Please see my response 2 days ago, it seems that you are missing flags in the input file.
/Nick On Thu, 10 Mar 2022, 22:02 Neculai PLUGARU, <neculai.plug...@imt.ro> wrote: > > Hi, Nick > > Thank you, very much, for the checks and your time. > > 1) your scat.fdf does not ask for transmission eigenvalues. I.e. I can't > find TBT.T.Eig in scat.fdf, this is also reflected in tbt.out which lists 0 > transmission eigenvalues should be calculated. So nothing wrong there. > Absolutely correct. The meaning of this piece of information was to show > that without specifications for additional data, particularly TBT.T.EIG, > the code works alright. > 2) your scat-dn and scat-up. The output of the tbtrans runs tbt-dn.out and > tbt-up.out have these lines: > > =================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > .... > > Correct. This happens when one follows the discussion since 2017, trying > to perform two calculations (but using TBT 4.1.5) for spin_UP/DN. The code > produces the (empty) scat.TBT_UP/DN.CEIG_Left files and huge > scat.TBT_UP/DN.nc files. It has been just a test of that approach, it > failed and this is understandable because it is a different version. Now, > just to complete the information, this is what one gets with TBT 4.1.5 > when using the attached scat.fdf input asking for specific output data (I > also attach the tbt.out) > > > 195116 Feb 12 18:54 scat.TBT.CC > 350488 Feb 12 19:19 scat.TBT_DN.ADOS_Left > 350488 Feb 12 19:19 scat.TBT_DN.ADOS_Right > 70103 Feb 12 19:19 scat.TBT_DN.AVADOS_Left > 70103 Feb 12 19:19 scat.TBT_DN.AVADOS_Right > 70074 Feb 12 19:19 scat.TBT_DN.AVTRANS_Left-Right > 350459 Feb 12 19:19 scat.TBT_DN.TRANS_Left-Right > 297 Feb 12 18:54 scat.TBT.KP > 350488 Feb 12 19:06 scat.TBT_UP.ADOS_Left > 350488 Feb 12 19:06 scat.TBT_UP.ADOS_Right > 70103 Feb 12 19:06 scat.TBT_UP.AVADOS_Left > 70103 Feb 12 19:06 scat.TBT_UP.AVADOS_Right > 70074 Feb 12 19:06 scat.TBT_UP.AVTRANS_Left-Right > 350459 Feb 12 19:06 scat.TBT_UP.TRANS_Left-Right > > Still, no output for > SystemLabel.TEIG_<1>_<2> > SystemLabel.BDOS_<> > SystemLabel.BTRANS_<> > SystemLabel.CORR_<> > SystemLabel.TRANS_<1>_<1> > as well as for SystemLabel.TBT_UP/DN.nc files, although tbt.out says that > the job was executed without error. > > I have just completed the ts_graphene test in the 4.1.5 release in a > spin-polarized configuration with transmission eigenvalues, and everything > seems correctly written. > > Please, is there anything wrong in the here-attached *fdf file comparing > with your input for the spin polarized graphene input ? > > Thank you, very much, for your comments and suggestion wrt the compilation > of TBT when using intel compilers; I have had painstaking experiences in > the past with that. I will ask the system administrator to recompile the > code paying more attention to the optimization flags, indeed. > Kind regards, > > Neculai > On 3/9/22 14:15, Nick Papior wrote: > > Hi, > > This is what I can find: > > 1) your scat.fdf does not ask for transmission eigenvalues. I.e. I can't > find TBT.T.Eig in scat.fdf, this is also reflected in tbt.out which lists 0 > transmission eigenvalues should be calculated. So nothing wrong there. > > 2) your scat-dn and scat-up. The output of the tbtrans runs tbt-dn.out and > tbt-up.out have these lines: > > =================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = RANK 46 PID 17638 RUNNING AT imt01 > = KILLED BY SIGNAL: 9 (Killed) > =================================================================================== > > > indicating a prematurely ending job. Always check whether your jobs are > done. That information could be of a number of reasons that I don't have > any knowledge about. > Sometimes intel compilers are extremely aggressive in optimizations, and > this could be what is causing problems. Try lowering the optimization > level, or ask the admins on your cluster why the jobs ended prematurely. > > I have just completed the ts_graphene test in the 4.1.5 release in a > spin-polarized configuration with transmission eigenvalues, and everything > seems correctly written. > > / Nick > > > Den man. 7. mar. 2022 kl. 17.32 skrev Neculai PLUGARU < > neculai.plug...@imt.ro>: > >> >> Hello, Nick >> >> Thank you for your help. I have delayed my message because I have made >> several tests to be more explicit about the problems I face with TBT 4.1.5. >> So, here are the answers to your questions: >> >> 1) I attach my input files; now there are three of them, because I found >> and followed this discussion since 2017-01-24, regarding TBT 4.1-b3, and >> somehow the present situation with TBT 4.1.5 is similar, but still >> different. >> >> https://bugs.launchpad.net/siesta/+bug/1658896 >> "spin polarized tbtrans calculation" >> >> In my calculations of the eigen channels, the first one (denoted here >> below scat-up) stops after producing the files for the spin UP. Then, in an >> independent TBT calculation, scat-dn, with the line >> >> TBT.Spin 2 >> >> included in *fdf, one obtains all the files for the spin-DOWN channel. >> However, the code gives the output for both spin channels (but not the >> files mentioned in my first message) in the case that one does not specify >> in the input the request for the eigen channels and other data,( this is >> calculation denoted scat). >> >> 2) I also attach the tbt.out files, for conformity; >> >> 3) Below, I list the files generated by TBtrans 4.1.5 for the two >> independent calculations spin-up/spin-dn, as well as for the calculation >> without the TBT.T.Eig 5, and other supplimentary lines. >> >> >> scat-up >> 195116 Mar 7 10:17 scat.TBT.CC >> 529 Mar 7 10:17 scat.TBT.KP >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzY3OCR0PzAsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/OmYxOmc0Njc6OjdmZmZgNDQwNGQ0Z2czMzY6OjI2ZDcxNDBnZ2ZmNSR2PzM0NjQ7MzI2OzMkc2tmPzAwQ0A6Q1p6MjA0MzcxLzAwQ0A6Q1szMjA0MzcxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzIkamZuPzI=&url=http%3a%2f%2fscat.TBT.KP> >> 630796 Mar 7 11:58 scat.TBT_UP.ADOS_Left >> 70103 Mar 7 11:58 scat.TBT_UP.AVADOS_Left >> 70070 Mar 7 11:58 scat.TBT_UP.AVBDOS_Left >> 70079 Mar 7 11:58 scat.TBT_UP.AVBTRANS_Left >> 70089 Mar 7 11:58 scat.TBT_UP.AVCORR_Left >> 630763 Mar 7 11:58 scat.TBT_UP.BDOS_Left >> 630772 Mar 7 11:58 scat.TBT_UP.BTRANS_Left >> 178 Mar 7 11:58 scat.TBT_UP.CEIG_Left >> 630782 Mar 7 11:58 scat.TBT_UP.CORR_Left >> 745686907872 Mar 7 11:58 scat.TBT_UP.nc >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzY3OCR0PzAsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/YTU0YWA6NTM0NDczMDdjMzc3YTE2M2AwNTFmMWdnMDs2YTRjNTZnMiR2PzM0NjQ7MzI2OzMkc2tmPzAwQ0A6Q1p6MjA0MzcxLzAwQ0A6Q1szMjA0MzcxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzIkamZuPzI=&url=http%3a%2f%2fscat.TBT_UP.nc> >> -- >> >> scat-dn >> 78116 Mar 7 14:29 scat.TBT.CC >> 252796 Mar 7 15:11 scat.TBT_DN.ADOS_Left >> 28103 Mar 7 15:11 scat.TBT_DN.AVADOS_Left >> 28070 Mar 7 15:11 scat.TBT_DN.AVBDOS_Left >> 28079 Mar 7 15:11 scat.TBT_DN.AVBTRANS_Left >> 28089 Mar 7 15:11 scat.TBT_DN.AVCORR_Left >> 252763 Mar 7 15:11 scat.TBT_DN.BDOS_Left >> 252772 Mar 7 15:11 scat.TBT_DN.BTRANS_Left >> 178 Mar 7 15:11 scat.TBT_DN.CEIG_Left >> 252782 Mar 7 15:11 scat.TBT_DN.CORR_Left >> 298284813762 Mar 7 15:11 scat.TBT_DN.nc >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzY3OCR0PzAsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/MTpkZmA7MDo0YzA6NzE0YWBhZjNkMDoyNWY2NjJgN2E7YGEzMDZnNCR2PzM0NjQ7MzI2OzMkc2tmPzAwQ0A6Q1p6MjA0MzcxLzAwQ0A6Q1szMjA0MzcxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzIkamZuPzI=&url=http%3a%2f%2fscat.TBT_DN.nc> >> 529 Mar 7 14:29 scat.TBT.KP >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzY3OCR0PzAsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/OmYxOmc0Njc6OjdmZmZgNDQwNGQ0Z2czMzY6OjI2ZDcxNDBnZ2ZmNSR2PzM0NjQ7MzI2OzMkc2tmPzAwQ0A6Q1p6MjA0MzcxLzAwQ0A6Q1szMjA0MzcxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzIkamZuPzI=&url=http%3a%2f%2fscat.TBT.KP> >> -- >> scat >> 195116 Feb 11 06:11 scat.TBT.CC >> 350488 Feb 11 06:36 scat.TBT_DN.ADOS_Left >> 350488 Feb 11 06:36 scat.TBT_DN.ADOS_Right >> 70103 Feb 11 06:36 scat.TBT_DN.AVADOS_Left >> 70103 Feb 11 06:36 scat.TBT_DN.AVADOS_Right >> 70074 Feb 11 06:36 scat.TBT_DN.AVTRANS_Left-Right >> 225823297 Feb 11 06:36 scat.TBT_DN.nc >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzY3OCR0PzAsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/MTpkZmA7MDo0YzA6NzE0YWBhZjNkMDoyNWY2NjJgN2E7YGEzMDZnNCR2PzM0NjQ7MzI2OzMkc2tmPzAwQ0A6Q1p6MjA0MzcxLzAwQ0A6Q1szMjA0MzcxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzIkamZuPzI=&url=http%3a%2f%2fscat.TBT_DN.nc> >> 350459 Feb 11 06:36 scat.TBT_DN.TRANS_Left-Right >> 297 Feb 11 06:11 scat.TBT.KP >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzY3OCR0PzAsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/OmYxOmc0Njc6OjdmZmZgNDQwNGQ0Z2czMzY6OjI2ZDcxNDBnZ2ZmNSR2PzM0NjQ7MzI2OzMkc2tmPzAwQ0A6Q1p6MjA0MzcxLzAwQ0A6Q1szMjA0MzcxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzIkamZuPzI=&url=http%3a%2f%2fscat.TBT.KP> >> 350488 Feb 11 06:24 scat.TBT_UP.ADOS_Left >> 350488 Feb 11 06:24 scat.TBT_UP.ADOS_Right >> 70103 Feb 11 06:24 scat.TBT_UP.AVADOS_Left >> 70103 Feb 11 06:24 scat.TBT_UP.AVADOS_Right >> 70074 Feb 11 06:24 scat.TBT_UP.AVTRANS_Left-Right >> 225823295 Feb 11 06:24 scat.TBT_UP.nc >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVw4MzY3OCR0PzAsMiRrZj8yMzgyMyRxa2VsY3Z3cGc/YTU0YWA6NTM0NDczMDdjMzc3YTE2M2AwNTFmMWdnMDs2YTRjNTZnMiR2PzM0NjQ7MzI2OzMkc2tmPzAwQ0A6Q1p6MjA0MzcxLzAwQ0A6Q1szMjA0MzcxJHBhcnY/cWtncXZjL25Cd2NvLGdxJGE/OzIkamZuPzI=&url=http%3a%2f%2fscat.TBT_UP.nc> >> 350459 Feb 11 06:24 scat.TBT_UP.TRANS_Left-Right >> -- >> >> I have also tested the example for graphene (spin unpolarized >> calculation) and it produced all required output, without error. >> I hope these information can be useful for you to detect either what I >> miss or has to be fixed in TBT. >> >> Kind regards, >> >> Neculai >> >> >> On 3/4/22 23:27, Nick Papior wrote: >> >> Hi, >> >> 1) what is your input file >> 2) what does the top 10 lines of the tbtrans output say? >> 3) do you have the netcdf file SystemLabel.TBT.nc >> <https://protection.puc.rediris.es/fmlurlsvc/?fewReq=:B:JVE3PDk4Nyt7MD8jPStkaTA9PDc9PCt+ZGpjbHl4f2gwbGw8NG86Pz04a2k/aTw0PzhoOTs7bmtpPDs0bz85aTk1bzo/NGg8bCt5MDw7OTs5PzQ/NDgrfGRpMD8/OUFeSEpJPT09OTw0ID8/OUFeSEpLPT09OTw0K39ufXkwfmRofnlsIGFNeGxgI2h+K24wND0rZWlhMD0=&url=http%3a%2f%2fSystemLabel.TBT.nc> >> present in your calculation folder? >> >> >> Den fre. 4. mar. 2022 kl. 22.07 skrev Neculai PLUGARU < >> neculai.plug...@imt.ro>: >> >>> Dear SIESTA Community >>> >>> I use SIESTA 4.1.5 and the associated TS and TBT. TBtrans was compiled >>> following the instructions in the TBtrans manual, using NETCDF-4 and MKL >>> libs. >>> >>> I want to calculate the eigen channels for the transmission matrix for a >>> spin-polarized system. For that purpose we have set the following flags in >>> the TBT input: >>> >>> TBT.Verbosity 8 >>> TBT.T.Bulk true >>> TBT.T.All true >>> TBT.T.Eig true >>> TBT.T.Eig 5 >>> TBT.T.Out true >>> TBT.Symmetry.TimeReversal F >>> TBT.Current.Orb true >>> >>> But the TBT calculation does not provide the files >>> >>> SystemLabel.TEIG_<1>_<2> >>> SystemLabel.BDOS_<> >>> SystemLabel.BTRANS_<> >>> SystemLabel.CORR_<> >>> SystemLabel.TRANS_<1>_<1> >>> >>> Is the information in these files listed only in the netcdf format >>> (*.nc files) ? >>> >>> Thank you for your help, >>> Neculai >>> ******************************************************* >>> Dr. Neculai Plugaru >>> National Institute for R&D in Microtechnologies (IMT-Bucharest) >>> Simulation, Modelling and Computer-Aided Design - Laboratory L5 >>> 126A, Erou Iancu Nicolae Street, 077190, Ilfov >>> Bucharest, ROMANIA >>> >>> E-mail: neculai.plug...@imt.ro >>> Tel: +4021 269 0777 >>> https://www.imt.ro >>> ******************************************************* >>> >>> >>> >>> -- >>> SIESTA is supported by the Spanish Research Agency (AEI) and by the >>> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) >>> >> >> >> -- >> Kind regards Nick >> >> > > -- > Kind regards Nick > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) >
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
