<div dir="ltr"><div><div><div>Dear Teo,<br><br></div>I've compiled it again on different machine with latest ubuntu.<br></div>fes.dat this time contains zeros and NaNs !!<br></div>I used exactly same files that I have sent to you!<br>
<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Mar 26, 2014 at 11:32 AM, Teodoro Laino <span dir="ltr"><<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div>mmm… strange.. it could really be some issue with the compiler..</div><div><br>
</div><div>Teo</div><br><div><div><div class="h5"><div>On 26 Mar 2014, at 16:15, Taha Salavati-fard <<a href="mailto:t.salav...@gmail.com" target="_blank">t.salav...@gmail.com</a>> wrote:</div><br></div></div>
<blockquote type="cite"><div><div class="h5"><div dir="ltr">here it is</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Mar 26, 2014 at 10:53 AM, Teodoro Laino <span dir="ltr"><<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">please, post that file.<div><br><div><div><div><div>On 26 Mar 2014, at 14:21, Taha Salavati-fard <<a href="mailto:t.salav...@gmail.com" target="_blank">t.salav...@gmail.com</a>> wrote:</div>
<br></div></div><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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<div><div><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></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>On Wed, Mar 26, 2014 at 1:09 AM, Teodoro Laino<span> </span><span dir="ltr"><<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>></span><span> </span>wrote:<br>
</div></div><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><div><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>
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</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></div></div><blockquote type="cite"><div>
<div><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> </span><span dir="ltr"><<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>></span><span> </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> </span><span dir="ltr"><<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>></span><span> </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>
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</div><span><fes.dat></span></blockquote></div><br></div><div class="HOEnZb"><div class="h5">
<p></p>
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