[CP2K:8962] calculation of a x-ray structure

[Matt W]

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 
>
>
> -- 
> ************************************************************* 
> 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 
>
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