[CP2K:4964] Outputting cell information and fractional coordinates

Efrem Braun efrem... at gmail.com
Wed Aug 2 22:05:41 CEST 2017


I'll note that I've since realized that an easy and safe option for 
converting the final snapshot into a cif file containing fractional 
coordinates is to post-process the restart file (which contains the full 
unit cell matrix) into a file type that uses this kind of information, such 
as the VASP POSCAR file format, and then use obabel to convert that file 
into a cif. I'm still interested in hearing the answer to the question, but 
it's less pertinent to my own work. Sorry for the excess emails!

On Wednesday, August 2, 2017 at 1:43:35 PM UTC+2, Efrem Braun wrote:
>
> Similar question applies when using pwtools. io.write_cif is happy to 
> write a cif file in fractional coordinates given a CP2K output pdb, but is 
> it assuming that CP2K was writing the pdb using a convention that CP2K 
> isn't using?
>
> On Wednesday, August 2, 2017 at 10:39:51 AM UTC+2, Efrem Braun wrote:
>>
>> Would someone be willing to explain this problem in some more detail? I'd 
>> like to convert the last snapshot of my pdb trajectory into a cif file 
>> containing fractional coordinates. I was planning to do this using obabel 
>> to get the cif file containing Cartesian coordinates, and then using obabel 
>> again to get a fractional coordinate file. However, I believe that obabel 
>> does the second conversion assuming that crytallographic conventions 
>> regarding the unit cell (
>> https://en.wikipedia.org/wiki/Fractional_coordinates#In_Crystallography) 
>> are followed, and per this thread, I'm not sure whether this is the case.
>>
>> Efrem Braun
>>
>> On Friday, January 31, 2014 at 4:34:37 PM UTC+1, FX Coudert wrote:
>>>
>>> > There is now an alternative dump format called DCD_ALIGNED_CELL which 
>>> dumps the coordinates based on a cell alignment as described which should 
>>> allow a reconstruction of the scaled coordinates only from the DCD dump 
>>> data (to single precision accuracy). 
>>>
>>> Thanks! 
>>>
>>> FX
>>
>>
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