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- correlate_vibrations(L_ref_p, L_tr_p, atom_pairs, U, remove_tr_rot=False, L_tr_rot_F_ref=None, L_tr_rot_F_tr=None)
- Calculate the similarity and overlap of two vibrations on a fragment.
The vibrations must be given as mass-weighted excursions.
Let us denote the first vibration as reference, and the second one as trial.
Positional arguments :
L_ref_p -- reference vibration (one-based ndarray)
shape : (1 + Natoms_ref, 4) with Natoms_ref being the
number of atoms in the reference molecule
L_tr_p -- trial vibration (one-based ndarray)
shape : (1 + Natoms_tr, 4) with Natoms_ref being the
number of atoms in the trial molecule
atom_pairs -- atom pairs comprising the fragment
(null-based ndarray)
shape : (Natoms_F, 2) with Natoms_F being the number of
atoms in the fragment
atom numbers are one-based
example : array([ [1, 1], [3, 3], [9, 9] ])
U -- rotation matrix found by superimposing the reference and
trial molecules on the fragment (one-based ndarray)
shape : (4, 4)
The trial vibration is rotated with this matrix.
if None, the rotation is not carried out.
refer to pyviblib.calc.qtrfit.fit()
Keyword arguments :
remove_tr_rot -- whether the non-vibrational contaminations are to be
removed (default False)
L_tr_rot_F_ref -- translations/rotations on the reference *FRAGMENT*
(one-based ndarray, default None)
shape : (4 + nrot_ref, Natoms_F, 4) with nrot_ref being the
number of rotational degrees of freedom in the reference
molecule
must be supplied if remove_tr_rot is True
L_tr_rot_F_tr -- translations/rotations on the trial *FRAGMENT*
(one-based ndarray, default None)
shape : (4 + nrot_tr, Natoms_F, 4) with nrot_tr being the
number of rotational degrees of freedom in the trial
molecule
must be supplied if remove_tr_rot is True
Return a dictionary with the following keys :
similarity -- similarity
overlap -- overlap
- correlate_vibrations_all(L_ref, L_tr_rot_ref, L_tr, L_tr_rot_tr, atom_pairs, U=None, include_tr_rot=False, remove_tr_rot=False, L_tr_rot_F_ref=None, L_tr_rot_F_tr=None)
- Correlate a set of vibrations on a fragment.
The vibrations to be correlated must be given as mass-weighted excursions.
Let us denote by reference the first set of vibrations and by trial the second
one.
Positional arguments :
L_ref -- vibrations of the reference molecule (one-based ndarray)
shape : (1 + NFreq_ref, 1 + Natoms_ref, 4) with NFreq_ref
being the number of vibrations in the reference molecule
and Natoms_ref the number of atoms in it
L_tr_rot_ref -- translations/rotations of the reference molecule
(one-based ndarray)
shape : (4 + nrot_ref, 1 + Natoms_ref, 4) with nrot_ref
being the number of rotational degrees of freedom in the
reference molecule
L_tr -- vibrations of the trial molecule (one-based ndarray)
shape : (1 + NFreq_tr, 1 + Natoms_tr, 4) with NFreq_tr
being the number of vibrations in the trial molecule
and Natoms_tr the number of atoms in it
L_tr_rot_tr -- translations/rotations of the trial molecule
(one-based ndarray)
shape : (4 + nrot_tr, 1 + Natoms_tr, 4) with nrot_tr
being the number of rotational degrees of freedom in the
trial molecule
atom_pairs -- atom pairs comprising the fragment
(null-based ndarray)
shape : (Natoms_F, 2) with Natoms_F being the number of
atoms in the fragment
atom numbers are one-based
example : array([ [1, 1], [3, 3], [9, 9] ])
Keyword arguments :
U -- rotation matrix found by superimposing the reference and
trial fragments (one-based ndarray, default None)
shape : (4, 4)
The trial vibrations are rotated with this matrix.
if None, the rotation is not carried out.
include_tr_rot -- include the translations/rotations explicitely in the
result overlaps and similarities matrices.
remove_tr_rot -- whether the non-vibrational contaminations are to be
removed (default False)
L_tr_rot_F_ref -- translations/rotations on the reference fragment
(one-based ndarray, default None)
shape : (4 + nrot_ref, Natoms_F, 4) with nrot_ref being the
number of rotational degrees of freedom in the reference
molecule and Natoms_F the number of atoms in the fragment
must be supplied if remove_tr_rot is True
L_tr_rot_F_tr -- translations/rotations on the trial fragment
(one-based ndarray, default None)
shape : (4 + nrot_tr, Natoms_F, 4) with nrot_tr being the
number of rotational degrees of freedom in the trial
molecule
must be supplied if remove_tr_rot is True
Return a dictionary with the following keys :
overlaps : overlaps matrix (one-based ndarray)
similarities : similarities matrix (one-based ndarray)
- create_dyad(L_p, atom_list=None)
- Create the dyad tensor for a vibration on a fragment.
Positional arguments :
L_p -- mass-weighted excursion for the vibration (one-based ndarray)
shape : (1 + Natoms, 4) with Natoms being the number of atoms
in the molecule
Keyword arguments :
atom_list -- atoms comprising the fragment (null-based ndarray, default None)
atom numbers are one-based
shape : (Natoms_F,) with Natoms_F being the number of atoms in
the fragment
if None, use all atoms
Return the dyad with the shape (1 + Natoms_F, 4, 1 + Natoms_F, 4).
- dcm_p(coords, Lx, nu)
- Calculate the distance change matrix (DCM) for a normal mode.
Positional arguments :
coords -- coordinates of the atoms (one-based ndarray)
shape : (1 + Natoms, 4) with Natoms being the number of atoms
Lx -- cartesian excursions (one-based ndarray)
shape : (1 + Natoms, 4)
nu -- wavenumber in cm**(-1)
The return value is an one-based ndarray with the
shape (1 + Natoms, 1 + Natoms).
- generate_tr_rot(L, coords, masses, atom_list=None)
- Generate translations/rotations for a fragment in a molecule.
Positional arguments :
L -- set of vibrations (one-based ndarray)
if given, the result translations/rotations will be made
orthogonal to the set
shape : (1 + Nvib, 1 + Natoms, 4) with Nvib being number of
vibrations, Natoms the number of atoms
coords -- coordinates of the atoms (one-based ndarray)
shape : (1 + Natoms, 4)
masses -- masses of the atoms (one-based ndarray)
shape : (1 + Natoms,)
Keyword arguments :
atom_list -- atoms comprising the fragment (null-based ndarray, default None)
atom numbers are one-based
shape : (Natoms_F,) with Natoms_F being the number of atoms in
the fragment
if None, use all atoms
The return value is a dictionary with the following keys :
L_tr_rot : set of the translations and rotations (one-based ndarray)
shape : (4 + nrot, 1 + Natoms_F, 4) with nrot being the number
of rotational degrees of freedom
The first three members are always translations.
The number of rotations nrot can vary.
I : principal axes of the inertia tensor (null-based ndarray)
shape : (3,)
I_values : principal values of the inertia tensor (null-based ndarray)
shape : (3,)
- omega_p(nu)
- Calculate the angular frequency.
omega_p = 200 * pi * C * nu.
Positional arguments :
nu -- wavenumber in cm**(-1)
The return value is expressed in inverse seconds.
- remove_contaminations(L_p, L_tr_rot_F, atoms)
- Remove the translational and rotational contaminations on a fragment.
Positional argument :
L_p -- mass-weighted excursion for the vibration (one-based ndarray)
shape : (1 + Natoms, 4) with Natoms being the number of atoms
in the molecule
L_tr_rot_F -- mass-weighted excursions for the translations/rotations on
the fragment (one-based ndarray)
shape : (4 + nrot, Natoms_F, 4) with nrot being the number of
rotational degrees of freedom and Natoms_F the number of atoms
in the fragment
atoms -- atoms comprising the fragment (null-based ndarray)
shape : (Natoms_F,)
atom numbers are one-based
Return the dyad for the vibration on the fragment, from which the
rotational/translational contaminations have been removed.
Shape : (1 + Natoms_F, 4, 1 + Natoms_F, 4)
- vib_amplitudes(Lx, nu, n_p=0)
- Calculate the amplitudes of atoms for a vibration.
Positional arguments :
Lx -- cartesian excursions (one-based ndarray)
shape : (1 + Natoms, 4) with Natoms being the number of atoms
nu -- wavenumber in cm**(-1)
Keyword arguments :
n_p -- vibrational number (default 0)
the default value instructs to calculate the zero-point amplitudes
The return value is an one-based ndarray with the shape (1 + Natoms,).
The units are angstroms.
- vibana(hessian, coords, masses)
- Perform the vibrational analysis.
For details refer to http://www.gaussian.com/g_whitepap/vib.htm.
This implementation generates the translations and rotations around
the pricipal axes of the inertia tensor.
Positional arguments :
hessian -- Hessian matrix (one-based ndarray)
shape : (1 + Natoms, 4, 1 + Natoms, 4)
coords -- coordinates of the atoms (one-based ndarray)
shape : (1 + Natoms, 4)
masses -- masses of the atoms (one-based ndarray)
shape : (1 + Natoms,)
Return a dictionary with the following keys :
freqs : frequencies array sorted in ascending order (one-based ndarray)
shape : (1 + NFreq,) with NFreq being the number of vibrations
L : set of mass-weighted excursions (one-based ndarray)
shape : (1 + NFreq, 1 + Natoms, 4)
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