CDTK.Tools.NormalModeAnalysis module

CDTK.Tools.NormalModeAnalysis.normal_modes_from_HessianCart(Hc, m, x0=None, proj=False, subgroups=None, **opts)

Normal modes analysis from the Cartesian Hessian matrix

Hc – Hessian matrix in Cartesian coordinates (in general non mass-weighted)

np.array, shape=(N,N) where N is the number of coordinates

m – Mass of each coordinate, 3N array for molecules in 3D space

np.array, shape=(N,)

x0 – Reference geometry on which the Hessian was calculated [optional] proj – Requires x0. If True, the overall translation and rotation of the molecule, as

well as the rotation of any given >subgroups are projected out before normal mode analysis [optional]

subgroups – Requires x0 and proj=True. May contain arrays of atomic indices that

each specify a rotating subgroup with respect to the atom index positions given in m. The rotation of this subgroup with the smallest moment of inertia is projected out before normal mode analysis [optional]

output:

omega – array with angular frequencies of each mode L – mass weighted normal modes (in columns)

CDTK.Tools.NormalModeAnalysis.q_mw_to_x(m, L)

Normal mode Mass weighted displacements to unweighted Cartesian

m – array with mass of each coordinate L – mass weighted normal modes

Returns:

2D array with normalized Cartesian normal modes in _rows_ This array can now be used to perform displacements in the unweighted Cartesian space.