- class matlantis_features.features.reaction.rest_scan.ScanDihedral(indices: Tuple[int, int, int, int], direction: int, destination: float, exceed: float = 1.0, fmax: float = 0.05, current: Optional[float] = None)#
-
Bases:
ScanRestraint
Scan for dihedral.
- Parameters
-
-
direction – 1 for scan towords large angle. -1 for scan for towards small angle.
-
destination – The scan will stop when the angle is rotated by 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.
-
current – The value required to restart scan. Normally, you can ignore this value.
-
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)observe
(atoms)todict
()- __init__(indices: Tuple[int, int, int, int], direction: int, destination: float, exceed: float = 1.0, fmax: float = 0.05, current: Optional[float] = None) 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 #
- observe(atoms: Atoms) None #
- todict() Dict[str, Any] #
Resource Library
matlantis_features.features.reaction.rest_scan.ScanDihedral