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, <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 <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 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 <http://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 <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
<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 <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
<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/)
