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./ NickDen 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 <http://scat.TBT.CC> 529 Mar 7 10:17 scat.TBT.KP <http://scat.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 <http://scat.TBT_UP.nc> -- scat-dn 78116 Mar 7 14:29 scat.TBT.CC <http://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 <http://scat.TBT_DN.nc> 529 Mar 7 14:29 scat.TBT.KP <http://scat.TBT.KP> -- scat 195116 Feb 11 06:11 scat.TBT.CC <http://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 <http://scat.TBT_DN.nc> 350459 Feb 11 06:36 scat.TBT_DN.TRANS_Left-Right 297 Feb 11 06:11 scat.TBT.KP <http://scat.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 <http://scat.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) andby the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)-- Kind regards Nick-- Kind regards Nick
scat.fdf
Description: application/vnd.fdf
TBtrans Version: 4.1.5
Architecture : x86_64_MPI_INTEL
Compiler flags: mpiifort -O3 -fPIC -xHost -ip -no-prec-div
PP flags : -DFC_HAVE_ABORT -DMPI -DCDF -DNCDF -DNCDF_4 -DTBTRANS
Libraries : libncdf.a libfdict.a -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
-lmkl_scalapacck_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
-lmkl_blacs_intelmpi_lp64 -lpthread -lm -ldl
PARALLEL version
NetCDF support
NetCDF-4 support
* Running on 48 nodes in parallel
>> Start of run: 12-FEB-2022 18:54:16
************************
* WELCOME TO TBtrans *
************************
reinit: Reading from standard input
************************** Dump of input data file ****************************
SystemLabel scat
NumberOfAtoms 360
NumberOfSpecies 5
%block ChemicalSpeciesLabel
1 8 O
2 38 Sr
3 44 Ru
4 56 Ba
5 22 Ti
%endblock ChemicalSpeciesLabel
#%block AtomicCoordinatesOrigin
# Shift the atomic positions into the cell#
#0.7 0. 0.
#%endblock
SpinPolarized T
%block DM.InitSpin
13 +
14 +
15 +
16 +
33 +
34 +
35 +
36 +
53 +
54 +
55 +
56 +
73 +
74 +
75 +
76 +
249 +
250 +
251 +
252 +
273 +
274 +
275 +
276 +
293 +
294 +
295 +
296 +
313 +
314 +
315 +
316 +
333 +
334 +
335 +
336 +
353 +
354 +
355 +
356 +
%endblock DM.InitSpin
%block kgrid_Monkhorst_Pack
3 0 0 0.0
0 3 0 0.0
0 0 100 0.0
%endblock kgrid_Monkhorst_Pack
PAO.BasisSize SZP
PAO.SplitNorm 0.24
MeshCutoff 150. Ry
XC.functional GGA
XC.authors PBE
SolutionMethod Transiesta
ElectronicTemperature 100 K
OccupationFunction FD
MinSCFIterations 5
MaxSCFIterations 500
DM.MixingWeight 0.05
DM.Tolerance 0.005
DM.NumberPulay 6
DM.UseSaveDM .true.
SCF.H.Converge .true.
SCF.H.Tolerance 0.1 eV
MD.NumCGSteps 0
LatticeConstant 1.0 Ang
AtomicCoordinatesFormat Ang
%block LatticeVectors
7.8486810000 0.0000000000 0.0000000000
0.0000000000 7.8486870000 0.0000000000
0.0000000000 0.0000000000 72.178493000
%endblock LatticeVectors
%block AtomicCoordinatesAndAtomicSpecies
-0.0227810 3.9943490 0.8885360 2
5.7443060 5.7302700 0.8885460 1
3.8670450 0.0701570 0.8885490 2
3.8892080 3.9821050 0.8885520 2
2.1716550 6.0788870 0.8885520 1
1.7854510 1.8060780 0.8885590 1
-0.0696470 0.0579130 0.8885650 2
6.0614810 2.1546950 0.8885660 1
0.0527010 6.0748690 2.6656640 1
3.9425270 2.1506770 2.6656770 1
1.8081270 3.9249370 2.6656950 1
5.6979530 0.0007460 2.6657090 1
5.9382820 5.8862880 2.8505050 3
2.0139420 5.8862880 2.8505050 3
1.9794270 1.9620960 2.8505180 3
5.9037680 1.9620960 2.8505180 3
6.1095830 3.9234460 3.0353280 1
2.1507280 -0.0007460 3.0353420 1
3.9751830 5.6977070 3.0353450 1
0.0163280 1.7735150 3.0353590 1
1.8562290 5.6936880 4.8124570 1
6.1322590 6.0423060 4.8124640 1
4.0285020 3.8662790 4.8124710 2
5.7460550 1.7694970 4.8124710 1
2.1734040 2.1181140 4.8124770 1
0.0696470 -0.0579130 4.8124850 2
0.0918100 3.8540350 4.8124870 2
3.9816360 -0.0701570 4.8125000 2
6.1096010 3.9234540 6.5895900 1
3.9751940 5.6977300 6.5896000 1
2.1507460 -0.0007380 6.5896040 1
0.0163390 1.7735390 6.5896130 1
2.0139360 5.8862880 6.7744240 3
5.9382770 5.8862880 6.7744240 3
5.9037620 1.9620960 6.7744370 3
1.9794220 1.9620960 6.7744370 3
0.0526780 6.0748450 6.9592470 1
3.9425040 2.1506530 6.9592610 1
1.8080970 3.9249300 6.9592710 1
5.6979230 0.0007380 6.9592840 1
-0.0227920 3.9943490 8.7363740 2
5.7442950 5.7302700 8.7363840 1
3.8670340 0.0701570 8.7363870 2
3.8891960 3.9821050 8.7363900 2
2.1716430 6.0788870 8.7363900 1
1.7854400 1.8060780 8.7363970 1
-0.0696590 0.0579130 8.7364030 2
6.0614690 2.1546950 8.7364040 1
5.6949130 0.0037680 10.4503770 1
0.0359770 6.0915830 10.4513290 1
3.9387530 2.1544470 10.4518180 1
1.7971840 3.9358570 10.4570740 1
1.9794240 1.9620960 10.6758460 3
2.0083740 5.8918470 10.6763860 3
5.9323550 5.8922050 10.6770220 3
5.9046360 1.9612240 10.6776740 3
2.1597600 -0.0097800 10.9189920 1
6.1153570 3.9176730 10.9195310 1
0.0225340 1.7673060 10.9196420 1
3.9752680 5.6976120 10.9214230 1
6.0954730 6.0790770 12.6515010 1
5.7203110 1.7952290 12.6519550 1
1.8211750 5.7287260 12.6522790 1
2.1473500 2.1441600 12.6540440 1
4.0214590 -0.1099790 12.6563850 2
0.1204280 3.8254120 12.6566240 2
4.0552680 3.8395020 12.6571900 2
0.1109110 -0.0992010 12.6575800 2
2.1625930 -0.0125930 14.4238390 1
3.9778980 5.6950130 14.4257130 1
0.0294480 1.7604220 14.4283670 1
6.1205960 3.9124540 14.4302270 1
1.9842720 1.9572390 14.6228300 3
5.9355340 5.8890260 14.6247410 3
5.9095880 1.9562620 14.6258020 3
2.0122440 5.8879670 14.6274600 3
1.8071630 3.9258580 14.8909880 1
5.7022690 -0.0036290 14.8918420 1
0.0441840 6.0833260 14.8926930 1
3.9449720 2.1481680 14.8944630 1
-0.0375800 4.0091200 16.5884350 2
3.8612930 0.0758770 16.5928460 2
3.8761250 3.9951750 16.5939100 2
-0.0772030 0.0654530 16.5960490 2
5.7418850 5.7326650 16.6454040 1
1.7939300 1.7975800 16.6455460 1
6.0700700 2.1460800 16.6467320 1
2.1729030 6.0776270 16.6487160 1
5.8379850 2.0110660 18.4663960 5
1.9133570 2.0111630 18.4665990 5
1.9139510 5.9350990 18.4667610 5
5.8380690 5.9355110 18.4687220 5
1.9370710 3.9497190 18.4704780 1
-0.0182390 5.9050300 18.4722260 1
3.9016710 1.9851190 18.4726130 1
5.8612000 0.0255900 18.4749620 1
5.8683350 3.9429850 18.6007540 1
1.9449690 0.0172910 18.6037370 1
-0.0152090 1.9774700 18.6050230 1
3.9137860 5.8975340 18.6054770 1
-0.0276310 3.9521610 20.5610990 4
3.8968550 0.0276750 20.5615810 4
-0.0276650 0.0276650 20.5623480 4
3.8971590 3.9519010 20.5624320 4
1.9372500 5.9118000 20.6369180 1
5.8620570 5.9115230 20.6376710 1
5.8607720 1.9882790 20.6376960 1
1.9366500 1.9878700 20.6379340 1
1.9264530 1.9980670 22.5188430 5
1.9265630 5.9224870 22.5189920 5
5.8509890 1.9980610 22.5190030 5
5.8511370 5.9224430 22.5193280 5
5.8633270 0.0234630 22.6247140 1
-0.0233260 5.9101160 22.6247680 1
1.9386190 3.9481710 22.6248230 1
3.9010140 1.9857760 22.6250670 1
1.9386040 0.0236560 22.6262550 1
3.9008360 5.9104840 22.6263050 1
-0.0238550 1.9861150 22.6264820 1
5.8629520 3.9483680 22.6266560 1
-0.0260770 3.9506070 24.6573450 4
3.8984300 0.0261000 24.6573550 4
-0.0261030 0.0261030 24.6573890 4
3.8984400 3.9506210 24.6574250 4
5.8633120 5.9102690 24.7369660 1
1.9387880 5.9102620 24.7370530 1
1.9387800 1.9857400 24.7371300 1
5.8633050 1.9857450 24.7372460 1
1.9258700 1.9986500 26.6206230 5
1.9258720 5.9231780 26.6206420 5
5.8504020 1.9986480 26.6206610 5
5.8504000 5.9231800 26.6206650 5
3.9053220 5.9059980 26.7323920 1
-0.0192340 5.9060240 26.7323990 1
1.9430750 0.0191850 26.7324050 1
5.8676380 0.0191520 26.7324430 1
1.9430070 3.9437830 26.7324490 1
-0.0192280 1.9814880 26.7324660 1
5.8675210 3.9437990 26.7324680 1
3.9053230 1.9814670 26.7324970 1
-0.0226570 0.0226570 28.7582150 4
-0.0226250 3.9471550 28.7582190 4
3.9018330 0.0226980 28.7582190 4
3.9018550 3.9472050 28.7582310 4
5.8672700 5.9063110 28.8351920 1
1.9427370 5.9063130 28.8352110 1
5.8672810 1.9817690 28.8352610 1
1.9427570 1.9817640 28.8353120 1
5.8520230 1.9970280 30.7152500 5
5.8520200 5.9215600 30.7152560 5
1.9274830 5.9215690 30.7152750 5
1.9274760 1.9970440 30.7153420 5
5.8725890 0.0142010 30.8265800 1
-0.0142250 5.9010150 30.8266000 1
3.9103310 5.9009900 30.8266010 1
5.8725750 3.9387460 30.8266010 1
3.9103520 1.9764380 30.8266590 1
1.9480700 0.0141900 30.8266630 1
-0.0142830 1.9765430 30.8266780 1
1.9480210 3.9387690 30.8266820 1
3.9065750 0.0179550 32.8670200 4
-0.0179600 0.0179600 32.8670260 4
-0.0179550 3.9424850 32.8670390 4
3.9065760 3.9424840 32.8670390 4
5.8713980 5.9021830 32.9476150 1
1.9468800 1.9776410 32.9476570 1
5.8714050 1.9776450 32.9476570 1
1.9468680 5.9021820 32.9476610 1
5.8598470 1.9892040 34.8333730 5
5.8598620 5.9137190 34.8333990 5
1.9353240 5.9137260 34.8334260 5
1.9353230 1.9891970 34.8335180 5
1.9501300 3.9366600 34.9451850 1
1.9501360 0.0121240 34.9451850 1
-0.0121330 1.9743930 34.9451930 1
3.9124030 1.9743870 34.9451970 1
-0.0121550 5.8989460 34.9452040 1
3.9123930 5.8989270 34.9452120 1
5.8746500 3.9366700 34.9452190 1
5.8746690 0.0121210 34.9452230 1
3.9087890 0.0157420 36.9891530 4
3.9088740 3.9401860 36.9891720 4
-0.0156190 0.0156190 36.9891800 4
-0.0155260 3.9400560 36.9891800 4
5.8733600 5.9002200 37.0729160 1
5.8733600 1.9756900 37.0731030 1
1.9488290 5.9002220 37.0732330 1
1.9488350 1.9756850 37.0735840 1
5.8616620 5.9119190 38.9604940 5
5.8616450 1.9874060 38.9609020 5
1.9371240 5.9119260 38.9610430 5
1.9371110 1.9874090 38.9618360 5
5.8754740 0.0113160 39.0730610 1
5.8753910 3.9359290 39.0730650 1
3.9132270 5.8980930 39.0730770 1
-0.0114190 5.8982090 39.0730840 1
-0.0114100 1.9736700 39.0732100 1
3.9132340 1.9735560 39.0732220 1
1.9508660 3.9359240 39.0732330 1
1.9509520 0.0113080 39.0732410 1
-0.0153160 0.0153160 41.1095640 4
3.9091280 3.9399320 41.1095830 4
3.9088410 0.0156890 41.1095870 4
-0.0150340 3.9395640 41.1095950 4
5.8737230 5.8998570 41.1913130 1
5.8736960 1.9753540 41.1918320 1
1.9491810 5.8998690 41.1919960 1
1.9491660 1.9753540 41.1932890 1
5.8597430 5.9138380 43.0754840 5
5.8596430 1.9894070 43.0769450 5
1.9351320 5.9139180 43.0775480 5
1.9350280 1.9894920 43.0807100 5
5.8766090 3.9347110 43.1894290 1
3.9148740 5.8964480 43.1895360 1
-0.0102050 5.8969950 43.1896650 1
5.8770610 0.0097300 43.1896730 1
-0.0101570 1.9724170 43.1900960 1
1.9524310 0.0098290 43.1901840 1
3.9147400 1.9720500 43.1902830 1
1.9521820 3.9346080 43.1903140 1
-0.0144060 0.0144060 45.2163150 4
3.9095880 0.0149420 45.2163680 4
-0.0138140 3.9383440 45.2165400 4
3.9100920 3.9389680 45.2165630 4
1.9499090 5.8991410 45.2946990 1
5.8742200 1.9748310 45.2949360 1
5.8745220 5.8990590 45.2971140 1
1.9495640 1.9749560 45.3007720 1
5.8659680 1.9830830 47.1802620 5
5.8669250 5.9066570 47.1803920 5
1.9420360 5.9070150 47.1811200 5
1.9413220 1.9831980 47.1931020 5
1.9491160 3.9376740 47.2815040 1
3.9153400 1.9714500 47.2817220 1
-0.0113270 5.8981170 47.2819010 1
1.9529560 0.0093040 47.2821640 1
5.8761630 0.0106270 47.2822440 1
-0.0133750 1.9756350 47.2827780 1
3.9146800 5.8966400 47.2833500 1
5.8754550 3.9358650 47.2835830 1
-0.0159350 0.0159350 49.3167980 4
3.9092070 0.0153230 49.3184460 4
3.9096510 3.9394090 49.3209820 4
-0.0132240 3.9377540 49.3229970 4
1.9549590 1.9695610 49.3324570 1
1.9561870 5.8928640 49.3446340 1
5.8789660 1.9700840 49.3497680 1
5.8824800 5.8911000 49.3525950 1
2.0016410 5.8985890 51.3827000 3
1.9763820 1.9651490 51.3828030 3
5.9266110 5.8979590 51.3863010 3
5.9016990 1.9641720 51.3867100 3
1.7961940 3.9368560 51.3913750 1
5.6957060 0.0029850 51.3921610 1
3.9398480 2.1533620 51.3970020 1
0.0326380 6.0949320 51.3970550 1
0.0141230 1.7757270 51.5725690 1
2.1516490 -0.0016590 51.5754070 1
3.9645600 5.7083320 51.5793140 1
6.1035600 3.9294810 51.5853640 1
3.9864950 -0.0750050 53.3886250 2
4.0208470 3.8739330 53.3887280 2
0.0877160 3.8581340 53.3899640 2
0.0752350 -0.0635050 53.3907460 2
6.0810280 6.0935320 53.4253680 1
1.8181410 5.7317800 53.4257300 1
2.1389460 2.1525740 53.4259590 1
5.7141800 1.8013700 53.4266880 1
2.1404350 0.0095750 55.1582440 1
6.0959660 3.9370940 55.1606090 1
3.9571080 5.7158120 55.1620850 1
0.0065010 1.7833790 55.1625240 1
1.9607250 1.9807950 55.3820370 3
5.9119540 5.9126170 55.3836580 3
5.8851920 1.9806680 55.3844360 3
1.9890260 5.9112040 55.3857860 3
1.7807820 3.9522480 55.6353020 1
0.0168430 6.1106770 55.6359580 1
3.9174190 2.1757410 55.6374920 1
5.6751410 0.0235190 55.6408180 1
1.7965480 1.7949720 57.3713480 1
5.7639920 5.7105690 57.3722860 1
2.1906000 6.0599400 57.3724080 1
6.0715330 2.1446280 57.3725420 1
3.8222500 0.1149310 57.3739720 2
3.8444690 4.0268420 57.3740140 2
-0.0694480 4.0409980 57.3747160 2
-0.1160930 0.1043530 57.3749600 2
0.0526320 6.0748690 59.1484920 1
3.9424580 2.1506770 59.1485030 1
1.8080580 3.9249370 59.1485220 1
5.6978840 0.0007460 59.1485340 1
5.9382140 5.8862880 59.3333330 3
2.0138730 5.8862880 59.3333330 3
1.9793590 1.9620960 59.3333440 3
5.9036990 1.9620960 59.3333440 3
6.1095140 3.9234460 59.5181550 1
2.1506590 -0.0007460 59.5181700 1
3.9751140 5.6977070 59.5181740 1
0.0162590 1.7735150 59.5181860 1
1.8561600 5.6936880 61.2952850 1
6.1321900 6.0423060 61.2952890 1
5.7459860 1.7694970 61.2952970 1
4.0284330 3.8662790 61.2953000 2
2.1733350 2.1181140 61.2953040 1
0.0695780 -0.0579130 61.2953120 2
0.0917410 3.8540350 61.2953120 2
3.9815670 -0.0701570 61.2953270 2
6.1095320 3.9234540 63.0724190 1
3.9751250 5.6977300 63.0724270 1
2.1506770 -0.0007380 63.0724310 1
0.0162700 1.7735390 63.0724420 1
2.0138670 5.8862880 63.2572490 3
5.9382080 5.8862880 63.2572490 3
5.9036930 1.9620960 63.2572640 3
1.9793530 1.9620960 63.2572640 3
0.0526090 6.0748450 63.4420750 1
3.9424350 2.1506530 63.4420860 1
1.8080280 3.9249300 63.4420980 1
5.6978540 0.0007380 63.4421130 1
-0.0228610 3.9943490 65.2192010 2
5.7442260 5.7302700 65.2192120 1
3.8669650 0.0701570 65.2192160 2
3.8891270 3.9821050 65.2192160 2
2.1715740 6.0788870 65.2192160 1
1.7853710 1.8060780 65.2192240 1
-0.0697280 0.0579130 65.2192320 2
6.0614000 2.1546950 65.2192320 1
0.0526200 6.0748690 66.9963270 1
3.9424460 2.1506770 66.9963430 1
1.8080470 3.9249370 66.9963620 1
5.6978730 0.0007460 66.9963730 1
5.9382020 5.8862880 67.1811690 3
2.0138620 5.8862880 67.1811690 3
1.9793470 1.9620960 67.1811840 3
5.9036880 1.9620960 67.1811840 3
6.1095030 3.9234460 67.3659940 1
2.1506480 -0.0007460 67.3660060 1
3.9751030 5.6977070 67.3660100 1
0.0162480 1.7735150 67.3660250 1
1.8561490 5.6936880 69.1431210 1
6.1321780 6.0423060 69.1431280 1
5.7459750 1.7694970 69.1431360 1
4.0284220 3.8662790 69.1431360 2
2.1733230 2.1181140 69.1431440 1
0.0695670 -0.0579130 69.1431510 2
0.0917300 3.8540350 69.1431510 2
3.9815560 -0.0701570 69.1431670 2
6.1095210 3.9234540 70.9202550 1
3.9751140 5.6977300 70.9202660 1
2.1506660 -0.0007380 70.9202700 1
0.0162590 1.7735390 70.9202780 1
2.0138560 5.8862880 71.1050880 3
5.9381960 5.8862880 71.1050880 3
5.9036820 1.9620960 71.1051030 3
1.9793410 1.9620960 71.1051030 3
0.0525980 6.0748450 71.2899140 1
3.9424240 2.1506530 71.2899260 1
1.8080170 3.9249300 71.2899370 1
5.6978430 0.0007380 71.2899480 1
%endblock AtomicCoordinatesAndAtomicSpecies
WriteMullikenPop 1
WriteDM T
WriteBands T
WriteKBands F
WriteCoorInitial T
WriteMDhistory F
WriteWaveFunctions T
WriteCoorXmol F
WriteForces T
SaveHS T
# Transiesta options
TS.Forces .true.
TS.SCF.dQ.Converge .true.
TS.SCF.dQ.Tolerance 1.D+1
TS.HS.Save .true.
TS.DE.Save .true.
ParallelOverK .true.
Diag.ParallelOverK .true.
#Transiesta------------------------------
#(;Noua metoda din carte:)#
# Bias voltage
TS.Voltage 0.0 eV
%block TS.ChemPots
Left
Right
%endblock TS.ChemPots
%block TS.ChemPot.Left
mu V/2
contour.eq
begin
c-Left
t-Left
end
%endblock TS.ChemPot.Left
%block TS.ChemPot.Right
mu -V/2
contour.eq
begin
c-Right
t-Right
end
%endblock TS.ChemPot.Right
TS.Elecs.Bulk true
TS.Elecs.DM.Update none
TS.Elecs.GF.ReUse false
#Electrodes-------
%block TS.Elecs
Left
Right
%endblock TS.Elecs
%block TS.Elec.Left
TSHS ../elec-1/elec-1.TSHS
chem-pot Left
semi-inf-dir -a3
elec-pos begin 1
%endblock TS.Elec.Left
%block TS.Elec.Right
TSHS ../elec-2/elec-2.TSHS
chem-pot Right
semi-inf-dir +a3
elec-pos begin 321
%endblock TS.Elec.Right
TS.Contours.Eq.Pole 2.5 eV
%block TS.Contour.c-Left
part circle
from -25.00000 eV + V/2 to -10. kT + V/2
points 34
method g-legendre
%endblock TS.Contour.c-Left
%block TS.Contour.t-Left
part tail
from prev to inf
points 12
method g-fermi
%endblock TS.Contour.t-Left
%block TS.Contour.c-Right
part circle
from -25.00000 eV - V/2 to -10. kT - V/2
points 34
method g-legendre
%endblock TS.Contour.c-Right
%block TS.Contour.t-Right
part tail
from prev to inf
points 12
method g-fermi
%endblock TS.Contour.t-Right
TS.Contours.nEq.Eta 0.0001 eV
%block TS.Contours.nEq
neq
%endblock TS.Contours.nEq
%block TS.Contour.nEq.neq
part line
from -|V|/2 - 5 kT to |V|/2 + 5 kT
delta 0.005 eV
method mid-rule
%endblock TS.Contour.nEq.neq
TBT.DOS.A.All T
TS.SolutionMethod btd
TS.BTD.Pivot atom+rev-CM+Left
%block TBT.k
diag 3 3 100
%endblock
%block TBT.Contours
line
%endblock TBT.Contours
%block TBT.Contour.line
part line
from -15. eV to 10. eV
delta 0.01 eV
method mid-rule
%endblock TBT.Contour.line
************************** End of input data file *****************************
reinit: -----------------------------------------------------------------------
reinit: System Name:
reinit: -----------------------------------------------------------------------
reinit: System Label: scat
reinit: -----------------------------------------------------------------------
Kpoints in: 6 . Kpoints trimmed: 5
tbt: Number of transport k-points = 5
tbt: Method = Monkhorst-Pack grid.
tbt: k-grid: Supercell and displacements
tbt: 3 0 0 0.000
tbt: 0 3 0 0.000
tbt: 0 0 1 0.000
tbt: **************************************************************
tbt: Electronic temperature (reference) = 99.9993 K
tbt: No applied bias
tbt: Calculate transmission only using diag(Gf) = F
tbt: Saving bulk transmission for electrodes = F
tbt: Saving DOS from bulk electrodes = F
tbt: Saving DOS from Green function = F
tbt: Saving DOS from all spectral functions = T
tbt: Saving bond currents (orb-orb) = F
tbt: Saving DM from Green function = F
tbt: Saving DM from spectral functions = F
tbt: Saving COOP from Green function = F
tbt: Saving COOP from spectral functions = F
tbt: Saving COHP from Green function = F
tbt: Saving COHP from spectral functions = F
tbt: Calc. # transmission eigenvalues = 0
tbt: Calc. T between all electrodes = F
tbt: Calc. total T out of electrodes = F
tbt: Calculate spin UP and DOWN
tbt: BTD creation algorithm = speed
tbt: BTD spectral function algorithm = propagation
tbt: Divide and conquer diagonalization = F
tbt: Assume LAPACK <i|S|j> = delta_ij = F
tbt: Saving downfolded self-energies = F
tbt: No delta Hamiltonian
tbt: No delta self-energy
tbt: Data files stored in current folder
tbt: No compression of TBT.nc files
tbt: Default NetCDF precision = single
tbt: Parallel MPI-IO not possible
tbt: >> Electrodes <<
tbt: >> Left
tbt: Electrode cell pivoting: E1, E2, E3 = A1, A2, A3
tbt: In-core self-energy calculation
tbt: Electrode TSHS file = ../elec-1/elec-1.TSHS
tbt: # atoms used in electrode = 40
tbt: Electrode Bloch unity [E1 x E2 x E3] = 1 x 1 x 1
tbt: Position in geometry = 1 -- 40
tbt: Semi-infinite direction for electrode = negative wrt. E3
tbt: Chemical shift = 0.000000 eV
tbt: Electronic temperature = 99.999269 K
tbt: Gamma-only electrode = F
tbt: Bulk H, S in electrode region = T
tbt: Manual delta-Ef shift = 0.000000 eV
tbt: Electrode self-energy imaginary Eta = 0.1000E-02 eV
tbt: Electrode self-energy accuracy = 0.1000E-12 eV
tbt: Electrode inter-layer distance (semi-inf) = 1.7771 Ang
tbt: >> Right
tbt: Electrode cell pivoting: E1, E2, E3 = A1, A2, A3
tbt: In-core self-energy calculation
tbt: Electrode TSHS file = ../elec-2/elec-2.TSHS
tbt: # atoms used in electrode = 40
tbt: Electrode Bloch unity [E1 x E2 x E3] = 1 x 1 x 1
tbt: Position in geometry = 321 -- 360
tbt: Semi-infinite direction for electrode = positive wrt. E3
tbt: Chemical shift = 0.000000 eV
tbt: Electronic temperature = 99.999269 K
tbt: Gamma-only electrode = F
tbt: Bulk H, S in electrode region = T
tbt: Manual delta-Ef shift = 0.000000 eV
tbt: Electrode self-energy imaginary Eta = 0.1000E-02 eV
tbt: Electrode self-energy accuracy = 0.1000E-12 eV
tbt: Electrode inter-layer distance (semi-inf) = 1.7771 Ang
ts: >> TBtrans contour <<
ts: Device Green function imaginary Eta = 0.000 eV
ts: Contour name = TBT.Contour.line
ts: line contour E_min = -15.0000 eV
ts: line contour E_max = 10.0000 eV
ts: line contour points = 2500
ts: line contour method = Mid-rule
tbt: **************************************************************
tbt: <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
%block TBT.Contours
line
%endblock TBT.Contours
%block TBT.Contour.line
from -15. eV to 10. eV
delta 0.01 eV
method mid-rule
%endblock TBT.Contour.line
tbt: <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
************************ Begin: TBT CHECKS AND WARNINGS ************************
************************ End: TBT CHECKS AND WARNINGS **************************
Device information (full):
<sparsity:scat.TSHS
nrows_g=2880 nrows=2880 sparsity=.6252 nnzs=5185846, refcount: 3>
Electrode information:
<sparsity:../elec-1/elec-1.TSHS
nrows_g=320 nrows=320 sparsity=3.9139 nnzs=400784, refcount: 3>
<sparsity:(TM [--,--, 0] of: ../elec-1/elec-1.TSHS)
nrows_g=320 nrows=320 sparsity=2.3112 nnzs=236672, refcount: 3>
<sparsity:(TM [--,--,-1] of: ../elec-1/elec-1.TSHS)
nrows_g=320 nrows=320 sparsity=.8013 nnzs=82056, refcount: 3>
Left principal cell is perfect!
<sparsity:../elec-2/elec-2.TSHS
nrows_g=320 nrows=320 sparsity=3.9139 nnzs=400784, refcount: 3>
<sparsity:(TM [--,--, 0] of: ../elec-2/elec-2.TSHS)
nrows_g=320 nrows=320 sparsity=2.3112 nnzs=236672, refcount: 3>
<sparsity:(TM [--,--, 1] of: ../elec-2/elec-2.TSHS)
nrows_g=320 nrows=320 sparsity=.8013 nnzs=82056, refcount: 3>
Right principal cell is perfect!
tbt: Analyzing electrode sparsity pattern and electrode pivot-tables
tbt: BTD pivoting scheme for electrode (Left): atom+Left
tbt: Analyzing device sparsity pattern and pivot-table
tbt: BTD pivoting scheme in device: atom+rev-CM+Left
tbt: Done analyzing electrode and device sparsity pattern and pivot-tables
tbt: Reducing matrix (H, S) sparsity patterns by: 164112
tbt: # of device region orbitals: 2240
Region (280): [A]-device
[ 41 -- 320 ]
tbt: # of Left downfolding orbitals: 568
tbt: # of Left device orbitals: 248
Region (40): [A]-Left folding region
[ 1 -- 40 ]
Region (32): [A]-Left folding in D
[ 41 -- 68, 73 -- 76 ]
tbt: # of Right downfolding orbitals: 636
tbt: # of Right device orbitals: 316
Region (40): [A]-Right folding region
[ 321 -- 360 ]
Region (40): [A]-Right folding in D
[ 281 -- 320 ]
tbt: Creating electrode tri-diagonal matrix blocks
tbt: Creating device tri-diagonal matrix blocks
Region (7): [TRI] device region
[ 72, 320, 426, [427] * 2, 372, 196 ]
tbt: Matrix elements in BTD: 2341212
tbt: Electrodes tri-diagonal matrices
Region (3): [TRI] Left
[ 1, 319, 248 ]
Region (3): [TRI] Right
[ 72, 248, 316 ]
tbt: Electrode memory: 15.284 MB
tbt: Sparse H, S and auxiliary matrices memory: 143.534 MB
tbt: Sum of electrode and sparse memory: 158.817 MB
tbt: Initializing data file: scat.TBT_UP.nc
tbt: Estimated file size of scat.TBT_UP.nc: 213.718 MB
tbt: LHS Green function padding / memory: 75 / 35.725 MB
tbt: RHS Green function padding / memory: 0 / 35.724 MB
tbt: Initial ETA in 612.121 s
tbt: Calculated 5.376 %, ETA in 484.491 s
tbt: Calculated 10.752 %, ETA in 584.826 s
tbt: Calculated 16.128 %, ETA in 591.150 s
tbt: Calculated 21.152 %, ETA in 573.761 s
tbt: Calculated 26.528 %, ETA in 510.201 s
tbt: Calculated 31.904 %, ETA in 485.756 s
tbt: Calculated 37.280 %, ETA in 456.551 s
tbt: Calculated 42.304 %, ETA in 420.042 s
tbt: Calculated 47.680 %, ETA in 374.571 s
tbt: Calculated 53.056 %, ETA in 338.640 s
tbt: Calculated 58.432 %, ETA in 303.495 s
tbt: Calculated 63.456 %, ETA in 264.829 s
tbt: Calculated 68.832 %, ETA in 225.200 s
tbt: Calculated 74.208 %, ETA in 187.609 s
tbt: Calculated 79.584 %, ETA in 149.723 s
tbt: Calculated 84.608 %, ETA in 111.512 s
tbt: Calculated 89.984 %, ETA in 72.733 s
tbt: Calculated 95.360 %, ETA in 33.852 s
tbt: Completed in 737.086 s
Currents (ensure entire Fermi function window):
Left -> Right, V [V] / I [A]: 0.00000 V / 0.00000 A
Left -> Right, V [V] / P [W]: 0.00000 V / 0.00000 W
tbt: Initializing data file: scat.TBT_DN.nc
tbt: Estimated file size of scat.TBT_DN.nc: 213.718 MB
tbt: LHS Green function padding / memory: 75 / 35.725 MB
tbt: RHS Green function padding / memory: 0 / 35.724 MB
tbt: Initial ETA in 617.951 s
tbt: Calculated 5.376 %, ETA in 518.233 s
tbt: Calculated 10.752 %, ETA in 606.151 s
tbt: Calculated 16.128 %, ETA in 605.443 s
tbt: Calculated 21.152 %, ETA in 584.354 s
tbt: Calculated 26.528 %, ETA in 514.993 s
tbt: Calculated 31.904 %, ETA in 490.703 s
tbt: Calculated 37.280 %, ETA in 460.223 s
tbt: Calculated 42.304 %, ETA in 423.518 s
tbt: Calculated 47.680 %, ETA in 376.113 s
tbt: Calculated 53.056 %, ETA in 339.308 s
tbt: Calculated 58.432 %, ETA in 304.042 s
tbt: Calculated 63.456 %, ETA in 265.299 s
tbt: Calculated 68.832 %, ETA in 225.099 s
tbt: Calculated 74.208 %, ETA in 187.697 s
tbt: Calculated 79.584 %, ETA in 149.809 s
tbt: Calculated 84.608 %, ETA in 111.599 s
tbt: Calculated 89.984 %, ETA in 72.683 s
tbt: Calculated 95.360 %, ETA in 33.840 s
tbt: Completed in 735.933 s
Currents (ensure entire Fermi function window):
Left -> Right, V [V] / I [A]: 0.00000 V / 0.00000 A
Left -> Right, V [V] / P [W]: 0.00000 V / 0.00000 W
Section Calls Walltime %
global_section 1 1495.300 100.00
tbtrans 1 1495.300 100.00
init-region+sp 1 0.793 0.05
pivot-elec 1 0.316 0.02
pivot 1 0.163 0.01
pivot-device 1 0.165 0.01
pivot 1 0.165 0.01
tri-init 1 2.073 0.14
tri-init-elec 1 1.355 0.09
TS-rgn2tri 1 0.002 0.00
TS-rgn2tri 1 0.013 0.00
TBT 1 1479.628 98.95
read-GS 530 743.075 49.69
SE-dwn 530 24.186 1.62
ts_expand 1040 0.506 0.03
Gf-prep 530 288.082 19.27
V_TM_Pinv 520 242.174 16.20
analysis 530 416.161 27.83
cdf2ascii 2 1.672 0.11
>> End of run: 12-FEB-2022 19:19:11
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
