NEBLog
- class atomman.lammps.NEBLog(neblog: str = 'log.lammps', replicalogs: str = 'log.lammps.*', rootdir: str | None = None)
Bases:
object- get_barrier(reverse: bool = False) float
Returns the barrier energy calculated from the final NEB simulation step.
- Parameters:
reverse (bool, optional) – Indicates if the energy barrier returned is the forward barrier relative to the first replica (False, default), or is the reverse barrier relative to the last replica (True).
- Returns:
The energy barrier relative to one of the endpoint replicas.
- Return type:
- get_neb_path(step: int) Tuple[ndarray, ndarray]
Retrieves the reaction coordinates and corresponding potential energies for a given simulation step.
- Parameters:
step (int) – The run step to retrieve values for.
- Returns:
reaction_coordinates (numpy.ndarray) – The reaction coordinates
potential_energies (numpy.ndarray) – The potential energies
- load(neblog: str = 'log.lammps', replicalogs: str = 'log.lammps.*', rootdir: str | None = None)
Loads LAMMPS NEB calculation log file data.
- Parameters:
neblog (str, optional) – The filename for the primary LAMMPS NEB log file. Default value is ‘log.lammps’.
replicalogs (str, optional) – The filename with wildcard for the LAMMPS NEB replica log files. Default value is ‘log.lammps.*’
rootdir (str, optional) – The root directory to use with respect to the neblog and replicalogs parameters. Default value is None, which will assume the current working directory for relative paths.