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 <[email protected]> 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 [[email protected]] im Auftrag von > > Peter Blaha [[email protected]] > > Gesendet: Donnerstag, 17. Mai 2018 12:32 > > An: [email protected] > > 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 [[email protected]] im Auftrag > > von Gavin Abo [[email protected]] > > > Gesendet: Dienstag, 15. Mai 2018 06:40 > > > An: [email protected] > > > 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 > > $fermits. > > > > > > I made a patch file called init_lapw.patch [ https://github.com/g > > sabo/WIEN2k-Patches/tree/master/17.1 ], which you should be able to > > apply and try simply using: > > > > > > username@computername:~/Desktop$ cd $WIENROOT > > > username@computername:~/WIEN2k$ wget https://raw.githubuserconten > > t.com/gsabo/WIEN2k-Patches/master/17.1/init_lapw.patch > > > username@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/[email protected]/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/[email protected] > > /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: [email protected]<mailto:[email protected]> > > > _______________________________________________ > > > Wien mailing list > > > [email protected] > > > 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: [email protected] WIEN2k: http://www.wien2k.at > > WWW: http://www.imc.tuwien.ac.at/TC_Blaha > > ----------------------------------------------------------------- > > --------- > > > > _______________________________________________ > > Wien mailing list > > [email protected] > > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > > SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus. > > theochem.tuwien.ac.at/index.html > > > > _______________________________________________ > Wien mailing list > [email protected] > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: http://www.mail-archive.com/[email protected] > eochem.tuwien.ac.at/index.html _______________________________________________ Wien mailing list [email protected] http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/[email protected]/index.html
