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

[Peterson, Andrew]

Perhaps there is a simple in-built solution that gets us most of the way.
We currently have the ability to save atoms as html:

from ase.build import molecule
molecule('trans-butane').write('butane.html')

The output is rotatable, translatable, and zoomable. See here
<http://www.brown.edu/Departments/Engineering/Labs/Peterson/images/butane.html>
(or here
<http://www.brown.edu/Departments/Engineering/Labs/Peterson/tips/BuildAButane/index.html>)
for the output, or try it yourself. You can get this to pop up in a new tab
from jupyter with a call like os.system('firefox butane.html').

The html output file is in simple X3D format, and some quick googling
sounds like there may be ways to get that to display within a jupyter
notebook, so it could be straightforward to convert this approach into a
simple inline viewer, if we are lucky.
​


On Fri, Dec 16, 2016 at 7:25 AM, James Kermode via ase-users <
ase-users at listserv.fysik.dtu.dk> wrote:

> Hi all
>
> There is an ASE interface to chemview in matscipy:
> https://github.com/libAtoms/matscipy/blob/master/matscipy/visualise.py
>
> If there is sufficient interest this could be merged into ASE.
>
> I’ve also had good success using imolecule in Jupyter notebooks.
>
> James
>
> On 16 Dec 2016, at 11:47, Łukasz Mentel via ase-users <
> ase-users at listserv.fysik.dtu.dk> wrote:
>
>
> Hi,
>
> For interactive visualizations you could try one of:
>
> - imolecule: http://futurefullers.com/imolecule/
> - chemview: http://chemview.readthedocs.io/en/latest/
>
> There are examples on how to embed those in the jupyter notebook, but
> there is no direct interface to ASE so you would have to convert the POSCAR
> into one of the more popular formats like cif or xyz and feed it to the
> viewer.
>
> Cheers,
> Lukasz
>
> On 16.12.2016 12:38, Adam Jackson via ase-users wrote:
>
> 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
>
> ![](poscar.png)
>
> 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,
> Adam
>
>
> Dr Adam J. Jackson
> Post-doctoral research associate
> Dept of Chemistry
> University College London
>
>
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-- 
Andrew Peterson
Assistant Professor
Brown University School of Engineering
Barus & Holley 247
184 Hope Street
Providence, RI 02912
(401) 863-2153
http://brown.edu/go/catalyst
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