On 06/13/2013 08:24 PM, Artem Baskin wrote:
Thank you Nick and Gabriele for your kind and very enlightening
answers and comments. I really appreciate them.
I have another question that might be of interest for the audience
(and of course for me). My question is how to calculate and visualize
the spatial distribution of the current (current density) in the system.
Dear Artem,
here's a bunch of references you will find interesting:
Physical Review B, 2003, 68, 075306
Reports on Progress in Physics, 2004, 67, 1497
Nature Chemistry, 2010, 2, 223-228 (see suppl. material)
For sure there's some more literature about it. In line of principle you
can calculate them from the hamiltonian and the non equilibrium green's
function. Whether there's an easy way to get them directly in
transiesta, I don't know.
Please note that there is difference whether you have overlap or not
(this issue is mentioned in ref. 2,3) and this can be a tricky point.
Gabriele
If I want to see where the current goes, how should I proceed to get
the answer to this query? This question is partially related to the
fact that in when we use TRANSIESTA as a SolutionMethod no PDOS and LDOS
are calculated since it requires SolutionMethod = diagon.
Thank you for any comment.
Artem
On Fri, Apr 26, 2013 at 3:06 AM, Nick Papior Andersen
<[email protected] <mailto:[email protected]>> wrote:
Dear Artem
2013/4/26 Akshu <[email protected] <mailto:[email protected]>>
Dear nick
I have a question about one of your notes
4) I also played with relaxation of the geometry of the SR. So I
used several CG steps to equilibrate the structure. I expected,
SIESTA first takes over and does the relaxation and then Transiesta
calculates the Gree's functions upon the relaxed geometry.
Instead, Transiesta calculates its stuff at each relaxation step.
Is it ok? Why is it so?
Then you just get the transiesta forces instead of the siesta
forces. So you relax against transiesta forces. You could try
and do siesta relaxation and compare. But don't relax the
electrodes.
What happens if the siesta forces are zero but the transiesta
forces are not, though the transiesta cycle converges. Is it
necessary to relax transiesta forces as well. And what do you
mean by don't relax the electrodes...please explain
I should have been more specific on the electrodes. The
requirement of transiesta is to have the electrodes fixed. I.e.
when you apply the self-energies they must "match" the structure
where they are put, hence if you do geometric optimization without
the constraint of the electrode atoms they could move away from
where the self-energy "lives".
As for the forces, I have never really done this my-self. But in
principle you could do siesta/transiesta cycle geometry relaxation
(but often this is overkill).
As a rule-of thumb (if you need transmission for the relaxed
structure):
1. relax geometry with siesta (separate CG-run)
2. Do transiesta on the geometry obtained from 1. (i.e. do not
further relax the structure)
3. Carefully go through your out-file and check the energies,
forces, etc.
4. If the forces are excessive, then you need to think about what
you want to achieve.
Note especially that if the forces are excessive with a bias, then
possibly (note that I am not saying "only if the forces are
excessive") other time and bias-dependent effects may be governing
the motion/position of the atoms. In this case you need to do
further studies of your system and relaxing in siesta/transiesta
might not provide the full picture.
Kind regards Nick
On 26-Apr-2013, at 1:16 AM, Nick Papior Andersen
<[email protected] <mailto:[email protected]>> wrote:
Dear Artem,
I will give some short notes on your questions.
2013/4/25 Artem Baskin <[email protected]
<mailto:[email protected]>>
Dear SIESTA/TRANSIESTA users,
I have recently read the paper (PRB 81, 205437) and found it very
interesting and enlightening. Since I want to reproduce these
results,
I faced with some questions that I want to address here, some of
them are technical
whereas others are conceptual. From now on I will refer to the
mentioned above paper and the
materials that I
foundhttp://unam.bilkent.edu.tr/mt2/transiesta/agnr8-transiesta/README.txt
1) What is (are) the particular reason(-s) to choose 8AGNR as
an electrode? In this case, the scattering region is defined in a
dummy
way since the only difference between scattering and electrode
regions is
for which area the charge neutrality is preserved and how many
atoms are
treated out of equilibrium. Am I right?
This is a structural choice, you want the electrodes to
represent a semi-infinite system which you put in contact
with the scattering region. The electrode atoms should be as
close (in electronic structure) to the bulk semi-infinite
electrode (as well explained in Brandbyge et al. paper: DOI:
10.1103/PhysRevB.65.165401)
I dont understand what you mean by "scattering region is
defined in a dummy way".
2) In the example
(http://unam.bilkent.edu.tr/mt2/transiesta/agnr8-transiesta/README.txt) I found
TS.NumUsedAtomsLeft/Right 16
TS.BufferAtomsLeft/Right 16
Is there any reason why to use these values?
It is the authors of the papers choice. Buffer atoms are also
well explained in the paper of Brandbyge et al. They are
simply not considered in the transiesta SCF.
3) I was trying to reproduce some of the results. I took 17AGNR as
an electrode with a standard
unit cell (38 atoms). As a scattering region, I choose the same
17AGNR of 4 and 6 unit cells long. I have arranged carefully
the atoms in the scattering regions so that first and last 38 atoms
correspond to the electrode regions. To my surprise,
for the scattering region with 4 unit cells I got a pretty decent
resulting transmission spectrum (step like) whereas for
the scattering region with 6 unit cells the transmission spectra is
just a set of delta-functions. Does anybody have a clue
why is it so? Moreover, when transiesta takes over and calculates
the Green's functions I see a very strange charge population
on atomic orbitals (H atoms at the edges get zero or even negative
charge!!!!) How it can be ok for the smaller SR and
terribly weird for just a two unit cells bigger SR? Do I need to
worry about parameters defining complex contour integration
options (I double checked the TS.ComplexContour.Emin to make sure
that it is below the min eigenvalue in both cases)?
I cannot really comment on this case as I haven't made any of
these calculations myself, have you read Ref. 24 in the paper
you mention?
You could also try to increase the electrode size in the
z-direction, take one more dimer, for instance, on both sides
(in fact I would probably make it two dimers bigger).
4) I also played with relaxation of the geometry of the SR. So I
used several CG steps to equilibrate the structure. I expected,
SIESTA first takes over and does the relaxation and then Transiesta
calculates the Gree's functions upon the relaxed geometry.
Instead, Transiesta calculates its stuff at each relaxation step.
Is it ok? Why is it so?
Then you just get the transiesta forces instead of the siesta
forces. So you relax against transiesta forces. You could try
and do siesta relaxation and compare. But don't relax the
electrodes.
5) Did anyone try to evaluate the Fermi wavelength for such a
system as
compared to the width of the ribbon to make sure that we deal with a
truly 1D system?
6) Due to the specific choice of the electrode for the set up (the
middle
part coincides with the leads) one may interpret the transmission
spectra
using the band structure of the electrode region only. From that
perspective it is unclear for me how one would explain the
conductance
profile for the non zero bias. Moreover, what if the electrodes
were of
the different material, say, gold or nikel?
7) Another technical issue arises when I try to apply this
"approach" to
the case when the electrode are made of different material as
compared to
the scattering region. The Siesta Manual says: "it is also crucial
that
the atomic positions specified at the left (right) EL calculation
must be
equivalent to the left (right) electrode part of the SR set up.
Here,
equivalent means that they can be made equal by a simple
translation in
space." In the examples provided in Siesta and in the case of paper
the EL and SR
are the same, that is why it is easy to provide the equivalence of
the
atoms of the electrodes and those of the SR just multiplying the
first two
lattice vectors for the EL by integer number(s). But what if the
lattice
constants for EL and SR are not commensurable, how can I get the
equivalence of the atomic positions for EL and SR? What is the
"electrode
part of the SR"?
I am not quite sure about your question, the electrode
coordinates have to be the same. If I understand you correct,
then you have to multiply your system until the unit-cell
vectors are equivalent for some integer values.
8) By definition, the whole set up in reality should not have the
translation symmetry, the scattering region does not have
translational
invariance. Yet, in TRANSIESTA set up we have to apply the periodic
boundary conditions in the xy-directions, moreover, we need to
apply the
periodic boundary conditions along the current direction (z). Can
anyone
comment on this? Why do we need them? If I want to analyse (and
visualise)
the wave functions of the scattering region then I have a problem to
decide for which k-point in 3D Brillouin-zone I need to construct
the wf
of a given eigenvalue. It is very counter-intuitive to consider the
scattering region as a chain (or even bulk) rather than a
"super-molecule"
with molecular orbitals as it is should be.
Transiesta k-points are only considered in the transverse
direction. So kz=0. for transiesta SCF.
9) Could you generally comment the meaning of
TS.NumUsedAtomsLeft/Right
TS.BufferAtomsLeft/Right
TS.ReplicateA1(A2)Left/Right
parameters in terms of their physical meaning and geometry of the
set up?
The geometry setup follow this order
1. Left buffer atoms (not used in transiesta)
2. atoms used in the left electrode TSHS x ReplicateA1 x
ReplicateA2
3. Scattering region
4. atoms used in the right electrode TSHS x ReplicateA1 x
ReplicateA2
5. right buffer atoms (not used in transiesta)
I believe I have made a reasonable explanation of the
replicate feature in the manual.
In short, the buffer atoms can be used to match non-equal
electrodes in the left/right side.
10) It is known that<SystemLabel>.TSDE contains the info about the
non-equilibrium density matrix. Manual says that .TSDE file can be
used to
analyse the non equilibrium charge density with the aid of DENCHAR.
However, Denchar needs .DM file but not .TSDE. I renamed .TSDE file
by .DM
file to see the difference but I did not see any difference between
equilibrium and non equilibrium charge density even when I applied
bias of 2 or
more Volts. Have you tried to do this, if so, please, share with me
what
you got and what we should get.
This is system dependent. If you have only tried one system,
then try on another system.
If anyone could comment on at least one of the issues listed above,
I would be very obliged.
Best,
Artem Baskin
Kind regards Nick
