[CP2K:8980] calculation of a x-ray structure

Jörg Saßmannshausen j.sassma... at ucl.ac.uk
Sat Apr 29 20:57:30 UTC 2017
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Hi Matt,

thanks for the feedback. 
I was actually using Mercury to save the file as xyz coordinates and that is 
running fine now. Sorry, I thought I had mentioned that in my last email. 

Now, what I am after are crystal packing effects. Does my current approach 
takes these effects in considerations or would it be better to use a supercell, 
i.e. expand the cell into all three dimensions?

I guess that was the original question I was after.

All the best from London

Jörg


On Samstag 29 April 2017 Matt W wrote:
> 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
> > 
> > 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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