[ase-users] ASE database website

[Michael Joseph Waters]

Currently, I see .xyz and .json .

I'd like a format that support lattice vectors. The .xyz files don't contain them on the comment line like some of the .xyz files produced by ASE.  CIF and POSCAR are common formats for on materials project/AFLOW/OQMD.

 I know .json isn't aimed at being nicely formatted for humans, so I don't want to use that alone.

Personally, I prefer not using CIFs because the format is overly complex for specifying arbitrary atoms in a periodic cell. Sometimes compatibility is tricky.

POSCAR is nearly perfect for my uses, but it's not a fixed standard, just the input format for VASP. And seeing as how the format can change (vasp4 vs. vasp5) and its various options like selective dynamics and optional elements, It might not be a good long-term format. It does have reasonably good support though.

I'd settle for POSCAR if the elements are specified in the VASP5 format and the direct/fractional/scaled positions are used. Overall, I am very open to suggestions!

Best,
-Mike
________________________________
From: Jens Jørgen Mortensen <jjmo at dtu.dk>
Sent: Wednesday, March 3, 2021 3:22 PM
To: Michael Joseph Waters <michael.j.waters at northwestern.edu>; ase-users <ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] ASE database website

Den 03.03.2021 kl. 17.22 skrev Michael Joseph Waters via ase-users:
> This is very helpful, thank you.
>
> I have a quick question about download formats. Is it possible to add an
> option for something other than xyz and json?

Yes, everything can be customized.  You can write your own row.html to
extend or replace ase/db/templates/row.html and you can also add your
own endpoints to ase.db.app.app.

We could also consider extending the possible download formats directly
in ASE.  What format do you have in mind?

Jens Jørgen

> Best,
> -Mike
> ------------------------------------------------------------------------
> *From:* Jens Jørgen Mortensen <jjmo at dtu.dk>
> *Sent:* Monday, March 1, 2021 1:53 AM
> *To:* Michael Joseph Waters <michael.j.waters at northwestern.edu>;
> ase-users <ase-users at listserv.fysik.dtu.dk>
> *Subject:* Re: [ase-users] ASE database website
> Den 26.02.2021 kl. 17.20 skrev Michael Joseph Waters via ase-users:
>> Hi all,
>>
>> I'd like to explore setting up a data base website as described here:
>> (https://urldefense.com/v3/__https://wiki.fysik.dtu.dk/ase/ase/db/db.html*browse-database-with-your-web-browser__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!HK-iJLgAxC_AcP-s5-LdtIm_yuxnCoNAY8XtVj3VfQYZtt21vzhNa80hK3JyU9BXckywM07-lskt$
>
>> <https://urldefense.com/v3/__https://wiki.fysik.dtu.dk/ase/ase/db/db.html*browse-database-with-your-web-browser__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!HK-iJLgAxC_AcP-s5-LdtIm_yuxnCoNAY8XtVj3VfQYZtt21vzhNa80hK3JyU9BXckywM07-lskt$
>  >)
>>
>> Following these instructions, I am presented with this warning:
>>
>>   * Serving Flask app "ase.db.app" (lazy loading)
>>   * Environment: production
>>     WARNING: This is a development server. Do not use it in a production
>> deployment.
>>     Use a production WSGI server instead.
>>
>> How do I make this into a production server?  Any tips for configuring
>> the rest of the server environment?
>
> This might help:
>
>
> https://urldefense.com/v3/__https://wiki.fysik.dtu.dk/ase/ase/db/db.html*running-a-postgresql-server__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!HK-iJLgAxC_AcP-s5-LdtIm_yuxnCoNAY8XtVj3VfQYZtt21vzhNa80hK3JyU9BXckywMzOLhsMe$
> <https://urldefense.com/v3/__https://wiki.fysik.dtu.dk/ase/ase/db/db.html*running-a-postgresql-server__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!HK-iJLgAxC_AcP-s5-LdtIm_yuxnCoNAY8XtVj3VfQYZtt21vzhNa80hK3JyU9BXckywMzOLhsMe$>
>
> https://urldefense.com/v3/__https://cmr.fysik.dtu.dk/server.html*the-cmr-database-server__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!HK-iJLgAxC_AcP-s5-LdtIm_yuxnCoNAY8XtVj3VfQYZtt21vzhNa80hK3JyU9BXckywM__ljGyf$
> <https://urldefense.com/v3/__https://cmr.fysik.dtu.dk/server.html*the-cmr-database-server__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!HK-iJLgAxC_AcP-s5-LdtIm_yuxnCoNAY8XtVj3VfQYZtt21vzhNa80hK3JyU9BXckywM__ljGyf$>
>
>
> Jens Jørgen
>
>> Best,
>> -Mike
>>
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>
>>
>
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