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

Michael Walter Michael.Walter at fmf.uni-freiburg.de
Fri Dec 16 08:34:35 CET 2016

2016-12-15 22:07 GMT+01:00 Protik Das via ase-users <
ase-users at listserv.fysik.dtu.dk>:

> 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
adding the possibility to use ase-gui in jupyter would be indeed a great
plus for ase. Maybe we can work on that when the gui is ported.


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 calculator?
> 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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> ase-users at listserv.fysik.dtu.dk
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PD Dr Michael Walter
- Fraunhofer IWM, Wöhlerstrasse 11, D-79108 Freiburg i. Br., Germany
  Tel.: +49 761 5142 296
- FIT Freiburg Centre for Interactive Materials and Bioinspired
Technologies, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
  Tel: +49 761 203 95072
email: Michael.Walter at fmf.uni-freiburg.de
www: http://www.functional-nanosystems.uni-freiburg.de/People/PDWalter/group
publications: http://scholar.google.com/citations?user=vlmryKEAAAAJ&hl=en
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