[CP2K:8977] calculation of a x-ray structure

Matt W mattwa... at gmail.com
Sat Apr 29 20:10:09 UTC 2017
Previous message (by thread): [CP2K:8977] calculation of a x-ray structure
Next message (by thread): [CP2K:8980] calculation of a x-ray structure
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
Hi,

On Saturday, April 29, 2017 at 8:37:49 AM UTC+1, sassy wrote:
>
> Hi Matt, 
>
> thanks for the quick reqply. I thought of doing that as well but I was not 
> quite sure what else, other than the coordinates, are being read from the 
> CIF 
> file. I am usually doing single molecules hence I am sticking more to what 
> people advice me to do, rather than exploring. 
>
> Well maybe save the structure as pdb (or indeed re-export a new cif) from 
mercury or gdis or other visualization code you have available?
 

> So, is there anything else I need to bear in mind? In particular, am I 
> right 
> to assume that for periodic calculations the POISSON_SOLVER needs to be 
> set to 
> the default, i.e.  PERIODIC? 
>
> Shouldn't be anything in particular, most cp2k defaults are set up for 
periodic systems. POISSON_SOLVER should be PERIODIC.

Matt

 

> Thanks again. 
>
> All the best from a sunny London 
>
> Jörg 
>
> On Freitag 28 April 2017 Matt W wrote: 
> > Hi Jörg, 
> > 
> > yes that error comes during reading the cif file. I'm not sure how 
> robust 
> > the CP2K cif parser is, the format can be fairly complex I think and 
> maybe 
> > with different standards. 
> > 
> > Can you save the (full, not just symmetry inequivalent) coordinates as 
> xyz 
> > or pdb and use those - if you just want things to work for now? 
> > 
> > Matt 
> > 
> > On Friday, April 28, 2017 at 10:59:50 PM UTC+1, sassy wrote: 
> > > Hi Juerg, 
> > > 
> > > thanks for the feedback. 
> > > 
> > > I have tried what you suggested and I failed miserably. 
> > > 
> > > I got this subsys section for the coordinates which are provided by 
> the 
> > > CIF 
> > > 
> > > file with ABC and ALPHA_BETA_GAMMA taken from the CIF file: 
> > >   &SUBSYS 
> > >   
> > >     &CELL 
> > >     
> > >       ABC [angstrom] 10.0980 16.7278 20.6290 
> > >       ALPHA_BETA_GAMMA 93.744 94.745 91.931 
> > >       PERIODIC xyz 
> > >     
> > >     &END CELL 
> > >     &TOPOLOGY 
> > >     
> > >       CONNECTIVITY OFF 
> > >       COORDINATE   CIF 
> > >       COORD_FILE_NAME 6d.cif 
> > >     
> > >     &END TOPOLOGY 
> > > 
> > > However, I get that error message which puzzles me: 
> > >  1 x 
> > >   
> > >    ? 
> > >   
> > > 
>  ************************************************************************ 
> > >  ******* 
> > >   
> > >  *   ___ 
> > > 
> > > * 
> > > 
> > >  *  /   \ 
> > > 
> > > * 
> > > 
> > >  * [ABORT] 
> > > 
> > > * 
> > > 
> > >  *  \___/            Syntax error in function string: Missing operator 
> > > 
> > > * 
> > > 
> > >  *    | 
> > > 
> > > * 
> > > 
> > >  *  O/| 
> > >  1 x 
> > >   
> > >    ? 
> > >     
> > >                                                                     * 
> > >   
> > >  * /| | 
> > >   
> > >                                                                      1 
> x 
> > >     
> > >    ? 
> > > 
> > > * 
> > > 
> > >  * / \ 
> > >  common/fparser.F:406 
> > > 
> > > * 
> > > 
> > > 
>  ************************************************************************ 
> > >  ******* 
> > >   
> > >   
> > >   
> > >  ===== Routine Calling Stack ===== 
> > >   
> > >             5 read_coordinate_cif 
> > >             4 coordinate_control_READ_COORDINATE 
> > >             3 coordinate_control 
> > >             2 topology_control 
> > >             1 CP2K 
> > >   
> > >  1 x 
> > >   
> > >    ? 
> > > 
> > > I played around with PERIODIC (NONE and XYZ) in vain. 
> > > 
> > > I don't get that error when I am using a xyz file. 
> > > 
> > > Am I right to assume that for periodic calculations the POISSON_SOLVER 
> > > needs 
> > > to be set to the default, i.e.  PERIODIC? 
> > > 
> > > For me it looks like the problem has to do with the CIF file but I am 
> > > unable to 
> > > deduct the problem. I can open the same CIF file with Mercury for 
> > > example. 
> > > 
> > > Could somebody help me please? 
> > > 
> > > All the best from a cold London 
> > > 
> > > Jörg 
> > > 
> > > On Freitag 21 April 2017 hut... at chem.uzh.ch <javascript:> wrote: 
> > > > Hi 
> > > > 
> > > > I would just do a periodic calculation (using the cif file). 
> > > > You get all the packing effects and the computational costs 
> > > > are not higher (or even lower) than for a cluster calculation. 
> > > > 
> > > > regards 
> > > > 
> > > > Juerg 
> > > > -------------------------------------------------------------- 
> > > > Juerg Hutter                         Phone : ++41 44 635 4491 
> > > > Institut für Chemie C                FAX   : ++41 44 635 6838 
> > > > Universität Zürich                   E-mail: hut... at chem.uzh.ch 
> > > 
> > > <javascript:> 
> > > 
> > > > Winterthurerstrasse 190 
> > > > CH-8057 Zürich, Switzerland 
> > > > --------------------------------------------------------------- 
> > > > 
> > > > -----cp... at googlegroups.com <javascript:> wrote: -----To: cp2k < 
> > > 
> > > cp... at googlegroups.com <javascript:>> 
> > > 
> > > > From: Jörg Saßmannshausen 
> > > > Sent by: cp... at googlegroups.com <javascript:> 
> > > > Date: 04/21/2017 01:17PM 
> > > > Subject: [CP2K:8961] calculation of a x-ray structure 
> > > > 
> > > > Dear all, 
> > > > 
> > > > when I am usually calculate structures from the data I am obtaining 
> via 
> > > 
> > > a 
> > > 
> > > > x- ray analysis, i.e. from the CIF file, I simply take the single 
> > > 
> > > molecule 
> > > 
> > > > and run that via some DFT functional. No periodic boundries, if 
> there 
> > > 
> > > are 
> > > 
> > > > two molecules in the unit cell I simply pick one. 
> > > > 
> > > > However, to find out whether a specific effect I am seeing is due to 
> > > > crystal packing or not, I actually want to calculate the complete 
> unit 
> > > > cell, which contains two molecules, and I want to calculated it as a 
> > > > lattice, i.e. one more cell in each direction. This way, I hope, I 
> > > > would see whether it is due to crystal packing effects what I am 
> > > > observing, or not. 
> > > > 
> > > > From the CIF file I know it is a triclinic cell and I also know the 
> > > > geometric parameters, i.e. a,b,c and the angles. 
> > > > 
> > > > If I plug that into the subsys section of the input file and I am 
> using 
> > > 
> > > the 
> > > 
> > > > MT POISSON_SOLVER, what else do I need to bear in mind? 
> > > > Does that actually make sense what I am trying to do or is that a 
> waste 
> > > 
> > > of 
> > > 
> > > > my time? I never done solid state calculations as I am more a single 
> > > > molecule person so your advice here would be much appreciated. 
> > > > 
> > > > Please let me know if you got any further questions. 
> > > > 
> > > > All the best from a dull London 
> > > > 
> > > > Jörg 
> > > 
> > > email: j.sas... at ucl.ac.uk <javascript:> 
> > > web: http://sassy.formativ.net 
> > > 
> > > Please avoid sending me Word or PowerPoint attachments. 
> > > See http://www.gnu.org/philosophy/no-word-attachments.html 
>
>
> -- 
> ************************************************************* 
> Dr. Jörg Saßmannshausen, MRSC 
> University College London 
> Department of Chemistry 
> 20 Gordon Street 
> London 
> WC1H 0AJ 
>
> email: j.sas... at ucl.ac.uk <javascript:> 
> web: http://sassy.formativ.net 
>
> Please avoid sending me Word or PowerPoint attachments. 
> See http://www.gnu.org/philosophy/no-word-attachments.html 
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20170429/f2846dd3/attachment.htm>
Previous message (by thread): [CP2K:8977] calculation of a x-ray structure
Next message (by thread): [CP2K:8980] calculation of a x-ray structure
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
More information about the CP2K-user mailing list