io

asext.io

Modules:

• readwrite –

readwrite

Functions:

• read_extxyz –

  Read extxyz file. The existing ase.io.read returns a single Atoms object if file contains only one frame. This function will return a list of Atoms object.

• write_extxyz –

  Write a list of Atoms object to an extxyz file. The existing ase.io.write function does not support writing file if the parent directory does not exist. This function will overcome this problem.

• read_lmpdump –

  Shortcut to ase.io.lammpsrun.read_lammps_dump function.

• write_lmpdata –

  Shortcut to ase.io.lammpsdata.write_lammps_data function.

• extxyz2lmpdata –

  Convert extxyz file to LAMMPS data file.

• lmpdata2extxyz –

  Convert LAMMPS data file to extxyz file.

• lmpdump2extxyz –

  Convert LAMMPS dump file to extxyz file.

read_extxyz(extxyz_file: str, index=':') -> list[Atoms]

Read extxyz file. The existing ase.io.read returns a single Atoms object if file contains only one frame. This function will return a list of Atoms object.

Parameters:

• extxyz_file (str) –

  Path to the output file.

• index (int | slice | str, default: ':' ) –

  integer or slice object (default: get all frames)

Returns:

• list ( list[Atoms] ) –

  List of Atoms object.

Note

• ase.io.read returns a single Atoms object or a list of Atoms object, depending on the index argument.
  • index=":" will always return a list.
  • index=0 or index=-1 will return a single Atoms object.
• this function will always return a list of Atoms object, even index=0 or index=-1

write_extxyz(outfile: str, structs: list[Atoms] | Atoms) -> None

Write a list of Atoms object to an extxyz file. The existing ase.io.write function does not support writing file if the parent directory does not exist. This function will overcome this problem.

Parameters:

• structs (list) –

  List of Atoms object.

• outfile (str) –

  Path to the output file.

read_lmpdump(lmpdump_file: str, index=-1, units='metal', **kwargs) -> list[Atoms]

Shortcut to ase.io.lammpsrun.read_lammps_dump function.

Parameters:

• lmpdump_file (str) –

  Path to the LAMMPS dump file.

• index (int | list[int], default: -1 ) –

  integer or slice object (default: get the last timestep)

• units (str, default: 'metal' ) –

  lammps units for unit transformation between lammps and ase

• order (bool) –

  sort atoms by id. Might be faster to turn off. Default: True

• specorder (list[str]) –

  list of species to map lammps types to ase-species. Default: None

• **kwargs –

  Additional arguments passed to ase.io.lammpsrun.read_lammps_dump

Returns:

• list ( list[Atoms] ) –

  List of Atoms object.

write_lmpdata(file: str, atoms: Atoms, *, specorder: list[str] | None = None, reduce_cell: bool = False, force_skew: bool = False, prismobj: Prism | None = None, write_image_flags: bool = False, masses: bool = True, velocities: bool = False, units: str = 'metal', bonds: bool = True, atom_style: str = 'atomic') -> None

Shortcut to ase.io.lammpsdata.write_lammps_data function.

Parameters:

• file (str) –

  File to which the output will be written.

• atoms (Atoms) –

  Atoms to be written.

• specorder (list[str], default: None ) –

  Chemical symbols in the order of LAMMPS atom types, by default None

• force_skew (bool, default: False ) –

  Force to write the cell as a triclinic <https://docs.lammps.org/Howto_triclinic.html> box, by default False

• reduce_cell (bool, default: False ) –

  Whether the cell shape is reduced or not, by default False

• prismobj (Prism | None, default: None ) –

  Prism, by default None

• write_image_flags (bool, default: False ) –

  default False. If True, the image flags, i.e., in which images of the periodic simulation box the atoms are, are written.

• masses (bool, default: True ) –

  Whether the atomic masses are written or not, by default True

• velocities (bool, default: False ) –

  Whether the atomic velocities are written or not, by default False

• units (str, default: 'metal' ) –

  LAMMPS units <https://docs.lammps.org/units.html>, by default 'metal'

• bonds (bool, default: True ) –

  Whether the bonds are written or not. Bonds can only be written for atom_style='full', by default True

• atom_style –

  {'atomic', 'charge', 'full'}, optional. LAMMPS atom style <https://docs.lammps.org/atom_style.html>, by default 'atomic'

Returns:

• None –

  None

extxyz2lmpdata(extxyz_file: str, lmpdata_file: str, masses: bool = True, units: str = 'metal', atom_style: str = 'atomic', **kwargs) -> tuple[list, list]

Convert extxyz file to LAMMPS data file.

Note

• need to save 'original_cell' to able to revert the original orientation of the crystal.
• Use atoms.arrays['type'] to set atom types when convert from extxyz to lammpsdata file.

lmpdata2extxyz(lmpdata_file: str, extxyz_file: str, original_cell_file: str | None = None)

Convert LAMMPS data file to extxyz file.

lmpdump2extxyz(lmpdump_file: str, extxyz_file: str, index: int | slice = -1, original_cell_file: str | None = None, stress_file: str | None = None, lammps_units: str = 'metal')

Convert LAMMPS dump file to extxyz file.

Parameters:

• lmpdump_file (str) –

  Path to the LAMMPS dump file.

• extxyz_file (str) –

  Path to the output extxyz file.

• index (int | slice | str, default: -1 ) –

  Integer, slice, or string to specify which frames to read from the LAMMPS dump file. Defaults to -1 (last frame).

• original_cell_file (str | None, default: None ) –

  Path to the text file contains original_cell. It should a simple text file that can write/read with numpy. If not provided, try to find in the same directory as lmpdump_file with the extension .original_cell. Defaults to None.

• stress_file (str | None, default: None ) –

  Path to the text file contains stress tensor. Defaults to None.

• lammps_units (str, default: 'metal' ) –

  LAMMPS units for unit transformation between LAMMPS and ASE. Defaults to "metal".

Restriction

• Current ver: stress is mapped based on frame_index, it requires that frames in text stress file must be in the same "length and order" as in the LAMMPS dump file.
• struct.info.get("timestep") is a new feature in ASE 3.25 ?