[Pw_forum] convert to cif file

[Filipe Camargo Dalmatti Alves Lima]

Open babel can do it for you.


First all you need is to create a .xyz file then convert to PDB format.
> After this, you just need do add an extra line with the crystal cell.
>
> I am pretty sure you can create your own shell script using sed, , awk,
> grep and open babel. The algorithm, could be something like this:
>
> - find nat flag on pwscf input. ( can be done with grep)
> - copy only the number (can be done using awk and defining = as delimiter )
> - write this number in a new file with cat or sed.
> - jump 1 line in the file (fixed format xyz issues)
> - find the flag ATOMIC_POSITIONS and copy all lines until K_POINTS flag
> (can be done using sed)
> - write it in your new xyz file.
> - run open babel to convert the format.
> Now the trick part might be the cell parameters since there are lot of
> different ways to define your cell. I would say this step can't be fully
> automated without tons of efforts to recognize and follow specific rules
> for each case (ibrav type. angles, etc). If you use only a single way to
> define your cells, use the same ideas as above and write a new line in your
> file with the cell size.
>
> If you try to develop the script I can help you fixing the bugs/issues on
> it and in the end you will learn how to make a new script. :-)
>
> Let me know if you need further assistance.
>
> Regards,
> Filipe
>


-- 
_________________________________________
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of São Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones:    (11) 3091-6881  (USP)
                (11) 97408-2755 (Vivo)
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