Polyhedral Template Matcher

PTM Displacement

Identifies atoms in a structure file that do not match a specified crystal structure (e.g., FCC) using Polyhedral Template Matching (PTM). It outputs the 0-based indices of these defect atoms (e.g., interstitials), which is useful for filtering or setting up atom lists for the displacements used for EON calculations.

rgpycrumbs eon ptmdisp

Analyzes FILENAME to find all atoms that are NOT the specified crystal structure type and prints their 0-based indices as a comma-separated list, suitable for use in other programs.

Usage

rgpycrumbs eon ptmdisp [OPTIONS] FILENAME

Options

-s, --structure-type <structure>

The crystal structure to identify and exclude.

Default:

<CrystalStructure.FCC: 'FCC'>

Options:

Other | FCC | HCP | BCC | Icosahedral

-v, --verbose

Enable verbose informational output to stderr.

--no-fcc-vacancy <no_fcc_vacancy>

Disable FCC vacancy processing.

Arguments

FILENAME

Required argument

Usage

$ python -m rgpycrumbs.cli eon ptmdisp --help
--> Dispatching to: uv run /home/runner/work/rgpycrumbs/rgpycrumbs/rgpycrumbs/eon/ptmdisp.py --help
Error: 'uv' command not found. Is it installed?

API Reference

For developer details and source code see rgpycrumbs.eon.ptmdisp.