<div dir="ltr">Hi, On Saturday, April 29, 2017 at 8:37:49 AM UTC+1, sassy wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">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. </blockquote><div>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?</div><div> </div><blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">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? </blockquote><div>Shouldn't be anything in particular, most cp2k defaults are set up for periodic systems. POISSON_SOLVER should be PERIODIC.</div><div> </div><div>Matt</div><div> </div><div> </div><blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">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 <a>hut...@chem.uzh.ch</a> <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: <a>hut...@chem.uzh.ch</a> > > > > <javascript:> > > > > > Winterthurerstrasse 190 > > > CH-8057 Zürich, Switzerland > > > --------------------------------------------------------------- > > > > > > -----<a>cp...@googlegroups.com</a> <javascript:> wrote: -----To: cp2k < > > > > <a>cp...@googlegroups.com</a> <javascript:>> > > > > > From: Jörg Saßmannshausen > > > Sent by: <a>cp...@googlegroups.com</a> <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: <a>j.sas...@ucl.ac.uk</a> <javascript:> > > web: <a href="http://sassy.formativ.net" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fsassy.formativ.net\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNE9o9WkpTCH9I54nkUfQDVTZ3MyXg';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fsassy.formativ.net\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNE9o9WkpTCH9I54nkUfQDVTZ3MyXg';return true;">http://sassy.formativ.net</a> > > > > Please avoid sending me Word or PowerPoint attachments. > > See <a href="http://www.gnu.org/philosophy/no-word-attachments.html" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.gnu.org%2Fphilosophy%2Fno-word-attachments.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEjON8UjWwcCChP9-0mlwmJs_iU7g';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.gnu.org%2Fphilosophy%2Fno-word-attachments.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEjON8UjWwcCChP9-0mlwmJs_iU7g';return true;">http://www.gnu.org/philosophy/no-word-attachments.html</a> -- ************************************************************* Dr. Jörg Saßmannshausen, MRSC University College London Department of Chemistry 20 Gordon Street London WC1H 0AJ email: <a href="javascript:" target="_blank" gdf-obfuscated-mailto="4TUN5kWMBgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">j.sas...@ucl.ac.uk</a> web: <a href="http://sassy.formativ.net" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fsassy.formativ.net\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNE9o9WkpTCH9I54nkUfQDVTZ3MyXg';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fsassy.formativ.net\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNE9o9WkpTCH9I54nkUfQDVTZ3MyXg';return true;">http://sassy.formativ.net</a> Please avoid sending me Word or PowerPoint attachments. See <a href="http://www.gnu.org/philosophy/no-word-attachments.html" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.gnu.org%2Fphilosophy%2Fno-word-attachments.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEjON8UjWwcCChP9-0mlwmJs_iU7g';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.gnu.org%2Fphilosophy%2Fno-word-attachments.html\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEjON8UjWwcCChP9-0mlwmJs_iU7g';return true;">http://www.gnu.org/philosophy/no-word-attachments.html</a> </blockquote></div>