<HTML> <div> <div> Dear Juerg,</div> <div>I have performed 20 ps MD simulation already of my system using D3 correction. The system is an organic framework and I study the diffusion of small molecules inside. Since the C9 term as implemented is not invariant to translations....Dos it mean that my trajectories are wrong?</div> <div>Regards!</div> <div>Petko</div> <div> </div> </div> <div> </div> <blockquote style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; 
BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px"> -----Original Message----- From: hut...@chem.uzh.ch To: cp...@googlegroups.com Date: Thu, 9 Oct 2014 15:21:04 +0200 Subject: Re: [CP2K:5712] Possible bug in DFT-D3 <div style="font-family: monospace, courier new, courier">Hi yes, this is a bug. The C9 term as implemented is not invariant to translations. I try to find a fix - fighting with unique triple lists. regards Juerg -------------------------------------------------------------- Juerg Hutter Phone : ++41 44 635 4491 Institut für Chemie C FAX : ++41 44 635 6838 Universität Zürich E-mail: hut...@chem.uzh.ch Winterthurerstrasse 190 CH-8057 Zürich, Switzerland --------------------------------------------------------------- -----cp...@googlegroups.com wrote: ----- To: cp...@googlegroups.com From: yakutovich Sent by: cp...@googlegroups.com Date: 10/07/2014 11:17AM Subject: Re: [CP2K:5710] Possible bug in DFT-D3 Dear Juerg, Sorry that I didn't post the coordinates file, now you can find it in the attachement (p.xyz). Following you suggestion I added the PRINT section in the DFTD3 part of input. Please find enclosed files 20-vacuum-PROJ-1_0.dftd and 40-vacuum-PROJ-1_0.dftd. I also tried an another thing: from DFTD3 section I removed the C9 tem. Then the vdW energies become the same for both structures (see 20-vacuum-no-C9-PROJ-1_0.dftd and 40-vacuum-no-C9-PROJ-1_0.dftd) So apparently there is a bug in calculating C9 term. Best regards Sasha On Tuesday, October 7, 2014 9:52:27 AM UTC+2, jgh wrote:Hi I cannot reproduce your problem using a simple input. Can you either send the coordinate file or rerun the jobs with additional output for the DFTD3 section: VERBOSE_OUTPUT &PRINT_DFTD &END By sending reproducible inputs/output you make our life easier. regards Juerg -------------------------------------------------------------- Juerg Hutter Phone : ++41 44 635 4491 Institut für Chemie C FAX : ++41 44 635 6838 Universität Zürich E-mail: hut...@chem.uzh.ch Winterthurerstrasse 190 CH-8057 Zürich, Switzerland --------------------------------------------------------------- -----cp...@googlegroups.com wrote: ----- To: cp...@googlegroups.com From: Leopold Talirz Sent by: cp...@googlegroups.com Date: 10/06/2014 04:17PM Subject: [CP2K:5703] Possible bug in DFT-D3 Dear all, a colleague in my lab found an unexpected dependence of the DFT-D3 dispersion energy on the amount of vacuum in a slab calculation, which could indicate a bug in the DFT-D3 implementation. Here the message from Sasha: I have a slab geometry for a slab that is ~20 A thick (less than 20) and I perforrm a fully periodic calculation. To test the convergence of the vacuum region i performed ENERGY calculations with a cell of 40 A (so 20 A of vacuum) and, afterwards, the same ENERGY calculation with a cell thickness of 60A (so 40 A of vacuum). I did define R_CUTOFF for the VDW as 8 A, i.e. less than half of the vacuum region. I was therefore expecting the dispersion energy to be exactly the same (?). The ENERGY calculations for the SAME geometry (file p.xyz) give rise to a difference of 1.8eV in the dispersion energy term for the DFT-D3 calculation, when i change the cell size. I repeated the same calculations with DFT-D2 and in this case there is no difference in the dispersion energy (as I would have expected). In the tar file you can find the input that I used for the four different calculations (DFT-D3 with 20 and 40 A of vacuum and DFT-D2 same two cases) as well as output files and the geometry p.xyz. Does anybody have an idea on what could be wrong? Thanks in advance for your help Kind regards, Sasha (and Leopold) -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+...@googlegroups.com. To post to this group, send email to cp...@googlegroups.com. Visit this group at <a target="_blank" href="http://groups.google.com/group/cp2k"> http://groups.google.com/group/cp2k</a>. For more options, visit <a target="_blank" href="https://groups.google.com/d/optout"> https://groups.google.com/d/optout</a>. [attachment "question.tar.gz" removed by Jürg Hutter/at/UZH] -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns...@googlegroups.com. To post to this group, send email to cp...@googlegroups.com. Visit this group at <a target="_blank" href="http://groups.google.com/group/cp2k"> http://groups.google.com/group/cp2k</a>. For more options, visit <a target="_blank" href="https://groups.google.com/d/optout"> https://groups.google.com/d/optout</a>. [attachment "20-vacuum-no-C9-PROJ-1_0.dftd" removed by Jürg Hutter/at/UZH] [attachment "20-vacuum-PROJ-1_0.dftd" removed by Jürg Hutter/at/UZH] [attachment "40-vacuum-no-C9-PROJ-1_0.dftd" removed by Jürg Hutter/at/UZH] [attachment "40-vacuum-PROJ-1_0.dftd" removed by Jürg Hutter/at/UZH] [attachment "p.xyz" removed by Jürg Hutter/at/UZH] -- You received this message because you are subscribed to the Google Groups "cp2k" group. To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns...@googlegroups.com. To post to this group, send email to cp...@googlegroups.com. Visit this group at <a target="_blank" href="http://groups.google.com/group/cp2k"> http://groups.google.com/group/cp2k</a>. For more options, visit <a target="_blank" href="https://groups.google.com/d/optout"> https://groups.google.com/d/optout</a>. </div> </blockquote> </HTML>