[ase-users] From CIF files to XYZ

[Landi, Alessandro]

Hello.


Obviously, I typed it wrong.


Here the right command lines I use:


atoms_ase=ase.io.read('filename.cif')
ase.io.write('filename.xyz', atoms_ase)


Anyway, I have the problem that the xyz file is wrong as I explained in my first e-mail: the molecules need to be reconnected (see files attached).


"pentacene.cif" is the cif file that I give as input to ASE;
"pentacene.xyz" is the xyz file written by ASE;
"realstructure.xyz" is the structure of the reconnected molecules (obtained using CCDC Mercury)


Any suggestions?


Best regards,

Alessandro


________________________________
Da: Oscar Xavier Guerrero <oscarxavier.ox at gmail.com>
Inviato: venerdì 8 dicembre 2017 18:36:10
A: Landi, Alessandro
Cc: ase-users at listserv.fysik.dtu.dk
Oggetto: Re: [ase-users] From CIF files to XYZ

Hello,

When you read the structure an Atoms object is created. You need to store that object on a variable and then you can write that one. As so:

First read the data:
from ase.io<http://ase.io> import read, write
atoms = read('filename.cif')
Then write:
write('filename.xyz<http://filename.xyz>', atoms)
or you can use:
atoms.write('filename.xyz<http://filename.xyz>')




2017-12-08 12:19 GMT+00:00 Landi, Alessandro via ase-users <ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>>:

Hello everyone.


I am using ASE to read some CIF files and (among other things) to convert the structure in xyz format.


However using the following commands:


ase.io.read('filename.cif', atoms_ase)
ase.io.write('filename.xyz<http://filename.xyz>', atoms_ase)

I obtain a wrong structure, since the molecules need to be reconnected. This happens for all the molecules I have tested (about 20).

Could you please explain me what I am doing wrong?

If could be of any help, I attached an example:
"pentacene.cif" is the cif file that I give as input to ASE;
"pentacene.xyz<http://pentacene.xyz>" is the xyz file written by ASE;
"realstructure.xyz<http://realstructure.xyz>" is the structure of the reconnected molecules (obtained using CCDC Mercury)

Best regards,
Alessandro


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