https://github.com/jarvist/julia-phonons
Julia codes to play with Phonons
https://github.com/jarvist/julia-phonons
phonons phonopy
Last synced: 3 months ago
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Julia codes to play with Phonons
- Host: GitHub
- URL: https://github.com/jarvist/julia-phonons
- Owner: jarvist
- License: mit
- Created: 2015-08-26T18:49:15.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2018-11-07T13:38:59.000Z (almost 7 years ago)
- Last Synced: 2025-04-14T10:52:28.710Z (6 months ago)
- Topics: phonons, phonopy
- Language: Julia
- Size: 302 KB
- Stars: 24
- Watchers: 4
- Forks: 11
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Julia-Phonons
Codes to play with Phonons, as output from Phonopy, in Julia.
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
- [x] 'Animated' .xyz files, with or without supercell expansion.
* ((I recommend `Pymol` to visualise, with `set grid_mode,1` and `show
spheres` ))
- [x] Decomposition to individual atoms, norm of Energy or Displacement weighted phonon eigenvectors
- [x] Decomposition to atom type, for generating %fractional contribution of structure to phonon modes
- [x] Inverse Participation Ratio (IPR) of the mode by Energy and Displacement, as
a localisation metric.
- [x] 'Conflation' animation of multiple modes, with the relative harmonies being displayed
- [x] Generates a synchronised audio-track 'warble' for the relative harmonies of the conflation: https://www.youtube.com/watch?v=7UoPgFJcRoI
## Future plans
- [ ] Symmetry / mode analysis
- [ ] Maybe with these exciting new 'distortion antisymmetry' ideas: http://dx.doi.org/10.1038/ncomms9818