Hi, And could you attach the input and output again... The last output clearly showed that you had not put those flags in. So I am guessing you are doing the same thing again....
Please, always attach input and output! And you write something about tbt.t.eig true which does not make sense... As I suggested previously, please check the output to see if it will write the things requested, when you attach the output, could you comment on the output and your interpretation of what it says about transmission eigenvalues etc. On Fri, 11 Mar 2022, 09:39 Neculai PLUGARU, <neculai.plug...@imt.ro> wrote: > Hi, All > > I have the following flags in the input: section for TBT : > > ... > > TBT.DOS.A.All true > > TS.SolutionMethod btd > > TS.BTD.Pivot atom+rev-CM+Left > > > > %block TBT.k > > diag 3 3 1 > > %endblock > > > > %block TBT.Contours > > line > > %endblock TBT.Contours > > %block TBT.Contour.line > > part line > > from -15. eV to 10. eV > > delta 0.02 eV > > method mid-rule > > %endblock TBT.Contour.line > > TBT.T.Bulk true > > TBT.DOS.Elecs true > > TBT.T.Eig 5 > > TBT.T.All true > > TBT.T.Out true > > TBT.Symmetry.TimeReversal false > > TBT.Current.Orb true > > However, the code does not yield "the equivalent eigenvalue files" for > TBT.T.Eig true > Nor the *.nc files for spin_UP/DN > Here I list the TBT output files I get: > > 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 > > What is wrong/missing in my TBT input ? > > Thank you for your comments, > Neculai > > > > On 3/11/22 07:36, Nick Papior wrote: > > 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/)
