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

[Zeyuan Tang]

Hi Protik Das


1. I'm not familiar with jupyter notebook, maybe others can offer some suggestions.

2. If you want to use vasp5 style POSCAR while using vasp calculator, you need to add parameter (vasp5=True) for write_vasp() function in ase/calculators/vasp.py

        write_vasp('POSCAR',
                   self.atoms_sorted,
                   symbol_count=self.symbol_count,
                   vasp5=True)
3. While running vasp through 'VASP_COMMAND' environment variable, vasp output can be found in vasp.out.


Best wishes
Zeyuan Tang


________________________________
From: ase-users-bounces at listserv.fysik.dtu.dk <ase-users-bounces at listserv.fysik.dtu.dk> on behalf of Protik Das via ase-users <ase-users at listserv.fysik.dtu.dk>
Sent: Friday, December 16, 2016 5:07 AM
To: ase-users at listserv.fysik.dtu.dk
Subject: [ase-users] viewing structure in jupyter notebook and vasp calculator

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 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.
VASP - ASE documentation<https://wiki.fysik.dtu.dk/ase/ase/calculators/vasp.html>
wiki.fysik.dtu.dk
Introduction¶ VASP is a density-functional theory code using pseudopotentials or the projector-augmented wave method and a plane wave basis set.




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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