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Julia-Phonons

Codes to play with Phonons, as output from Phonopy, in Julia.

MAPI Phonon decomposition Per atom energy-mode decomposition.

A work in progress.

These codes read a mesh.yaml from a Phonopy calculation (Gamma only, save the eigenvectors); and a VASP POSCAR file on this structure, to collect coordinate and atom information.

Using this

Beware - Dragons!

  • First do a standard Phonopy calculation pipeline, to get your FORCE_SETS etc., then output the Eigenvectors to your mesh.yaml.

  • The animation part of this package assumes that the mode is at Gamma, but (touch wood), the Inverse Participation Ratio and Atomic decomposition by energy and displacement should also work when there's a complex phase factor, BUT THIS IS AS YET UNTESTED.

To generate a Gamma point Eigenvectors file, your Phonopy input should contain something like:

DIM = 2 2 2
FC_SYMMETRY = 1
MP = 1 1 1

EIGENVECTORS=.TRUE.

Then take your POSCAR and mesh.yaml, put them in a suitable directory with these codes, and then edit phonopy_projector.jl to do something useful with them.

Features

  • 'Animated' .xyz files, with or without supercell expansion.
    • ((I recommend Pymol to visualise, with set grid_mode,1 and show spheres ))
  • Decomposition to individual atoms, norm of Energy or Displacement weighted phonon eigenvectors
  • Decomposition to atom type, for generating %fractional contribution of structure to phonon modes
  • Inverse Participation Ratio (IPR) of the mode by Energy and Displacement, as a localisation metric.
  • 'Conflation' animation of multiple modes, with the relative harmonies being displayed
  • Generates a synchronised audio-track 'warble' for the relative harmonies of the conflation: https://www.youtube.com/watch?v=7UoPgFJcRoI

Future plans