<div dir="ltr">Hi Jörg,<div> </div><div>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.</div><div> </div><div>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?</div><div> </div><div>Matt</div><div> </div><div>On Friday, April 28, 2017 at 10:59:50 PM UTC+1, sassy wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">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 href="javascript:" target="_blank" gdf-obfuscated-mailto="Va4oortsBgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">hut...@chem.uzh.ch</a> 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 href="javascript:" target="_blank" gdf-obfuscated-mailto="Va4oortsBgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">hut...@chem.uzh.ch</a> > Winterthurerstrasse 190 > CH-8057 Zürich, Switzerland > --------------------------------------------------------------- > > -----<a href="javascript:" target="_blank" gdf-obfuscated-mailto="Va4oortsBgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a> wrote: -----To: cp2k <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="Va4oortsBgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a>> > From: Jörg Saßmannshausen > Sent by: <a href="javascript:" target="_blank" gdf-obfuscated-mailto="Va4oortsBgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">cp...@googlegroups.com</a> > 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: <a href="javascript:" target="_blank" gdf-obfuscated-mailto="Va4oortsBgAJ" 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></div>