[CP2K:4964] Outputting cell information and fractional coordinates
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 (
>> 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).
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