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

[Jörg Saßmannshausen]

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 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
> Winterthurerstrasse 190
> CH-8057 Zürich, Switzerland
> ---------------------------------------------------------------
> 
> -----cp... at googlegroups.com wrote: -----To: cp2k <cp... at googlegroups.com>
> From: Jörg Saßmannshausen
> Sent by: cp... at googlegroups.com
> 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.sassma... at ucl.ac.uk
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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