[ase-users] From CIF files to XYZ

Tom Daff tdd20 at cam.ac.uk
Mon Dec 11 11:55:40 CET 2017 

Just to expand a little further, the xyz file produced by ase is an 'extended' xyz format that includes information on the periodic boundaries. When that file is loaded in the ase gui (or ovito or atomeye...) the boundaries are conserved and the periodic images can be repeated to show the extended crystal structure. Molden and VMD do not read the lattice information from the xyz and hence show isolated fragments. You can probably enter the boundaries manually in both of those programs to regenerate the periodicity.

I have found vesta to be very nice for dealing with cif files (I have not used mercury). Opening the cif you sent immediately demonstrates the periodic nature of the structure with the molecules crossing the boundaries.

Tom

-----Original Message-----
From: ase-users-bounces at listserv.fysik.dtu.dk [mailto:ase-users-bounces at listserv.fysik.dtu.dk] On Behalf Of Ask Hjorth Larsen via ase-users
Sent: 11 December 2017 10:25
To: Landi, Alessandro <Alessandro.Landi at liverpool.ac.uk>
Cc: ase-users at listserv.fysik.dtu.dk
Subject: Re: [ase-users] From CIF files to XYZ

Hi,

The molecules are divided over the cell boundary.  This is a bit ugly, but not wrong because it is just a displacement in a periodic cell.
If you repeat the cell, molecules will indeed appear 'correctly'
connected over the boundaries.  Unless there is some convention of the cif specification about the origin of the structure, the conversion appears to be correct in this case.  You can displace by (probably) half the cell and re-wrap the positions to obtain a structure that is valid without a repeated cell, but then that's a physically different structure (molecule) than in the cif file (bulk).

Best regards
Ask

2017-12-11 10:58 GMT+01:00 Landi, Alessandro via ase-users
<ase-users at listserv.fysik.dtu.dk>:
> Hello.
>
>
> With "reconnected" I mean that the coordinates are consistent with 
> entire molecules and not with fragments at distances greater than bond length.
>
>
> It's not a matter of ordering in the list of atoms, simply all the 
> atoms constituting each molecule should be at a distance equal to bond 
> length in the xyz file.
>
>
> If you try to open the two xyz files with a visualization software 
> like Molden or VMD, you will see that, while "realstructure.xyz" shows 
> two "connected" molecules, "pentacene.xyz" has isolated fragments 
> which needs to be "reconnected", i.e. to be shifted to a distance 
> equal to bond length, in order to reconstruct 2 molecules of pentacene.
>
>
> I hope to have made a clearer description of my problem.
>
>
> Best regards,
>
> Alessandro
>
>
>
> ________________________________
> Da: ase-users-bounces at listserv.fysik.dtu.dk
> <ase-users-bounces at listserv.fysik.dtu.dk> per conto di Eric Hermes via 
> ase-users <ase-users at listserv.fysik.dtu.dk>
> Inviato: venerdì 8 dicembre 2017 19:08:01
> A: ase-users at listserv.fysik.dtu.dk
>
> Oggetto: Re: [ase-users] From CIF files to XYZ
>
> On Fri, 2017-12-08 at 18:48 +0000, Landi, Alessandro via ase-users
> wrote:
>> 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).
>
> I don't understand what you mean by "reconnected". Neither xyz file 
> that you uploaded contains any information regarding connectivity, and 
> ASE doesn't have any conception of connectivity anyway (aside from a 
> distance-based metric used in the ASE GUI to draw sticks between 
> nearby atoms). The atom ordering produced by ASE is more consistent 
> than the "realstructure.xyz" file as compared to the original cif 
> ordering. It might be that whatever program you are using with the xyz 
> files expects connected atoms to be contiguous; to the best of my 
> knowledge this is not typical. If you want to ensure this ordering 
> within ASE, you will need to manually rearrange the Atoms object.
>
> Eric
>
>>
>> "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 import read, write
>> atoms = read('filename.cif')
>> Then write:
>> write('filename.xyz', atoms)
>> or you can use:
>> atoms.write('filename.xyz')
>>
>>
>>
>>
>> 2017-12-08 12:19 GMT+00:00 Landi, Alessandro via ase-users <ase-users
>> @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', 
>> > 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" is the xyz file written by ASE; "realstructure.xyz" 
>> > is the structure of the reconnected molecules (obtained using CCDC 
>> > Mercury)
>> >
>> > Best regards,
>> > Alessandro
>> >
>> >
>> > _______________________________________________
>> > ase-users mailing list
>> > ase-users at listserv.fysik.dtu.dk
>> > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>> >
>>
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