Visualize phonon vibrational modes.
This project aims to provide a simple way to visualize the lattice vibrations of different materials. The temperature of a material is related to the agitation of its atoms. The atoms can move in any of the three cartesian directions. Combining the different possible ways the atoms can vibrate we obtain the eigenvectors. Each mode has associated a frequency of vibration that is related with the forces between the atoms.
In the phonon section you can click on any point in the dispersion relation and see an animation of how the atoms vibrate in that particular mode.
By default you can visualize the phonon dispersion of some materials we calculated.
If you want to see your own calculations, we currently support phonon calculations form Abinit, Quantum Espresso and phononpy.
You can visualize your own phonopy files by clicking on the Choose files button and selecting a band.yaml file. The following options should be present in the band.conf file:
EIGENVECTORS = .TRUE.
BAND_CONNECTION = .TRUE.
BAND_LABELS = Gamma M K
BAND = (x1,y1,z1) (x2,y2,z2) (x3,y3,z3)
This only works with the newer version of phonopy as new tags were added to 'band.yaml' to have information about the atomic positions and the supercell.
To read a phonon dispersion form Abinit we provide some python scripts to convert the data to a .json format.
You can obtain these scripts from the Github page. To install them just do:
python setup.py install --user
In the folder where you ran anaddb you will find a netCDF file (if your Abinit version has netCDF compiled) with the name anaddb.out_PHBST.nc. To convert it to .json format just run:
read_anaddb_phonon.py anaddb.out_PHBST.nc <name_of_your_material>
You can then select the resulting .json file with the Choose files button.
To read a Quantum Espresso calculation you need two files <prefix>.scf and <prefix>.modes. The first one is the input file for pw.x the second one can be generated with dynmat.x. The file that should be used is the one set with the 'filout' tag in the dynmat input file as in it the modes are normalized with the atomic masses.
After installing the python scripts (as in the case of an Abinit calculation) you can obtain the .json files:
read_qe_phonon.py prefix <name_of_your_material>
You can then select the resulting .json file with the Choose files button.
You can export the lattice distorted according to the currently selected phonon mode to a .xsf or POSCAR file.
The phase and amplitude sliders define a complex number that is multiplied by the phonon eigenvectors to obtain the displacements.
You can export a animated .gif with a particular mode using the gif button in the Export movie section.
If you want to share your own data with someone else you can add to the url tags with the following format:
http://henriquemiranda.github.io/phononwebsite/phonon.html?tag1=a&tag2=b
The available tags are:
json = link to a json file
yaml = link to a yaml file
name = name of the material
Here are some examples of what can be added to the website link:
- ?yaml=http://henriquemiranda.github.io/phononwebsite/tests/phonopy/band.yaml
- ?json=http://henriquemiranda.github.io/phononwebsite/graphene/data.json
You are free to use all the images generated with this website in your publications and presentations as long as you cite this work (a link to the website is enough). For the license terms of the data from phonodb please refer to their website.
In polar materials the LO-TO splitting is missing, we are working on adding these corrections.
This project is the continuation of the work of Raoul Weber during an internship in the University of Luxembourg for 2 months in the Theoretical Solid State Physics group under the supervision of Ludger Wirtz and technical help from me.
I decided to continue the project by optimizing the implementation, cleaning up the design and replacing JSmol by a self made applet using Three.js and WebGL called VibCrystal.
Currently the website works also as a web application which means the user can visualize his own calculations made with phonopy.
For more information about us and our work visit:
http://wwwen.uni.lu/
The original implementation by Raoul Weber:
http://tssphysics.jpsfs.com
My personal webpage:
http://henriquemiranda.github.io
Contact me:
miranda.henrique at gmail.com
Ludger Wirtz for the original idea and important scientific advices. Atsushi Togo the creator of phonopy for providing phonon dispersion data from his phonodb phonon database. José Pedro Silva for very helpful advices on technical issues and the best web technologies to use.
Fonds National de la Recherche Luxembourg (2013-present): http://www.fnr.lu/
University of Luxembourg (2013-present): http://wwwen.uni.lu/
The project is still under development!
You can leave your suggestions and feature requests here:
https://github.com/henriquemiranda/phononwebsite/issues
If you would like to see some of your calculations published on this website please contact me.
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The WebGL visualization is made using
Three.js: http://threejs.org/ -
The phonon dispersion is plotted using
highcharts: http://www.highcharts.com/ -
The export animation is provided using
CCapture.js: https://github.com/spite/ccapture.js -
The gif animation is uses
gif.js: http://jnordberg.github.io/gif.js/ -
Abinit: http://www.abinit.org/ -
Quantum Espresso: http://www.quantum-espresso.org/ -
phonopy: http://atztogo.github.io/phonopy/