[Wien] formation energy
Dear WIEN2k user: I am interested in the formation energy. I've searched the mailing address, but I still can't get it. I found the definition of formation energy is like this (Ga15MnN16 for example) : formation energy = total ENE of Ga15MnN16 -15*total ENE for Ga metal in standard state structure - 1* total ENE for Mn metal in standard state structure - 16* total ENE for N in standard structure In our system, it's TbOCl, does that mean: formation energy = = total ENE of TbOCl - tot ENE for Tb metal in standard state structure - tot ENE for O in standard state - Cl in standard state. ? If that is correct, what is the standard state structure for O and Cl? Do we need to do several other calculations for Tb metal or O standard state to get the formation energy? Thanks very much. Sincerely Wangwei Lan ___ Wien mailing list Wien@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@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] time difference among nodes
Dear Prof. Marks, As I suspected, users can not use ganglia. Our administrators are very jealous !! Dear Elias Assmann, Many thanks for your comments. I will try to comment on some of them. First of all, I wonder: To what extent is this problem reproducible? > E.g., does your job always run on the same 4 nodes? Yes. > Is it always the > same node(s) that are slow? Yes > Does the problem also show up in other > calculations (maybe just changing the number of k-points, or > restarting the same case from scratch). The strangest part: at the beginning of this month, the same calculation was running properly. I had a crash for convergence problems and when I reduced the "mixing factor" in case.inm (it is now 0.04 in pre-convergence scf cycle) the problems started. Obviously, I do not believe that the mixing factor is the problem. > Is it only lapw1 that is slow? > No. All the executables are running slowly in the problematic node. > > Second, how did you make those ‘top’s? As for ‘lapw0’ and ‘lapw1’, I > am guessing that this is just because the snapshots were taken at > different times (notice that the CPU times of lapw0 on the two nodes > are quite different, too). > Users can do nothing. The administrator sent me the "top's" and I have asked him for simultaneous ones. > > About the CPU usage on ‘n2’, I find this very suspicious. If it is as > Peter said that the jobs are in the initialization and therefore not > computing much, that may be fine; but I have to disagree with his > assessment, because the memory usage of lapw1 on the two nodes is > basically the same (if anything, the image sizes on ‘n2’ are slightly > larger). Note also that it is *not* the case that other processes are > using the CPU; the total usage is at 7.5 %. > > It would be good to clarify that by getting a ‘top’ such that we know > that lapw1 had been running for a while. To this end, top has an ‘-n’ > option which says how many frames to output, e.g. ‘top -bn 10’. > > I am also curious about the load averages. ‘n2’ has larger “mid-term” > and “long-term” load averages than the others, and its “short-term” > average is just as large. I am not sure what that means. > > On 09/23/2015 02:21 PM, Luis Ogando wrote: > > I can not access the nodes. SSH among them is forbidden ! We have > > to ask the administrators for anything !! It is the hell !! Of > > course, only the PBS jobs can "travel" among the nodes. > > I do not know about PBS Pro, but Torque and SGE have an option (I > think ‘-I’ in either case) to submit an interactive job where you get > a login on a node. Of course that is only a realistic option when the > queuing time is not too long. Otherwise, any information that a more > sophisticated tool can give you will also be available from the > command line (just more painful to extract!) via ‘top’, ‘ps’, ‘/proc’, > etc. You can also put these things in a jobs script (which you > apparently already did with ‘top’). > > > Good luck, > > Elias > Finally, I would like to thank all the comments and say that if I did not comment on them is because the administrators said they can not be the origin of the problem, "everything is 0K" (?). All the best, Luis ___ Wien mailing list Wien@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@zeus.theochem.tuwien.ac.at/index.html
[Wien] Regarding spin orbit coupling calculations (SOC)
Dear All I have one query regarding the spin orbit coupling calculations. Ca n I did the SO-calculations with out apply U and spin polarization. If yes, then please help me that, how to calculate the density of states. I means the commands for calculating the density of states. Regards Azam ___ Wien mailing list Wien@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@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Fwd: Problem in Gap
Hi, Send the file case.scf such that we can have a look. F. Tran On Wed, 23 Sep 2015, Marzieh Gh wrote: -- Forwarded message -- From: Marzieh Gh Date: Wed, Sep 23, 2015 at 11:18 AM Subject: Problem in Gap To: wien@zeus.theochem.tuwien.ac.at Dear Prof.Blaha & Tran I'm calculating electronic band structure of KTiOPO4 & isostructural crystals by using YSPBE0(with α opt. KTP crystals are semiconductors, But my calculations show metallic. According to these calculations the bottom of the conduction band crosses the fermi level,The gap is located in Valance band. In case.scf: Gap: -9. Ry = - eV (metallic) why? please help me Regards -- Marzieh Ghoohestani PhD Student of Computational Nano Physics Nano Research Center, Department of Physics University of Technology, Isfahan, Iran -- Marzieh Ghoohestani PhD Student of Computational Nano Physics Nano Research Center, Department of Physics University of Technology, Isfahan, Iran ___ Wien mailing list Wien@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@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] time difference among nodes
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Luis, First of all, I wonder: To what extent is this problem reproducible? E.g., does your job always run on the same 4 nodes? Is it always the same node(s) that are slow? Does the problem also show up in other calculations (maybe just changing the number of k-points, or restarting the same case from scratch). Is it only lapw1 that is slow? Second, how did you make those ‘top’s? As for ‘lapw0’ and ‘lapw1’, I am guessing that this is just because the snapshots were taken at different times (notice that the CPU times of lapw0 on the two nodes are quite different, too). About the CPU usage on ‘n2’, I find this very suspicious. If it is as Peter said that the jobs are in the initialization and therefore not computing much, that may be fine; but I have to disagree with his assessment, because the memory usage of lapw1 on the two nodes is basically the same (if anything, the image sizes on ‘n2’ are slightly larger). Note also that it is *not* the case that other processes are using the CPU; the total usage is at 7.5 %. It would be good to clarify that by getting a ‘top’ such that we know that lapw1 had been running for a while. To this end, top has an ‘-n’ option which says how many frames to output, e.g. ‘top -bn 10’. I am also curious about the load averages. ‘n2’ has larger “mid-term” and “long-term” load averages than the others, and its “short-term” average is just as large. I am not sure what that means. On 09/23/2015 02:21 PM, Luis Ogando wrote: > I can not access the nodes. SSH among them is forbidden ! We have > to ask the administrators for anything !! It is the hell !! Of > course, only the PBS jobs can "travel" among the nodes. I do not know about PBS Pro, but Torque and SGE have an option (I think ‘-I’ in either case) to submit an interactive job where you get a login on a node. Of course that is only a realistic option when the queuing time is not too long. Otherwise, any information that a more sophisticated tool can give you will also be available from the command line (just more painful to extract!) via ‘top’, ‘ps’, ‘/proc’, etc. You can also put these things in a jobs script (which you apparently already did with ‘top’). Good luck, Elias -BEGIN PGP SIGNATURE- Version: GnuPG v1 Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iQIcBAEBAgAGBQJWA7M8AAoJEE/4gtQZfOqPu5AQAJERPcJ8VBgVJdiVmDPSmfC0 9lJ+NUXWbNKxP9oXVChniwB/p0TUn588xVtVGIiXuviIW6jWM/reh7aU4NkXfxz/ J3zQq+yZ/gqMnK3JseNpq5hosU6f8keG4dGvq/qz3a+fDefe3Q1KoaTotG3oOyzY foq3RJjIoY0M7Yl2VJXhhDU6fLWNuu2Uixd9DpbWDmUzhY2o7y8zUZrCdEN0CMN7 OcaUWAkPzFwAdGY/ZVzmc4AvBICXAndBRd29KIMF5JJAxKqwXzbCbROZC14spCl5 Yt8A3deCiUrCGKTuT8w4or8shtkfGxFXXWAEKxY9kKpsHRGmbcOmIVljXk3x6JpV VOo5y3xHOEmaGOGGRZSDRGK0AWpkiep71us9zOYmnTd0GVuulOOAfi6m4FyTS0vc 3FPws2FUaOZWHm+K0AEMJyyxY5Sz6NwN6sTmiPfelvUdKLDHpDDVyig1a0X+x39+ jfgOx/J927rCYvyWA1/n5h6Mqj7ByUYA3zM9nrrTt3mw5YM/fgCyqlFp8M9cWWRF cW54Aes9cnV2GdhnbLy7cuOwXK5J7FV6uyQFPipaAkuGEG7ynvUWQdvnftX9j1hL O8S6WOzZDUYduB3mXJ5XT2iV2jjRd3zEk1niQcRfyFuQUYneY9zuGjpxkknmxEln 5KaBqwFCLo4XnRrvlDkg =PO9e -END PGP SIGNATURE- ___ Wien mailing list Wien@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@zeus.theochem.tuwien.ac.at/index.html
