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

Protik Das protik77 at gmail.com
Thu Dec 15 22:07:27 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.

2. While using the vasp calculator, I have found that the POSCAR created by
ASE is vasp v4 style. That means the 6th line does not have the name of the
element. Is there any way to produce vasp v5 style POSCAR while using vasp

3. For running my VASP calculation I am following this tutorial:
https://wiki.fysik.dtu.dk/ase/ase/calculators/vasp.html . I am using PBS
job scheduling to run calculations. Usually with PBS or slum I could
redirect the vasp output to a log file. But while using ASE, the output
file only have the print outputs of python script and the vasp outputs are
lost. Is there any way to redirect the vasp output to a file? For some
cases like structural optimization this output file can come in handy.

Your help regarding this is really appreciated. Thanks.
Protik Das,
ECE Graduate Student,
LATTE (http://latte.ece.ucr.edu),
University of California, Riverside.
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