<div dir="ltr">I also have the same problem with E vs c/a plot. Then when I replace <a href="http://optimize.pl">optimize.pl</a> your attached one the I get an error<br><pre>Failed to exec /home/dipraj/wien2k/SRC_w2web/htdocs/exec/<a href="http://optimize.pl">optimize.pl</a> : Permission denied</pre></div><div class="gmail_extra"><br><div class="gmail_quote">On 17 May 2018 at 17:00, Fecher, Gerhard <span dir="ltr"><<a href="mailto:fecher@uni-mainz.de" target="_blank">fecher@uni-mainz.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hallo Peter,<br>
thanks for the files.<br>
unforunately, the <a href="http://otimize.pl" rel="noreferrer" target="_blank">otimize.pl</a> still doesn't show the result of the fit (plot is there)<br>
output is in a shortened version:<br>
<span class=""><br>
Fit of: E = a1 + a2*x + a3*x^2 + a4*x^3 + a5*x^4<br>
</span>a1 1.000 <br>
a2 0.000 1.000 <br>
a3 -0.725 -0.000 1.000 <br>
a4 -0.000 -0.930 0.000 1.000 <br>
a5 0.648 0.000 -0.985 -0.000 1.000 <br>
<br>
the line 174 should contain at least tail -15 (instead of -5) what results in the output of the parameters and the correlation matrix <br>
<span class=""><br>
Fit of: E = a1 + a2*x + a3*x^2 + a4*x^3 + a5*x^4<br>
</span>Final set of parameters Asymptotic Standard Error<br>
======================= ==========================<br>
a1 = -5573.9 +/- 3.634e-06 (6.519e-08%)<br>
a2 = 4.23124e-06 +/- 9.205e-06 (217.5%)<br>
a3 = 0.000137795 +/- 2.93e-05 (21.26%)<br>
a4 = 7.61902e-06 +/- 1.037e-05 (136.1%)<br>
a5 = -1.43164e-05 +/- 2.725e-05 (190.3%)<br>
<br>
correlation matrix of the fit parameters:<br>
a1 a2 a3 a4 a5 <br>
a1 1.000 <br>
a2 0.000 1.000 <br>
a3 -0.725 -0.000 1.000 <br>
a4 -0.000 -0.930 0.000 1.000 <br>
a5 0.648 0.000 -0.985 -0.000 1.000<br>
<br>
or shorter versuion is to use tail -15 fit.log | head -7 because I don't think that the correlation matrix is needed in the w2web output (it's found in fit.log anyway)<br>
the result is then only<br>
<span class=""> <br>
Fit of: E = a1 + a2*x + a3*x^2 + a4*x^3 + a5*x^4<br>
</span>Final set of parameters Asymptotic Standard Error<br>
======================= ==========================<br>
a1 = -5573.9 +/- 3.634e-06 (6.519e-08%)<br>
a2 = 4.23124e-06 +/- 9.205e-06 (217.5%)<br>
a3 = 0.000137795 +/- 2.93e-05 (21.26%)<br>
a4 = 7.61902e-06 +/- 1.037e-05 (136.1%)<br>
a5 = -1.43164e-05 +/- 2.725e-05 (190.3%)<br>
<br>
the <a href="http://optimize.pl" rel="noreferrer" target="_blank">optimize.pl</a> file changed in the latter way is attached<br>
<span class=""><br>
<br>
Ciao<br>
Gerhard<br>
<br>
DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:<br>
"I think the problem, to be quite honest with you,<br>
is that you have never actually known what the question is."<br>
<br>
==============================<wbr>======<br>
Dr. Gerhard H. Fecher<br>
Institut of Inorganic and Analytical Chemistry<br>
Johannes Gutenberg - University<br>
55099 Mainz<br>
and<br>
Max Planck Institute for Chemical Physics of Solids<br>
01187 Dresden<br>
______________________________<wbr>__________<br>
</span>Von: Wien [<a href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at">wien-bounces@zeus.theochem.<wbr>tuwien.ac.at</a>] im Auftrag von Peter Blaha [<a href="mailto:pblaha@theochem.tuwien.ac.at">pblaha@theochem.tuwien.ac.at</a>]<br>
Gesendet: Donnerstag, 17. Mai 2018 12:32<br>
An: <a href="mailto:wien@zeus.theochem.tuwien.ac.at">wien@zeus.theochem.tuwien.ac.<wbr>at</a><br>
Betreff: Re: [Wien] Problems when trying to plot E vs c/a<br>
<div class="HOEnZb"><div class="h5"><br>
Thanks for the report.<br>
<br>
Modified eplot_lapw<br>
and<br>
SRC_w2web/htdocs/exec/<a href="http://optimize.pl" rel="noreferrer" target="_blank">optimize<wbr>.pl</a><br>
<br>
attached.<br>
<br>
On 05/16/2018 04:20 PM, Fecher, Gerhard wrote:<br>
> Dear c/a fitters,<br>
> This concerns the latest Wien2k version<br>
> I receive only the content of<br>
> test_opt.analysis<br>
> when I try with w2web to plot E vs c/a<br>
> but neither the result of the fit nor the plot are shown,<br>
> this seems to be a problem with the present version of the<br>
> eplot<br>
> script<br>
><br>
> when I use the eplot script of version 14.2 it is nearly ok, however,<br>
> there are still two issues: instead of the result of the fit, the "correlation matrix of the fit parameters" is shown<br>
> and the figure is missing.<br>
> Reason is that eplot and <a href="http://optimize.pl" rel="noreferrer" target="_blank">optimize.pl</a> do not work well together:<br>
> <a href="http://optimize.pl" rel="noreferrer" target="_blank">optimize.pl</a><br>
> prints the last 5 lines of fit.log (but the result is before these lines) and expects the graph as case.c_over_a.png (but has a different name .coa.)<br>
><br>
> this can be solved by changing the two lines<br>
> line 169 change "CASE.c_over_a.png"<br>
> $umps = qx(cp $DIR/$CASE.coa.png $tempdir/$SID-$$.png);<br>
> line 173 change "tail -5"<br>
> $OUT .= qx(cd $DIR;echo ' ';echo "Fit of: E = a1 + a2*x + a3*x^2 + a4*x^3 + a5*x^4";tail -15 fit.log);<br>
><br>
> or indeed, by changing eplot (I just did not find fast how to supress the output of the correlation matrix)<br>
><br>
> It would also nice to have the minimum (should be prepared by findmincoa called in eplot) in the fit.log and w2web output.<br>
><br>
><br>
><br>
> Ciao<br>
> Gerhard<br>
><br>
> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:<br>
> "I think the problem, to be quite honest with you,<br>
> is that you have never actually known what the question is."<br>
><br>
> ==============================<wbr>======<br>
> Dr. Gerhard H. Fecher<br>
> Institut of Inorganic and Analytical Chemistry<br>
> Johannes Gutenberg - University<br>
> 55099 Mainz<br>
> and<br>
> Max Planck Institute for Chemical Physics of Solids<br>
> 01187 Dresden<br>
> ______________________________<wbr>__________<br>
> Von: Wien [<a href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at">wien-bounces@zeus.theochem.<wbr>tuwien.ac.at</a>] im Auftrag von Gavin Abo [<a href="mailto:gsabo@crimson.ua.edu">gsabo@crimson.ua.edu</a>]<br>
> Gesendet: Dienstag, 15. Mai 2018 06:40<br>
> An: <a href="mailto:wien@zeus.theochem.tuwien.ac.at">wien@zeus.theochem.tuwien.ac.<wbr>at</a><br>
> Betreff: Re: [Wien] Finite temperature DFT: electronic free energy<br>
><br>
> I think you found a bug in init_lapw. The fix seems like it should be simple though. On line 498 in the init_lapw script in the sed command, it looks like $fermit just needs changed to $fermits.<br>
><br>
> I made a patch file called init_lapw.patch [ <a href="https://github.com/gsabo/WIEN2k-Patches/tree/master/17.1" rel="noreferrer" target="_blank">https://github.com/gsabo/<wbr>WIEN2k-Patches/tree/master/17.<wbr>1</a> ], which you should be able to apply and try simply using:<br>
><br>
> username@computername:~/<wbr>Desktop$ cd $WIENROOT<br>
> username@computername:~/<wbr>WIEN2k$ wget <a href="https://raw.githubusercontent.com/gsabo/WIEN2k-Patches/master/17.1/init_lapw.patch" rel="noreferrer" target="_blank">https://raw.githubusercontent.<wbr>com/gsabo/WIEN2k-Patches/<wbr>master/17.1/init_lapw.patch</a><br>
> username@computername:~/<wbr>WIEN2k$ patch -b init_lapw init_lapw.patch<br>
> patching file init_lapw<br>
><br>
> Maybe F is the :ENE (TOTAL ENERGY) in case.scf.<br>
><br>
> I tried following what a previous user did [ <a href="https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10319.html" rel="noreferrer" target="_blank">https://www.mail-archive.com/<wbr>wien@zeus.theochem.tuwien.ac.<wbr>at/msg10319.html</a> ] but with a quick TiC calculation using run_lapw in WIEN2k 17.1:<br>
><br>
> T = 1000 K = 0.00633 Ry<br>
> init_lapw -b -fermits 0.00633<br>
> TiC.scf::ENE : ********** TOTAL ENERGY IN Ry = -1783.95041939<br>
> TiC.output2: Kb * T = 0.00633000<br>
> TiC.output2: -T*Entr = -0.00054181<br>
><br>
> T = 0 K = 0.0 Ry<br>
> init_lapw -b -fermits 0.0<br>
> TiC.scf::ENE : ********** TOTAL ENERGY IN Ry = -1783.94928338<br>
> TiC.output2: Kb * T = 0.00180000<br>
> TiC.output2: -T*Entr = -0.00005329<br>
><br>
> F_1000K - F_0K = (E - T*S) - (E - 0) = -T*S = -1783.95041939 - (-1783.94928338) = -0.001136 => -T*S = -0.001136<br>
><br>
> If -T*S divided by 2:<br>
><br>
> -T*S = -0.001136/2 = - 0.000568 <- This seems reasonably close to the above -0.00054181 for T = 1000 K.<br>
><br>
> As I recall, the -T*S term was doubled in WIEN2k versions after 2014 [ <a href="https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10319.html" rel="noreferrer" target="_blank">https://www.mail-archive.com/<wbr>wien@zeus.theochem.tuwien.ac.<wbr>at/msg10319.html</a> ].<br>
><br>
> Though, there may be a flaw in my above calculation.<br>
><br>
> On 5/14/2018 5:35 PM, Sabry Moustafa wrote:<br>
><br>
> Hi;<br>
><br>
> I am interested in the electronic free energy (F=E-TS) using the finite temperature DFT using Fermi-Dirac statistics (i.e., Mermin's extension to 0 K DFT) -- i.e., I am not just looking for Fermi-Dirac as a broadening/smearing technique. So,how this can be done in WIEN2k?<br>
><br>
> It looks like I have to define "-fermits X" in the init_lapw command (where X= kT, in Ry). But when I did (T=1000K in my case):<br>
><br>
> init_lapw -b -fermits 0.00633<br>
><br>
> I got "fermit: Undefined variable." at the end. This is fixed though when defined fermit as well:<br>
><br>
> init_lapw -b -fermit 0.00633 -fermits 0.00633<br>
><br>
> So, do I have to define both?<br>
><br>
><br>
> Also, where can I find this "free energy F". It does not seem to be the "TOTAL ENERGY" in case.scf. Seems like I need to add this "TOTAL ENERGY" (E) to "-T*Entr" (-TS) in case.output2 file to get F?<br>
><br>
><br>
> Thanks ;<br>
><br>
> Sabry<br>
><br>
> :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-<wbr>:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-<wbr>:-:-:-:-:-:-:-:-:-:<br>
> Sabry G. Moustafa, Ph.D.<br>
> Department of Chemical and Biological Engineering,<br>
> University at Buffalo, The State University of New York.<br>
> 511 Furnas Hall<br>
> Buffalo, NY 14260-4200<br>
> 716-645-1186 (office)<br>
> 716-239-8543 (cell)<br>
> E-mail: <a href="mailto:sabrygad@buffalo.edu">sabrygad@buffalo.edu</a><mailto:<a href="mailto:sabrygad@buffalo.edu">sa<wbr>brygad@buffalo.edu</a>><br>
> ______________________________<wbr>_________________<br>
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><br>
<br>
--<br>
<br>
P.Blaha<br>
------------------------------<wbr>------------------------------<wbr>--------------<br>
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna<br>
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982<br>
Email: <a href="mailto:blaha@theochem.tuwien.ac.at">blaha@theochem.tuwien.ac.at</a> WIEN2k: <a href="http://www.wien2k.at" rel="noreferrer" target="_blank">http://www.wien2k.at</a><br>
WWW: <a href="http://www.imc.tuwien.ac.at/TC_Blaha" rel="noreferrer" target="_blank">http://www.imc.tuwien.ac.at/<wbr>TC_Blaha</a><br>
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<br></blockquote></div><br></div>