NEBLog

class atomman.lammps.NEBLog(neblog: str = 'log.lammps', replicalogs: str = 'log.lammps.*', rootdir: Optional[str] = None)

Bases: object

property climbrun: DataFrame

The NEB log data for the barrier climb steps.

Type:

pandas.DataFrame

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:

float

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: Optional[str] = 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.

property logs: List[Log]

The LAMMPS log files for each replica.

Type:

list of atomman.lammps.log

property minrun: DataFrame

The NEB log data for the minimization steps.

Type:

pandas.DataFrame

property nreplicas: int

The number of replicas

Type:

int