class matlantis_features.features.reaction.rest_scan.ScanDistance(indices: Tuple[int, int], direction: int, destination: float, exceed: float = 0.1, fmax: float = 0.05)#

Bases: ScanRestraint

Scan for distance.

Parameters

  • direction – 1 for scan towords large distance. -1 for scan for towards small distance.

  • destination – The scan finish when the distance reach this value.

  • exceed – In this class, scan force is turned off when it reaches the destination.
    This is a value indicating how far the scan can exceed the destination.
    This value is defined to smooth out the force field that Optimizer feels.

  • fmax – Rsstraint scan force.

Methods

__init__(indices, direction, destination[, …])

adjust_forces(atoms, forces)

adjust_momenta(atoms, momenta)

adjust_positions(atoms, positions)

get_coefficient(atoms)

get_colvar(atoms)

get_colvar_forces(atoms)

get_removed_dof(atoms)

index_shuffle(atoms, ind)

todict()
__init__(indices: Tuple[int, int], direction: int, destination: float, exceed: float = 0.1, fmax: float = 0.05) → None#
adjust_forces(atoms: Atoms, forces: ndarray) → None#
adjust_momenta(atoms: Atoms, momenta: ndarray) → None#
adjust_positions(atoms: Atoms, positions: ndarray) → None#
get_coefficient(atoms: Atoms) → float#
get_colvar(atoms: Atoms) → float#
get_colvar_forces(atoms: Atoms) → ndarray#
get_removed_dof(atoms: Atoms) → int#
index_shuffle(atoms: Atoms, ind: ndarray) → None#
todict() → Dict[str, Any]#