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

[Jörg Saßmannshausen]

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. 

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?

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.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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