[Wien] Problems when trying to plot E vs c/a
Pavel Ondračka
pavel.ondracka at email.cz
Fri May 18 16:52:47 CEST 2018
Riyajul Islam píše v Pá 18. 05. 2018 v 19:25 +0530:
> I also have the same problem with E vs c/a plot. Then when I replace
> optimize.pl your attached one the I get an error
> Failed to exec /home/dipraj/wien2k/SRC_w2web/htdocs/exec/optimize.pl
> : Permission denied
Dear Riyajul,
you probably have wrong file permissions, try:
chmod +x /home/dipraj/wien2k/SRC_w2web/htdocs/exec/optimize.pl
Best regards
Pavel
> On 17 May 2018 at 17:00, Fecher, Gerhard <fecher at uni-mainz.de> wrote:
> > Hallo Peter,
> > thanks for the files.
> > unforunately, the 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 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] im Auftrag von
> > Peter Blaha [pblaha at theochem.tuwien.ac.at]
> > Gesendet: Donnerstag, 17. Mai 2018 12:32
> > An: 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
> >
> > 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 do not work well together:
> > > 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] im Auftrag
> > von Gavin Abo [gsabo at crimson.ua.edu]
> > > Gesendet: Dienstag, 15. Mai 2018 06:40
> > > An: 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
> > $fermits.
> > >
> > > I made a patch file called init_lapw.patch [ https://github.com/g
> > sabo/WIEN2k-Patches/tree/master/17.1 ], which you should be able to
> > apply and try simply using:
> > >
> > > username at computername:~/Desktop$ cd $WIENROOT
> > > username at computername:~/WIEN2k$ wget https://raw.githubuserconten
> > t.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-arc
> > hive.com/wien at 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>
> > > _______________________________________________
> > > Wien mailing list
> > > Wien at zeus.theochem.tuwien.ac.at
> > > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> > > SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeu
> > s.theochem.tuwien.ac.at/index.html
> > >
> >
> > --
> >
> > P.Blaha
> > -----------------------------------------------------------------
> > ---------
> > Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> > Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> > Email: blaha at theochem.tuwien.ac.at WIEN2k: http://www.wien2k.at
> > WWW: http://www.imc.tuwien.ac.at/TC_Blaha
> > -----------------------------------------------------------------
> > ---------
> >
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> >
>
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