rgpycrumbs.eon.ptmdisp

Identifies non-crystalline atoms using polyhedral template matching.

Added in version 0.0.2.

Identifies atoms in a structure file that do not match a specified crystal structure (e.g., FCC) and prints their 0-based indices to standard output. By default, the script is quiet. Use –verbose for progress messages.

Attributes

log
STRUCTURE_TYPE_MAP

Classes

StrEnum	Backport for Python 3.10.
CrystalStructure	Enum where members are also (and must be) strings

Functions

find_mismatch_indices(→ numpy.ndarray)	Analyzes a structure file with PTM, identifies the interstitial defect,
main(filename, structure, verbose, no_fcc_vacancy)	Analyzes FILENAME to find all atoms that are NOT the specified

Module Contents

class rgpycrumbs.eon.ptmdisp.StrEnum

Bases: str, enum.Enum

Backport for Python 3.10.

rgpycrumbs.eon.ptmdisp.log

class rgpycrumbs.eon.ptmdisp.CrystalStructure

Bases: enum.StrEnum

Enum where members are also (and must be) strings

OTHER = 'Other'

FCC = 'FCC'

HCP = 'HCP'

BCC = 'BCC'

ICO = 'Icosahedral'

rgpycrumbs.eon.ptmdisp.STRUCTURE_TYPE_MAP

rgpycrumbs.eon.ptmdisp.find_mismatch_indices(filename: str, target_structure: CrystalStructure, remove_fcc_vacancy: bool = False, view_selection: bool = True, selection_radius: float = 5) → numpy.ndarray

Analyzes a structure file with PTM, identifies the interstitial defect, and returns the indices of the interstitial atoms plus all atoms within a sphere of radius selection_radius.

rgpycrumbs.eon.ptmdisp.main(filename: str, structure: CrystalStructure, verbose: bool, no_fcc_vacancy: bool)

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.