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trajectory

TrajectoryObserver 

TrajectoryObserver(atoms, file, interval=1, mode='a', write_kwargs=None, **observer_kwargs)

Bases: TextObserver

Parameters:

  • atoms (Atoms) –

    The ASE Atoms object to write to the trajectory file.

  • file (IO | str | Path) –

    The file or path to the trajectory file.

  • interval (int, default: 1 ) –

    The interval at which to write the trajectory, by default 1.

  • mode (str, default: 'a' ) –

    The mode in which to open the file (e.g., 'a' for append), by default "a".

  • write_kwargs (dict[str, Any] | None, default: None ) –

    Additional keyword arguments to pass to the writing function, by default None.

  • **observer_kwargs (Any, default: {} ) –

    Additional keyword arguments for the observer class.

Source code in quansino/io/trajectory.py 
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def __init__(
    self,
    atoms: Atoms,
    file: IO | Path | str,
    interval: int = 1,
    mode: str = "a",
    write_kwargs: dict[str, Any] | None = None,
    **observer_kwargs: Any,
) -> None:
    """
    Initialize the `TrajectoryObserver` with mode, and other parameters. In `quansino`, trajectory files are written in the XYZ format using ASE's `write_xyz` function.

    Parameters
    ----------
    atoms : Atoms
        The ASE Atoms object to write to the trajectory file.
    file : IO | str | Path
        The file or path to the trajectory file.
    interval : int, optional
        The interval at which to write the trajectory, by default 1.
    mode : str, optional
        The mode in which to open the file (e.g., 'a' for append), by default "a".
    write_kwargs : dict[str, Any] | None, optional
        Additional keyword arguments to pass to the writing function, by default None.
    **observer_kwargs : Any
        Additional keyword arguments for the observer class.
    """
    super().__init__(file=file, interval=interval, mode=mode, **observer_kwargs)

    self.atoms = proxy(atoms)
    self.write_kwargs = write_kwargs or {}

__call__ 

__call__()

Call the function to write the trajectory to the file.

Source code in quansino/io/trajectory.py 
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def __call__(self) -> None:
    """Call the function to write the trajectory to the file."""
    write_xyz(self._file, images=self.atoms, **self.write_kwargs)
    self._file.flush()