atomistics.calculators.lammps.helpers.lammps_get_structure

atomistics.calculators.lammps.helpers.lammps_get_structure(structure: Atoms, lmp_instance: LammpsASELibrary, set_velocities: bool = True, scale_atoms: bool = True, set_cell: bool = True) → Atoms

Capture the current cell, positions, and velocities of a live LAMMPS session as a standalone ase.Atoms snapshot.

The returned snapshot can be passed back into lammps_run (with an input template that does not re-initialise velocities, e.g. omitting the LAMMPS_VELOCITY command) to resume the session state later – there is no pylammpsmpi API to set velocities on an existing session directly, so a full session rebuild from such a snapshot is the only way to restore them.

Chemical symbols are copied unchanged from structure; callers that need to change species (e.g. after a Monte Carlo swap) should call structure.set_chemical_symbols(...) before passing structure in.

Parameters:

• structure (Atoms) – Template structure to copy (species, constraints, etc.); its cell, positions, and velocities are overwritten from lmp_instance.

• lmp_instance (LammpsASELibrary) – An active LAMMPS library instance.

• set_velocities (bool) – Whether to copy velocities from the LAMMPS session. Set to False if the caller intends to re-initialise velocities later.

• scale_atoms (bool) – Whether to scale atomic positions when setting the cell. Defaults to True to preserve fractional coordinates; set to False

• set_cell (bool) – Whether to copy the cell from the LAMMPS session. Defaults to True.

Returns:

A new Atoms snapshot of the current session state.

Return type:

Atoms