[Wien] Problems when trying to plot E vs c/a
Fecher, Gerhard
fecher at uni-mainz.de
Fri May 18 22:39:02 CEST 2018
Permission denied ==> seems you are not allowed to execute the script, check the permissions
Ciao
Gerhard
DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."
====================================
Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden
________________________________________
Von: Wien [wien-bounces at zeus.theochem.tuwien.ac.at] im Auftrag von Riyajul Islam [riyajul80 at gmail.com]
Gesendet: Freitag, 18. Mai 2018 15:55
An: A Mailing list for WIEN2k users
Betreff: Re: [Wien] Problems when trying to plot E vs c/a
I also have the same problem with E vs c/a plot. Then when I replace optimize.pl<http://optimize.pl> your attached one the I get an error
Failed to exec /home/dipraj/wien2k/SRC_w2web/htdocs/exec/optimize.pl<http://optimize.pl> : Permission denied
On 17 May 2018 at 17:00, Fecher, Gerhard <fecher at uni-mainz.de<mailto:fecher at uni-mainz.de>> wrote:
Hallo Peter,
thanks for the files.
unforunately, the otimize.pl<http://otimize.pl> still doesn't show the result of the fit (plot is there)
output is in a shortened version:
Fit of: E = a1 + a2*x + a3*x^2 + a4*x^3 + a5*x^4
a1 1.000
a2 0.000 1.000
a3 -0.725 -0.000 1.000
a4 -0.000 -0.930 0.000 1.000
a5 0.648 0.000 -0.985 -0.000 1.000
the line 174 should contain at least tail -15 (instead of -5) what results in the output of the parameters and the correlation matrix
Fit of: E = a1 + a2*x + a3*x^2 + a4*x^3 + a5*x^4
Final set of parameters Asymptotic Standard Error
======================= ==========================
a1 = -5573.9 +/- 3.634e-06 (6.519e-08%)
a2 = 4.23124e-06 +/- 9.205e-06 (217.5%)
a3 = 0.000137795 +/- 2.93e-05 (21.26%)
a4 = 7.61902e-06 +/- 1.037e-05 (136.1%)
a5 = -1.43164e-05 +/- 2.725e-05 (190.3%)
correlation matrix of the fit parameters:
a1 a2 a3 a4 a5
a1 1.000
a2 0.000 1.000
a3 -0.725 -0.000 1.000
a4 -0.000 -0.930 0.000 1.000
a5 0.648 0.000 -0.985 -0.000 1.000
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)
the result is then only
Fit of: E = a1 + a2*x + a3*x^2 + a4*x^3 + a5*x^4
Final set of parameters Asymptotic Standard Error
======================= ==========================
a1 = -5573.9 +/- 3.634e-06 (6.519e-08%)
a2 = 4.23124e-06 +/- 9.205e-06 (217.5%)
a3 = 0.000137795 +/- 2.93e-05 (21.26%)
a4 = 7.61902e-06 +/- 1.037e-05 (136.1%)
a5 = -1.43164e-05 +/- 2.725e-05 (190.3%)
the optimize.pl<http://optimize.pl> file changed in the latter way is attached
Ciao
Gerhard
DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."
====================================
Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden
________________________________________
Von: Wien [wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at>] im Auftrag von Peter Blaha [pblaha at theochem.tuwien.ac.at<mailto:pblaha at theochem.tuwien.ac.at>]
Gesendet: Donnerstag, 17. Mai 2018 12:32
An: wien at zeus.theochem.tuwien.ac.at<mailto:wien at zeus.theochem.tuwien.ac.at>
Betreff: Re: [Wien] Problems when trying to plot E vs c/a
Thanks for the report.
Modified eplot_lapw
and
SRC_w2web/htdocs/exec/optimize.pl<http://optimize.pl>
attached.
On 05/16/2018 04:20 PM, Fecher, Gerhard wrote:
> Dear c/a fitters,
> This concerns the latest Wien2k version
> I receive only the content of
> test_opt.analysis
> when I try with w2web to plot E vs c/a
> but neither the result of the fit nor the plot are shown,
> this seems to be a problem with the present version of the
> eplot
> script
>
> when I use the eplot script of version 14.2 it is nearly ok, however,
> there are still two issues: instead of the result of the fit, the "correlation matrix of the fit parameters" is shown
> and the figure is missing.
> Reason is that eplot and optimize.pl<http://optimize.pl> do not work well together:
> optimize.pl<http://optimize.pl>
> 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.)
>
> this can be solved by changing the two lines
> line 169 change "CASE.c_over_a.png"
> $umps = qx(cp $DIR/$CASE.coa.png $tempdir/$SID-$$.png);
> line 173 change "tail -5"
> $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);
>
> or indeed, by changing eplot (I just did not find fast how to supress the output of the correlation matrix)
>
> It would also nice to have the minimum (should be prepared by findmincoa called in eplot) in the fit.log and w2web output.
>
>
>
> Ciao
> Gerhard
>
> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
> "I think the problem, to be quite honest with you,
> is that you have never actually known what the question is."
>
> ====================================
> Dr. Gerhard H. Fecher
> Institut of Inorganic and Analytical Chemistry
> Johannes Gutenberg - University
> 55099 Mainz
> and
> Max Planck Institute for Chemical Physics of Solids
> 01187 Dresden
> ________________________________________
> Von: Wien [wien-bounces at zeus.theochem.tuwien.ac.at<mailto:wien-bounces at zeus.theochem.tuwien.ac.at>] im Auftrag von Gavin Abo [gsabo at crimson.ua.edu<mailto:gsabo at crimson.ua.edu>]
> Gesendet: Dienstag, 15. Mai 2018 06:40
> An: wien at zeus.theochem.tuwien.ac.at<mailto:wien at zeus.theochem.tuwien.ac.at>
> Betreff: Re: [Wien] Finite temperature DFT: electronic free energy
>
> 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 $fermits.
>
> I made a patch file called init_lapw.patch [ https://github.com/gsabo/WIEN2k-Patches/tree/master/17.1 ], which you should be able to apply and try simply using:
>
> username at computername:~/Desktop$ cd $WIENROOT
> username at computername:~/WIEN2k$ wget https://raw.githubusercontent.com/gsabo/WIEN2k-Patches/master/17.1/init_lapw.patch
> username at computername:~/WIEN2k$ patch -b init_lapw init_lapw.patch
> patching file init_lapw
>
> Maybe F is the :ENE (TOTAL ENERGY) in case.scf.
>
> I tried following what a previous user did [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10319.html ] but with a quick TiC calculation using run_lapw in WIEN2k 17.1:
>
> T = 1000 K = 0.00633 Ry
> init_lapw -b -fermits 0.00633
> TiC.scf::ENE : ********** TOTAL ENERGY IN Ry = -1783.95041939
> TiC.output2: Kb * T = 0.00633000
> TiC.output2: -T*Entr = -0.00054181
>
> T = 0 K = 0.0 Ry
> init_lapw -b -fermits 0.0
> TiC.scf::ENE : ********** TOTAL ENERGY IN Ry = -1783.94928338
> TiC.output2: Kb * T = 0.00180000
> TiC.output2: -T*Entr = -0.00005329
>
> F_1000K - F_0K = (E - T*S) - (E - 0) = -T*S = -1783.95041939 - (-1783.94928338) = -0.001136 => -T*S = -0.001136
>
> If -T*S divided by 2:
>
> -T*S = -0.001136/2 = - 0.000568 <- This seems reasonably close to the above -0.00054181 for T = 1000 K.
>
> As I recall, the -T*S term was doubled in WIEN2k versions after 2014 [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10319.html ].
>
> Though, there may be a flaw in my above calculation.
>
> On 5/14/2018 5:35 PM, Sabry Moustafa wrote:
>
> Hi;
>
> 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?
>
> 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):
>
> init_lapw -b -fermits 0.00633
>
> I got "fermit: Undefined variable." at the end. This is fixed though when defined fermit as well:
>
> init_lapw -b -fermit 0.00633 -fermits 0.00633
>
> So, do I have to define both?
>
>
> 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?
>
>
> Thanks ;
>
> Sabry
>
> :-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:
> Sabry G. Moustafa, Ph.D.
> Department of Chemical and Biological Engineering,
> University at Buffalo, The State University of New York.
> 511 Furnas Hall
> Buffalo, NY 14260-4200
> 716-645-1186 (office)
> 716-239-8543 (cell)
> E-mail: sabrygad at buffalo.edu<mailto:sabrygad at buffalo.edu><mailto:sabrygad at buffalo.edu<mailto:sabrygad at buffalo.edu>>
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--
P.Blaha
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