Phonon Calculations
The Phonon class allows to compute the normal modes
and vibration energies of a system using a machine
learning trained model.
- class mlcalcdriver.workflows.phonon.Phonon(posinp, calculator, relax=True, finite_difference=False, translation_amplitudes=None)[source]
Bases:
objectThis class allows to run all the calculations enabling the computation of the phonon energies of a given system, using machine learning models.
To get the phonon energies of the system, one needs to find the eigenvalues of the dynamical matrix, that is closely related to the Hessian matrix. To build these matrices, one must find the derivatives of the forces when each coordinate of each atom is translated by a small amount around the equilibrium positions.
The initial position fo the atoms are taken from the init_state Posinp instance. If they are not part of a relaxed geometry, the relax parameter should stay at True.
WARNING: Relaxed geometries are dependent on the model chosen to define the calculator. In doubt, relax parameter should be ignored.
The distance of the displacement in each direction is controlled by translation_amplitudes.
Phonon energies and normal modes are calculated using the run()`method. This method creates the additional structures needed, passes them to a `Job instance, then post-processes the obtained forces to obtain them.
- Parameters
posinp (mlcaldriver.Posinp) – Initial positions of the system under consideration.
calculator (Calculator) – mlcalcdriver.Calculator instance that will be used in the created Jobs to evaluate properties.
relax (bool) – Wether the initial positions need to be relaxed or not. Default is True.
finite_difference (bool) – If True, the hessian matrix is calculated using finite displacements of atoms. Default is False. Mostly there for legacy reasons.
translation_amplitudes (list of length 3) – Amplitudes of the translations to be applied to each atom along each of the three space coordinates (in angstroms). Only relevant if finite_difference is True.
- property posinp
- Returns
posinp – Initial positions of the system for which phonon properties will be calculated.
- Return type
- property calculator
- Returns
The Calculator object to use for the Jobs necessary to perform the phonons calculations.
- Return type
- property translation_amplitudes
- Returns
translation_amplitudes – Displacements of atoms in all three dimensions to calculate the phonon properties. Default is 0.03 Angstroms.
- Return type
float
- property relax
- Returns
relax – If True, which is default, the initial positions are relaxed before the phonon properties are calculated. Recommended, especially if more than one model is used.
- Return type
bool
- property finite_difference
- Returns
finite_difference – If True, the hessian matrix is calculated using small finite movements on the atoms. Default is False.
- Return type
bool
- property energies
- Returns
Phonon energies of the system (units: cm^-1).
- Return type
numpy.array or None
- property dyn_mat
- Returns
Dynamical matrix deduced from the calculations.
- Return type
numpy.array or None
- property normal_modes
- Returns
Normal modes of the system found as eigenvectors of the dynamical matrix.
- Return type
numpy.array or None