base.Vibration

base.Vibration(self, geom, freq=None, mw_disp=None, mw_hess=None, unit_xyz='Bohr', unit_xyz_hess='Bohr', unit_omega='Hartree', unit_mass='a.u.', disp=None)

Main Vibraion class

This class allows localization and visualization of vibrational modes.

Attributes

Name	Type	Description
unit	str	Unit of displacement vector. Defaults to Bohr.
freq	(Optional, List[float])	The list of frequencies in cm-1.
mw_disp	(Optional, List[List[float]])	The list of mass-weighted displacement vectors. disp[imode][iatom_xyz] gives displacement from refernce coordinates.
mw_hess	(Optional, np.ndarray)	mass-weighted hessian
geom	List[List[str, Tuple[float, flotat, float]]]	Referenece geometry. geom[iatom][0] gives element symbol. geom[iatom][1] gives the refernce cartesian coordinate.
bond	List[List[Tuple[int, int]]]	The pair of atom coordinates which bonded each other.
nmode	int	Number of modes.
natom	int	Number of atoms.
Q_mat	numpy.ndarray	Unitary matrix aligned displacement vectors.

Parameters

Name	Type	Description	Default
geom	List[List[str, Tuple[float, float, float]]]	Referenece geometry. geom[iatom][0] gives element symbol. geom[iatom][1] gives the refernce cartesian coordinate.	required
freq	List[float]	The list of frequencies in cm-1.	None
disp	List[List[float]]	The list of displacement vectors. disp[imode][iatom_xyz] gives displacement from refernce coordinates.	None

Methods

Name	Description
group_localize	Generate Group Localized Coordinate from mass-weighted hessian
localize	Localize vibrational modes.
visualize	Visualize vibrational modes.

group_localize

base.Vibration.group_localize(mw_hess, domain, unit_xyz='au', unit_omega='au', unit_mass='au')

Generate Group Localized Coordinate from mass-weighted hessian

Parameters

Name	Type	Description	Default
mwhess	np.ndarray	mass-weighted hessian	required
domain	List[List[float]]	atomic domain such as [[0,1,2],[3,4]]	required

localize

base.Vibration.localize(option='Pipek-Mezey', window=400)

Localize vibrational modes.

Vibration mode localization with local_cls module.

• Pipek-Mezey metric

\[ \xi_{\mathrm{at}}\left(\widetilde{\boldsymbol{Q}}^{\mathrm{sub}}\right)=\sum_{p=1}^{k} \sum_{i=1}^{n}\left(\tilde{C}_{i p}^{\mathrm{sub}}\right)^{2} \\ \tilde{C}_{i p}^{\mathrm{sub}}=\sum_{\alpha=x, y, z}\left(\tilde{Q}_{i \alpha, p}^{\mathrm{sub}}\right)^{2} \]

• Boys metric

\[ \xi_{\mathrm{dist}}\left(\widetilde{\boldsymbol{Q}}^{\mathrm{sub}}\right)=\sum_{p=1}^{k}\left(\boldsymbol{R}_{p}^{\text {center }}\right)^{2} \\ \boldsymbol{R}_{p}^{\text {center }}=\sum_{i=1}^{n} \tilde{C}_{i p}^{\mathrm{sub}} \boldsymbol{R}_{i} \]

Parameters

Name	Type	Description	Default
option	str	The metric of localization. Boys or Pipek-Mezey.	'Pipek-Mezey'
window	float	window frequency in cm-1.	400

Examples

>>> sim = Vibration(geom, freq, disp)
>>> sim.localize()

visualize

base.Vibration.visualize(arrow_scale=100, blender=False, atom_number=False)

Visualize vibrational modes.

Vibration mode visualization with Matplotlib and tinker.

Parameters

Name	Type	Description	Default
arrow_scale	float	The scale of displacement arrows. Defaults to 1.	100
blender	Optional[bool]	View by blender.	False
atom_number	Optional[bool]	Plot atom number	False

Examples

>>> sim = Vibration(geom, freq, disp)
>>> sim.visualize()