[CP2K:8980] calculation of a x-ray structure
Matt W
mattwa... at gmail.com
Sat Apr 29 21:38:56 UTC 2017
Hi again,
I'm a little confused, but if you take the periodic structure that comes
from the XRD, and run it using the default periodic setup specifying the
appropriate unit cell, you'll have the crystal packing effects included.
Matt
On Saturday, April 29, 2017 at 9:57:45 PM UTC+1, sassy wrote:
>
> 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.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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