Re: [SIESTA-L] TBtrans output
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 <http://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, 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 <http://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 <http://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, 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 <http://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 <http://scat.TBT.KP> 350488 Feb 12 19:06 scat.TBT_UP.ADOS_Left 350488 F
Re: [SIESTA-L] [***RedIris: Posible SPAM***] [***RedIris: Posible SPAM***] Re: TBtrans output
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 <http://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 <http://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, 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 <http://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 <http://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 an
[SIESTA-L] [***RedIris: Posible SPAM***] [***RedIris: Posible SPAM***] Re: TBtrans output
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 : 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 chan
[SIESTA-L] TBtrans output
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 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/)
Re: [SIESTA-L] transiesta yields negative total energy and TBTrans starts with positive total energy
Hello Nick Thank you, very much, for your insightful comments. Indeed, we have started with a 0 V calculation in all our tests, and the reported issue appears for V= 0 V. It also manifested when, after performing a successful 0 V calculation on the same heterostructure prior being relaxed in the slab geometry ( so only preoptimized cells in the electrodes and barrier, we call it "ideal") and increased the bias to 0.001 V or 0.5 V, independent calculations. Also, the points: - " you started a biased calculation (V) from a previous TranSiesta calculation (V'), ..." - "- your mixing weight is too high" -"- your convergence parameters too loose during the Siesta SCF can be discarded. We shall check the remaining of your comments and further report to the forum. Kind regards from Bucharest, Neculai *********** Neculai Plugaru National Institute for R 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 *** On 2021-11-15 11:37, Nick Papior wrote: Please use 4.1.5, it has checks for these kinds of things. Probably what you are seeing is that the charge is leaking out of the device region during your SCF. This is an indication of one or a combination of the following: - your initial Hamiltonian is far from the open-boundary one. I.e. your electrode regions are too close to the scattering in the device - your mixing weight is too high - your convergence parameters too loose during the Siesta SCF - your integration variables in TranSiesta could be better (more points) - you started a biased calculation (V) from a previous TranSiesta calculation (V'), and the difference V - V' is too large for the system to converge properly, try a smaller dV There may be other things as well. Also, I hope you are doing a 0 V calculation to start with. Den fre. 12. nov. 2021 kl. 22.08 skrev Neculai PLUGARU : Dear SIESTA community I attempt to perform conductance calculations on a heterostructure with two interfaces, (slab geometry) which was previously relaxed and then the SCF calculation produced correct results. I use SIESTA v4.1-b4, Compiler version: ifort (IFORT) 18.0.5 20180823, PARALLEL version. However, although the SIESTA cycle in the transport calculation converges and the Harris, KS and Free energies are negative, TS starts from (huge) positive energy values, then the calculation converges according to the DM tolerance criterion, the energies are still positive, the forces on atoms are huge and the populations on orbitals are wrong. The leads are cut from the electrodes, so that the scattering region comprises the interfaces and the leads still are about one nanometer long each. I would greatly appreciate your comments to solve this issue. Thank you, Neculai *** N. Plugaru National Institute for R 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 -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
[SIESTA-L] correction to subject: transiesta yields negative total energy and TBTrans starts with positive total energy
Hi, Sorry for the error in the subject of the previous message: it should be "SIESTA yields negative total energy and TranSIESTA starts with positive total energy" Neculai *** N. Plugaru National Institute for R 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/)
[SIESTA-L] transiesta yields negative total energy and TBTrans starts with positive total energy
Dear SIESTA community I attempt to perform conductance calculations on a heterostructure with two interfaces, (slab geometry) which was previously relaxed and then the SCF calculation produced correct results. I use SIESTA v4.1-b4, Compiler version: ifort (IFORT) 18.0.5 20180823, PARALLEL version. However, although the SIESTA cycle in the transport calculation converges and the Harris, KS and Free energies are negative, TS starts from (huge) positive energy values, then the calculation converges according to the DM tolerance criterion, the energies are still positive, the forces on atoms are huge and the populations on orbitals are wrong. The leads are cut from the electrodes, so that the scattering region comprises the interfaces and the leads still are about one nanometer long each. I would greatly appreciate your comments to solve this issue. Thank you, Neculai *** N. Plugaru National Institute for R 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/)
