degeneracy_class module

This module contains methods and classes treating degenerate orbital energies while post-processing NMFD/ENMFD displacements to obtain phonon-renormalizations of the single-particle levels.

Danger

Most probably you would never need to use this basic classes. Only use if you know what you are doing.

class degeneracy_class.degeneracy(logfile, eigval_file, overlap_file=None, degeneracy_cutoff=0.002)

Bases: object

This class will read the Kohn Sham eigenvalues from a file and divide it into defferent set of degenerate eigenvalues based on a defined degeneracy cut_off.

Arguments:

logfile = Logfile path

eigval_file = A file path where each column defined KS eigenvalue (band energies) with a particular orbital-index.

overlap_file = overlap_file path contains overlap matrix to map orbitals between two normal-mode displaced structures.

degeneracy_cutoff = Any two elements within a degenerate set would be smaller than this value.

rewrite_ks_eigval(filename)

Method to rewrite the modified eigenvalues in a separate file. Argument: filename

Warning

Usually used for debugging.

class degeneracy_class.align_band_energies(logfile, eigval_file, overlap_file=None, degeneracy_cutoff=0.002)

Bases: degeneracy_class.degeneracy

This class will read the Kohn Sham eigenvalues (band energies) from a file for several snapshots obtained from simulations with independent mode approximation then align their energies with respect to the energies of the optimized geometry. This alignment would be done based on maximum overlap, therefore for each snapshot an overlap-matrix with respect to optimized geometry must be supplied. If the difference between two bands are smaller than a user specified cut-off they would be treated as degenerate.

Arguments:

logfile = Logfile path

eigval_file = A file path where each column defined KS eigenvalues (band energies) with a particular orbital-index.

overlap_file = overlap_file path contains overlap matrix to map orbitals between displaced & optimized geometry

degeneracy_cutoff = Any two elements within a degenerate set would be smaller than this value.

..warning::

Only to be used with simulations with independent mode approximation when each phonon modes are excited one by one. This should not be used to align energies when all phonon modes are excited at once such as standard MD or MC simulations.