CDTK.Interfaces.EmbeddingInterface module
- class CDTK.Interfaces.EmbeddingInterface.embedding(atomlist, atomnums, atommass3, xcart, **opts)[source]
Bases:
objectThis defines a class to embedd a QM interface into a MM region.
- energy_gradient(X, V=None, S=0, Time=0.0, SH=False, **opts)[source]
Calculates the energy and gradient of the system using an ONIOM scheme: :math: E = E_{MM}(MM+QM) + E_{QM}(QM) - E_{MM}(QM) For the electrostatic embedding calculation, the Coulomb interaction in the QM region and the QM-MM Coulomb interaction are calculated with QCE. In this case, only the MM Coulomb energy is calculated with the forcefield.
- Parameters:
X ((n_atoms, 3) ndarray of floats.) – Atomic positions, in Bohr (au).
V ((n_atoms, 3) ndarray of floats., optional) – Atomic velocities in au, by default None
S (int, optional) – Current electronic state, by default 0
Time (float, optional) – Current propagation time in au, by default 0.0
SH (bool, optional) – Whether to run surface hopping or not for QM energy, by default False
- Returns:
e (float) – Energy in atomic units
g ((n_atoms, 3) ndarray of floats.) – Gradient in atomic units.
- getConstraintsCorrection(vec0, vec1, dt, case)[source]
Calculates the correction to the position or velocities of atoms in case there are constraints. For now, only RATTLE algorithm implemented.
- Parameters:
vec0 ((3 * n_atoms) ndarray of float.) – Array with position or velocities of atoms
vec1 ((3 * n_atoms) ndarray of float.) – Array with position or velocities of atoms
dt (float) – Timestep
case (str) – Flag for different types of correction
- Returns:
correction – Array with correction for position or velocities.
- Return type:
(3 * n_atoms) ndarray of float.
- getD(X, V, t=0.0, **opts)[source]
Return matrix with kinetic couplings.
- Parameters:
X ((n_atoms, 3) ndarray of floats.) – Array of atomic positions, in Bohr (au).
V ((n_atoms, 3) ndarray of floats.) – Array with atomic velocities in au.
t (float, optional) – Current propagation time in au, by default 0.0
- Returns:
Matrix with kinetic couplings in au.
- Return type:
_type_
- getPartialCharges(chargetype='mulliken', state=0)[source]
returns partial charges of all atoms
- Parameters:
chargetype (str, optional) – Type. Defaults to ‘mulliken’.
state (int, optional) – state index. Defaults to 0.
- getW(X, V=None, t=0.0, **opts)[source]
Diagonal matrix with all adiabatic energies.
- Parameters:
X ((n_atoms, 3) ndarray of floats.) – Atomic positions, in Bohr (au).
V ((n_atoms, 3) ndarray of floats., optional) – Atomic velocities in au, by default None
t (float, optional) – Current propagation time in au, by default 0.0
- Returns:
e – Diagonal matrix with adiabatic energies in atomic units.
- Return type:
__type__
- hasConstraints()[source]
Checks wether there are constraints in the parts of the geometry modelled by forcefields.
- nac(X, SI, SJ, V, t=0.0, **opts)[source]
Nonadiabatic coupling vector between states SI and SJ.
- Parameters:
X ((n_atoms, 3) ndarray of floats.) – Atomic positions, in Bohr (au).
SI (int) – Current electronic state index.
SJ (int) – Index of state to which the coupling is calculated.
V ((n_atoms, 3) ndarray of floats.) – Atomic velocities in au.
t (float, optional) – Current propagation time in au, by default 0.0
- Returns:
coupling – Nonadiabatic coupling vector.
- Return type:
(n_atoms) ndarray of complex.