[ase-users] ASE database website

Thu Mar 4 08:54:19 CET 2021

Den 04.03.2021 kl. 00.59 skrev Michael Joseph Waters via ase-users:
> 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'm also not a fan of CIF and POSCAR.  We should fix the xyz writing so 
that it will include the lattice vectors.  I think you will need to 
change 'xyz' to 'extxyz' in the ase.db.app module.  Would you like to do 
that?

Jens Jørgen

>   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$> 
> 
>> <https://urldefense.com/v3/__https://wiki.fysik.dtu.dk/ase/ase/db/db.html*running-a-postgresql-server__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!HK-iJLgAxC_AcP-s5-LdtIm_yuxnCoNAY8XtVj3VfQYZtt21vzhNa80hK3JyU9BXckywMzOLhsMe$ 
> <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$> 
> 
>> <https://urldefense.com/v3/__https://cmr.fysik.dtu.dk/server.html*the-cmr-database-server__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!HK-iJLgAxC_AcP-s5-LdtIm_yuxnCoNAY8XtVj3VfQYZtt21vzhNa80hK3JyU9BXckywM__ljGyf$ 
> <https://urldefense.com/v3/__https://cmr.fysik.dtu.dk/server.html*the-cmr-database-server__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!HK-iJLgAxC_AcP-s5-LdtIm_yuxnCoNAY8XtVj3VfQYZtt21vzhNa80hK3JyU9BXckywM__ljGyf$>> 
> 
>> 
>> 
>> Jens Jørgen
>> 
>>> Best,
>>> -Mike
>>> 
>>> _______________________________________________
>>> ase-users mailing list
>>> ase-users at listserv.fysik.dtu.dk
>>> https://urldefense.com/v3/__https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users__;!!Dq0X2DkFhyF93HkjWTBQKhk!HK-iJLgAxC_AcP-s5-LdtIm_yuxnCoNAY8XtVj3VfQYZtt21vzhNa80hK3JyU9BXckywM8iT1dYO$ 
> <https://urldefense.com/v3/__https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users__;!!Dq0X2DkFhyF93HkjWTBQKhk!HK-iJLgAxC_AcP-s5-LdtIm_yuxnCoNAY8XtVj3VfQYZtt21vzhNa80hK3JyU9BXckywM8iT1dYO$> 
> 
>> <https://urldefense.com/v3/__https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users__;!!Dq0X2DkFhyF93HkjWTBQKhk!HK-iJLgAxC_AcP-s5-LdtIm_yuxnCoNAY8XtVj3VfQYZtt21vzhNa80hK3JyU9BXckywM8iT1dYO$ 
> <https://urldefense.com/v3/__https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users__;!!Dq0X2DkFhyF93HkjWTBQKhk!HK-iJLgAxC_AcP-s5-LdtIm_yuxnCoNAY8XtVj3VfQYZtt21vzhNa80hK3JyU9BXckywM8iT1dYO$>> 
> 
>> 
>>> 
>> 
>> _______________________________________________
>> ase-users mailing list
>> ase-users at listserv.fysik.dtu.dk
>> https://urldefense.com/v3/__https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users__;!!Dq0X2DkFhyF93HkjWTBQKhk!HtMtzSScGV2BqTzKd4DRWkiS3JzTxxkezLDYg_sNkwg7uZ36I3kbl44YZsmF_W8QE3w7s5eTmRLP$ 
> <https://urldefense.com/v3/__https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users__;!!Dq0X2DkFhyF93HkjWTBQKhk!HtMtzSScGV2BqTzKd4DRWkiS3JzTxxkezLDYg_sNkwg7uZ36I3kbl44YZsmF_W8QE3w7s5eTmRLP$> 
> 
>> 
> 
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
> 