<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> <meta name="Generator" content="Microsoft Word 15 (filtered medium)"> <style></style> </head> <body lang="DE" link="blue" vlink="purple"> <div class="WordSection1"> <p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US">Both atoms could be fixed to preserve their distance using </span><span style="mso-fareast-language:EN-US"><a href="https://manual.cp2k.org/cp2k-7_1-branch/CP2K_INPUT/MOTION/CONSTRAINT/FIXED_ATOMS.html"><span lang="EN-GB">https://manual.cp2k.org/cp2k-7_1-branch/CP2K_INPUT/MOTION/CONSTRAINT/FIXED_ATOMS.html</span></a></span><span lang="EN-GB" style="mso-fareast-language:EN-US"><o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p> <p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US">Matthias<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p> <div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="margin-left:35.4pt"><b>Von:</b> cp...@googlegroups.com <...@googlegroups.com> <b>Im Auftrag von </b>Matt W<br> <b>Gesendet:</b> Samstag, 25. April 2020 14:00<br> <b>An:</b> cp2k <...@googlegroups.com><br> <b>Betreff:</b> Re: [CP2K:13169] fixing the bond distance between two atoms (non bonded)<o:p></o:p></p> </div> <p class="MsoNormal" style="margin-left:35.4pt"><o:p> </o:p></p> <div> <p class="MsoNormal" style="margin-left:35.4pt">This setting only works with MD, to my knowledge, not for GEO_OPT type runs. We don't (as far as I know) have any internal way of fixing particular bond lengths etc.<o:p></o:p></p> <div> <p class="MsoNormal" style="margin-left:35.4pt"><br> On Saturday, April 25, 2020 at 9:14:47 AM UTC+1, Patrick Gono wrote:<o:p></o:p></p> <blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"> <div> <p class="MsoNormal" style="margin-left:35.4pt">Dear Rupesh,<o:p></o:p></p> <div> <p class="MsoNormal" style="margin-left:35.4pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt">You need to declare a collective variable representing the distance between the two atoms in the SUBSYS part of the FORCE_EVAL section. You specify the atoms by their indexes. Atoms are indexed in the order they appear in the coordinate section or the coordinate file. Indexing starts at 1:<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt"> &SUBSYS<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt"> ...<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt"> &COLVAR<br> &DISTANCE<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt"> ATOMS 11 35<br> &END DISTANCE<br> &END COLVAR<br> &END SUBSYS<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt">Next, in the MOTION section, you set the collective variable to the desired value:<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt"> &CONSTRAINT<br> &COLLECTIVE<br> TARGET 5.0833 ! this value is in bohr<br> INTERMOLECULAR T<br> COLVAR 1 ! index of the collective variable, in order of appearance in the SUBSYS section<br> &END COLLECTIVE<br> &END CONSTRAINT<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt">I attach a sample input file for your convenience.<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt">Yours sincerely,<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt">Patrick Gono<o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt"><o:p> </o:p></p> </div> </div> <p class="MsoNormal" style="margin-left:35.4pt"><o:p> </o:p></p> <div> <div> <p class="MsoNormal" style="margin-left:35.4pt">On Sat, 25 Apr 2020 at 06:26, Sun Peng <<a href="javascript:" target="_blank">sp...@gmail.com</a>> wrote:<o:p></o:p></p> </div> <blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"> <div> <p class="MsoNormal" style="margin-left:35.4pt">Hi, Rajaraman,<o:p></o:p></p> <div> <p class="MsoNormal" style="margin-left:35.4pt">In my opinion, you can just fix the two atoms in three directions by adding the &CONSTRAINT subsection under the section MOTION. For more details, you can check the reference manual website: <a href="https://manual.cp2k.org/cp2k-7_1-branch/CP2K_INPUT/MOTION/CONSTRAINT.html" target="_blank"> https://manual.cp2k.org/cp2k-7_1-branch/CP2K_INPUT/MOTION/CONSTRAINT.html</a><o:p></o:p></p> <div> <p class="MsoNormal" style="margin-left:35.4pt"><o:p> </o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt">Penson <o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt">Sun Yat-sen University<o:p></o:p></p> </div> </div> </div> <p class="MsoNormal" style="margin-left:35.4pt"><o:p> </o:p></p> <div> <div> <p class="MsoNormal" style="margin-left:35.4pt">On Sat, 25 Apr 2020 at 10:46, RUPESH TIWARI <<a href="javascript:" target="_blank">rup...@gmail.com</a>> wrote:<o:p></o:p></p> </div> <blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"> <div> <p class="MsoNormal" style="margin-left:35.4pt">Dear all,<o:p></o:p></p> <div> <p class="MsoNormal" style="margin-left:35.4pt"> I want to fix the distance between two atoms (non bonded) and optimise the whole systems using DFT in cp2k. Can anyone please tell me, how to fix the distance between two atoms. <br clear="all"> <o:p></o:p></p> <div> <p class="MsoNormal" style="margin-left:35.4pt"><o:p> </o:p></p> </div> <p class="MsoNormal" style="margin-left:35.4pt">-- <o:p></o:p></p> <div> <div> <div> <div> <p class="MsoNormal" style="margin-left:35.4pt"><span style="font-family:"Comic Sans MS";color:fuchsia;background:white">Rupesh Kumar Tiwari </span><o:p></o:p></p> <div> <p class="MsoNormal" style="margin-left:35.4pt"><span style="font-family:"Comic Sans MS";color:fuchsia;background:white">C/o: Prof. Gopalan Rajaraman</span><o:p></o:p></p> </div> <p class="MsoNormal" style="margin-left:35.4pt"><span style="font-family:"Comic Sans MS";color:fuchsia;background:white">Junior Research Fellow (CSIR)</span><o:p></o:p></p> <div> <p class="MsoNormal" style="margin-left:35.4pt"><span style="font-family:"Comic Sans MS";color:fuchsia;background:white">Department of Chemistry</span><o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt"><span style="font-family:"Comic Sans MS";color:fuchsia;background:white">IIT Bombay</span><o:p></o:p></p> </div> <div> <p class="MsoNormal" style="margin-left:35.4pt"><span style="font-family:"Comic Sans MS";color:fuchsia;background:white">Mumbai- 400076</span><o:p></o:p></p> </div> </div> </div> </div> </div> </div> </div> <p class="MsoNormal" style="margin-left:35.4pt">-- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="javascript:" target="_blank">c...@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/CAHo%2BLD5_Hpm-WRj2pX-t9-9GoYqrFJWGW2XFBhERjtAS5eYT5w%40mail.gmail.com?utm_medium=email&utm_source=footer" target="_blank"> https://groups.google.com/d/msgid/cp2k/CAHo%2BLD5_Hpm-WRj2pX-t9-9GoYqrFJWGW2XFBhERjtAS5eYT5w%40mail.gmail.com</a>.<o:p></o:p></p> 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