<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">please, post that file.<div><br><div><div>On 26 Mar 2014, at 14:21, Taha Salavati-fard <<a href="mailto:t.salav...@gmail.com">t.salav...@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div dir="ltr">Thanks Teo.<div>Problem might be due to old linux on the cluster I am using. I am going to try it again on my laptop and will let you know.</div><div>Thanks for great helps.</div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Mar 26, 2014 at 1:09 AM, Teodoro Laino<span class="Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>></span><span class="Apple-converted-space"> </span>wrote:<br><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;"><div style="word-wrap: break-word;">On my laptop, when I run:<div><br></div><div><div style="margin: 0px; font-size: 10px; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);">fes.sopt -cpmd -ndim 2</div><div><div><br></div><div>I get the fes.dat file attached. Which is everything but not zero.</div><div>Can you please attach your fes.dat output file generated by fes.sopt ?</div><div><br></div><div>Teo</div><div><br></div><div></div></div></div></div><br>--<br>You received this message because you are subscribed to a topic in the Google Groups "cp2k" group.<br>To unsubscribe from this topic, visit<span class="Apple-converted-space"> </span><a href="https://groups.google.com/d/topic/cp2k/NgPWFuuJ3ak/unsubscribe" target="_blank">https://groups.google.com/d/topic/cp2k/NgPWFuuJ3ak/unsubscribe</a>.<br>To unsubscribe from this group and all its topics, send an email to<span class="Apple-converted-space"> </span><a href="mailto:cp2k%2Bun...@googlegroups.com">cp2k+uns...@googlegroups.com</a>.<br>To post to this group, send email to<span class="Apple-converted-space"> </span><a href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a>.<br>Visit this group at<span class="Apple-converted-space"> </span><a href="http://groups.google.com/group/cp2k" target="_blank">http://groups.google.com/group/cp2k</a>.<br>For more options, visit<span class="Apple-converted-space"> </span><a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/optout</a>.<br><br><div style="word-wrap: break-word;"><div><div></div><div><br></div><div>On 25 Mar 2014, at 16:25, Taha Salavati-fard <<a href="mailto:t.salav...@gmail.com" target="_blank">t.salav...@gmail.com</a>> wrote:</div><br><blockquote type="cite"><div dir="ltr">Yes of course,<div>Here they are!</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Mar 25, 2014 at 11:16 AM, Teodoro Laino<span class="Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>></span><span class="Apple-converted-space"> </span>wrote:<br><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;"><div style="word-wrap: break-word;">can you post your files?<div><br><div><div>On 25 Mar 2014, at 16:10, Taha Salavati-fard <<a href="mailto:t.salav...@gmail.com" target="_blank">t.salav...@gmail.com</a>> wrote:</div><br><blockquote type="cite"><div dir="ltr">Dear Teo,<div><br></div><div>I've tried that but still zeros!</div><div><br></div><div><div>FES| Parsing file: <colvar_mtd></div><div><br></div><div>**********************************************************************</div><div>FES| Parameters for FES:</div><div><br></div><div>FES| NDIM :: 2</div><div>FES| NWD :: 2</div><div>FES| HILLS :: 2156</div><div>FES| COLVAR # 1 :: ( 2.294 , 10.688) ( MAPPED)</div><div>FES| COLVAR # 2 :: ( 2.278 , 10.693) ( MAPPED)</div><div>FES| NGRID :: 100 100</div><div>FES| DX :: 0.085 0.085</div><div>FES| CUTOFF :: .10000E-06</div><div>**********************************************************************</div><div><br></div><div><br></div><div>FES| Computing Free Energy Surface</div><div>FES| Mapping Gaussians :: 10 %</div><div>FES| Mapping Gaussians :: 20 %</div><div>FES| Mapping Gaussians :: 30 %</div><div>FES| Mapping Gaussians :: 40 %</div><div>FES| Mapping Gaussians :: 50 %</div><div>FES| Mapping Gaussians :: 60 %</div><div>FES| Mapping Gaussians :: 70 %</div><div>FES| Mapping Gaussians :: 80 %</div><div>FES| Mapping Gaussians :: 90 %</div><div>FES| Mapping Gaussians :: 100 %</div><div>FES| Dumping FES structure in file: < fes.dat ></div><div><br></div><div>FES| NORMAL FES TERMINATION.</div></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Mar 25, 2014 at 3:13 AM, Teodoro Laino<span class="Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>></span><span class="Apple-converted-space"> </span>wrote:<br><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;"><div style="word-wrap: break-word;">fes.sopt -help<div><br></div><div>will give you an help.. Try to go though it.</div><div><br></div><div>You’ll have to specify -ndim and also -ndw (if I remember correctly).</div><div><br></div><div>Teo</div><div><br><div><div><div>On 25 Mar 2014, at 00:50, T. Salavati fard <<a href="mailto:t.salav...@gmail.com" target="_blank">t.salav...@gmail.com</a>> wrote:</div><br></div><blockquote type="cite"><div><div dir="ltr">Thanks all for your reply.<div>I've compiled fes and it seems working. But the problem is when I use it, in fes.dat all values are zero.</div><div>I've used following synatax:</div><div>fes.sopt [-cpmd] in a folder which contains colvar and parvar files.</div><div>any ideas?</div><div>Thanks in advance--<br><br>On Monday, March 24, 2014 2:36:48 AM UTC-4, Teo wrote:<blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;"><div style="word-wrap: break-word;"><br><div><div>On 24 Mar 2014, at 00:00, Ole Schütt <<a>o....@schuett.name</a>> wrote:</div><br><blockquote type="cite"><div style="font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><br>Actually, if you are using the latest svn version you now have to type "make graph", because the names of the make-targets now match the names of the executables. Alternatively, you can just call make without any targets, which will build all executables including the fes tool.<br><br></div></blockquote><div><br></div><div>Not entirely true - using the SVN version, one can still compile FES, by typing </div><div><br></div><div>> make fes</div><div><br></div><div>alternatively also </div><div><br></div><div>> make graph</div><div><br></div><div>works..</div><div><br></div><div>Teo</div><div><br></div><br><blockquote type="cite"><div style="font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><br>-Ole<br><br><br><br>On 2014-03-23 22:39, Ari Paavo Seitsonen wrote:<br><blockquote type="cite">Dear T. Salavati fard,<br> <span> </span>In <cp2k-root>/src/metadyn_tools/<u></u>, if you are using the latest<br>version? It used to be in <cp2k-root>/tools/metadyn/ earlier. One<br>compiles by typing "make fes" in '<cp2k-root>/makefiles'.<br> <span> </span>Greetings from Zurich,<br> apsi<br>2014-03-23 21:52 GMT+01:00 T. Salavati fard<br><<a>t.sal...@gmail.com</a>>:<br><blockquote type="cite">Dear all<br>I am CPMD user. I am doing metadynamics calculations and I need to<br>reconstruct FES. I know there is a code by Teo to reconstruct free<br>energy surface using colvar and parvar files.<br>My problem is finding FES program source!! I couldn't find that code<br>to compile and try..<br>I appreciate your helps--Thanks<br>--<br>You received this message because you are subscribed to the Google<br>Groups "cp2k" group.<br>To unsubscribe from this group and stop receiving emails from it,<br>send an email to<span class="Apple-converted-space"> </span><a>cp2k+uns...@googlegroups.<u></u>com</a>.<br>To post to this group, send email to<span class="Apple-converted-space"> </span><a>cp...@googlegroups.com</a>.<br>Visit this group at<span> </span><a href="http://groups.google.com/group/cp2k" target="_blank">http://groups.google.com/<u></u>group/cp2k</a><span> </span>[1].<br>For more options, visit<span> </span><a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.<u></u>com/d/optout</a><span> </span>[2].<br></blockquote>--<br>-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=<u></u>*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=<u></u>-=*=-=*=-=*=-=*=-<br> Ari Paavo Seitsonen /<span> </span><a>Ari.P...@iki.fi</a><span> </span>/<br><a 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options, visit<span class="Apple-converted-space"> </span><a href="https://groups.google.com/d/optout" target="_blank">https://groups.google.com/d/optout</a>.<br><span><colvar_mtd></span><span><parvar_mtd></span></blockquote></div><br></div><br></blockquote></div><br></div><div><br class="webkit-block-placeholder"></div>--<span class="Apple-converted-space"> </span><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="mailto:cp2k+uns...@googlegroups.com">cp2k+uns...@googlegroups.com</a>.<br>To post to this group, send email to<span class="Apple-converted-space"> </span><a href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a>.<br>Visit this group at<span class="Apple-converted-space"> </span><a href="http://groups.google.com/group/cp2k">http://groups.google.com/group/cp2k</a>.<br>For more options, visit<span class="Apple-converted-space"> 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