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

[James Kermode]

Hi all

There is an ASE interface to chemview in matscipy:
https://github.com/libAtoms/matscipy/blob/master/matscipy/visualise.py <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/ <http://futurefullers.com/imolecule/>
> - chemview: http://chemview.readthedocs.io/en/latest/ <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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