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Messages - nori

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16
You should write 'numpy.linspace(-2,2,201)' to get the same interval as 'numpy.linspace(-0.05,0.05,6)'.
Anyway, it can be possible that you obtain different results because the energy points are still different and  the electron temperature also affects the results.

In addition, your transmission spectrum is so small that you should interpret it as  just numerical error and ZERO in practice.

17
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the time computing transmission spectrum with no scf in atk-se is much longer than that in atk-DFT for the same structure.
It hardly (never?) occurs in SCF but it can be possible in transmission.
Because the calculation time of transmission mainly depends on the size of transmission matrix, in other words, the total number of orbitals.
For instance, if you use SZ in DFT and Cerda in SE for Silicon, the number of orbitals per atom is 4(s:1, p:3) in DFT while 9(s:1, p:3, d:5) in SE.
In such a case, the calculation of transmission for SE costs time more than that for DFT.

18
You can download the scripts for 11.2 here ;)
You can realize that the electronic property of ZnO Nanowire strongly depends on the surface structure by calculating and comparing NW1 and NW2.

19
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The transmission spectra for each bias did not have any negative value
Apparently there are negative values in the transmission spectra.
They are probably due to inaccuracy of Krylov method (and of course have no physical meaning).
That's why your problem would be solved by using Recursion method or Direct method instead.

20
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But can we get the DOS and bandstructure of electrodes by ATK?
Electrodes are defined as Bulk system, that's why it can be easily done ;)

21
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Where do the nonzero transmission values in the original band gap come from? How to understand these phenomena?
It's a band-to-band tunneling from a valence band to a conduction band.

on the other hand,
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the transport spectra move further away from the Fermi level as well as the suppressed amplitude for a wide range of energies.
"the suppressed amplitude" comes from breaking the periodicity of effective potential by applying bias voltage and mismatch of Bloch States.
"move further away" is due to the shift of Fermi-level of electrodes.
In order to have finite transmission coefficient at some energies in coherent transport, there should be DOS in electrodes and central region simultaneously at the same energy.

22
It seems that there is no mistake in your calculation, so it would make some sense physically.
One possible reason is that the band to band tunneling around the Fermi level is forbidden.
Why don't you calculate transmission eigenstates at the fermi level under bias voltage 2.0V?

23
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Can it handle incoherent transport in an amorphous nano-scale material?
Unfortunately at least current version of ATK only supports coherent transport.
If you requests incoherent transport to QuantumWise staff, it may be on the road map for future release ;)

24
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Is ATK able to reproduce the experimental IV curve for bulk gold?
No, it isn't because ATK treats coherent transport properties of nano-scale system, which is lost in macro-scale.
So transport properties calculated with ATK don't obey ohm's law.
In your case, the transport is ballistic and the conductance does not depend on the length of the central region.

25
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The k-point of transmission spectra and current need to be equivalent,is that right?
Exactly.

You should be more careful about the k-point sampling for the armchair because Dirac point is not located at Gamma point.
(On the other hand, You can easily include gamma point in the case of the zigzag by using odd k points)
That's why you should analyse the k-resolved transmission coefficient at the fermi level in order to check that Dirac point indeed is included. 

26
General Questions and Answers / Re: Three Terminal device
« on: September 21, 2011, 17:32 »
I think  the energy spectrum of the molecule under a negative gate voltage is elevated because an electron has a negative charge.

27
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Should I use DirectSelfEnergy or RecursionSelfEnergy for the self-consistent calculation or just for transmission spectrum calculation after scf?
In 0 bias calculation, the recursion method is used as default.
Even if the calculation was under finite bias, I think it's OK because you could converge the SCF normally.
Please note that the sensitivity to self energy method is different between SCF and transmission.

Krylov method ignores fast decaying modes (= almost 0) while Recursion and Direct method include all decaying modes.
such ignored modes don't usually affect accuracy but in some cases cause inaccuracy.

28
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Is there any physical meaning for a negative transmission coefficient?
No, always the negative transmission coefficient in ATK is an artifact or due to bugs.
I feel the magnitude of negative coefficients is relatively large so it may be better that you use DirectSelfEnergy or RecursionSelfEnergy instead of KrylovSelfEnergy.

29
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there might be some bonds accross the interface,
If so, they are not dangling bonds because the unit cell interacts physically with the adjacent cell.

So you don't need to worry about it.
Instead, if you add the passivation with hydrogen, your calculation will result in wrong one.

30
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But it turned out that current in structure in which an atom was missing was high
I guess it would be possible in your case because AGNR is a semi-conductor.
In ATK formalism, the electron transport between semiconductive electrodes is not ballistic but is derived from band-to-band tunneling and the central region play a role as a tunneling barrier.

Defects in central region effect the change of tunneling barrier's shape, and there is no guarantee that this change leads to the decrease of conductivity. 

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