"""Defects analysis module."""
from pathlib import Path
from typing import Any
import numpy as np
from numpy import typing as npt
from irradiapy.analysis.defectsidentifier import DefectsIdentifier
from irradiapy.io import BZIP2LAMMPSReader, LAMMPSReader, LAMMPSWriter
[docs]
def identify_defects(
lattice: str,
a0: float,
data_atoms: dict[str, Any],
a1: float | None = None,
pos_pka: npt.NDArray[np.float64] | None = None,
theta_pka: float | None = None,
phi_pka: float | None = None,
transform: bool = False,
debug: bool = False,
) -> dict[str, Any]:
"""Identify defects in a given atomic structure.
Parameters
----------
lattice : str
Lattice type. Currently only "bcc" is supported.
a0 : float
Lattice parameter.
data_atoms : dict[str, Any]
Dictionary containing simulation data as given by the LAMMPSReader and similar readers.
Must include keys: 'atoms', 'boundary', 'xlo', 'xhi', 'ylo', 'yhi', 'zlo',
'zhi', 'timestep'.
a1 : float | None, optional (default=None)
Final lattice parameter. If provided, defect positions are rescaled to this value
(independently of the `transform` value).
pos_pka : npt.NDArray[np.float64] | None, optional (default=None)
Position vector of the PKA. If provided with theta_pka and phi_pka, defects are
recentered and aligned.
theta_pka : float | None, optional (default=None)
Polar angle (in radians) for the PKA direction.
phi_pka : float | None, optional (default=None)
Azimuthal angle (in radians) for the PKA direction.
transform : bool, optional (default=False)
If True, defects are recentered and aligned with the PKA direction (if provided). If
True but no PKA parameters are provided, defects are recentered based on their
average position. Note that the box boundaries are not modified for visualization
purposes, only the atomic positions are transformed.
debug : bool, optional (default=False)
If `True`, enables debug mode for additional output.
Returns
-------
dict[str, Any]
Snapshot data containing the identified defects in its ``"atoms"`` entry.
"""
defects_finder = DefectsIdentifier(lattice=lattice, a0=a0, debug=debug)
defects = defects_finder.identify(
data_atoms=data_atoms,
a1=a1,
pos_pka=pos_pka,
theta_pka=theta_pka,
phi_pka=phi_pka,
transform=transform,
)
return defects
[docs]
def identify_lammps_dump(
lattice: str,
a0: float,
dump_path: Path,
dump_defects_path: Path,
a1: float | None = None,
pos_pka: npt.NDArray[np.float64] | None = None,
theta_pka: float | None = None,
phi_pka: float | None = None,
transform: bool = False,
overwrite: bool = False,
debug: bool = False,
) -> None:
"""Identify defects in a LAMMPS dump file.
Parameters
----------
lattice : str
Lattice type. Currently only "bcc" is supported.
a0 : float
Lattice parameter.
dump_path : Path
Path to the LAMMPS dump file to read. Can be compressed with `.bz2` or not.
dump_defects_path : Path
Path to the output file where identified defects will be written (in text format).
a1 : float | None, optional (default=None)
Final lattice parameter. If provided, defect positions are rescaled to this value
(independently of the `transform` value).
pos_pka : npt.NDArray[np.float64] | None, optional (default=None)
Position vector of the PKA. If provided with theta_pka and phi_pka, defects are
recentered and aligned.
theta_pka : float | None, optional (default=None)
Polar angle (in radians) for the PKA direction.
phi_pka : float | None, optional (default=None)
Azimuthal angle (in radians) for the PKA direction.
transform : bool, optional (default=False)
If True, defects are recentered and aligned with the PKA direction (if provided). If
True but no PKA parameters are provided, defects are recentered based on their
average position. Note that the box boundaries are not modified for visualization
purposes, only the atomic positions are transformed.
overwrite : bool, optional (default=False)
If True, allows overwriting the output file if it already exists.
debug : bool, optional (default=False)
If `True`, enables debug mode for additional output.
"""
if dump_defects_path.exists():
if overwrite:
dump_defects_path.unlink()
else:
raise FileExistsError(f"Defects file {dump_defects_path} already exists.")
if debug:
print(f"Identifying defects in {dump_path}")
if dump_path.suffix == ".bz2":
reader = BZIP2LAMMPSReader(dump_path)
else:
reader = LAMMPSReader(dump_path)
writer = LAMMPSWriter(dump_defects_path, mode="a")
defects_finder = DefectsIdentifier(lattice=lattice, a0=a0, debug=debug)
for data_atoms in reader:
if debug:
print(f"Timestep {data_atoms['timestep']}")
defects = defects_finder.identify(
data_atoms,
a1=a1,
pos_pka=pos_pka,
theta_pka=theta_pka,
phi_pka=phi_pka,
transform=transform,
)
writer.write(defects)