[ase-users] viewing structure in jupyter notebook and vasp calculator

Adam Jackson a.j.jackson at physics.org
Fri Dec 16 12:38:16 CET 2016

Hi everyone, 
I need help regarding some issues. I thought it would be best to put them 
in one email rather than sending a bunch. 
1. For ase related coding I use jupyter notebook a lot. For that I would 
like to view my structures in the browser. Is there any interactive 
plotting library that works well with ase? I don't need anything fancy, 
just need to make sure that my structure is looking right 
I tried a few but they need a lot modification. Also the ase view gives me 
the following error: 
FileNotFoundError: [WinError 2] The system cannot find the file specified 
I am using conda3 in windows 10. 

Hi Protik,

the method I usually use is to generate a PNG file with something like

import ase.io
atoms = ase.io.read('POSCAR')
atoms.write('poscar.png', show_unit_cell=True, radii=0.5)

and then follow that code cell with a Markdown cell displaying the generated file


The only catch I find with this approach is that the image will not automatically refresh when the file is changed;
to update the image I need to save the Jupyter notebook and refresh the browser window.

I would not be surprised if a more elegant approach exists, but this works for me!
(A similar approach is useful for org-babel documents in Emacs.)

All the best,

Dr Adam J. Jackson
Post-doctoral research associate
Dept of Chemistry
University College London

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