis.

New Contributors

• @mailhexu made their first contribution in https://github.com/mzkhalid039/DWBuilder/pull/1

Full Changelog: https://github.com/mzkhalid039/DWBuilder/compare/v1.1.0...v2.0.0

Scientific Software - Peer-reviewed - Python
Published by mzkhalid039 almost 2 years ago

DWBuilder - DWBuilder1.1.0

Full Changelog: https://github.com/mzkhalid039/DWBuilder/commits/main/

Scientific Software - Peer-reviewed - Python
Published by mzkhalid039 about 2 years ago

DWBuilder - Domain wall and interface builder

Full Changelog: https://github.com/mzkhalid039/DWBuilder/commits/v1.0.0

Scientific Software - Peer-reviewed - Python
Published by mzkhalid039 about 3 years ago