[Wien] Problems when trying to plot E vs c/a
Riyajul Islam
riyajul80 at gmail.com
Fri May 18 22:57:02 CEST 2018
I can plot E vs volume but not E vs c/a with the previous optimize.pl.
On Sat, 19 May 2018, 2:09 am Fecher, Gerhard, <fecher at uni-mainz.de> wrote:
> 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>>
> > _______________________________________________
> > Wien mailing list
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> > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> > SEARCH the MAILING-LIST at:
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> >
>
> --
>
> 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<mailto:blaha at theochem.tuwien.ac.at>
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