Great it got sorted out! On Tue, 15 Mar 2022, 10:30 Neculai PLUGARU, <neculai.plug...@imt.ro> wrote:
> > Dear Nick, Dear All > > I wish to thank you for your great help in finding out what went wrong in > my calculations with TBT 4.1.5, on large, spin polarized systems, (about > 400 atoms). The tests cost me about 10 days and lots of worries. (being an > inexperienced SIESTA user, obviously). > > Well, the explanation has proven to be the compilation of the code - as > you pointed out in a previous reply. After a careful compilation with the > libraries stated in the manual: > > Loading Siesta/4.1.5-intel-2021a > Loading requirement: GCCcore/10.3.0 zlib/1.2.11-GCCcore-10.3.0 > binutils/2.36.1-GCCcore-10.3.0 intel-compilers/2021.2.0 > numactl/2.0.14-GCCcore-10.3.0 UCX/1.10.0-GCCcore-10.3.0 > impi/2021.2.0-intel-compilers-2021.2.0 iimpi/2021a > imkl/2021.2.0iimpi-2021a > intel/2021a Szip/2.1.1-GCCcore-10.3.0 HDF5/1.10.7-iimpi-2021a OpenSSL/1.1 > > cURL/7.76.0-GCCcore-10.3.0 netCDF/4.8.0-iimpi-2021a > netCDF-Fortran/4.5.3-iimpi-2021a METIS/5.1.0-GCCcore-10.3.0 > ELPA/2021.05.001-intel-2021a > > --- > > the code works perfectly. The first lines of TNTrans.out are: > > TBtrans Version: 4.1.5 > > Architecture : unknown > > Compiler flags: mpiifort -fPIC -O2 -xHost -fp-model precise > > PP flags : -DFC_HAVE_ABORT -DF2003 -DMPI -DCDF -DNCDF -DNCDF_4 > -DNCDF_PARALLEL -I/cm/shaared/apps/ > Libraries : libncdf.a libfdict.a -Wl,-Bstatic -Wl,--start-group > -lmkl_scalapack_lp64 -lmkkl_blacs_i > PARALLEL version > > NetCDF support > > NetCDF-4 support > > NetCDF-4 MPI-IO support > > METIS ordering support > > > > * Running on 48 nodes in parallel > > >> Start of run: 14-MAR-2022 15:13:47 > > > > ************************ > > * WELCOME TO TBtrans * > > ************************ > ... > --- > > and thereafter the code produces all files in the output that were > required in the TBT input, here below is an example. > > I hope that other users may find the information useful. > > Kind regards, > Neculai > --- > 48866 Mar 14 13:56 scat.TBT.CC > 158296 Mar 14 14:49 scat.TBT_DN.ADOS_Left > 158296 Mar 14 14:49 scat.TBT_DN.ADOS_Right > 17603 Mar 14 14:49 scat.TBT_DN.AVADOS_Left > 17603 Mar 14 14:49 scat.TBT_DN.AVADOS_Right > 17570 Mar 14 14:49 scat.TBT_DN.AVBDOS_Left > 17570 Mar 14 14:49 scat.TBT_DN.AVBDOS_Right > 17579 Mar 14 14:49 scat.TBT_DN.AVBTRANS_Left > 17579 Mar 14 14:49 scat.TBT_DN.AVBTRANS_Right > 57601 Mar 14 14:49 scat.TBT_DN.AVCEIG_Left > 57601 Mar 14 14:49 scat.TBT_DN.AVCEIG_Right > 17589 Mar 14 14:49 scat.TBT_DN.AVCORR_Left > 17589 Mar 14 14:49 scat.TBT_DN.AVCORR_Right > 57586 Mar 14 14:49 scat.TBT_DN.AVTEIG_Left-Right > 57586 Mar 14 14:49 scat.TBT_DN.AVTEIG_Right-Left > 17574 Mar 14 14:49 scat.TBT_DN.AVTRANS_Left-Left > 17574 Mar 14 14:49 scat.TBT_DN.AVTRANS_Left-Right > 17574 Mar 14 14:49 scat.TBT_DN.AVTRANS_Right-Left > 17574 Mar 14 14:49 scat.TBT_DN.AVTRANS_Right-Right > 158263 Mar 14 14:49 scat.TBT_DN.BDOS_Left > 158263 Mar 14 14:49 scat.TBT_DN.BDOS_Right > 158272 Mar 14 14:49 scat.TBT_DN.BTRANS_Left > 158272 Mar 14 14:49 scat.TBT_DN.BTRANS_Right > 518294 Mar 14 14:49 scat.TBT_DN.CEIG_Left > 518294 Mar 14 14:49 scat.TBT_DN.CEIG_Right > 158282 Mar 14 14:49 scat.TBT_DN.CORR_Left > 158282 Mar 14 14:49 scat.TBT_DN.CORR_Right > 186434408061 Mar 14 14:49 scat.TBT_DN.nc > 518279 Mar 14 14:49 scat.TBT_DN.TEIG_Left-Right > 518279 Mar 14 14:49 scat.TBT_DN.TEIG_Right-Left > 158267 Mar 14 14:49 scat.TBT_DN.TRANS_Left-Left > 158267 Mar 14 14:49 scat.TBT_DN.TRANS_Left-Right > 158267 Mar 14 14:49 scat.TBT_DN.TRANS_Right-Left > 158267 Mar 14 14:49 scat.TBT_DN.TRANS_Right-Right > 529 Mar 14 13:56 scat.TBT.KP > 158296 Mar 14 14:22 scat.TBT_UP.ADOS_Left > 158296 Mar 14 14:22 scat.TBT_UP.ADOS_Right > 17603 Mar 14 14:22 scat.TBT_UP.AVADOS_Left > 17603 Mar 14 14:22 scat.TBT_UP.AVADOS_Right > 17570 Mar 14 14:22 scat.TBT_UP.AVBDOS_Left > 17570 Mar 14 14:22 scat.TBT_UP.AVBDOS_Right > 17579 Mar 14 14:22 scat.TBT_UP.AVBTRANS_Left > 17579 Mar 14 14:22 scat.TBT_UP.AVBTRANS_Right > 57601 Mar 14 14:22 scat.TBT_UP.AVCEIG_Left > 57601 Mar 14 14:22 scat.TBT_UP.AVCEIG_Right > 17589 Mar 14 14:22 scat.TBT_UP.AVCORR_Left > 17589 Mar 14 14:22 scat.TBT_UP.AVCORR_Right > 57586 Mar 14 14:22 scat.TBT_UP.AVTEIG_Left-Right > 57586 Mar 14 14:22 scat.TBT_UP.AVTEIG_Right-Left > 17574 Mar 14 14:22 scat.TBT_UP.AVTRANS_Left-Left > 17574 Mar 14 14:22 scat.TBT_UP.AVTRANS_Left-Right > 17574 Mar 14 14:22 scat.TBT_UP.AVTRANS_Right-Left > 17574 Mar 14 14:22 scat.TBT_UP.AVTRANS_Right-Right > 158263 Mar 14 14:22 scat.TBT_UP.BDOS_Left > 158263 Mar 14 14:22 scat.TBT_UP.BDOS_Right > 158272 Mar 14 14:22 scat.TBT_UP.BTRANS_Left > 158272 Mar 14 14:22 scat.TBT_UP.BTRANS_Right > 518294 Mar 14 14:22 scat.TBT_UP.CEIG_Left > 518294 Mar 14 14:22 scat.TBT_UP.CEIG_Right > 158282 Mar 14 14:22 scat.TBT_UP.CORR_Left > 158282 Mar 14 14:22 scat.TBT_UP.CORR_Right > 186434408059 Mar 14 14:22 scat.TBT_UP.nc > 518279 Mar 14 14:22 scat.TBT_UP.TEIG_Left-Right > 518279 Mar 14 14:22 scat.TBT_UP.TEIG_Right-Left > 158267 Mar 14 14:22 scat.TBT_UP.TRANS_Left-Left > 158267 Mar 14 14:22 scat.TBT_UP.TRANS_Left-Right > 158267 Mar 14 14:22 scat.TBT_UP.TRANS_Right-Left > 158267 Mar 14 14:22 scat.TBT_UP.TRANS_Right-Right > --- > > > > On 3/11/22 15:08, Nick Papior wrote: > > 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/)
